Changed FeatureDataframe to subclass of pd.DataFrame #186
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* Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Release/0.9.3.1 (#152) * Preparing minor release * Disabling test * Minor bug fixes * Minor refactor of IRACE configure method * test update * Updating changelog and version number and adding distributable (#154) * Release + Fixes (#155) * Release/0.9.3.1 (#151) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Preparing minor release * Disabling test --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * release prep * Release/0.9.3.2 (#153) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Release/0.9.3.1 (#152) * Preparing minor release * Disabling test * Minor bug fixes * Minor refactor of IRACE configure method * test update * Updating changelog and version number and adding distributable --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * Removing handmade dists for automatic releases fix * Bugfix --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * template fix * SPRK 373 - Enable selection over algorithm configurations (#165) * First step * Remove file * Adding code to extract and pivot data to a table containins multiple configurations * update * Adding configurations to portfolio core * test update to avoid file writing * Implementing changes to run portfolio with various configurations * more changes * Update comments to be more informative * Performance dataframe update to present configurations as columns * Adding/removing solvers bug fix * Updating functionality to be more flexible * Updating configurator (SMAC2) to work with new PDF structure for configs * Irace update * SMAC3 update * Paramils fix * delete old component * Have SMAC3 use the same resource limit as smac2 * Refactor code * BUgfixes and refactoring * Replacing test file with new setting * Bugfixes marginal contribution test * smac2 test fix * Test fixes * Test bugfixes * Update snapshots * Integration test updates * remove print statements * remove dead code * Test fix * marginal contribution test fix * Report generation bugfixes * Ablation test fix * Refactoring and updating todos * test fix * Changelog update * test fix * test files sorted update * ASF-lib downgrade due to bug * Test fix, version fix * Delete unnecessary files, attempted test fix * Remove duplicate test * Snapshot fixes * test file fix * Sprk 162 (#166) * Solver wrapper update * print fix * Minor fixes * Solver update, bugfixes * wrapper echo fix * remove old comment * cli bugfix * Implementing check function for solvers, updating solver wrappers to handle kill signals, removing tmp/log dir from sparkle executables * Adding feature extractor tests to check command * Adding instance set to check function * Extra test * Updating wrappers documentation * bugfix * Update changelog * Bugfixes * Bugfix for default value overriding user input * Fixing name change * Name change * Solver wrapper bugfix * Sprk 150 (#157) * fixed typos and errors of SPRK-372 * test ssh connection * split run_parallel_portfolio function into seperate functions * Adjust test of run_parallel_portfolio to its new version * added missing part for writing output to csv * Remove redundant file * Argument parser always at the top of a file * delete run_parallel_portfolio, write results in PerformanceDataFrame * added create performance dataframe function * change function place * adjust test file according to new changes * fix type mismatching in test file * fix typos in test file * fix attribute typo * delete unnecessary print --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 161 (#168) * First big update for reporting changes * update argument name for clarity * extractor bugfix * Updating selector to use SelectionScenario * Renaming example extractor * Code update for extractor rename * test file update * remove dead files * First rebuild of report generation for selection scenarios * remove dead line * Minor fixes * Updating configuration scenario to contain number of runs and generate steady config ids * remove print statements * Updating configuration output processing and report generation * Bugfixes Paramils + smac2 configuration in one report * Adding ablation scenario to the new generation structure * Removing comments * Add parallel portfolio reporting * Remove dead files * cleanup * Updating tests * pytest fix * bugfix * pytest update * irace testfix * pytest fix smac3 scenario * smac2 scenario init fix * paramils test update * ablation test fixes * selector test update * settings bugfix * test snapshot fix * snapshot fixes * config report generation bugfixes * Test file fix * Update changelog * bugfix * parallel portfolio update * snapshot fix * marginal contribution fixes * selector test update * report bugfixes * configured snapshot fixes * snapshot instance bugfix * Refreshing scenarios bugfix * Kaleido/Plotly upgrade and configscenario timestamp bugfix * Sprk 352 (#167) * Merged with current development branch * Merge * Fixed merging errors * Formatting * Fixed test and merging errors * Fixed indexing error * Snapshot fixes for github * setup missing kaleido for some reason * Review changes * Adjusted portfolio constructor and instance tests * disable report tests on github * changelog update * removing comments --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 171 - Modularity of configurators (#172) * Moving files to prepare for on-the-fly installation of configurators and reduce installation size of sparkle * URL update * Updating downloaders of SMAC2 and ParamILS * Fixing IRACE installation to be handled by configurator class * Irace install bugfixes * Updating configurator class * Fixing tests, removing redundant code * test b ugfixes * changelog update * ablation path fix * initialise fix for non interactive sessions * Test update * fix configurator test * test fix github attempt * test fix attempt * Attempt test fix input * Adding install option to configure solver command * irace bugfix * test fix return value * pytest update * updating test stability * Post merge update for URLs * adding test file * job list bugfix * Various bugfixes for report generation * selection example bugfixes * pytest bugfix * Test fix * update contributing text * merge main fix * delete dead code * fix file pathing * contributing fix * Updating print statements * Example update and minor bugfix * Update examples * Release/0.9.4 (#173) * updating documentation and version log * package gen update * Updating contributing * Changelog date fix * Sprk 175 - Refactoring settings and command line arguments (#176) * First push refactor settings * First changes to refactor options in sparkle for both settings and CLI args * Updating settings with new workflow for options and creating pytests accordingly * Updating arguments * command fixes * Minor bugfixes * pytest fix * test fix * snapshots fix * minor bugfix * pytest expansion * Various bugfixes for settings handling * enum bugfix * logging fix * logging fix * selector scenario bugfix * test fixes * snapshot fix * test speed up * pytest fixes * Removing print statement * Remove comments * Changelog * typo * typos * SPRK 177 - Refactor marginal contribution command out of Sparkle (#178) * removing marginal contribution as CLI method * adding new test files * Replacing run_portfolio core with selector_cli * Test fix * Test fix * changelog * serialisation bugfix * Updating cli and adding tests * improved coverage * update tests * test fixes * test fix * Check fix incase runsolver is not present * Issue #169 (#180) * Issue #169 * Changed timestamp generation moment and fixed failing tests * ablation snapshot fix * Refactored resolving the directories * Adjusted find_scenario --------- Co-authored-by: Thijs Snelleman <[email protected]> * Feature dataframe tests (#183) Co-authored-by: Thijs Snelleman <[email protected]> * Refactoring compute features from CLI into package * Changed FeatureDataframe to subclass of pd.DataFrame (#186) * Changed FeatureDataframe to subclass of pd.DataFrame * Changed feature dataframe access in the codebase * Replace flake8 in Sparkle with Ruff (#187) * Ruff config * Formatted code and fixed linting errors * Fixed pre-commit config * Updated github linter action * Disabled linter check for line-length because formatter may exceed line-length * Removed flake8 mentions * Bugfix for passing configurator to CLI * remove print statement * Implemented seed functionality (#191) * Implemented seed functionality * Incorporated feedback * Added seed logging * Adjusted the header for the log file * Changelog update * Sprk 170 (#190) * generate appendix with max cols per table logic * splitting cells and column headers logic after a fixed length * rename variable names for readability and adjust comments * fix break logic during for loop in append_dataframe_longtable * add functionality: path segment remove and centering the header of the multicolumn * isolating appendix section * putting the helper functions inside append_dataframe_longtable, fix naming issues, fix tabulator * Add appendicies arg to argparse * Add argument container of appendix to argparse_custom * Add appendix to general section of settings as option * Change AppendixReportArgument to action:store_store * Change _abstract_getter to read bool value of appendix from settings * delete unnecessary custom argparse for appendix * Change custom argparse to using option for appendix * adjust kwargs property for handling "action" * Issue 188 - Added test for high concurrency writing to PDF (#193) * First test updates * Bugfixes pytest * Fix comment * bugfixes * solver test update * bugfixes * file fix * Fixing speed up for PDF loading duplicate values * Adding new test, fixing bugs * bugfix * minor fixes * smac2 seed bugfix * Updating settings for git and pytest * Fixing cleanup to also correct PDF from logs * test fix * Disable performance tests for running "all" due to heavy load * ParamILS seed fix * Updating cleanup functionality to remove empty configs * config scenarios bugfixes * Adding minimum marginal contribution option * print statement update * irace scenario bugfix * typo * jobname fix * minor refactor * Adding notes * remove print statement * Preparing release * Updating examples * Updating command descs * Updating package info * Configurator bugfix * remove old file * Fixing merge errors from main * Fixing another settings error --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]>
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* Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Release/0.9.3.1 (#152) * Preparing minor release * Disabling test * Minor bug fixes * Minor refactor of IRACE configure method * test update * Updating changelog and version number and adding distributable (#154) * Release + Fixes (#155) * Release/0.9.3.1 (#151) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Preparing minor release * Disabling test --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * release prep * Release/0.9.3.2 (#153) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Release/0.9.3.1 (#152) * Preparing minor release * Disabling test * Minor bug fixes * Minor refactor of IRACE configure method * test update * Updating changelog and version number and adding distributable --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * Removing handmade dists for automatic releases fix * Bugfix --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * template fix * SPRK 373 - Enable selection over algorithm configurations (#165) * First step * Remove file * Adding code to extract and pivot data to a table containins multiple configurations * update * Adding configurations to portfolio core * test update to avoid file writing * Implementing changes to run portfolio with various configurations * more changes * Update comments to be more informative * Performance dataframe update to present configurations as columns * Adding/removing solvers bug fix * Updating functionality to be more flexible * Updating configurator (SMAC2) to work with new PDF structure for configs * Irace update * SMAC3 update * Paramils fix * delete old component * Have SMAC3 use the same resource limit as smac2 * Refactor code * BUgfixes and refactoring * Replacing test file with new setting * Bugfixes marginal contribution test * smac2 test fix * Test fixes * Test bugfixes * Update snapshots * Integration test updates * remove print statements * remove dead code * Test fix * marginal contribution test fix * Report generation bugfixes * Ablation test fix * Refactoring and updating todos * test fix * Changelog update * test fix * test files sorted update * ASF-lib downgrade due to bug * Test fix, version fix * Delete unnecessary files, attempted test fix * Remove duplicate test * Snapshot fixes * test file fix * Sprk 162 (#166) * Solver wrapper update * print fix * Minor fixes * Solver update, bugfixes * wrapper echo fix * remove old comment * cli bugfix * Implementing check function for solvers, updating solver wrappers to handle kill signals, removing tmp/log dir from sparkle executables * Adding feature extractor tests to check command * Adding instance set to check function * Extra test * Updating wrappers documentation * bugfix * Update changelog * Bugfixes * Bugfix for default value overriding user input * Fixing name change * Name change * Solver wrapper bugfix * Sprk 150 (#157) * fixed typos and errors of SPRK-372 * test ssh connection * split run_parallel_portfolio function into seperate functions * Adjust test of run_parallel_portfolio to its new version * added missing part for writing output to csv * Remove redundant file * Argument parser always at the top of a file * delete run_parallel_portfolio, write results in PerformanceDataFrame * added create performance dataframe function * change function place * adjust test file according to new changes * fix type mismatching in test file * fix typos in test file * fix attribute typo * delete unnecessary print --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 161 (#168) * First big update for reporting changes * update argument name for clarity * extractor bugfix * Updating selector to use SelectionScenario * Renaming example extractor * Code update for extractor rename * test file update * remove dead files * First rebuild of report generation for selection scenarios * remove dead line * Minor fixes * Updating configuration scenario to contain number of runs and generate steady config ids * remove print statements * Updating configuration output processing and report generation * Bugfixes Paramils + smac2 configuration in one report * Adding ablation scenario to the new generation structure * Removing comments * Add parallel portfolio reporting * Remove dead files * cleanup * Updating tests * pytest fix * bugfix * pytest update * irace testfix * pytest fix smac3 scenario * smac2 scenario init fix * paramils test update * ablation test fixes * selector test update * settings bugfix * test snapshot fix * snapshot fixes * config report generation bugfixes * Test file fix * Update changelog * bugfix * parallel portfolio update * snapshot fix * marginal contribution fixes * selector test update * report bugfixes * configured snapshot fixes * snapshot instance bugfix * Refreshing scenarios bugfix * Kaleido/Plotly upgrade and configscenario timestamp bugfix * Sprk 352 (#167) * Merged with current development branch * Merge * Fixed merging errors * Formatting * Fixed test and merging errors * Fixed indexing error * Snapshot fixes for github * setup missing kaleido for some reason * Review changes * Adjusted portfolio constructor and instance tests * disable report tests on github * changelog update * removing comments --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 171 - Modularity of configurators (#172) * Moving files to prepare for on-the-fly installation of configurators and reduce installation size of sparkle * URL update * Updating downloaders of SMAC2 and ParamILS * Fixing IRACE installation to be handled by configurator class * Irace install bugfixes * Updating configurator class * Fixing tests, removing redundant code * test b ugfixes * changelog update * ablation path fix * initialise fix for non interactive sessions * Test update * fix configurator test * test fix github attempt * test fix attempt * Attempt test fix input * Adding install option to configure solver command * irace bugfix * test fix return value * pytest update * updating test stability * Post merge update for URLs * adding test file * job list bugfix * Various bugfixes for report generation * selection example bugfixes * pytest bugfix * Test fix * update contributing text * merge main fix * delete dead code * fix file pathing * contributing fix * Updating print statements * Example update and minor bugfix * Update examples * Release/0.9.4 (#173) * updating documentation and version log * package gen update * Updating contributing * Changelog date fix * Sprk 175 - Refactoring settings and command line arguments (#176) * First push refactor settings * First changes to refactor options in sparkle for both settings and CLI args * Updating settings with new workflow for options and creating pytests accordingly * Updating arguments * command fixes * Minor bugfixes * pytest fix * test fix * snapshots fix * minor bugfix * pytest expansion * Various bugfixes for settings handling * enum bugfix * logging fix * logging fix * selector scenario bugfix * test fixes * snapshot fix * test speed up * pytest fixes * Removing print statement * Remove comments * Changelog * typo * typos * SPRK 177 - Refactor marginal contribution command out of Sparkle (#178) * removing marginal contribution as CLI method * adding new test files * Replacing run_portfolio core with selector_cli * Test fix * Test fix * changelog * serialisation bugfix * Updating cli and adding tests * improved coverage * update tests * test fixes * test fix * Check fix incase runsolver is not present * Issue #169 (#180) * Issue #169 * Changed timestamp generation moment and fixed failing tests * ablation snapshot fix * Refactored resolving the directories * Adjusted find_scenario --------- Co-authored-by: Thijs Snelleman <[email protected]> * Feature dataframe tests (#183) Co-authored-by: Thijs Snelleman <[email protected]> * Refactoring compute features from CLI into package * Changed FeatureDataframe to subclass of pd.DataFrame (#186) * Changed FeatureDataframe to subclass of pd.DataFrame * Changed feature dataframe access in the codebase * Replace flake8 in Sparkle with Ruff (#187) * Ruff config * Formatted code and fixed linting errors * Fixed pre-commit config * Updated github linter action * Disabled linter check for line-length because formatter may exceed line-length * Removed flake8 mentions * Bugfix for passing configurator to CLI * remove print statement * Implemented seed functionality (#191) * Implemented seed functionality * Incorporated feedback * Added seed logging * Adjusted the header for the log file * Changelog update * Sprk 170 (#190) * generate appendix with max cols per table logic * splitting cells and column headers logic after a fixed length * rename variable names for readability and adjust comments * fix break logic during for loop in append_dataframe_longtable * add functionality: path segment remove and centering the header of the multicolumn * isolating appendix section * putting the helper functions inside append_dataframe_longtable, fix naming issues, fix tabulator * Add appendicies arg to argparse * Add argument container of appendix to argparse_custom * Add appendix to general section of settings as option * Change AppendixReportArgument to action:store_store * Change _abstract_getter to read bool value of appendix from settings * delete unnecessary custom argparse for appendix * Change custom argparse to using option for appendix * adjust kwargs property for handling "action" * Issue 188 - Added test for high concurrency writing to PDF (#193) * First test updates * Bugfixes pytest * Fix comment * bugfixes * solver test update * bugfixes * file fix * Fixing speed up for PDF loading duplicate values * Adding new test, fixing bugs * bugfix * minor fixes * smac2 seed bugfix * Updating settings for git and pytest * Fixing cleanup to also correct PDF from logs * test fix * Disable performance tests for running "all" due to heavy load * ParamILS seed fix * Updating cleanup functionality to remove empty configs * config scenarios bugfixes * Adding minimum marginal contribution option * print statement update * irace scenario bugfix * typo * jobname fix * minor refactor * Adding notes * remove print statement * Release/0.9.5 (#196) * Release/0.9.4 (#174) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fi…
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* Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Release/0.9.3.1 (#152) * Preparing minor release * Disabling test * Minor bug fixes * Minor refactor of IRACE configure method * test update * Updating changelog and version number and adding distributable (#154) * Release + Fixes (#155) * Release/0.9.3.1 (#151) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Preparing minor release * Disabling test --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * release prep * Release/0.9.3.2 (#153) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Release/0.9.3.1 (#152) * Preparing minor release * Disabling test * Minor bug fixes * Minor refactor of IRACE configure method * test update * Updating changelog and version number and adding distributable --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * Removing handmade dists for automatic releases fix * Bugfix --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * template fix * SPRK 373 - Enable selection over algorithm configurations (#165) * First step * Remove file * Adding code to extract and pivot data to a table containins multiple configurations * update * Adding configurations to portfolio core * test update to avoid file writing * Implementing changes to run portfolio with various configurations * more changes * Update comments to be more informative * Performance dataframe update to present configurations as columns * Adding/removing solvers bug fix * Updating functionality to be more flexible * Updating configurator (SMAC2) to work with new PDF structure for configs * Irace update * SMAC3 update * Paramils fix * delete old component * Have SMAC3 use the same resource limit as smac2 * Refactor code * BUgfixes and refactoring * Replacing test file with new setting * Bugfixes marginal contribution test * smac2 test fix * Test fixes * Test bugfixes * Update snapshots * Integration test updates * remove print statements * remove dead code * Test fix * marginal contribution test fix * Report generation bugfixes * Ablation test fix * Refactoring and updating todos * test fix * Changelog update * test fix * test files sorted update * ASF-lib downgrade due to bug * Test fix, version fix * Delete unnecessary files, attempted test fix * Remove duplicate test * Snapshot fixes * test file fix * Sprk 162 (#166) * Solver wrapper update * print fix * Minor fixes * Solver update, bugfixes * wrapper echo fix * remove old comment * cli bugfix * Implementing check function for solvers, updating solver wrappers to handle kill signals, removing tmp/log dir from sparkle executables * Adding feature extractor tests to check command * Adding instance set to check function * Extra test * Updating wrappers documentation * bugfix * Update changelog * Bugfixes * Bugfix for default value overriding user input * Fixing name change * Name change * Solver wrapper bugfix * Sprk 150 (#157) * fixed typos and errors of SPRK-372 * test ssh connection * split run_parallel_portfolio function into seperate functions * Adjust test of run_parallel_portfolio to its new version * added missing part for writing output to csv * Remove redundant file * Argument parser always at the top of a file * delete run_parallel_portfolio, write results in PerformanceDataFrame * added create performance dataframe function * change function place * adjust test file according to new changes * fix type mismatching in test file * fix typos in test file * fix attribute typo * delete unnecessary print --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 161 (#168) * First big update for reporting changes * update argument name for clarity * extractor bugfix * Updating selector to use SelectionScenario * Renaming example extractor * Code update for extractor rename * test file update * remove dead files * First rebuild of report generation for selection scenarios * remove dead line * Minor fixes * Updating configuration scenario to contain number of runs and generate steady config ids * remove print statements * Updating configuration output processing and report generation * Bugfixes Paramils + smac2 configuration in one report * Adding ablation scenario to the new generation structure * Removing comments * Add parallel portfolio reporting * Remove dead files * cleanup * Updating tests * pytest fix * bugfix * pytest update * irace testfix * pytest fix smac3 scenario * smac2 scenario init fix * paramils test update * ablation test fixes * selector test update * settings bugfix * test snapshot fix * snapshot fixes * config report generation bugfixes * Test file fix * Update changelog * bugfix * parallel portfolio update * snapshot fix * marginal contribution fixes * selector test update * report bugfixes * configured snapshot fixes * snapshot instance bugfix * Refreshing scenarios bugfix * Kaleido/Plotly upgrade and configscenario timestamp bugfix * Sprk 352 (#167) * Merged with current development branch * Merge * Fixed merging errors * Formatting * Fixed test and merging errors * Fixed indexing error * Snapshot fixes for github * setup missing kaleido for some reason * Review changes * Adjusted portfolio constructor and instance tests * disable report tests on github * changelog update * removing comments --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 171 - Modularity of configurators (#172) * Moving files to prepare for on-the-fly installation of configurators and reduce installation size of sparkle * URL update * Updating downloaders of SMAC2 and ParamILS * Fixing IRACE installation to be handled by configurator class * Irace install bugfixes * Updating configurator class * Fixing tests, removing redundant code * test b ugfixes * changelog update * ablation path fix * initialise fix for non interactive sessions * Test update * fix configurator test * test fix github attempt * test fix attempt * Attempt test fix input * Adding install option to configure solver command * irace bugfix * test fix return value * pytest update * updating test stability * Post merge update for URLs * adding test file * job list bugfix * Various bugfixes for report generation * selection example bugfixes * pytest bugfix * Test fix * update contributing text * merge main fix * delete dead code * fix file pathing * contributing fix * Updating print statements * Example update and minor bugfix * Update examples * Release/0.9.4 (#173) * updating documentation and version log * package gen update * Updating contributing * Changelog date fix * Sprk 175 - Refactoring settings and command line arguments (#176) * First push refactor settings * First changes to refactor options in sparkle for both settings and CLI args * Updating settings with new workflow for options and creating pytests accordingly * Updating arguments * command fixes * Minor bugfixes * pytest fix * test fix * snapshots fix * minor bugfix * pytest expansion * Various bugfixes for settings handling * enum bugfix * logging fix * logging fix * selector scenario bugfix * test fixes * snapshot fix * test speed up * pytest fixes * Removing print statement * Remove comments * Changelog * typo * typos * SPRK 177 - Refactor marginal contribution command out of Sparkle (#178) * removing marginal contribution as CLI method * adding new test files * Replacing run_portfolio core with selector_cli * Test fix * Test fix * changelog * serialisation bugfix * Updating cli and adding tests * improved coverage * update tests * test fixes * test fix * Check fix incase runsolver is not present * Issue #169 (#180) * Issue #169 * Changed timestamp generation moment and fixed failing tests * ablation snapshot fix * Refactored resolving the directories * Adjusted find_scenario --------- Co-authored-by: Thijs Snelleman <[email protected]> * Feature dataframe tests (#183) Co-authored-by: Thijs Snelleman <[email protected]> * Refactoring compute features from CLI into package * Changed FeatureDataframe to subclass of pd.DataFrame (#186) * Changed FeatureDataframe to subclass of pd.DataFrame * Changed feature dataframe access in the codebase * Replace flake8 in Sparkle with Ruff (#187) * Ruff config * Formatted code and fixed linting errors * Fixed pre-commit config * Updated github linter action * Disabled linter check for line-length because formatter may exceed line-length * Removed flake8 mentions * Bugfix for passing configurator to CLI * remove print statement * Implemented seed functionality (#191) * Implemented seed functionality * Incorporated feedback * Added seed logging * Adjusted the header for the log file * Changelog update * Sprk 170 (#190) * generate appendix with max cols per table logic * splitting cells and column headers logic after a fixed length * rename variable names for readability and adjust comments * fix break logic during for loop in append_dataframe_longtable * add functionality: path segment remove and centering the header of the multicolumn * isolating appendix section * putting the helper functions inside append_dataframe_longtable, fix naming issues, fix tabulator * Add appendicies arg to argparse * Add argument container of appendix to argparse_custom * Add appendix to general section of settings as option * Change AppendixReportArgument to action:store_store * Change _abstract_getter to read bool value of appendix from settings * delete unnecessary custom argparse for appendix * Change custom argparse to using option for appendix * adjust kwargs property for handling "action" * Issue 188 - Added test for high concurrency writing to PDF (#193) * First test updates * Bugfixes pytest * Fix comment * bugfixes * solver test update * bugfixes * file fix * Fixing speed up for PDF loading duplicate values * Adding new test, fixing bugs * bugfix * minor fixes * smac2 seed bugfix * Updating settings for git and pytest * Fixing cleanup to also correct PDF from logs * test fix * Disable performance tests for running "all" due to heavy load * ParamILS seed fix * Updating cleanup functionality to remove empty configs * config scenarios bugfixes * Adding minimum marginal contribution option * print statement update * irace scenario bugfix * typo * jobname fix * minor refactor * Adding notes * remove print statement * Release/0.9.5 (#196) * Release/0.9.4 (#174) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a te…
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* Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Release/0.9.3.1 (#152) * Preparing minor release * Disabling test * Minor bug fixes * Minor refactor of IRACE configure method * test update * Updating changelog and version number and adding distributable (#154) * Release + Fixes (#155) * Release/0.9.3.1 (#151) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Preparing minor release * Disabling test --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * release prep * Release/0.9.3.2 (#153) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Release/0.9.3.1 (#152) * Preparing minor release * Disabling test * Minor bug fixes * Minor refactor of IRACE configure method * test update * Updating changelog and version number and adding distributable --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * Removing handmade dists for automatic releases fix * Bugfix --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * template fix * SPRK 373 - Enable selection over algorithm configurations (#165) * First step * Remove file * Adding code to extract and pivot data to a table containins multiple configurations * update * Adding configurations to portfolio core * test update to avoid file writing * Implementing changes to run portfolio with various configurations * more changes * Update comments to be more informative * Performance dataframe update to present configurations as columns * Adding/removing solvers bug fix * Updating functionality to be more flexible * Updating configurator (SMAC2) to work with new PDF structure for configs * Irace update * SMAC3 update * Paramils fix * delete old component * Have SMAC3 use the same resource limit as smac2 * Refactor code * BUgfixes and refactoring * Replacing test file with new setting * Bugfixes marginal contribution test * smac2 test fix * Test fixes * Test bugfixes * Update snapshots * Integration test updates * remove print statements * remove dead code * Test fix * marginal contribution test fix * Report generation bugfixes * Ablation test fix * Refactoring and updating todos * test fix * Changelog update * test fix * test files sorted update * ASF-lib downgrade due to bug * Test fix, version fix * Delete unnecessary files, attempted test fix * Remove duplicate test * Snapshot fixes * test file fix * Sprk 162 (#166) * Solver wrapper update * print fix * Minor fixes * Solver update, bugfixes * wrapper echo fix * remove old comment * cli bugfix * Implementing check function for solvers, updating solver wrappers to handle kill signals, removing tmp/log dir from sparkle executables * Adding feature extractor tests to check command * Adding instance set to check function * Extra test * Updating wrappers documentation * bugfix * Update changelog * Bugfixes * Bugfix for default value overriding user input * Fixing name change * Name change * Solver wrapper bugfix * Sprk 150 (#157) * fixed typos and errors of SPRK-372 * test ssh connection * split run_parallel_portfolio function into seperate functions * Adjust test of run_parallel_portfolio to its new version * added missing part for writing output to csv * Remove redundant file * Argument parser always at the top of a file * delete run_parallel_portfolio, write results in PerformanceDataFrame * added create performance dataframe function * change function place * adjust test file according to new changes * fix type mismatching in test file * fix typos in test file * fix attribute typo * delete unnecessary print --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 161 (#168) * First big update for reporting changes * update argument name for clarity * extractor bugfix * Updating selector to use SelectionScenario * Renaming example extractor * Code update for extractor rename * test file update * remove dead files * First rebuild of report generation for selection scenarios * remove dead line * Minor fixes * Updating configuration scenario to contain number of runs and generate steady config ids * remove print statements * Updating configuration output processing and report generation * Bugfixes Paramils + smac2 configuration in one report * Adding ablation scenario to the new generation structure * Removing comments * Add parallel portfolio reporting * Remove dead files * cleanup * Updating tests * pytest fix * bugfix * pytest update * irace testfix * pytest fix smac3 scenario * smac2 scenario init fix * paramils test update * ablation test fixes * selector test update * settings bugfix * test snapshot fix * snapshot fixes * config report generation bugfixes * Test file fix * Update changelog * bugfix * parallel portfolio update * snapshot fix * marginal contribution fixes * selector test update * report bugfixes * configured snapshot fixes * snapshot instance bugfix * Refreshing scenarios bugfix * Kaleido/Plotly upgrade and configscenario timestamp bugfix * Sprk 352 (#167) * Merged with current development branch * Merge * Fixed merging errors * Formatting * Fixed test and merging errors * Fixed indexing error * Snapshot fixes for github * setup missing kaleido for some reason * Review changes * Adjusted portfolio constructor and instance tests * disable report tests on github * changelog update * removing comments --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 171 - Modularity of configurators (#172) * Moving files to prepare for on-the-fly installation of configurators and reduce installation size of sparkle * URL update * Updating downloaders of SMAC2 and ParamILS * Fixing IRACE installation to be handled by configurator class * Irace install bugfixes * Updating configurator class * Fixing tests, removing redundant code * test b ugfixes * changelog update * ablation path fix * initialise fix for non interactive sessions * Test update * fix configurator test * test fix github attempt * test fix attempt * Attempt test fix input * Adding install option to configure solver command * irace bugfix * test fix return value * pytest update * updating test stability * Post merge update for URLs * adding test file * job list bugfix * Various bugfixes for report generation * selection example bugfixes * pytest bugfix * Test fix * update contributing text * merge main fix * delete dead code * fix file pathing * contributing fix * Updating print statements * Example update and minor bugfix * Update examples * Release/0.9.4 (#173) * updating documentation and version log * package gen update * Updating contributing * Changelog date fix * Sprk 175 - Refactoring settings and command line arguments (#176) * First push refactor settings * First changes to refactor options in sparkle for both settings and CLI args * Updating settings with new workflow for options and creating pytests accordingly * Updating arguments * command fixes * Minor bugfixes * pytest fix * test fix * snapshots fix * minor bugfix * pytest expansion * Various bugfixes for settings handling * enum bugfix * logging fix * logging fix * selector scenario bugfix * test fixes * snapshot fix * test speed up * pytest fixes * Removing print statement * Remove comments * Changelog * typo * typos * SPRK 177 - Refactor marginal contribution command out of Sparkle (#178) * removing marginal contribution as CLI method * adding new test files * Replacing run_portfolio core with selector_cli * Test fix * Test fix * changelog * serialisation bugfix * Updating cli and adding tests * improved coverage * update tests * test fixes * test fix * Check fix incase runsolver is not present * Issue #169 (#180) * Issue #169 * Changed timestamp generation moment and fixed failing tests * ablation snapshot fix * Refactored resolving the directories * Adjusted find_scenario --------- Co-authored-by: Thijs Snelleman <[email protected]> * Feature dataframe tests (#183) Co-authored-by: Thijs Snelleman <[email protected]> * Refactoring compute features from CLI into package * Changed FeatureDataframe to subclass of pd.DataFrame (#186) * Changed FeatureDataframe to subclass of pd.DataFrame * Changed feature dataframe access in the codebase * Replace flake8 in Sparkle with Ruff (#187) * Ruff config * Formatted code and fixed linting errors * Fixed pre-commit config * Updated github linter action * Disabled linter check for line-length because formatter may exceed line-length * Removed flake8 mentions * Bugfix for passing configurator to CLI * remove print statement * Implemented seed functionality (#191) * Implemented seed functionality * Incorporated feedback * Added seed logging * Adjusted the header for the log file * Changelog update * Sprk 170 (#190) * generate appendix with max cols per table logic * splitting cells and column headers logic after a fixed length * rename variable names for readability and adjust comments * fix break logic during for loop in append_dataframe_longtable * add functionality: path segment remove and centering the header of the multicolumn * isolating appendix section * putting the helper functions inside append_dataframe_longtable, fix naming issues, fix tabulator * Add appendicies arg to argparse * Add argument container of appendix to argparse_custom * Add appendix to general section of settings as option * Change AppendixReportArgument to action:store_store * Change _abstract_getter to read bool value of appendix from settings * delete unnecessary custom argparse for appendix * Change custom argparse to using option for appendix * adjust kwargs property for handling "action" * Issue 188 - Added test for high concurrency writing to PDF (#193) * First test updates * Bugfixes pytest * Fix comment * bugfixes * solver test update * bugfixes * file fix * Fixing speed up for PDF loading duplicate values * Adding new test, fixing bugs * bugfix * minor fixes * smac2 seed bugfix * Updating settings for git and pytest * Fixing cleanup to also correct PDF from logs * test fix * Disable performance tests for running "all" due to heavy load * ParamILS seed fix * Updating cleanup functionality to remove empty configs * config scenarios bugfixes * Adding minimum marginal contribution option * print statement update * irace scenario bugfix * typo * jobname fix * minor refactor * Adding notes * remove print statement * Release/0.9.5 (#196) * Release/0.9.4 (#174) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test *…
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* Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Release/0.9.3.1 (#152) * Preparing minor release * Disabling test * Minor bug fixes * Minor refactor of IRACE configure method * test update * Updating changelog and version number and adding distributable (#154) * Release + Fixes (#155) * Release/0.9.3.1 (#151) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Preparing minor release * Disabling test --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * release prep * Release/0.9.3.2 (#153) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * Expanded testing for IRACE parsing/exporting * Setting up SMAC2 exporter * SMAC2 Exporter bugfixes * Various bug fixes, placing PCSConverter into Solver class * Fixes regarding IRACE submissions * Environment updates + changelog * Pytest fixes * Refactoring PCS file contents * renaming file to be more representative * Fix * Various bugs and pytest fixes * Bug fix * Regex bugfix * Adding two extra test files provided by marie * Updating runrunner version * Updating settings and docs * Bugfixes for parsing ParamILS * test bugfix * test bugfix * parameter fix for paramils * Updating slurm script prepends * Updating docs * irace test fixes * smac2 test fix * Settings bugfixes * typo * Bugfixes for ablation * Update test name * Logging fix attempt * Attempted bugfix for tests on github * Comment * Ablation bug fixes * Review fixes * Update ParamILS * Fixes for github pytests * github pytest bugfixess * test fix for github * cluster name getting fix * SMAC3 mapping update * smac2 regex update * smac2 parsing bugfix * params fix smac2 * Parallel portfolio bugfixes * test bugfixes * Bugfixes for portfolio running * Log dir fix * Runrunner bugfixes * Sprk 353 (#143) * Implemented unit tests for the selector class. * Formatted code * Fixed formatting issues * Added checks for add_to_queue parameters * Pytest fix attempt * Fix attempt --------- Co-authored-by: Thijs Snelleman <[email protected]> * Release/0.9.3 (#145) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Release/0.9.2 (#134) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline --------- Co-authored-by: Hadar Shavit <[email protected]> * Documentation update * Removing example files from configurators to reduce repo/tarball size * New version tarball * Set change log date --------- Co-authored-by: Hadar Shavit <[email protected]> * Sprk 349 (#147) * test for create_configuration_file * test for create_instance_file_train_set * test for create_instance_file_test_set * take back the changes to update the branch * Recovering the codes * Created test files for ablation scenarios * Create missing variable * ablation tests done * Update missing variable with init value * Update and extend test cases * Update test create configuration file * Update return value of function * Update test case create_instance_file, add explanations * Sprk 372 (#148) * Created test .csv file * test_run_parallel_portfolio function done * deleting unnecessary files * Delete unnecessary variables, reformat the code for more readability * Create new class FakeJob to mimick the jobs for testing * add cases to test_run_parallel_portfolio to test different status cases * added test function for parser_function * test_main function updated, getting error cause of the format of the input * Update test_main function, still getting error from parser * test_main function update, still error from parser * added tests cases to test_main, change structure of test file * fixed typo on comment * Delete unnecessary comments * Test fix * Typo * Bugfix regarding passing job prepend to runrunner * More bugfixes * More bugfix * Release/0.9.3.1 (#152) * Preparing minor release * Disabling test * Minor bug fixes * Minor refactor of IRACE configure method * test update * Updating changelog and version number and adding distributable --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * Removing handmade dists for automatic releases fix * Bugfix --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: emirpisirici <[email protected]> Co-authored-by: Max van Gemmeren <[email protected]> * template fix * SPRK 373 - Enable selection over algorithm configurations (#165) * First step * Remove file * Adding code to extract and pivot data to a table containins multiple configurations * update * Adding configurations to portfolio core * test update to avoid file writing * Implementing changes to run portfolio with various configurations * more changes * Update comments to be more informative * Performance dataframe update to present configurations as columns * Adding/removing solvers bug fix * Updating functionality to be more flexible * Updating configurator (SMAC2) to work with new PDF structure for configs * Irace update * SMAC3 update * Paramils fix * delete old component * Have SMAC3 use the same resource limit as smac2 * Refactor code * BUgfixes and refactoring * Replacing test file with new setting * Bugfixes marginal contribution test * smac2 test fix * Test fixes * Test bugfixes * Update snapshots * Integration test updates * remove print statements * remove dead code * Test fix * marginal contribution test fix * Report generation bugfixes * Ablation test fix * Refactoring and updating todos * test fix * Changelog update * test fix * test files sorted update * ASF-lib downgrade due to bug * Test fix, version fix * Delete unnecessary files, attempted test fix * Remove duplicate test * Snapshot fixes * test file fix * Sprk 162 (#166) * Solver wrapper update * print fix * Minor fixes * Solver update, bugfixes * wrapper echo fix * remove old comment * cli bugfix * Implementing check function for solvers, updating solver wrappers to handle kill signals, removing tmp/log dir from sparkle executables * Adding feature extractor tests to check command * Adding instance set to check function * Extra test * Updating wrappers documentation * bugfix * Update changelog * Bugfixes * Bugfix for default value overriding user input * Fixing name change * Name change * Solver wrapper bugfix * Sprk 150 (#157) * fixed typos and errors of SPRK-372 * test ssh connection * split run_parallel_portfolio function into seperate functions * Adjust test of run_parallel_portfolio to its new version * added missing part for writing output to csv * Remove redundant file * Argument parser always at the top of a file * delete run_parallel_portfolio, write results in PerformanceDataFrame * added create performance dataframe function * change function place * adjust test file according to new changes * fix type mismatching in test file * fix typos in test file * fix attribute typo * delete unnecessary print --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 161 (#168) * First big update for reporting changes * update argument name for clarity * extractor bugfix * Updating selector to use SelectionScenario * Renaming example extractor * Code update for extractor rename * test file update * remove dead files * First rebuild of report generation for selection scenarios * remove dead line * Minor fixes * Updating configuration scenario to contain number of runs and generate steady config ids * remove print statements * Updating configuration output processing and report generation * Bugfixes Paramils + smac2 configuration in one report * Adding ablation scenario to the new generation structure * Removing comments * Add parallel portfolio reporting * Remove dead files * cleanup * Updating tests * pytest fix * bugfix * pytest update * irace testfix * pytest fix smac3 scenario * smac2 scenario init fix * paramils test update * ablation test fixes * selector test update * settings bugfix * test snapshot fix * snapshot fixes * config report generation bugfixes * Test file fix * Update changelog * bugfix * parallel portfolio update * snapshot fix * marginal contribution fixes * selector test update * report bugfixes * configured snapshot fixes * snapshot instance bugfix * Refreshing scenarios bugfix * Kaleido/Plotly upgrade and configscenario timestamp bugfix * Sprk 352 (#167) * Merged with current development branch * Merge * Fixed merging errors * Formatting * Fixed test and merging errors * Fixed indexing error * Snapshot fixes for github * setup missing kaleido for some reason * Review changes * Adjusted portfolio constructor and instance tests * disable report tests on github * changelog update * removing comments --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 171 - Modularity of configurators (#172) * Moving files to prepare for on-the-fly installation of configurators and reduce installation size of sparkle * URL update * Updating downloaders of SMAC2 and ParamILS * Fixing IRACE installation to be handled by configurator class * Irace install bugfixes * Updating configurator class * Fixing tests, removing redundant code * test b ugfixes * changelog update * ablation path fix * initialise fix for non interactive sessions * Test update * fix configurator test * test fix github attempt * test fix attempt * Attempt test fix input * Adding install option to configure solver command * irace bugfix * test fix return value * pytest update * updating test stability * Post merge update for URLs * adding test file * job list bugfix * Various bugfixes for report generation * selection example bugfixes * pytest bugfix * Test fix * update contributing text * merge main fix * delete dead code * fix file pathing * contributing fix * Updating print statements * Example update and minor bugfix * Update examples * Release/0.9.4 (#173) * updating documentation and version log * package gen update * Updating contributing * Changelog date fix * Sprk 175 - Refactoring settings and command line arguments (#176) * First push refactor settings * First changes to refactor options in sparkle for both settings and CLI args * Updating settings with new workflow for options and creating pytests accordingly * Updating arguments * command fixes * Minor bugfixes * pytest fix * test fix * snapshots fix * minor bugfix * pytest expansion * Various bugfixes for settings handling * enum bugfix * logging fix * logging fix * selector scenario bugfix * test fixes * snapshot fix * test speed up * pytest fixes * Removing print statement * Remove comments * Changelog * typo * typos * SPRK 177 - Refactor marginal contribution command out of Sparkle (#178) * removing marginal contribution as CLI method * adding new test files * Replacing run_portfolio core with selector_cli * Test fix * Test fix * changelog * serialisation bugfix * Updating cli and adding tests * improved coverage * update tests * test fixes * test fix * Check fix incase runsolver is not present * Issue #169 (#180) * Issue #169 * Changed timestamp generation moment and fixed failing tests * ablation snapshot fix * Refactored resolving the directories * Adjusted find_scenario --------- Co-authored-by: Thijs Snelleman <[email protected]> * Feature dataframe tests (#183) Co-authored-by: Thijs Snelleman <[email protected]> * Refactoring compute features from CLI into package * Changed FeatureDataframe to subclass of pd.DataFrame (#186) * Changed FeatureDataframe to subclass of pd.DataFrame * Changed feature dataframe access in the codebase * Replace flake8 in Sparkle with Ruff (#187) * Ruff config * Formatted code and fixed linting errors * Fixed pre-commit config * Updated github linter action * Disabled linter check for line-length because formatter may exceed line-length * Removed flake8 mentions * Bugfix for passing configurator to CLI * remove print statement * Implemented seed functionality (#191) * Implemented seed functionality * Incorporated feedback * Added seed logging * Adjusted the header for the log file * Changelog update * Sprk 170 (#190) * generate appendix with max cols per table logic * splitting cells and column headers logic after a fixed length * rename variable names for readability and adjust comments * fix break logic during for loop in append_dataframe_longtable * add functionality: path segment remove and centering the header of the multicolumn * isolating appendix section * putting the helper functions inside append_dataframe_longtable, fix naming issues, fix tabulator * Add appendicies arg to argparse * Add argument container of appendix to argparse_custom * Add appendix to general section of settings as option * Change AppendixReportArgument to action:store_store * Change _abstract_getter to read bool value of appendix from settings * delete unnecessary custom argparse for appendix * Change custom argparse to using option for appendix * adjust kwargs property for handling "action" * Issue 188 - Added test for high concurrency writing to PDF (#193) * First test updates * Bugfixes pytest * Fix comment * bugfixes * solver test update * bugfixes * file fix * Fixing speed up for PDF loading duplicate values * Adding new test, fixing bugs * bugfix * minor fixes * smac2 seed bugfix * Updating settings for git and pytest * Fixing cleanup to also correct PDF from logs * test fix * Disable performance tests for running "all" due to heavy load * ParamILS seed fix * Updating cleanup functionality to remove empty configs * config scenarios bugfixes * Adding minimum marginal contribution option * print statement update * irace scenario bugfix * typo * jobname fix * minor refactor * Adding notes * remove print statement * Release/0.9.5 (#196) * Release/0.9.4 (#174) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Release/0.9.1.2 (#126) (#127) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * Fixed command specification * Adding images to platform documentation * Sprk 364 (#128) * Fixing Feature data for SMAC2 configuration * Updating SMAC3 to take features from FDF * Adding feature data to IRACE * Bugfixes smac3 tests * SMAC2 test update * Irace fixes * Changelog update * Add prefix for cli options (#129) * Sprk 367 - Tutorial tips bug fixes (#130) * Fixing warning messages * Adding python3 infront of python script calls to avoid execution right issues * Changing command log dir naming * Updating Sparkle wait to give better information * Fixing table to change layout once finished * Fixing platform bug where changing dir does not happen on time when executing commands in subdir * Various fixes based on tutorial * Adding documentation for venv * updating logging pytest * Updating Venv installation manual * Adding CLI cores option to SMAC2 * flake8 * Bugfix settings * Bugfixes regarding overscheduling of jobs, adding better names to configuration jobs * Enabling terminal autocompletion of commands (#71) * environment yml fix * Adding in autocompletion to the CLI functionalities * Adding readme * Changelog * Better names * Renamiong file * updating install msg * Script bugfixes * Updating solution verifier argument docs * Changelog fix * flake8 * bugfixes * various cli bugfixes for autocomplete * Adding sparkle autocomplete to bash profile for installation * Updating documentation * RunRunner upgrade * SPRK 343: Merging wait and cancel command into jobs command (#132) * Updating sparkle cancel command to have all functionalities from sparkle wait * Adding comments * Minor bug fixes and performance updates * Renaming cancel command to jobs, adapting CLI args accordingly * Deleting wait command as it is now handled by the jobs command, updating docs accordingly * Changelog mistake * Bugfixes for interactive table * Release/0.9.2 (#133) * Release/0.9.1.2 (#126) * Sprk 361 - Merging run configured solver into run solvers (#123) * Updating run solvers to start a job per solver instead of per instance/run combination * Merging run_configured_solver into run_solvers * updating file names to be more clear, adding place holder test for run solvers * Test fix * Fixing specific configuration running * Update changelog * Bugfixes for selection example * Removing Validation directory from Platform * Reference_List moving into Settings directory * Bugfixes for snapshots * Adding sparkle citation * CLI execution rights fix * Release/0.9.1.1 (#125) * Pathing typos * Updating changelog * Adding init to core module * Patchfix * New distributable * Changelog update, version change, shell script updates * New release tarball * Attempted bug fixes for Github pipeline * Sprk 331 (#135) * Updating FastVC2+p wrapper * updating MinVC solver wrapper * Update tutorial * Updating venv docs * adding flushing to jobs table (spacebar) (#136) * adding flushing to jobs table (spacebar) * Changelog * 2 small fixes (#131) * Print enum value * Add postfix to solvers params * Fixup * Update postfix in docstring * Add type for postfix * fixup * flake8 fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Test matrix (#137) * Add matrix testing for unittest * Update changelog * Updating unittest run condition * Formatting --------- Co-authored-by: Thijs Snelleman <[email protected]> * CLI update (#138) * Sprk 369 (#139) * Updating configure solver to add new runs as 'empty' configurations * Bugfix reporting scenario * Adding check to report generation * Performance dataframe bugfix * Replacing AutoFolio with ASF-lib (#141) * Removing AutoFolio from Sparkle * Removing autofolio pt 2 * Adding pypi publish action for github * intermittent check in * updating asf lib version * Patching data conversion and prediction to new style * Fixing construction process of selectors * ASF total fix * New asflib version * Naming bugfix * PairwiseClassifier replacement * Docs update * Re-adding smac3 to the setup * typo * xgboost requirement * Making hadar happy * First ParamILS (#111) * First ParamILS * Fixes and preps * Updating configurators to latest version of Sparkle * Adding ParamILS 2016 version to Sparkle * Adding execution rights * Removing validation scripts as sparkle validates internally * Replacing smac jar for bugfixes (?) * Updating ParamILS class * Prepping paramils settings * Adding paramils specific settings to sparkle * Adding paramils parameters to the correct dict * Updates to scenario setting files * Update to sparkle settings * Updating docstring * Import bugfix * Bugfixes for ParamILS * Adding pytest for paramils * Parsing + PCS bugfixes for ParamILS * Target algorithm bugfixes, Parameter space conversion bugfixes * Updating paramils output parsing * Updating ParamILS settings handling * Settings bugfixes for ParamILS * Fixing report generation for ParamILS * Updating report text * Removing number of runs from Unit tests as it is directory dependent * Updating sparkle documentation for ParamILS * paramils scenario test fixes --------- Co-authored-by: Thijs Snelleman <[email protected]> * Sprk 350 (#140) * Added test case for constructor of Extractor class * SPRK350: Edited test case for constructor of Extractor class * SPRK-350: Added test for Extractor.features * SPRK350: Update test Extractor.features * SPRK350: Update comments * SPRK350: Update test features * SPRK350: Added test_feature_groups * SPRK350: Update test feature groups * SPRK350: Update test features * SPRK350: Added test feature groups for empty groups * SPRK350: Added test output dimension * SPRK350: Update test output dimension * SPRK350: Update extractor class removed dead variable * SPRK350: Update test empty feature groups * SPRK350: Update test output dimension * SPRK350: Added test groupwise computation * SPRK350: Update test output dimension * SPRK350: Removed comments * SPRK 346: Full PCSParser rework (#142) * First update on new PCS conversion, fixed SMAC2 parsing * Setting up IRACE + test * Add new irace version * Updating IRACE packages * Updating IRACE to v 4.2.0 * Adding source test file in yaml format * Fixing IRACE with a test * E…
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The FeatureDataFrame is now a subclass of pd.Dataframe instead of relying on a dataframe attribute.