Version 0.6.0

What's Changed

• fix: let raw_pathway_df handle present headers but no data by @tristan-f-r in #236
• Param tuning: ensembling (version 2 but all the same code as version 1) by @ntalluri in #212
• refactor: redo PRM properties by @tristan-f-r in #285
• test: make sure all inputs exist by @tristan-f-r in #313
• refactor: don't use globals in runner by @tristan-f-r in #287
• feat: ResponseNet by @tristan-f-r in #241
• style: drop unused imports by @tristan-f-r in #343
• docs: light reorganization by @tristan-f-r in #338
• Param tuning code integration: pca chosen by @ntalluri in #209
• test(evaluate): dynamically serialize data.pickle by @tristan-f-r in #340
• docs(rtd): prms by @tristan-f-r in #286
• chore: typos by @tristan-f-r in #347
• docs: display "edit on github" links by @tristan-f-r in #346
• chore: bump dependencies by @tristan-f-r in #310
• fix: typo by @tristan-f-r in #353
• chore: add devcontainer by @tristan-f-r in #312
• docs: responsenet by @tristan-f-r in #350
• chore: run pre-commit on all files by @agitter in #356
• ci: use pre-commit from conda by @tristan-f-r in #352
• fix: preserve pathway.txt files by @tristan-f-r in #360
• fix: make merged files less ambigious by @tristan-f-r in #359
• Make ResponseNet output path Windows compatible by @agitter in #366
• refactor!: config parsing by @tristan-f-r in #292
• docs(rtd): mv contributing guide by @tristan-f-r in #337
• Param tuning code integration:no param tuning by @ntalluri in #208
• docs(contributing): reorganize by @tristan-f-r in #367
• refactor: common validate_required_inputs by @tristan-f-r in #290
• chore: bump pip by @tristan-f-r in #376
• docs(oi1): dummy_mode, r default reasoning by @tristan-f-r in #371
• feat: add new summary statistics by @ntalluri in #368
• ci: split by @tristan-f-r in #282
• docs(pre-commit): drop redundant comment by @tristan-f-r in #384
• test(btb): singularity by @tristan-f-r in #383
• ci: use main branch by @tristan-f-r in #386
• fix: correct oi1 container by @tristan-f-r in #389
• docs(devcontainer): apptainer over singularity by @tristan-f-r in #392
• feat: update evaluation to use edge files by @ntalluri in #375
• docs(htcondor): mention container_framework by @tristan-f-r in #397
• docs(htcondor): 0.2.0 -> 0.5.0 by @tristan-f-r in #396
• Profiling by @jhiemstrawisc in #260
• ci: label merge conflicts by @tristan-f-r in #401
• docs(rtd): update fordevs by @tristan-f-r in #399
• fix: make omicsintegrator2 work offline by @tristan-f-r in #226
• docs(APSP): Link to current location of APSP source by @agitter in #405
• docs(htcondor): mv by @tristan-f-r in #400
• feat: container error handling by @tristan-f-r in #275
• docs: tutorials for COMBINE25 by @ntalluri in #369
• chore: remove Go dependency from environment.yml by @agitter in #412
• ci: re-enable pre-commit by @tristan-f-r in #414
• docs: add readme badge by @tristan-f-r in #416
• docs: highlight yaml by @tristan-f-r in #415
• docs: on parallelization and HPC by @tristan-f-r in #420
• test(btb): drop useless pathloading by @tristan-f-r in #419
• chore(environment.yml): bump pip by @tristan-f-r in #417
• docs: usage typo by @agitter in #422
• docs: naming conventions by @tristan-f-r in #418
• docs: move input file documentation over by @tristan-f-r in #423
• docs: updating tutorial for COMBINE25 by @ntalluri in #421
• ci: don't fail fast by @tristan-f-r in #427
• fix(rwr,strwr): directionality conversions by @tristan-f-r in #426
• refactor!: move container options to shared containers key by @tristan-f-r in #387
• refactor: broaden container settings args by @tristan-f-r in #390
• test(ml): use pathlib by @tristan-f-r in #435
• fix(meo): use non-deprecated base image by @tristan-f-r in #436

Full Changelog: 0.5.0...0.6.0