·
13 commits
to main
since this release
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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,
rdefault 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
containerskey 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