v3.0.0.dev0

What's Changed

• Multiple species returned in one run by @ChristopherMancuso in #375
• Add Clustering Functionality by @ChristopherMancuso in #381
• initial adding of domino by @ChristopherMancuso in #403
• changed to one-sided p-val test by @ChristopherMancuso in #413
• refactored default params for API and CLI by @ChristopherMancuso in #415
• fixed file name issue in #404 by @ChristopherMancuso in #416
• fix and update pytests by @ChristopherMancuso in #417
• Add documentation for clustering and saving additions by @ChristopherMancuso in #419
• Bump to 3.0.0.dev0 by @ChristopherMancuso in #422

Full Changelog: v2.0.4...v3.0.0.dev0

v2.0.4

Full Changelog: v2.0.3...v2.0.4
Changed from last version due to README.md pointing to wrong data

v2.0.3

What's Changed

• Bump statsmodels from 0.14.2 to 0.14.4 by @dependabot in #357
• Bump pytest-order from 1.1.0 to 1.3.0 by @dependabot in #356
• Bump pytest from 7.4.2 to 8.3.4 by @dependabot in #355
• Bump requests-mock from 1.11.0 to 1.12.1 by @dependabot in #354
• Fixes for changing bug in scaling by @ChristopherMancuso in #368
• Bump pyyaml from 6.0.1 to 6.0.2 by @dependabot in #360
• Bump pytest-cov from 4.1.0 to 6.0.0 by @dependabot in #361
• Bump setuptools from 75.5.0 to 75.8.0 by @dependabot in #362
• Bump requests from 2.31.0 to 2.32.3 by @dependabot in #363
• changes to Zenodo downloader by @ChristopherMancuso in #372
• Bump pystow from 0.6.1 to 0.7.0 by @dependabot in #369
• Bump tox from 4.23.2 to 4.24.1 by @dependabot in #370
• Bump scikit-learn from 1.6.0 to 1.6.1 by @dependabot in #371

Full Changelog: v2.0.2...v2.0.3

v2.0.2

What's Changed

• updated package version in places by @ChristopherMancuso in #353
• update v2.0.1 to v2.0.2 by @ChristopherMancuso in #358

Full Changelog: v2.0.1...v2.0.2

v2.0.1

Full Changelog: v2.0.0...v2.0.1

Update for PYPI project description from README.md. Major release changes in v2.0.0

v2.0.0

What's Changed

• Add sp_trn and sp_tst options by @ChristopherMancuso in #301
• change making sim dfs only from GSC by @ChristopherMancuso in #307
• basic api runs with all parameters by @ChristopherMancuso in #309
• added check if Entrez might not be correct species by @ChristopherMancuso in #311
• Mondo and prop by @ChristopherMancuso in #313
• Api functionality updates by @ChristopherMancuso in #325
• Zenodo and downloads by @ChristopherMancuso in #328
• Fixes to setters and custom by @ChristopherMancuso in #330
• multiple updates to CLI by @ChristopherMancuso in #331
• updated tst to res and code comments by @ChristopherMancuso in #332
• Fix the pytests by @ChristopherMancuso in #333
• updated the example directory by @ChristopherMancuso in #337
• remove custom from read the docs by @ChristopherMancuso in #338
• Pytests, package builds and documentation by @ChristopherMancuso in #339
• added parameter availablity tables by @ChristopherMancuso in #342
• Fix how parameters are set by @ChristopherMancuso in #343
• min positives for training by @ChristopherMancuso in #345
• Added FAQs section by @ChristopherMancuso in #346
• updated the faqs by @ChristopherMancuso in #347
• Bump pystow from 0.5.0 to 0.6.1 by @dependabot in #348
• Bump pytest-mock from 3.11.1 to 3.14.0 by @dependabot in #310
• Bump scikit-learn from 1.3.0 to 1.6.0 by @dependabot in #349
• Bump tqdm from 4.65.0 to 4.67.1 by @dependabot in #350

Full Changelog: v1.0.1...v2.0.0

v2.0.0.dev

What's Changed

• Add sp_trn and sp_tst options by @ChristopherMancuso in #301
• change making sim dfs only from GSC by @ChristopherMancuso in #307
• basic api runs with all parameters by @ChristopherMancuso in #309
• added check if Entrez might not be correct species by @ChristopherMancuso in #311
• Mondo and prop by @ChristopherMancuso in #313
• Api functionality updates by @ChristopherMancuso in #325
• Zenodo and downloads by @ChristopherMancuso in #328
• Fixes to setters and custom by @ChristopherMancuso in #330
• multiple updates to CLI by @ChristopherMancuso in #331
• updated tst to res and code comments by @ChristopherMancuso in #332
• Fix the pytests by @ChristopherMancuso in #333
• updated the example directory by @ChristopherMancuso in #337
• remove custom from read the docs by @ChristopherMancuso in #338
• Pytests, package builds and documentation by @ChristopherMancuso in #339
• added parameter availablity tables by @ChristopherMancuso in #342
• Fix how parameters are set by @ChristopherMancuso in #343
• min positives for training by @ChristopherMancuso in #345
• Added FAQs section by @ChristopherMancuso in #346
• updated the faqs by @ChristopherMancuso in #347
• Bump pystow from 0.5.0 to 0.6.1 by @dependabot in #348
• Bump pytest-mock from 3.11.1 to 3.14.0 by @dependabot in #310
• Bump scikit-learn from 1.3.0 to 1.6.0 by @dependabot in #349
• Bump tqdm from 4.65.0 to 4.67.1 by @dependabot in #350

Full Changelog: v1.0.1...v2.0.0.dev

v1.0.1

What's Changed

• changed to using sphinx.ext.napoleon not sphinxcontrib.napoleon by @ChristopherMancuso in #288
• update rtd config by @RemyLau in #296

Dependencies

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #279
• Bump pyyaml from 6.0 to 6.0.1 by @dependabot in #276
• Bump pytest from 7.2.0 to 7.4.2 by @dependabot in #291
• Bump tox from 4.6.4 to 4.11.4 by @dependabot in #295

Full Changelog: v1.0.0...v1.0.1

v1.0.0

What's Changed

• Update data v1.2, download zip files instead by @RemyLau in #64
• Test custom module by @RemyLau in #65
• Hotfix doc by @RemyLau in #66
• Multithreaded GET with persistent HTTP sessions by @RemyLau in #67
• References and license by @RemyLau in #68
• Fix typo and add LICENSE by @RemyLau in #70
• Patch CLI by @RemyLau in #91
• Patch data directories by @RemyLau in #92
• Check param via property by @RemyLau in #93
• Use zip instead of tar gz for windows users by @RemyLau in #94
• Download debug log by @RemyLau in #95
• Warn overwriting files by @RemyLau in #96
• Dump config by @RemyLau in #97
• Test dump config by @RemyLau in #98
• Create dependabot.yml by @RemyLau in #99
• Custom network validation by @RemyLau in #104
• Patch cross validation by @RemyLau in #110
• Overwrite option by @RemyLau in #112
• CLI skip model similarity analysis, save run log by @RemyLau in #114
• Max download retry by @RemyLau in #115
• Add more support by @RemyLau in #118
• Doc overview by @RemyLau in #116
• Minor doc fixes by @RemyLau in #126
• Update API examples and defaults by @RemyLau in #128
• Download log by @RemyLau in #133
• Add explicit links to doc by @RemyLau in #137
• Add option for skipping cross validation by @RemyLau in #145
• Improve custom network and gsc checks by @RemyLau in #148
• Bump numpy from 1.22.3 to 1.22.4 by @dependabot in #147
• Update docs by @RemyLau in #156
• Update docs (consistent notation + reorganize) by @RemyLau in #160
• Updated overview figure and product list by @ChristopherMancuso in #174
• Custom check by @ChristopherMancuso in #179
• Download tests by @ChristopherMancuso in #189
• fix typo by @RemyLau in #202
• fix file handler not closed issue on windows machines by @RemyLau in #203
• change software license to BSD3 by @RemyLau in #211
• added eval info to docs by @ChristopherMancuso in #212

New Contributors

• @dependabot made their first contribution in #100
• @pre-commit-ci made their first contribution in #108
• @ChristopherMancuso made their first contribution in #174

Full Changelog: v0.4...v1.0.0

v1.0.0-dev.5

What's Changed

• Updated overview figure and product list by @ChristopherMancuso in #174
• Custom check by @ChristopherMancuso in #179

Dependencies version bumps

• Bump pystow from 0.4.4 to 0.4.5 by @dependabot in #163
• Bump pytest-mock from 3.7.0 to 3.8.1 by @dependabot in #159
• Bump tox from 3.25.0 to 3.25.1 by @dependabot in #161
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #164
• Bump requests from 2.28.0 to 2.28.1 by @dependabot in #162
• Bump pytest-mock from 3.8.1 to 3.8.2 by @dependabot in #165
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #166
• Bump sphinx from 5.0.2 to 5.1.1 by @dependabot in #171
• Bump pystow from 0.4.5 to 0.4.6 by @dependabot in #170
• Bump sphinx-autodoc-typehints from 1.18.3 to 1.19.2 by @dependabot in #178
• Bump scikit-learn from 1.1.1 to 1.1.2 by @dependabot in #177
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #169

New Contributors

• @ChristopherMancuso made their first contribution in #174

Full Changelog: v1.0.0-dev.4...v1.0.0-dev.5