Geneplexus

What's Changed
* changed to using sphinx.ext.napoleon not sphinxcontrib.napoleon by ChristopherMancuso in https://github.com/krishnanlab/PyGenePlexus/pull/288
* update rtd config by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/296

Dependencies

* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PyGenePlexus/pull/279
* Bump pyyaml from 6.0 to 6.0.1 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/276
* Bump pytest from 7.2.0 to 7.4.2 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/291
* Bump tox from 4.6.4 to 4.11.4 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/295

**Full Changelog**: https://github.com/krishnanlab/PyGenePlexus/compare/v1.0.0...v1.0.1

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

New Contributors
* dependabot made their first contribution in https://github.com/krishnanlab/PyGenePlexus/pull/100
* pre-commit-ci made their first contribution in https://github.com/krishnanlab/PyGenePlexus/pull/108
* ChristopherMancuso made their first contribution in https://github.com/krishnanlab/PyGenePlexus/pull/174

**Full Changelog**: https://github.com/krishnanlab/PyGenePlexus/compare/v0.4...v1.0.0

What's Changed
* Updated overview figure and product list by ChristopherMancuso in https://github.com/krishnanlab/PyGenePlexus/pull/174
* Custom check by ChristopherMancuso in https://github.com/krishnanlab/PyGenePlexus/pull/179

Dependencies version bumps
* Bump pystow from 0.4.4 to 0.4.5 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/163
* Bump pytest-mock from 3.7.0 to 3.8.1 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/159
* Bump tox from 3.25.0 to 3.25.1 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/161
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PyGenePlexus/pull/164
* Bump requests from 2.28.0 to 2.28.1 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/162
* Bump pytest-mock from 3.8.1 to 3.8.2 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/165
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PyGenePlexus/pull/166
* Bump sphinx from 5.0.2 to 5.1.1 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/171
* Bump pystow from 0.4.5 to 0.4.6 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/170
* Bump sphinx-autodoc-typehints from 1.18.3 to 1.19.2 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/178
* Bump scikit-learn from 1.1.1 to 1.1.2 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/177
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PyGenePlexus/pull/169

New Contributors
* ChristopherMancuso made their first contribution in https://github.com/krishnanlab/PyGenePlexus/pull/174

**Full Changelog**: https://github.com/krishnanlab/PyGenePlexus/compare/v1.0.0-dev.4...v1.0.0-dev.5

What's Changed
* Bump scikit-learn from 1.0.2 to 1.1.1 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/144
* Add option for skipping cross validation by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/145
* Improve custom network and gsc checks by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/148
* Bump numpy from 1.22.3 to 1.22.4 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/147
* Update docs by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/156
* Bump sphinx from 4.5.0 to 5.0.2 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/157
* Bump sphinx-autodoc-typehints from 1.18.1 to 1.18.3 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/155
* Bump requests from 2.27.1 to 2.28.0 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/154
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PyGenePlexus/pull/152
* Bump pystow from 0.4.3 to 0.4.4 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/153
* Update docs (consistent notation + reorganize) by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/160


**Full Changelog**: https://github.com/krishnanlab/PyGenePlexus/compare/v1.0.0-dev.3...v1.0.0-dev.4

What's Changed
* Doc overview by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/116
* Bump pystow from 0.4.0 to 0.4.1 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/125
* Minor doc fixes by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/126
* Update API examples and defaults by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/128
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PyGenePlexus/pull/129
* Bump tox from 3.24.5 to 3.25.0 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/130
* Bump sphinx-autodoc-typehints from 1.17.0 to 1.17.1 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/131
* Bump pystow from 0.4.1 to 0.4.2 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/132
* Download log by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/133
* Bump sphinx-autodoc-typehints from 1.17.1 to 1.18.1 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/134
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PyGenePlexus/pull/135
* Bump pytest from 7.1.1 to 7.1.2 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/138
* Bump pystow from 0.4.2 to 0.4.3 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/139
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PyGenePlexus/pull/140
* Add explicit links to doc by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/137


**Full Changelog**: https://github.com/krishnanlab/PyGenePlexus/compare/v1.0.0-dev.2...v1.0.0-dev.3

What's Changed
* Patch CLI by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/91
* Patch data directories by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/92
* Check param via property by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/93
* Use zip instead of tar gz for windows users by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/94
* Download debug log by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/95
* Warn overwriting files by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/96
* Dump config by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/97
* Test dump config by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/98
* Create dependabot.yml by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/99
* Bump requests from 2.25.1 to 2.27.1 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/100
* Bump pytest from 7.0.1 to 7.1.1 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/101
* Bump sphinx from 4.4.0 to 4.5.0 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/103
* Bump tqdm from 4.60.0 to 4.63.1 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/102
* Custom network validation by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/104
* Bump tqdm from 4.63.1 to 4.64.0 by dependabot in https://github.com/krishnanlab/PyGenePlexus/pull/105
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PyGenePlexus/pull/108
* Patch cross validation by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/110
* Overwrite option by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/112
* CLI skip model similarity analysis, save run log by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/114
* Max download retry by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/115
* Add more support by RemyLau in https://github.com/krishnanlab/PyGenePlexus/pull/118

New Contributors
* dependabot made their first contribution in https://github.com/krishnanlab/PyGenePlexus/pull/100
* pre-commit-ci made their first contribution in https://github.com/krishnanlab/PyGenePlexus/pull/108

**Full Changelog**: https://github.com/krishnanlab/PyGenePlexus/compare/v1.0.0-dev.1...v1.0.0-dev.2