Novartis/scar

✨ Feature

• feat(scar): support MPS, but not recommend due to lower speed than CPU on Mac ([`9c3145c`](https://github.com/Novartis/scar/commit/9c3145c11ad03c47157cd4303ad3a50def859cb3))

📦 Unknown

• Develop (#75)
• fix: refactor pyproject.toml file, delete setup.cfg
• fix: refactor pyproject.toml file, delete setup.cfg
• fix: refactor pyproject.toml file, delete setup.cfg
• chore: update workflow file
• refactor codes (#73) (#74)
• fix: refactor pyproject.toml file, delete setup.cfg
• fix: refactor pyproject.toml file, delete setup.cfg
• + 5 more

📋 Changes

• Update release notes
• Require setuptools>=68.1.2 instead of >=42 to be compatible with pytorch-cuda12

📋 What's Changed

• Develop by @CaibinSh in https://github.com/Novartis/scar/pull/67
• fix: update python=3.8.6 -> python=3.10 to fix numpy & pandas conflict by @CaibinSh in https://github.com/Novartis/scar/pull/69
• Full Changelog: https://github.com/Novartis/scar/compare/v0.5.2...v0.5.3

📋 What's Changed

• clip the predicted ambient counts by @CaibinSh in https://github.com/Novartis/scar/pull/60
• new release by @CaibinSh in https://github.com/Novartis/scar/pull/61
• Default clip_to_obs to False by @CaibinSh in https://github.com/Novartis/scar/pull/63
• feat: add a feature/tutorial for denoising scATACseq by @CaibinSh in https://github.com/Novartis/scar/pull/65
• Full Changelog: https://github.com/Novartis/scar/compare/v0.5.0...v0.5.2

✨ Feature

• Update dependencies ([`40e906e`](https://github.com/Novartis/scar/commit/40e906e2789509eaa493658d0775f074d571f04c))
• Default clip_to_obs to False, as it leads to overall over-correction ([`944f09a`](https://github.com/Novartis/scar/commit/944f09aef2a1d9b97200fa90efb4a19eacaa7160))
• Support AnnData object as the input ([`24a1ab6`](https://github.com/Novartis/scar/commit/24a1ab67b64d870f4a785ad8ca13dbb4b45c8293))
• Estimate the ambient profile for all features together, add ambient_profile_all to adata.uns ([`e1913fd`](https://github.com/Novartis/scar/commit/e1913fd15fdf5546619f750c23e03debbcf1d63e))

🐛 Fix

• setup: Change sample and n_batch parameters to allow using all droplets by default ([`4f5e05f`](https://github.com/Novartis/scar/commit/4f5e05fa5bf6aa413287fb2be73d6ad01a3fc9b3))
• setup: Fix setupdata ([`63afe9d`](https://github.com/Novartis/scar/commit/63afe9dd8fbc701360715e1a4318f6be8f07e58b))

📝 Documentation

• tutorials: Update tutorials ([`a21e2ec`](https://github.com/Novartis/scar/commit/a21e2ecd507f0c2b9f0e876af04a477927443205))
• Print message ([`7659672`](https://github.com/Novartis/scar/commit/76596727389acc484c3dce78d6f2a262dec33a0e))
• Print message ([`203687f`](https://github.com/Novartis/scar/commit/203687fb03f098a1bd2f1f3940d49c7e83421f22))

✨ Feature

• *: Remove tensorboard parameter ([`98717e7`](https://github.com/Novartis/scar/commit/98717e7c55f4c4184309cb6d3956097fde661046))
• model: Add an option to clip the prediction ([`b250ebf`](https://github.com/Novartis/scar/commit/b250ebfcb412d41430ebcb1fe01b0c4f1b415b11))

📝 Documentation

• Update dependency ([`03cf19e`](https://github.com/Novartis/scar/commit/03cf19e2adfcb84714b7845914feaa45f7b0ae83))
• Update dependencies ([`9bd7f1c`](https://github.com/Novartis/scar/commit/9bd7f1c164e7f3e1b30af73dcf9f6b8737d26019))
• Update documentations ([`418996c`](https://github.com/Novartis/scar/commit/418996c2dcd3796444d7e01b3b2f1c897c0f7b0d))
• Update dependencies ([`1bde351`](https://github.com/Novartis/scar/commit/1bde351ad7f027d36de75f3a60f471e7ef75a6bf))
• main: Add link to anndata and scanpy ([`8436e05`](https://github.com/Novartis/scar/commit/8436e0514f5d9f9cdd9ed2c3b9ef036f23232b31))
• main: Update dependencies ([`984df35`](https://github.com/Novartis/scar/commit/984df3562f1d4f753ca66caf88619d7305089dcd))
• main: Update documentation for .h5 file ([`2a309e0`](https://github.com/Novartis/scar/commit/2a309e0d44eddb75fd1ddf5cdf69fe59e3e40280))
• Add a link of binary installers ([`2faed3e`](https://github.com/Novartis/scar/commit/2faed3e56b98027e4ecda68d73044e0c29c369a1))
• + 9 more

⚡ Performance

• main: Command line tool supports a new input: filtered_feature_bc_matrix.h5 ([`73bc13e`](https://github.com/Novartis/scar/commit/73bc13e2741d97885840c67177cc985c23749e96))
• setup: Add an error raise statement ([`f4fb1a8`](https://github.com/Novartis/scar/commit/f4fb1a8fe915e8deb89c05bf319f85684cbbc853))

🐛 Fix

• setup: Fix a bug to allow sample reasonable numbers of droplets ([`ef6f7e4`](https://github.com/Novartis/scar/commit/ef6f7e4e58fcb1ce8cf463bed3697883f561eba9))
• main: Fix a bug in main to set default NN number ([`794ff17`](https://github.com/Novartis/scar/commit/794ff17ac349148aaae24ca9c9927d0179ccd3f4))

📝 Documentation

• main: Add scanpy as dependency ([`252a492`](https://github.com/Novartis/scar/commit/252a492a4d545ed485e9acb208f8e18a25886206))

⚡ Performance

• main: Set a separate batchsize_infer parameter for inference ([`8727f04`](https://github.com/Novartis/scar/commit/8727f04da3c934de9d1b14358bee434a972d7849))
• setup: Add an option of random sampling droplets to speed up calculation ([`ce042dd`](https://github.com/Novartis/scar/commit/ce042dd120fbe592a089a48b4d584629e63797ca))
• setup: Enable manupulate large-scale emptydroplets ([`15f1840`](https://github.com/Novartis/scar/commit/15f18408dcd2ef4bdb1de84b55a136da03fb6244))

📝 Documentation

• Update dependencies ([`784ea63`](https://github.com/Novartis/scar/commit/784ea63a1a55b98592dc69be79d15b3f0c22317c))
• Update dependencies ([`cbf1fc6`](https://github.com/Novartis/scar/commit/cbf1fc6614bd1e559e3b80054f99bd7c05fd3958))
• Change background of logo ([`de267ed`](https://github.com/Novartis/scar/commit/de267ed6546fd9e1aba50594223bbddc57199f56))
• Update readme ([`e97dbf1`](https://github.com/Novartis/scar/commit/e97dbf1f14a9c3fc75fbdbf46c11e22630ddd362))
• Modify scAR_logo ([`1f6e890`](https://github.com/Novartis/scar/commit/1f6e890b662e105e810cda5b4354e0ec3476d8a9))
• Update logo ([`18b51e7`](https://github.com/Novartis/scar/commit/18b51e789d1d2a9bb4a078dff71d93dfb854c640))

⚡ Performance

• Add a setup_anndata method ([#54](https://github.com/Novartis/scar/issues/54)) ([`923b1e5`](https://github.com/Novartis/scar/commit/923b1e5f267f50a6aba765f0c2966080dc375a0f))
• Change sparsity to 1 for scCRISPR-seq and cell indexing ([`d4b2c3d`](https://github.com/Novartis/scar/commit/d4b2c3d4083c9619a205d1c66e361d634ebcb13b))

✨ Feature

• inference: add a round_to_int parameter to round the counts (float) for easy interpretation and better integration into other methods ([#47](https://github.com/Novartis/scar/issues/47)) ([`902a2b9`](https://github.com/Novartis/scar/commit/8694239b1efb4afd24871943e97ad006fab355f8)) ([`8694239`](https://github.com/Novartis/scar/commit/04d30678d29e28ceadd71622c9748edaa7ca8769))

📦 Build

• setup: replace setup.py with setup.cfg and pyproject.toml ([#51](https://github.com/Novartis/scar/pull/51)) ([`3dc999a`](https://github.com/Novartis/scar/pull/51/commits/c30f4f0270c4a6263bf23c5c3f3619f4436f2890))

📦 Chore

• unittest: refactor unittest ([#51](https://github.com/Novartis/scar/pull/51)) ([`a597c5f`](https://github.com/Novartis/scar/commit/c34f362697ce88a3604bc8b476b7038165699fe4))
• main: refactor device ([#51](https://github.com/Novartis/scar/pull/51)) ([`d807404`](https://github.com/Novartis/scar/commit/a597c5fd57a79cec921daf2133423ec8a8926019699fe4))

📝 Documentation

• readthedocs: add scAR_logo image ([#51](https://github.com/Novartis/scar/pull/51)) ([`c34f362`](https://github.com/Novartis/scar/commit/902a2b9cefffd8f883963450712825e939869569))
• tutorials: add ci=None to speed up plotting ([#51](https://github.com/Novartis/scar/pull/51)) ([`902a2b9`](https://github.com/Novartis/scar/commit/3dc999a7d475d08446663bd780d943ba4dffe56c))

📦 Contributor

• @CaibinSh and @mdmanurung
• Full Changelog: https://github.com/Novartis/scar/compare/v0.4.0...v0.4.1

✨ Feature

• scar.model: Addition of a sparsity parameter ([#44](https://github.com/Novartis/scAR/issues/44)) ([`0c30046`](https://github.com/Novartis/scAR/commit/0c30046aa8d20be88f516b8756789d9fab515b10))
• scar.main: Introduce a sparsity parameter ([`cd33fdd`](https://github.com/Novartis/scAR/commit/cd33fddbd6d7117f459e12b57a936148cde0563f))

📝 Documentation

• Modify Changlog.md ([`deb920c`](https://github.com/Novartis/scAR/commit/deb920cdaa3b81a7d6dbccc85231bfa87236cee6))

📝 Documentation

• Delete API.rst ([`497b080`](https://github.com/Novartis/scAR/commit/497b080eff15143a34c4d75649ba2e130e1d3006))
• Update documentations ([`5ad9986`](https://github.com/Novartis/scAR/commit/5ad998607ec41b91a318ef4bc2c46694ad034dcc))
• Update documentations ([`11fa2b8`](https://github.com/Novartis/scAR/commit/11fa2b858ae2162052dd6906d237b16a4f3955de))

🐛 Fix

• *: Changelog ([`b9171a3`](https://github.com/Novartis/scAR/commit/b9171a3015350ac37b0bc44cdb00e4c7aa3c2a67))
• *: Changelog ([`44a4409`](https://github.com/Novartis/scAR/commit/44a4409fadf8d124d9b5177cf15f53f00e4524ff))

📝 Documentation

• Autodoc command line interface ([`0efae6c`](https://github.com/Novartis/scAR/commit/0efae6c26a409553bb8caad5de03c2f38842c139))

🐛 Fix

• *: Addition of semantic releasing ([`6e83c3d`](https://github.com/Novartis/scAR/commit/6e83c3db418945e8d297b17112371b331e44e2de))

📋 What's Changed

• Implementation of [readthedocs documentation](https://scar-tutorials.readthedocs.io/en/latest/). Tutorials, installations and API are available.
• Code refactoring
• > Renaming module names, e.g. changing "scAR" -> "scar"
• > Renaming parameter names, e.g.
• > > "scRNAseq_tech" -> "feature_type"
• > > "model" -> "count_model"
• > > "empty_profile" -> "ambient_profile"
• > > ...
• + 2 more

📦 Contributor

• @CaibinSh @fgypas @mr-nvs @Tobias-Ternent
• Full Changelog: https://github.com/Novartis/scAR/compare/v0.2.3...v0.3.0

📋 Changes

• Add integration test
• Black formating
• Bump version to 0.2.3

📋 What's Changed

• Develop by @CaibinSh in https://github.com/Novartis/scAR/pull/19
• Full Changelog: https://github.com/Novartis/scAR/compare/v0.2.2...v0.2.3

📋 Changes

• Remove torchaudio
• Add test data for integration tests
• Bump version to 0.2.2

📋 What's Changed

• Remove torchaudio, add test data and bump version to 0.2.2 by @fgypas in https://github.com/Novartis/scAR/pull/15
• Full Changelog: https://github.com/Novartis/scAR/compare/v0.2.1-beta...v0.2.2

📋 Changes

• fix a typo in scAR-gpu.yml
• reorganise init.py files

📋 What's Changed

• Develop by @CaibinSh in https://github.com/Novartis/scAR/pull/12
• Full Changelog: https://github.com/Novartis/scAR/compare/v0.2.0-beta...v0.2.1-beta

📋 Changes

• Support for training of the model with CPUs
• Addition of two yaml files for CPU/GPU installation
• Refactor of setup.py and structure of the package
• Addition of tests with pytest
• Addition of lint checks
• Automate build with github actions (install package and run lint checks and pytest)
• Update documentation
• Version 0.2.0

📋 What's Changed

• 0.2.0-release by @fgypas in https://github.com/Novartis/scAR/pull/11
• Full Changelog: https://github.com/Novartis/scAR/commits/v0.2.0-beta