RTD config #333
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RTD config #333
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Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Zethson
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Aug 21, 2023
* RTD config Signed-off-by: zethson <[email protected]> * RTD config Signed-off-by: zethson <[email protected]> * RTD config (#333) * RTD config Signed-off-by: zethson <[email protected]> * RTD config Signed-off-by: zethson <[email protected]> * RTD config Signed-off-by: zethson <[email protected]> * RTD config Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Update CellLineMetaData (#334) * update cell line annotation * add LookUp object * pass nox test * fix test * keep downloaded files * improve error message and lookup initialize * add annotate_from_gdsc * add metadata source in the docstring * fix typo * update test script and speed up downloading metadata * add remotezip dependency * parametrize Pytest fixture * fix import error * poetry update Signed-off-by: zethson <[email protected]> * Fix fixture Signed-off-by: zethson <[email protected]> * fix test error * Refactor Signed-off-by: zethson <[email protected]> * Refactor Signed-off-by: zethson <[email protected]> * Refactor Signed-off-by: zethson <[email protected]> * improve LookUp object * add openpyxl Signed-off-by: zethson <[email protected]> * update lookup * replace dict with namedtuple --------- Signed-off-by: zethson <[email protected]> Co-authored-by: Lukas Heumos <[email protected]> * Remove whitespace in bulk RNA expression (#337) * remove whitespace in bulk RNA annotation * reformat * add details of random whitespace issue * [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.8 to 1.8.10 (#342) Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.8 to 1.8.10. - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](pypa/gh-action-pypi-publish@v1.8.8...v1.8.10) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [DEPENDABOT]: Bump mypy from 1.4.1 to 1.5.0 (#341) Bumps [mypy](https://github.com/python/mypy) from 1.4.1 to 1.5.0. - [Commits](python/mypy@v1.4.1...v1.5.0) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [DEPENDABOT]: Bump coverage from 7.2.7 to 7.3.0 (#340) Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.2.7 to 7.3.0. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](nedbat/coveragepy@7.2.7...7.3.0) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Python 3.11 support Signed-off-by: zethson <[email protected]> * palette support for da_neighborhoods (#343) * palette support for da_neighborhoods Signed-off-by: zethson <[email protected]> * Remove custom css Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Fix #284 Signed-off-by: zethson <[email protected]> * Switch to scverse cookiecutter (#349) * Remove cookietemple Signed-off-by: zethson <[email protected]> * pre-commit Signed-off-by: zethson <[email protected]> * pyproject toml Signed-off-by: zethson <[email protected]> * pre-commit Signed-off-by: zethson <[email protected]> * Add new wfs Signed-off-by: zethson <[email protected]> * RTD config Signed-off-by: zethson <[email protected]> * references Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * RTD config Signed-off-by: zethson <[email protected]> * sphinx-design Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Xichen Wu <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Zethson
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Oct 5, 2023
* Add new distances * add tests * add kl-divergence * re-implement kl-divergence implement T-test statistic rename the distances * implement rbf and quadratic polynomial mmd distances * RTD config Signed-off-by: zethson <[email protected]> * RTD config Signed-off-by: zethson <[email protected]> * RTD config (#333) * RTD config Signed-off-by: zethson <[email protected]> * RTD config Signed-off-by: zethson <[email protected]> * RTD config Signed-off-by: zethson <[email protected]> * RTD config Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Add Negative Binomial NLL distance * speedup Signed-off-by: zethson <[email protected]> * Less aggressive subsampling Signed-off-by: zethson <[email protected]> * Conditional subsampling Signed-off-by: zethson <[email protected]> * Fix NBNLL * Enable counts_layer for Distances Signed-off-by: zethson <[email protected]> * Formatting Signed-off-by: zethson <[email protected]> * Fix test Signed-off-by: zethson <[email protected]> * Further distance fixes Signed-off-by: zethson <[email protected]> * Enable layers for DistanceTests Signed-off-by: zethson <[email protected]> * use future annotation imports Signed-off-by: zethson <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * bug fix, convert to distance, check sparse csr * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add test for sparse matrices * use the internal __call__ method in pairwise * rename nb-nll to nb-ll * rename distances + add epsilon to kl-divergance and t-test * fix * add mse distance * add Kendall Tau distance * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Change handling of cell_wise_metric in distances Moved from argument to Distance class attribute. Affects how precomputed distances are stored and named. Changed metric used in Edistance to sqeuclidean as in original paper. Also fixed / added some tests. * Add fix again that was lost during merge resolve * Fix CINEMA OT test --------- Signed-off-by: zethson <[email protected]> Co-authored-by: zethson <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Yuge Ji <[email protected]> Co-authored-by: stefanpeidli <[email protected]>
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