Update CellLineMetaData #334
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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]>
Signed-off-by: zethson <[email protected]>
Zethson
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Aug 7, 2023
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All of the "overview of available stuff" and "what it contains" etc are things that I think we should document in the docstring and not necessarily always print out.
For the general design of everything please also have a look at https://github.com/laminlabs/bionty
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This PR should also be related to #266 |
Signed-off-by: zethson <[email protected]>
Zethson
added a commit
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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>
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