Set theme fix #1886
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Set theme fix #1886
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Codecov Report
@@ Coverage Diff @@
## master #1886 +/- ##
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Coverage 71.22% 71.22%
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Files 92 92
Lines 11181 11181
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Hits 7964 7964
Misses 3217 3217
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giovp
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Aug 1, 2021
…, explicit typing of output, adding theta input check
ivirshup
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Mar 29, 2022
* adding core functions and documentation for pearson residual normalization and hvg selection * adding Pearson residual+PCA bundles, minor bug fixes * some style cleanup, minor fixes * adapting _normalize_pearson_residuals() to cleaned-up _normalized_total() from #1667 * updating layer management as in #1667 for _highly_variable_pearson_residuals() as well * slight performance improvement for sparse input * style cleanup * fixing import issue, fixing docstring style, adding check_values param and warning as in #1642 * fixed small NameError, simplified clip argument * remove pd.categorical() * adding check_values to docstrings and remaining pearson residual functions * np.empty instead of np.nan * add references to docstrings, add HVG details to docstring * exposing pca keyword arguments to the user for the bundle/recipe functions * removed unneeded reversal in hvg, fix kwargs_pca bug, consistent defaults across files * fixing handling of `inplace` and `subset` arguments (see issue #1886), explicit typing of output, adding theta input check * renaming output fields for consistency, fixing minor bug * renaming output fields for consistency * adding function that prepares testdata (used for pearson residual tests) * adding tests for all pearson residual functions * fix precommit high_var_genes * try to get precommit to work * try to get precommit to work * fix recipes * fix normalization * remove relative imports * fix docstrings * retry to build docs * fix highvar docstring * more fixing docstrings * docs build locally ? 🔨 * minor cleanup test normalization * more minor cleanups * final cleanup normalization * fixes high var * init experimental module * fix column ordering for batch case * moving to experimental, minor fix for experimental version of hvg selection * linking tests to new experimental submodule, style cleanup * adapt input arguments and docstring for experimental version of hvg selection function * add recipes * fix docs * add correct module docs * fix recipe docstrings * try fix indentation * fix indentation * fix * new indentation * add space * fixing typo in docstring * renaming pca output fields * adapting tests to new output fieldname * fix docs 🔨 * update docs * fix test 🔨 * ensure argument and docstring consistency * update citation year * cleaning imports in `preprocessing` functions * making inputcheck tests specific to error/warning messages * making inputcheck tests specific to error/warning messages * resolve HVGs across batches more cleanly, fix dtype issue * renaming pca input arguments * renaming pca input arguments * _pca bundle: more efficient copy handling, added input check. both _pca and _recipe: varm field for PCs, adapted tests and docs * move repeated inputcheck code to helpers * merging tests *_values and *_general * condense code in pearson hvg selection test, smaller test data for speedup * condensing code in normalization tests * add asteriks for keyword * updating refs to Genome Biology publication * cleanup helpers.py * cleanup main files as requested by @ivirshup * revert unneeded settingWithCopy fix * cache data * use doc_params for doc * fix doc_params var * finalize docs * fix param doc * wrong var still * add cached datasets module and test on high_var_genes tests * use new cache dataset module for tests * fix precommit * fix docs * fix reference and add notebook to tutorials * add release note * add release note * fix release note * typo * remove duplicate reference * fixing black flake etc requirements * add _pca function to release note * last edits to docs * fix release and tutorial image * try fix pre-commit * minor docs * Remove accidentally included files from merge Co-authored-by: giovp <[email protected]> Co-authored-by: Isaac Virshup <[email protected]>
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If you call
sns.set_palette, seaborn sets the default color palette as rgb tuples. matplotlib sometimes complains about this, and something this causes errors with our other code. We were putting these tuples intoadata.uns[f"{key}_colors"]without validation. Now we validate this.Fixes #1885.