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Normalization and gene selection by analytical Pearson residuals #1715

Merged
merged 106 commits into from
Mar 29, 2022
Merged

Normalization and gene selection by analytical Pearson residuals #1715

merged 106 commits into from
Mar 29, 2022

Commits on Mar 10, 2021

  1. adding core functions and documentation for pearson residual normaliz… 

    …ation and hvg selection
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  2. adding Pearson residual+PCA bundles, minor bug fixes

    @jlause
    jlause committed Mar 10, 2021
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  3. some style cleanup, minor fixes

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  4. adapting _normalize_pearson_residuals() to cleaned-up _normalized_tot… 

    …al() from scverse#1667
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  5. updating layer management as in scverse#1667 for _highly_variable_pea… 

    …rson_residuals() as well
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  6. slight performance improvement for sparse input

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  7. style cleanup

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Commits on Mar 12, 2021

  1. fixing import issue, fixing docstring style, adding check_values para… 

    …m and warning as in scverse#1642
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  2. fixed small NameError, simplified clip argument

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  3. remove pd.categorical()

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  4. adding check_values to docstrings and remaining pearson residual func… 

    …tions
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  5. np.empty instead of np.nan

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Commits on Mar 15, 2021

  1. add references to docstrings, add HVG details to docstring

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  2. exposing pca keyword arguments to the user for the bundle/recipe func… 

    …tions
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  3. removed unneeded reversal in hvg, fix kwargs_pca bug, consistent defa… 

    …ults across files
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Commits on Jun 11, 2021

  1. fixing handling of inplace and subset arguments (see issue scvers… 

    …e#1886), explicit typing of output, adding theta input check
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  2. renaming output fields for consistency, fixing minor bug

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  3. renaming output fields for consistency

    @jlause
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  4. adding function that prepares testdata (used for pearson residual tests)

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  5. adding tests for all pearson residual functions

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Commits on Jun 28, 2021

  1. fix precommit high_var_genes

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  2. try to get precommit to work

    @giovp
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  3. Merge branch 'master' into pearson_residuals_1.7

    @giovp
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  4. try to get precommit to work

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  5. fix recipes

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  6. fix normalization

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  7. remove relative imports

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  8. fix docstrings

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  9. retry to build docs

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Commits on Jun 29, 2021

  1. Merge branch 'master' into pearson_residuals_1.7

    @giovp
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  2. fix highvar docstring

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  3. more fixing docstrings

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  4. docs build locally ? 🔨

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Commits on Jul 5, 2021

  1. minor cleanup test normalization

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  2. more minor cleanups

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  3. final cleanup normalization

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  4. fixes high var

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  5. init experimental module

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Commits on Jul 14, 2021

  1. fix column ordering for batch case

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  2. moving to experimental, minor fix for experimental version of hvg sel… 

    …ection
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  3. linking tests to new experimental submodule, style cleanup

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  4. adapt input arguments and docstring for experimental version of hvg s… 

    …election function
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Commits on Aug 1, 2021

  1. Merge branch 'master' into pearson_residuals_1.7

    @giovp
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  2. Merge branch 'pearson_residuals_1.7' of github.com:jlause/scanpy into… 

    … pearson_residuals_1.7
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  3. add recipes

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  4. fix docs

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  5. add correct module docs

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  6. fix recipe docstrings

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  7. try fix indentation

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  8. fix indentation

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  9. fix

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  10. new indentation

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Commits on Aug 2, 2021

  1. add space

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  2. fixing typo in docstring

    @jlause
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  3. renaming pca output fields

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  4. adapting tests to new output fieldname

    @jlause
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Commits on Aug 6, 2021

  1. fix docs 🔨

    @giovp
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  2. update docs

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  3. fix test 🔨

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Commits on Aug 10, 2021

  1. ensure argument and docstring consistency

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  2. update citation year

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Commits on Aug 17, 2021

  1. cleaning imports in preprocessing functions

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  2. making inputcheck tests specific to error/warning messages

    @jlause
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  3. making inputcheck tests specific to error/warning messages

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Commits on Aug 20, 2021

  1. resolve HVGs across batches more cleanly, fix dtype issue

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  2. renaming pca input arguments

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  3. renaming pca input arguments

    @jlause
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  4. _pca bundle: more efficient copy handling, added input check. both _p… 

    …ca and _recipe: varm field for PCs, adapted tests and docs
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Commits on Aug 22, 2021

  1. move repeated inputcheck code to helpers

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Commits on Aug 23, 2021

  1. merging tests *_values and *_general

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  2. condense code in pearson hvg selection test, smaller test data for sp… 

    …eedup
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  3. condensing code in normalization tests

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Commits on Aug 31, 2021

  1. add asteriks for keyword

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Commits on Sep 14, 2021

  1. updating refs to Genome Biology publication

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  2. Merge branch 'pearson_residuals_1.7' of github.com:jlause/scanpy into… 

    … pearson_residuals_1.7
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Commits on Oct 26, 2021

  1. Merge branch 'master' into pearson_residuals_1.7

    @ivirshup
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Commits on Dec 24, 2021

  1. cleanup helpers.py

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  2. cleanup main files as requested by @ivirshup

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  3. revert unneeded settingWithCopy fix

    @jlause
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Commits on Feb 23, 2022

  1. cache data

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  2. use doc_params for doc

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  3. fix doc_params var

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Commits on Feb 24, 2022

  1. Merge branch 'master' into pearson_residuals_1.7

    @giovp
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  2. finalize docs

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  3. fix param doc

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  4. wrong var still

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Commits on Feb 28, 2022

  1. add cached datasets module and test on high_var_genes tests

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  2. use new cache dataset module for tests

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  3. Merge branch 'master' into pearson_residuals_1.7

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  4. fix precommit

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  5. fix docs

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Commits on Mar 9, 2022

  1. fix reference and add notebook to tutorials

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  2. add release note

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  3. add release note

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  4. fix release note

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  5. typo

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  6. remove duplicate reference

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Commits on Mar 12, 2022

  1. fixing black flake etc requirements

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  2. add _pca function to release note

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Commits on Mar 13, 2022

  1. last edits to docs

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Commits on Mar 16, 2022

  1. fix release and tutorial image

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  2. Merge branch 'master' into pearson_residuals_1.7

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  3. try fix pre-commit

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  4. minor docs

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Commits on Mar 29, 2022

  1. Merge branch 'master' into pearson_residuals_1.7

    @ivirshup
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  2. Remove accidentally included files from merge

    @ivirshup
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