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add flake8 pre-commit#1689

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ivirshup merged 87 commits intomasterscverse/scanpy:masterfrom feature/flake8scverse/scanpy:feature/flake8Copy head branch name to clipboardMar 18, 2021

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Commits on Feb 24, 2021

• add flake8 pre-commit

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• fix pre-commit

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• add E402 to flake8 ignore

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• revert neighbors

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• Merge branch 'master' into feature/flake8

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• fix flake8

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Commits on Feb 25, 2021

• address review

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• fix comment character in .flake8

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• fix test

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• black

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• review round 2

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• review round 3

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• readded double comments

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• Ignoring E262 & reverted comment

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• using self for obs_tidy

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Commits on Mar 1, 2021

• Restore setup.py

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Commits on Mar 15, 2021

• rm call of black test (#1690)

  

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• Fix print_versions for python<3.8 (#1691)

  

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• add codecov so we can have a badge to point to (#1693)

  

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• Attempt server-side search (#1672)

  

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• Fix paga_path (#1047)

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• Switch to flit

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• add setup.py while leaving it ignored

  

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• Update install instructions

  

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• Circumvent new pip check (see pypa/pip#9628)

  

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• Go back to regular pip (#1702)

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• codecov comment (#1704)

  

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• Use joblib for parallelism in regress_out (#1695)

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• Add sparsificiation step before sparse-dependent Scrublet calls (#1707)

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• Fix version on Travis (#1713)

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• sc.metrics module (add confusion matrix & Geary's C methods) (#915)

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• Fix clipped images in docs (#1717)

  

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• Cleanup normalize_total (#1667)

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• deprecate scvi (#1703)

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• updated ecosystem.rst to add triku (#1722)

  

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• Minor addition to contributing docs (#1726)

  

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• Preserve category order when groupby is a list (#1735)

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• Asymmetrical diverging colormaps and vcenter (#1551)

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• add flake8 pre-commit

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• add E402 to flake8 ignore

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• revert neighbors

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• address review

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• black

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• using self for obs_tidy

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• rebased

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• rebasing

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• rebasing

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• rebasing

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• Merge branch 'master' into feature/flake8

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• add flake8 to dev docs

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• add autopep8 to pre-commits

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• add flake8 ignore docs

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• add exception todos

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• add ignore directories

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• reinstated lambdas

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• fix tests

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• fix tests

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• fix tests

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• fix tests

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• fix tests

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Commits on Mar 16, 2021

• Add E741 to allowed flake8 violations.

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• Add F811 flake8 ignore for tests

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• Fix mask comparison

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• Fix mask comparison

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• fix flake8 config file

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• readded autopep8

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• import Literal

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• revert literal import

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• fix scatterplot pca import

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• false comparison & unused vars

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• Add cleaner level determination

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• Fix comment formatting

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• Add smoother dev documentation

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• fix flake8

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• Readd long comment

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• Assuming X as array like

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• fix flake8

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• fix flake8 config

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• reverted rank_genes

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• fix disp_mean_bin formatting

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• fix formatting

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• add final todos

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Commits on Mar 17, 2021

• boolean checks with is

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• _dpt formatting

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• literal fixes

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• links to leafs

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Commits on Mar 18, 2021

• revert paga variable naming

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