A Python adaption of Augur to prioritize cell types in perturbation analysis.

Overview
Comments
  • Feature/calculateauc

    Feature/calculateauc

    Description of changes Implementation to calculate the AUC with respect to CellType along with test files.

    Still missing right now:

    • is a nice results output. (Current version returns huge dictionary with everything..)
    • feature importances (still not sure 1. how to best return them - eg. do I take the average if multiple importances are captured and 2. feature importances for logistic regression -> Issue.)
    • progress bar for calculations
    enhancement 
    opened by antschum 11
  • Feature/crossvalidation

    Feature/crossvalidation

    Implementation of cross validation (which will be used to calculate the overall AUC) Updated load function to transfer categorical data into dummy variables (so that sklearn random forest classifier and logistic regression classifier can fit the data) Fixed small errors.

    enhancement 
    opened by antschum 3
  • Feature/workingversion

    Feature/workingversion

    Fixed handing in multiple labels so that the user decides in the loading function which labels he will be comparing. Added log1p normalisation. Happens automatically if values are too large or too small / Value error is thrown because something is infinity. Adjusted expected test values accordingly.

    enhancement 
    opened by antschum 2
  • feature importance logistic regression

    feature importance logistic regression

    (Not sure if issues are intended to be used this way, but.)

    I would like to add the feature importances for the random forest and logistic regression. In the case of the random forest I propose to use the build in function. For logistic regression there is no äquivalent on sklearn. Augur used standardized coefficients with Agresti method and linked this: https://think-lab.github.io/d/205/#3.

    I have not had time to fully dive into it but was wondering if @Zethson you know any other way or have preferences :) (This is not integral to creating a cell type ranking so its not super urgent.)

    enhancement 
    opened by antschum 2
  • loosen dependencies

    loosen dependencies

    Think we should make many of the dependencies more loose and work with >= instead of '^='. But we can do that in a follow up PR. Or I can do that :)

    Originally posted by @Zethson in https://github.com/theislab/augurpy/pull/32#discussion_r768560977

    opened by antschum 2
  • [DEPENDABOT]: Bump types-requests from 2.27.7 to 2.27.14

    [DEPENDABOT]: Bump types-requests from 2.27.7 to 2.27.14

    Bumps types-requests from 2.27.7 to 2.27.14.

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    opened by dependabot[bot] 1
  • [DEPENDABOT]: Bump types-requests from 2.27.7 to 2.27.12

    [DEPENDABOT]: Bump types-requests from 2.27.7 to 2.27.12

    Bumps types-requests from 2.27.7 to 2.27.12.

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    DEPENDABOT 
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  • [DEPENDABOT]: Bump pytest from 6.2.5 to 7.1.0

    [DEPENDABOT]: Bump pytest from 6.2.5 to 7.1.0

    Bumps pytest from 6.2.5 to 7.1.0.

    Release notes

    Sourced from pytest's releases.

    7.1.0

    pytest 7.1.0 (2022-03-13)

    Breaking Changes

    • #8838: As per our policy, the following features have been deprecated in the 6.X series and are now removed:

      • pytest._fillfuncargs function.
      • pytest_warning_captured hook - use pytest_warning_recorded instead.
      • -k -foobar syntax - use -k 'not foobar' instead.
      • -k foobar: syntax.
      • pytest.collect module - import from pytest directly.

      For more information consult Deprecations and Removals in the docs.

    • #9437: Dropped support for Python 3.6, which reached end-of-life at 2021-12-23.

    Improvements

    • #5192: Fixed test output for some data types where -v would show less information.

      Also, when showing diffs for sequences, -q would produce full diffs instead of the expected diff.

    • #9362: pytest now avoids specialized assert formatting when it is detected that the default __eq__ is overridden in attrs or dataclasses.

    • #9536: When -vv is given on command line, show skipping and xfail reasons in full instead of truncating them to fit the terminal width.

    • #9644: More information about the location of resources that led Python to raise ResourceWarning{.interpreted-text role="class"} can now be obtained by enabling tracemalloc{.interpreted-text role="mod"}.

      See resource-warnings{.interpreted-text role="ref"} for more information.

    • #9678: More types are now accepted in the ids argument to @pytest.mark.parametrize. Previously only [str]{.title-ref}, [float]{.title-ref}, [int]{.title-ref} and [bool]{.title-ref} were accepted; now [bytes]{.title-ref}, [complex]{.title-ref}, [re.Pattern]{.title-ref}, [Enum]{.title-ref} and anything with a [__name__]{.title-ref} are also accepted.

    • #9692: pytest.approx{.interpreted-text role="func"} now raises a TypeError{.interpreted-text role="class"} when given an unordered sequence (such as set{.interpreted-text role="class"}).

      Note that this implies that custom classes which only implement __iter__ and __len__ are no longer supported as they don't guarantee order.

    Bug Fixes

    • #8242: The deprecation of raising unittest.SkipTest{.interpreted-text role="class"} to skip collection of tests during the pytest collection phase is reverted - this is now a supported feature again.
    • #9493: Symbolic link components are no longer resolved in conftest paths. This means that if a conftest appears twice in collection tree, using symlinks, it will be executed twice.

    ... (truncated)

    Commits
    • 1dbffcc [pre-commit.ci] auto fixes from pre-commit.com hooks
    • d53a5fb Prepare release version 7.1.0
    • d306ec0 Update upcoming trainings (#9744)
    • 3e4c14b Merge pull request #9751 from fabianegli/main
    • 7f924b1 Fix typo in deprecation documentation
    • 4a8f8ad build(deps): Bump django from 4.0.2 to 4.0.3 in /testing/plugins_integration ...
    • c0fd2d8 build(deps): Bump pytest-asyncio from 0.18.1 to 0.18.2 in /testing/plugins_in...
    • 843e018 Merge pull request #9732 from nicoddemus/9730-toml-failure
    • bc43d66 [automated] Update plugin list (#9733)
    • e38d1ca Improve error message for malformed pyproject.toml files
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    DEPENDABOT 
    opened by dependabot[bot] 1
  • [DEPENDABOT]: Bump types-requests from 2.27.7 to 2.27.11

    [DEPENDABOT]: Bump types-requests from 2.27.7 to 2.27.11

    Bumps types-requests from 2.27.7 to 2.27.11.

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    DEPENDABOT 
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  • [DEPENDABOT]: Bump actions/setup-python from 2 to 3.0.0

    [DEPENDABOT]: Bump actions/setup-python from 2 to 3.0.0

    Bumps actions/setup-python from 2 to 3.0.0.

    Release notes

    Sourced from actions/setup-python's releases.

    v3.0.0

    What's Changed

    Breaking Changes

    With the update to Node 16, all scripts will now be run with Node 16 rather than Node 12.

    This new major release removes support of legacy pypy2 and pypy3 keywords. Please use more specific and flexible syntax to specify a PyPy version:

    jobs:
      build:
        runs-on: ubuntu-latest
        strategy:
          matrix:
            python-version:
            - 'pypy-2.7' # the latest available version of PyPy that supports Python 2.7
            - 'pypy-3.8' # the latest available version of PyPy that supports Python 3.8
            - 'pypy-3.8-v7.3.8' # Python 3.8 and PyPy 7.3.8
        steps:
        - uses: actions/checkout@v2
        - uses: actions/setup-python@v3
          with:
            python-version: ${{ matrix.python-version }}
    

    See more usage examples in the documentation

    Update primary and restore keys for pip

    In scope of this release we include a version of python in restore and primary cache keys for pip. Besides, we add temporary fix for Windows caching issue, that the pip cache dir command returns non zero exit code or writes to stderr. Moreover we updated node-fetch dependency.

    Update actions/cache version to 1.0.8

    We have updated actions/cache dependency version to 1.0.8 to support 10GB cache upload

    Support caching dependencies

    This release introduces dependency caching support (actions/setup-python#266)

    Caching dependencies.

    The action has a built-in functionality for caching and restoring pip/pipenv dependencies. The cache input is optional, and caching is turned off by default.

    Besides, this release introduces dependency caching support for mono repos and repositories with complex structure.

    By default, the action searches for the dependency file (requirements.txt for pip or Pipfile.lock for pipenv) in the whole repository. Use the cache-dependency-path input for cases when you want to override current behaviour and use different file for hash generation (for example requirements-dev.txt). This input supports wildcards or a list of file names for caching multiple dependencies.

    Caching pip dependencies:

    steps:
    - uses: actions/checkout@v2
    - uses: actions/setup-python@v2
      with:
        python-version: '3.9'
    </tr></table> 
    

    ... (truncated)

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    DEPENDABOT 
    opened by dependabot[bot] 1
  • [DEPENDABOT]: Bump coverage from 6.2 to 6.3.2

    [DEPENDABOT]: Bump coverage from 6.2 to 6.3.2

    Bumps coverage from 6.2 to 6.3.2.

    Changelog

    Sourced from coverage's changelog.

    Version 6.3.2 — 2022-02-20

    • Fix: adapt to pypy3.9's decorator tracing behavior. It now traces function decorators like CPython 3.8: both the @-line and the def-line are traced. Fixes issue 1326_.

    • Debug: added pybehave to the list of :ref:cmd_debug and :ref:cmd_run_debug options.

    • Fix: show an intelligible error message if --concurrency=multiprocessing is used without a configuration file. Closes issue 1320_.

    .. _issue 1320: nedbat/coveragepy#1320 .. _issue 1326: nedbat/coveragepy#1326

    .. _changes_631:

    Version 6.3.1 — 2022-02-01

    • Fix: deadlocks could occur when terminating processes. Some of these deadlocks (described in issue 1310_) are now fixed.

    • Fix: a signal handler was being set from multiple threads, causing an error: "ValueError: signal only works in main thread". This is now fixed, closing issue 1312_.

    • Fix: --precision on the command-line was being ignored while considering --fail-under. This is now fixed, thanks to Marcelo Trylesinski <pull 1317_>_.

    • Fix: releases no longer provide 3.11.0-alpha wheels. Coverage.py uses CPython internal fields which are moving during the alpha phase. Fixes issue 1316_.

    .. _issue 1310: nedbat/coveragepy#1310 .. _issue 1312: nedbat/coveragepy#1312 .. _issue 1316: nedbat/coveragepy#1316 .. _pull 1317: nedbat/coveragepy#1317

    .. _changes_63:

    Version 6.3 — 2022-01-25

    • Feature: Added the lcov command to generate reports in LCOV format. Thanks, Bradley Burns <pull 1289_>. Closes issues 587 <issue 587_> and 626 <issue 626_>_.

    ... (truncated)

    Commits
    • 0f99e89 build: prep for 6.3.2
    • 84ea58f docs: latest sample HTML
    • bf5a760 build: tox understands "pypy38" on its own
    • 9d90ebd fix: pypy3.9 traces decorators like CPython 3.8
    • c778139 style: remove pylint exclusions only needed for 2/3
    • cae2884 build: make upgrade
    • 32ff871 fix: provide an intelligible error message for multiprocessing with no config...
    • dacea2d refactor(test): simplify these tests
    • 5f29141 test: dropping old Python versions mean we no longer need optimize_if_not_deb...
    • b60b789 test: nicer way to test debug=pybehave
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    DEPENDABOT 
    opened by dependabot[bot] 1
  • [DEPENDABOT]: Bump types-requests from 2.27.7 to 2.27.15

    [DEPENDABOT]: Bump types-requests from 2.27.7 to 2.27.15

    Bumps types-requests from 2.27.7 to 2.27.15.

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    DEPENDABOT 
    opened by dependabot[bot] 0
  • [DEPENDABOT]: Bump pytest from 6.2.5 to 7.1.1

    [DEPENDABOT]: Bump pytest from 6.2.5 to 7.1.1

    Bumps pytest from 6.2.5 to 7.1.1.

    Release notes

    Sourced from pytest's releases.

    7.1.1

    pytest 7.1.1 (2022-03-17)

    Bug Fixes

    • #9767: Fixed a regression in pytest 7.1.0 where some conftest.py files outside of the source tree (e.g. in the [site-packages]{.title-ref} directory) were not picked up.

    7.1.0

    pytest 7.1.0 (2022-03-13)

    Breaking Changes

    • #8838: As per our policy, the following features have been deprecated in the 6.X series and are now removed:

      • pytest._fillfuncargs function.
      • pytest_warning_captured hook - use pytest_warning_recorded instead.
      • -k -foobar syntax - use -k 'not foobar' instead.
      • -k foobar: syntax.
      • pytest.collect module - import from pytest directly.

      For more information consult Deprecations and Removals in the docs.

    • #9437: Dropped support for Python 3.6, which reached end-of-life at 2021-12-23.

    Improvements

    • #5192: Fixed test output for some data types where -v would show less information.

      Also, when showing diffs for sequences, -q would produce full diffs instead of the expected diff.

    • #9362: pytest now avoids specialized assert formatting when it is detected that the default __eq__ is overridden in attrs or dataclasses.

    • #9536: When -vv is given on command line, show skipping and xfail reasons in full instead of truncating them to fit the terminal width.

    • #9644: More information about the location of resources that led Python to raise ResourceWarning{.interpreted-text role="class"} can now be obtained by enabling tracemalloc{.interpreted-text role="mod"}.

      See resource-warnings{.interpreted-text role="ref"} for more information.

    • #9678: More types are now accepted in the ids argument to @pytest.mark.parametrize. Previously only [str]{.title-ref}, [float]{.title-ref}, [int]{.title-ref} and [bool]{.title-ref} were accepted; now [bytes]{.title-ref}, [complex]{.title-ref}, [re.Pattern]{.title-ref}, [Enum]{.title-ref} and anything with a [__name__]{.title-ref} are also accepted.

    • #9692: pytest.approx{.interpreted-text role="func"} now raises a TypeError{.interpreted-text role="class"} when given an unordered sequence (such as set{.interpreted-text role="class"}).

      Note that this implies that custom classes which only implement __iter__ and __len__ are no longer supported as they don't guarantee order.

    ... (truncated)

    Commits
    • 0ffe9e0 Prepare release version 7.1.1
    • 6f2c1ec Merge pull request #9784 from pytest-dev/backport-9768-to-7.1.x
    • a65c47a Merge pull request #9783 from pytest-dev/backport-9780-to-7.1.x
    • 30d995e [pre-commit.ci] auto fixes from pre-commit.com hooks
    • 10a14d1 [7.1.x] testing: fix tests when run under -v or -vv
    • f4cfc59 [pre-commit.ci] auto fixes from pre-commit.com hooks
    • f1df807 [7.1.x] config: restore pre-pytest 7.1.0 confcutdir exclusion behavior
    • 7d4d1ec Merge pull request #9758 from pytest-dev/release-7.1.0
    • 1dbffcc [pre-commit.ci] auto fixes from pre-commit.com hooks
    • d53a5fb Prepare release version 7.1.0
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    DEPENDABOT 
    opened by dependabot[bot] 0
  • Feature/docs

    Feature/docs

    Working documentation draft. Now showing all parameters for all functions. Updated augurpys READme. Changed default mode to light mode because in dark mode it was hard to see some colours.

    enhancement 
    opened by antschum 0
  • [DEPENDABOT]: Bump actions/setup-python from 2 to 3

    [DEPENDABOT]: Bump actions/setup-python from 2 to 3

    Bumps actions/setup-python from 2 to 3.

    Release notes

    Sourced from actions/setup-python's releases.

    v3.0.0

    What's Changed

    Breaking Changes

    With the update to Node 16, all scripts will now be run with Node 16 rather than Node 12.

    This new major release removes support of legacy pypy2 and pypy3 keywords. Please use more specific and flexible syntax to specify a PyPy version:

    jobs:
      build:
        runs-on: ubuntu-latest
        strategy:
          matrix:
            python-version:
            - 'pypy-2.7' # the latest available version of PyPy that supports Python 2.7
            - 'pypy-3.8' # the latest available version of PyPy that supports Python 3.8
            - 'pypy-3.8-v7.3.8' # Python 3.8 and PyPy 7.3.8
        steps:
        - uses: actions/checkout@v2
        - uses: actions/setup-python@v3
          with:
            python-version: ${{ matrix.python-version }}
    

    See more usage examples in the documentation

    Update primary and restore keys for pip

    In scope of this release we include a version of python in restore and primary cache keys for pip. Besides, we add temporary fix for Windows caching issue, that the pip cache dir command returns non zero exit code or writes to stderr. Moreover we updated node-fetch dependency.

    Update actions/cache version to 1.0.8

    We have updated actions/cache dependency version to 1.0.8 to support 10GB cache upload

    Support caching dependencies

    This release introduces dependency caching support (actions/setup-python#266)

    Caching dependencies.

    The action has a built-in functionality for caching and restoring pip/pipenv dependencies. The cache input is optional, and caching is turned off by default.

    Besides, this release introduces dependency caching support for mono repos and repositories with complex structure.

    By default, the action searches for the dependency file (requirements.txt for pip or Pipfile.lock for pipenv) in the whole repository. Use the cache-dependency-path input for cases when you want to override current behaviour and use different file for hash generation (for example requirements-dev.txt). This input supports wildcards or a list of file names for caching multiple dependencies.

    Caching pip dependencies:

    steps:
    - uses: actions/checkout@v2
    - uses: actions/setup-python@v2
      with:
        python-version: '3.9'
    </tr></table> 
    

    ... (truncated)

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  • [DEPENDABOT]: Bump actions/download-artifact from 2.1.0 to 3

    [DEPENDABOT]: Bump actions/download-artifact from 2.1.0 to 3

    Bumps actions/download-artifact from 2.1.0 to 3.

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  • [DEPENDABOT]: Bump actions/upload-artifact from 2.3.1 to 3

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