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Added compatibility with MDAnalysis 2.4 #36

Merged
merged 28 commits into from
Feb 3, 2023
Merged

Added compatibility with MDAnalysis 2.4 #36

merged 28 commits into from
Feb 3, 2023

Commits on Jan 27, 2023

  1. Added compatibility with MDAnalysis 2.4 

    - Removed the `get_propka` function (next version must be 2.0.0)
- PropkaTraj constructor accepts atom indices for selections
- Pandas Index with a dtype of float64 instead of Float64Index,
  per deprecation warning from Pandas
- Removed removed tests for `get_propka` and changed the baseanalysis
  test names to be being the standard
- Expanded parameters for `test_single_frame_regression`
- Removed MDAnalysis version constraint in setup.py
    @ianmkenney
    ianmkenney committed Jan 27, 2023
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  2. Added GitHub actions workflow

    @ianmkenney
    ianmkenney committed Jan 27, 2023
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  3. updated dev environment requiremnets

    @ianmkenney
    ianmkenney committed Jan 27, 2023
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  4. pytest -n from a plugin?

    @ianmkenney
    ianmkenney committed Jan 27, 2023
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  5. Missing pkatraj variable in revised test

    @ianmkenney
    ianmkenney committed Jan 27, 2023
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  6. Including pylintrc from MDAKit cookiecutter

    @ianmkenney
    ianmkenney committed Jan 27, 2023
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  7. Python 2 style super call confuses pylint?

    @ianmkenney
    ianmkenney committed Jan 27, 2023
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Commits on Jan 31, 2023

  1. Added GitHub CI badge for master

    @ianmkenney
    ianmkenney committed Jan 31, 2023
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  2. Removed find_packages import, added py3.8+ requirement, removed six i… 

    …nstall requirement
    @ianmkenney
    ianmkenney committed Jan 31, 2023
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  3. Added py311 to tested versions

    @ianmkenney
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  4. MDA>=2.0.0 needed, remove six

    @ianmkenney
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  5. Remove support for selection by index/list 

    Remove dependence on six
    @ianmkenney
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  6. test_single_frame_regression parameters changed 

    - instead of original 'protein' use 'default'
- added 'protein' to replace 'ag'
- New selections can be added move conveniently now, but the use
  of `PSF_FRAME_ZERO_PKA` gets in the way. Selecting a file from a
  dictionary based on the selection string would fix this.
    @ianmkenney
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  7. Pylint probably failing because MDA not installed

    @ianmkenney
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  8. Fix required python and MDA versions

    @ianmkenney
    ianmkenney committed Jan 31, 2023
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Commits on Feb 1, 2023

  1. Removed __future__ imports

    @ianmkenney
    ianmkenney committed Feb 1, 2023
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Commits on Feb 2, 2023

  1. Formatting for gh-ci.yaml

    @ianmkenney
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  2. Moved all results from PropkaTraj to results container

    @ianmkenney
    ianmkenney committed Feb 2, 2023
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  3. Improved selection handling of test_single_frame_regression

    @ianmkenney
    ianmkenney committed Feb 2, 2023
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  4. Set license to GPLv2+

    @ianmkenney
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  5. Simplified test_single_frame_regression 

    - Only test for selection methods of 'protein'
    @ianmkenney
    ianmkenney committed Feb 2, 2023
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Commits on Feb 3, 2023

  1. Updated documentation to reflect the use of the results container

    @ianmkenney
    ianmkenney committed Feb 3, 2023
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  2. Example notebook should use container

    @ianmkenney
    ianmkenney committed Feb 3, 2023
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  3. documentation updates 

    - document attributes
- fix sphinx rst
    @orbeckst
    orbeckst authored Feb 3, 2023
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  4. fixed my doc changes

    @orbeckst
    orbeckst authored Feb 3, 2023
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  5. more docs update

    @orbeckst
    orbeckst authored Feb 3, 2023
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  6. docfix

    @orbeckst
    orbeckst authored Feb 3, 2023
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  7. Formatting and license fix 

    - PEP8 requirement ignored in favor of clarity
- setup.py license: v2+ -> v2 or later
    @ianmkenney
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