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add active PRs to black ignore #4815

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Dec 19, 2024
Merged

add active PRs to black ignore #4815

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0eff624
add active PRs to black ignore
marinegor Dec 2, 2024
d123b17
limit black extensions to files with updatedAt within 2 months (after…
marinegor Dec 8, 2024
b93b5a5
remove already formatted files
marinegor Dec 9, 2024
a011864
merge upstream/develop
marinegor Dec 9, 2024
fa2dbd8
add active_files*.lst to mainainer dir
marinegor Dec 18, 2024
f83109d
update pyproject.toml accordingly
marinegor Dec 18, 2024
ceebd1a
format active_files_{package,testsuite} to be directly pastable to py…
marinegor Dec 18, 2024
e3a98e4
add unformatted output containing PR information for each file
marinegor Dec 18, 2024
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137 changes: 137 additions & 0 deletions maintainer/active_files.lst
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# 4841 add `relprop` for atom selection and corresponding UT
package/MDAnalysis/core/selection.py
testsuite/MDAnalysisTests/core/test_atomselections.py
# ---------------------
# 4822 Enabling of parallelization of `analysis.atomicdistances.AtomicDistances`
package/CHANGELOG
package/MDAnalysis/analysis/atomicdistances.py
testsuite/MDAnalysisTests/analysis/test_atomicdistances.py
# ---------------------
# 4816 Implementation of `CMSParser`
package/MDAnalysis/topology/CMSParser.py
package/MDAnalysis/topology/__init__.py
# ---------------------
# 4815 add active PRs to black ignore
maintainer/active_files_package.lst
maintainer/active_files_testsuite.lst
package/pyproject.toml
testsuite/pyproject.toml
# ---------------------
# 4812 Bump the github-actions group with 4 updates
.github/workflows/deploy.yaml
.github/workflows/gh-ci.yaml
# ---------------------
# 4800 Transfer of `fasteners` dependency to `filelock`
.github/actions/setup-deps/action.yaml
azure-pipelines.yml
maintainer/conda/environment.yml
package/CHANGELOG
package/MDAnalysis/coordinates/XDR.py
package/pyproject.toml
package/requirements.txt
testsuite/MDAnalysisTests/coordinates/test_xdr.py
# ---------------------
# 4790 Implementation of SugarSelection
package/MDAnalysis/core/selection.py
testsuite/MDAnalysisTests/core/test_atomselections.py
testsuite/MDAnalysisTests/data/6kya.pdb
testsuite/MDAnalysisTests/data/GLYCAM_sugars.pdb
testsuite/MDAnalysisTests/datafiles.py
# ---------------------
# 4745 'MDAnalysis.analysis.diffusionmap' parallelization
package/MDAnalysis/analysis/diffusionmap.py
testsuite/MDAnalysisTests/analysis/conftest.py
testsuite/MDAnalysisTests/analysis/test_diffusionmap.py
# ---------------------
# 4738 'MDAnalysis.analysis.align' parallelization
package/MDAnalysis/analysis/align.py
testsuite/MDAnalysisTests/analysis/conftest.py
testsuite/MDAnalysisTests/analysis/test_align.py
# ---------------------
# 4734 distopia 0.3.0 compatibility changes
.github/actions/setup-deps/action.yaml
package/CHANGELOG
package/MDAnalysis/lib/_distopia.py
package/MDAnalysis/lib/distances.py
testsuite/MDAnalysisTests/lib/test_distances.py
# ---------------------
# 4714 Dask timeseries prototype
.gitignore
package/MDAnalysis/analysis/dasktimeseries.py
package/MDAnalysis/coordinates/H5MD.py
tmp/env.yaml
tmp/lazyts.ipynb
# ---------------------
# 4712 Implementing `gemmi`-based mmcif reader (with easy extension to PDB/PDBx and mmJSON)
.github/actions/setup-deps/action.yaml
package/MDAnalysis/coordinates/MMCIF.py
package/MDAnalysis/coordinates/__init__.py
package/MDAnalysis/topology/MMCIFParser.py
package/MDAnalysis/topology/PDBParser.py
package/MDAnalysis/topology/__init__.py
package/MDAnalysis/topology/tpr/utils.py
package/pyproject.toml
testsuite/MDAnalysisTests/coordinates/test_mmcif.py
testsuite/MDAnalysisTests/data/mmcif/1YJP.cif
testsuite/MDAnalysisTests/data/mmcif/1YJP.cif.gz
testsuite/MDAnalysisTests/data/mmcif/7ETN.cif
testsuite/MDAnalysisTests/data/mmcif/7ETN.cif.gz
testsuite/MDAnalysisTests/datafiles.py
testsuite/MDAnalysisTests/topology/test_mmcif.py
# ---------------------
# 4681 [WIP] Cif reader
package/MDAnalysis/coordinates/CIF.py
package/MDAnalysis/coordinates/PDBx.py
package/MDAnalysis/coordinates/__init__.py
package/MDAnalysis/topology/PDBxParser.py
package/MDAnalysis/topology/__init__.py
package/doc/sphinx/source/documentation_pages/coordinates/PDBx.rst
testsuite/MDAnalysisTests/coordinates/test_cif.py
# ---------------------
# 4584 Limit threads usage in numpy during test to avoid time-out
testsuite/MDAnalysisTests/analysis/test_encore.py
testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py
# ---------------------
# 4535 Pathlib object handling for Universe, SingleFrameReaderBase and Toplogy parsers (Issue #3937)
package/CHANGELOG
package/MDAnalysis/coordinates/base.py
package/MDAnalysis/core/universe.py
package/MDAnalysis/topology/base.py
testsuite/MDAnalysisTests/coordinates/base.py
testsuite/MDAnalysisTests/coordinates/test_gro.py
testsuite/MDAnalysisTests/topology/base.py
# ---------------------
# 4533 Fix: modernise HBA to use AG as objects internally instead of selection strings - code only PR (Issue #3933)
package/AUTHORS
package/CHANGELOG
package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py
testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py
# ---------------------
# 4417 Accessible Surface Area calculations
package/AUTHORS
package/CHANGELOG
package/MDAnalysis/analysis/sasa.py
package/doc/sphinx/source/documentation_pages/analysis/sasa.rst
package/doc/sphinx/source/references.bib
testsuite/MDAnalysisTests/analysis/test_sasa.py
# ---------------------
# 4334 Deprecate `ts` argument to _read_next_timestep
package/MDAnalysis/coordinates/DCD.py
package/MDAnalysis/coordinates/DLPoly.py
package/MDAnalysis/coordinates/GMS.py
package/MDAnalysis/coordinates/MOL2.py
package/MDAnalysis/coordinates/PDB.py
package/MDAnalysis/coordinates/TRJ.py
package/MDAnalysis/coordinates/TRR.py
package/MDAnalysis/coordinates/TRZ.py
package/MDAnalysis/coordinates/TXYZ.py
package/MDAnalysis/coordinates/XTC.py
package/MDAnalysis/coordinates/XYZ.py
package/MDAnalysis/coordinates/base.py
package/MDAnalysis/coordinates/chain.py
package/MDAnalysis/coordinates/chemfiles.py
package/MDAnalysis/coordinates/memory.py
# ---------------------
# 4046 Added an info method to Universe Class
package/MDAnalysis/core/universe.py
# ---------------------
44 changes: 44 additions & 0 deletions maintainer/active_files_package.lst
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package/MDAnalysis/core/selection\.py
| package/MDAnalysis/analysis/atomicdistances\.py
| package/MDAnalysis/topology/CMSParser\.py
| package/MDAnalysis/topology/__init__\.py
| package/MDAnalysis/coordinates/XDR\.py
| package/MDAnalysis/core/selection\.py
| package/MDAnalysis/analysis/diffusionmap\.py
| package/MDAnalysis/analysis/align\.py
| package/MDAnalysis/lib/_distopia\.py
| package/MDAnalysis/lib/distances\.py
| package/MDAnalysis/analysis/dasktimeseries\.py
| package/MDAnalysis/coordinates/H5MD\.py
| package/MDAnalysis/coordinates/MMCIF\.py
| package/MDAnalysis/coordinates/__init__\.py
| package/MDAnalysis/topology/MMCIFParser\.py
| package/MDAnalysis/topology/PDBParser\.py
| package/MDAnalysis/topology/__init__\.py
| package/MDAnalysis/topology/tpr/utils\.py
| package/MDAnalysis/coordinates/CIF\.py
| package/MDAnalysis/coordinates/PDBx\.py
| package/MDAnalysis/coordinates/__init__\.py
| package/MDAnalysis/topology/PDBxParser\.py
| package/MDAnalysis/topology/__init__\.py
| package/MDAnalysis/coordinates/base\.py
| package/MDAnalysis/core/universe\.py
| package/MDAnalysis/topology/base\.py
| package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis\.py
| package/MDAnalysis/analysis/sasa\.py
| package/MDAnalysis/coordinates/DCD\.py
| package/MDAnalysis/coordinates/DLPoly\.py
| package/MDAnalysis/coordinates/GMS\.py
| package/MDAnalysis/coordinates/MOL2\.py
| package/MDAnalysis/coordinates/PDB\.py
| package/MDAnalysis/coordinates/TRJ\.py
| package/MDAnalysis/coordinates/TRR\.py
| package/MDAnalysis/coordinates/TRZ\.py
| package/MDAnalysis/coordinates/TXYZ\.py
| package/MDAnalysis/coordinates/XTC\.py
| package/MDAnalysis/coordinates/XYZ\.py
| package/MDAnalysis/coordinates/base\.py
| package/MDAnalysis/coordinates/chain\.py
| package/MDAnalysis/coordinates/chemfiles\.py
| package/MDAnalysis/coordinates/memory\.py
| package/MDAnalysis/core/universe\.py
21 changes: 21 additions & 0 deletions maintainer/active_files_testsuite.lst
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testsuite/MDAnalysisTests/core/test_atomselections\.py
| testsuite/MDAnalysisTests/analysis/test_atomicdistances\.py
| testsuite/MDAnalysisTests/coordinates/test_xdr\.py
| testsuite/MDAnalysisTests/core/test_atomselections\.py
| testsuite/MDAnalysisTests/datafiles\.py
| testsuite/MDAnalysisTests/analysis/conftest\.py
| testsuite/MDAnalysisTests/analysis/test_diffusionmap\.py
| testsuite/MDAnalysisTests/analysis/conftest\.py
| testsuite/MDAnalysisTests/analysis/test_align\.py
| testsuite/MDAnalysisTests/lib/test_distances\.py
| testsuite/MDAnalysisTests/coordinates/test_mmcif\.py
| testsuite/MDAnalysisTests/datafiles\.py
| testsuite/MDAnalysisTests/topology/test_mmcif\.py
| testsuite/MDAnalysisTests/coordinates/test_cif\.py
| testsuite/MDAnalysisTests/analysis/test_encore\.py
| testsuite/MDAnalysisTests/parallelism/test_multiprocessing\.py
| testsuite/MDAnalysisTests/coordinates/base\.py
| testsuite/MDAnalysisTests/coordinates/test_gro\.py
| testsuite/MDAnalysisTests/topology/base\.py
| testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis\.py
| testsuite/MDAnalysisTests/analysis/test_sasa\.py
48 changes: 47 additions & 1 deletion package/pyproject.toml
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Expand Up @@ -137,5 +137,51 @@ tables\.py
| MDAnalysis/transformations/.*\.py
)
'''
extend-exclude = '__pycache__'
extend-exclude = '''
(
__pycache__
| MDAnalysis/core/selection\.py
| MDAnalysis/analysis/atomicdistances\.py
| MDAnalysis/topology/CMSParser\.py
| MDAnalysis/topology/__init__\.py
| MDAnalysis/coordinates/XDR\.py
| MDAnalysis/core/selection\.py
| MDAnalysis/analysis/diffusionmap\.py
| MDAnalysis/analysis/align\.py
| MDAnalysis/analysis/dasktimeseries\.py
| MDAnalysis/coordinates/H5MD\.py
| MDAnalysis/coordinates/MMCIF\.py
| MDAnalysis/coordinates/__init__\.py
| MDAnalysis/topology/MMCIFParser\.py
| MDAnalysis/topology/PDBParser\.py
| MDAnalysis/topology/__init__\.py
| MDAnalysis/topology/tpr/utils\.py
| MDAnalysis/coordinates/CIF\.py
| MDAnalysis/coordinates/PDBx\.py
| MDAnalysis/coordinates/__init__\.py
| MDAnalysis/topology/PDBxParser\.py
| MDAnalysis/topology/__init__\.py
| MDAnalysis/coordinates/base\.py
| MDAnalysis/core/universe\.py
| MDAnalysis/topology/base\.py
| MDAnalysis/analysis/hydrogenbonds/hbond_analysis\.py
| MDAnalysis/analysis/sasa\.py
| MDAnalysis/coordinates/DCD\.py
| MDAnalysis/coordinates/DLPoly\.py
| MDAnalysis/coordinates/GMS\.py
| MDAnalysis/coordinates/MOL2\.py
| MDAnalysis/coordinates/PDB\.py
| MDAnalysis/coordinates/TRJ\.py
| MDAnalysis/coordinates/TRR\.py
| MDAnalysis/coordinates/TRZ\.py
| MDAnalysis/coordinates/TXYZ\.py
| MDAnalysis/coordinates/XTC\.py
| MDAnalysis/coordinates/XYZ\.py
| MDAnalysis/coordinates/base\.py
| MDAnalysis/coordinates/chain\.py
| MDAnalysis/coordinates/chemfiles\.py
| MDAnalysis/coordinates/memory\.py
| MDAnalysis/core/universe\.py
)
'''
required-version = '24'
26 changes: 25 additions & 1 deletion testsuite/pyproject.toml
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Expand Up @@ -164,5 +164,29 @@ setup\.py
| MDAnalysisTests/transformations/.*\.py
)
'''
extend-exclude = '__pycache__'
extend-exclude = '''
(
__pycache__
| testsuite/MDAnalysisTests/core/test_atomselections\.py
| testsuite/MDAnalysisTests/analysis/test_atomicdistances\.py
| testsuite/MDAnalysisTests/coordinates/test_xdr\.py
| testsuite/MDAnalysisTests/core/test_atomselections\.py
| testsuite/MDAnalysisTests/datafiles\.py
| testsuite/MDAnalysisTests/analysis/conftest\.py
| testsuite/MDAnalysisTests/analysis/test_diffusionmap\.py
| testsuite/MDAnalysisTests/analysis/conftest\.py
| testsuite/MDAnalysisTests/analysis/test_align\.py
| testsuite/MDAnalysisTests/coordinates/test_mmcif\.py
| testsuite/MDAnalysisTests/datafiles\.py
| testsuite/MDAnalysisTests/topology/test_mmcif\.py
| testsuite/MDAnalysisTests/coordinates/test_cif\.py
| testsuite/MDAnalysisTests/analysis/test_encore\.py
| testsuite/MDAnalysisTests/parallelism/test_multiprocessing\.py
| testsuite/MDAnalysisTests/coordinates/base\.py
| testsuite/MDAnalysisTests/coordinates/test_gro\.py
| testsuite/MDAnalysisTests/topology/base\.py
| testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis\.py
| testsuite/MDAnalysisTests/analysis/test_sasa\.py
)
'''
required-version = '24'
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