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add active PRs to black ignore (#4815)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,137 @@ | ||
| # 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 | ||
| # --------------------- |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| 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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| 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 |
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