From 4f143fdf02ddf9cdb43b0e69edc7cb41bb455556 Mon Sep 17 00:00:00 2001 From: Egor Marin Date: Thu, 19 Dec 2024 23:57:40 +0300 Subject: [PATCH] add active PRs to black ignore (#4815) --- maintainer/active_files.lst | 137 ++++++++++++++++++++++++++ maintainer/active_files_package.lst | 44 +++++++++ maintainer/active_files_testsuite.lst | 21 ++++ package/pyproject.toml | 48 ++++++++- testsuite/pyproject.toml | 26 ++++- 5 files changed, 274 insertions(+), 2 deletions(-) create mode 100644 maintainer/active_files.lst create mode 100644 maintainer/active_files_package.lst create mode 100644 maintainer/active_files_testsuite.lst diff --git a/maintainer/active_files.lst b/maintainer/active_files.lst new file mode 100644 index 00000000000..525bb70720e --- /dev/null +++ b/maintainer/active_files.lst @@ -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 +# --------------------- diff --git a/maintainer/active_files_package.lst b/maintainer/active_files_package.lst new file mode 100644 index 00000000000..a1889549c1e --- /dev/null +++ b/maintainer/active_files_package.lst @@ -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 diff --git a/maintainer/active_files_testsuite.lst b/maintainer/active_files_testsuite.lst new file mode 100644 index 00000000000..4898eafde48 --- /dev/null +++ b/maintainer/active_files_testsuite.lst @@ -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 diff --git a/package/pyproject.toml b/package/pyproject.toml index 05bce424867..5853b74a210 100644 --- a/package/pyproject.toml +++ b/package/pyproject.toml @@ -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' diff --git a/testsuite/pyproject.toml b/testsuite/pyproject.toml index 359430e131e..9c660c95482 100644 --- a/testsuite/pyproject.toml +++ b/testsuite/pyproject.toml @@ -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'