pre-commit inconsistent between local and remote execution

[ianmkenney]

From a fresh clone of gufe, it seems like we're not getting consistent results between local and remote (bot) run pre-commit execution.

cd `mktemp -d`
git clone https://github.com/openfreeenergy/gufe && cd gufe
git checkout 10fef9b  # check out main as it currently is
micromamba create -p ../env/ python=3.11 pre-commit --yes  # keep the env out of pre-commits way
micromamba -p ../env/ run pre-commit run --all-files

From the output of the last step we see that it would reformat (many) files. I figured that the files would be consistent with the merge of #421, but that doesn't seem to be the case.

check for added large files..............................................Passed
check for case conflicts.................................................Passed
check that executables have shebangs.................(no files to check)Skipped
check for broken symlinks............................(no files to check)Skipped
check toml...............................................................Passed
check yaml...............................................................Passed
debug statements (python)................................................Passed
detect destroyed symlinks................................................Passed
fix end of files.........................................................Failed
- hook id: end-of-file-fixer
- exit code: 1
- files were modified by this hook

Fixing .github/PULL_REQUEST_TEMPLATE/pull_request_template.md

trim trailing whitespace.................................................Passed
black....................................................................Failed
- hook id: black
- files were modified by this hook

reformatted gufe/chemicalsystem.py
reformatted gufe/mapping/atom_mapper.py
reformatted gufe/components/solventcomponent.py
reformatted gufe/components/explicitmoleculecomponent.py
reformatted gufe/custom_codecs.py
reformatted gufe/network.py
reformatted gufe/protocols/protocol.py
reformatted gufe/ligandnetwork.py
reformatted gufe/mapping/ligandatommapping.py
reformatted gufe/storage/externalresource/memorystorage.py
reformatted gufe/storage/externalresource/filestorage.py
reformatted gufe/settings/models.py
reformatted gufe/tests/test_chemicalsystem.py
reformatted gufe/tests/test_mapping.py
reformatted gufe/protocols/protocoldag.py
reformatted gufe/components/proteincomponent.py
reformatted gufe/tests/test_protocoldag.py
reformatted gufe/tests/conftest.py
reformatted gufe/tests/test_mapping_visualization.py
reformatted gufe/tests/test_ligandatommapping.py
reformatted gufe/tests/test_solvents.py
reformatted gufe/tests/test_proteincomponent.py
reformatted gufe/tests/test_serialization_migration.py
reformatted gufe/utils.py
reformatted gufe/tests/test_ligand_network.py
reformatted gufe/tests/test_transformation.py
reformatted gufe/transformations/transformation.py
reformatted gufe/vendor/pdb_file/PdbxReader.py
reformatted gufe/tests/test_tokenization.py
reformatted gufe/tests/test_protocol.py
reformatted gufe/vendor/pdb_file/element.py
reformatted gufe/tokenization.py
reformatted gufe/vendor/pdb_file/unitcell.py
reformatted gufe/vendor/pdb_file/pdbfile.py
reformatted gufe/visualization/mapping_visualization.py
reformatted gufe/vendor/pdb_file/pdbxfile.py
reformatted gufe/vendor/pdb_file/PdbxContainers.py
reformatted gufe/vendor/pdb_file/topology.py
reformatted gufe/vendor/pdb_file/pdbstructure.py

All done! ✨ 🍰 ✨
39 files reformatted, 38 files left unchanged.

black-jupyter............................................................Passed
isort....................................................................Failed
- hook id: isort
- files were modified by this hook

Fixing /tmp/tmp.G5QwXeH9YD/gufe/gufe/__init__.py
Fixing /tmp/tmp.G5QwXeH9YD/gufe/gufe/settings/__init__.py
Fixing /tmp/tmp.G5QwXeH9YD/gufe/gufe/tests/storage/test_externalresource.py
Fixing /tmp/tmp.G5QwXeH9YD/gufe/gufe/tests/test_models.py
Fixing /tmp/tmp.G5QwXeH9YD/gufe/gufe/tests/test_protocolunit.py

interrogate..............................................................Passed
pyupgrade................................................................Failed
- hook id: pyupgrade
- exit code: 1
- files were modified by this hook

Rewriting gufe/vendor/pdb_file/pdbstructure.py
Rewriting gufe/vendor/pdb_file/PdbxContainers.py

I get similar behavior when running some of the tools manually. Although it's not a required step for merging it is a bit of a headache. @jthorton might have more to add here as well.

Any idea why this might be happening @mikemhenry?