Add Ruff to pre-commit #819
Conversation
updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0) - [github.com/psf/black: 24.3.0 → 24.4.0](psf/black@24.3.0...24.4.0)
updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0) - [github.com/psf/black: 24.3.0 → 24.4.2](psf/black@24.3.0...24.4.2)
…mso into pre-commit-ci-update-config
for more information, see https://pre-commit.ci
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
| ryckaert_connection_type = convert_opls_to_ryckaert( | ||
| opls_connection_type | ||
| ) | ||
| ryckaert_connection_type = convert_opls_to_ryckaert(opls_connection_type) |
Check notice
Code scanning / CodeQL
Unused local variable Note
| ryckaert_connection_type = convert_opls_to_ryckaert( | ||
| opls_connection_type | ||
| ) | ||
| ryckaert_connection_type = convert_opls_to_ryckaert(opls_connection_type) |
Check warning
Code scanning / CodeQL
Variable defined multiple times Warning
| connection_lines = open(filename, "r").readlines()[ | ||
| i + 2 : i + n_connections + 2 | ||
| ] | ||
| connection_lines = open(filename, "r").readlines()[i + 2 : i + n_connections + 2] |
Check warning
Code scanning / CodeQL
File is not always closed Warning
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Looks like the pre-commit has a lot of recommendations for changes. @daico007 I think we should look at some custom parsing, because notes like the |
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If the only issue is the F401 errors in the See this in the documentation |
Yes that would be good. We may have to do that with a few of the different files this way because it's a bunch of files across the project. |
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Reading the ruff documentation https://docs.astral.sh/ruff/linter/#error-suppression We can add |
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The rest of the suggested changes seem pretty reasonable I think. What do you all think @CalCraven @daico007 ? |
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I would say we should ignore things for the |
for more information, see https://pre-commit.ci
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I think I got most of the errors fixed (even in the tests). There are some lingering ones about not using I think we should fix the bare excepts, I just don't know what the errors should be off the top of my head. We use |
| forcefield_selection_with_paths[residue] = ( | ||
| ff_names_path_iteration | ||
| ) | ||
| read_xlm_iteration = minidom.parse(ff_names_path_iteration) # noqa: F841 |
Check warning
Code scanning / CodeQL
Variable defined multiple times Warning
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https://github.com/BrianPugh/python-template/blob/main/.pre-commit-config.yaml Going to link to a cookie-cutter version of a ruff linter, check out the pyproject.toml as well for some additional formatting stuff we could consider implementing, such as type checking and isort. |
.pre-commit-config.yaml
Outdated
| hooks: | ||
| # Run the linter. | ||
| - id: ruff | ||
| args: [--line-length=80] |
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Should we add the fix flag back in, so that easy formatting fixes are automatically made and comitted on PRs?
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yeah, sure! we can always turn it off later if it's become troublesome.
This is just a test PR to test the linting with Ruff, which is recommended by pydocstyle as a replacement and used by other big python package.