chore: update CI with decoupled way of running pytest #114
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This file has special meaning in the GitHub interface and it is good practice to have it:
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| ## Recommended Installation | |||
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| The package `prymer` requires installation of [Primer3](https://github.com/primer3-org/primer3) and [interactive `bwa`](https://github.com/fulcrumgenomics/bwa-aln-interactive). | |||
| The package `prymer` requires installation of [interactive `bwa`](https://github.com/fulcrumgenomics/bwa-aln-interactive). | |||
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Looks like primer3 is nuked, so I got rid of that.
docs/CONTRIBUTING.md
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This soft-link ensure there is only 1 source of contributor/developer documentation and it will show up nicely in GitHub and also get compiled into our docs website too.
| [tool.git-cliff.changelog] | ||
| header = "" | ||
| trim = true | ||
| body = """ | ||
| {% for group, commits in commits | group_by(attribute="group") %} | ||
| ## {{ group | upper_first }} | ||
| {% for commit in commits %} | ||
| - {{ commit.message | upper_first }} ({{ commit.id | truncate(length=8, end="") }})\ | ||
| {% endfor %} | ||
| {% endfor %}\n | ||
| """ |
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Since this is repo/CI configuration, I moved it to the bottom.
So the flow of the pyproject.toml goes:
- Python project config
- Project config
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| [tool.mypy] | ||
| files = ["prymer", "tests"] | ||
| python_version = "3.12" |
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For the reasons here: https://github.com/fulcrumgenomics/python-template/pull/19
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Ah, yes, thanks! I got bitten by this earlier this week!
| ignore_missing_imports = true | ||
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| [tool.pytest.ini_options] | ||
| minversion = "7.4" | ||
| addopts = [ | ||
| "--import-mode=importlib", |
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Being explicit here I think is best practice.
pyproject.toml
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| [tool.ruff] | |||
| include = ["prymer/**/*.py", "tests/**/*.py"] | |||
| line-length = 100 | |||
| target-version = "py311" | |||
| target-version = "py312" | |||
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Looks like the project is now Py3.12+?
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For now. I'd like to re-enable 3.11 when we're doing making big changes.
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It doesn't make a difference right now so I reverted to py311.
| # TODO: fixup the documentation so we can remove the following lints from the ignore list: | ||
| "ARG001", # unused function argument | ||
| "ARG003", # unused class method argument | ||
| "D102", # missing docstring in public method | ||
| "D103", # missing docstring in public function | ||
| "D105", # missing docstring in magic method | ||
| "D107", # missing docstring in __init__ | ||
| "D214", # section is over-indented | ||
| "D200", # one-line docstring should fit on one line | ||
| "D202", # no blank lines allowed after function docstring | ||
| "D205", # 1 blank line required between summary line and description | ||
| "D209", # multi-line docstring closing quotes should be on a separate line | ||
| "D213", # multi-line docstring summary should start at the second line | ||
| "D412", # no blank lines allowed between a section header and its content ("Example") | ||
| "D414", # section has no content | ||
| "D415", # first line should end with a period, question mark, or exclamation point | ||
| "D417", # missing argument description in the docstring | ||
| "F841", # local variable `x` is assigned to but never used | ||
| "N815", # variable `x` in class scope should not be mixedCase |
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I added in our ruff lints but then ignored all the ones that failed.
Fixing these will make the API docs render even more nicely.
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
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