From cb96861de3fbc1224250a64c1110beead78bad80 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Thu, 22 Feb 2024 18:34:29 +0000 Subject: [PATCH] Update template to v0.3.1 --- .cruft.json | 7 ++++--- .github/workflows/release.yaml | 2 +- .pre-commit-config.yaml.rej | 34 ++++++++++++++++++++++++++++++++++ docs/contributing.md | 3 ++- pyproject.toml | 23 +++++++++++++---------- 5 files changed, 54 insertions(+), 15 deletions(-) create mode 100644 .pre-commit-config.yaml.rej diff --git a/.cruft.json b/.cruft.json index 27eb611..97edd3b 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,7 +1,7 @@ { "template": "https://github.com/scverse/cookiecutter-scverse", - "commit": "8e96abb5c3e2d5078c44713958da672711cf2a48", - "checkout": "v0.3.0", + "commit": "586b1652162ff7994b0070a034023d64289ae416", + "checkout": "v0.3.1", "context": { "cookiecutter": { "project_name": "scvi-hub-models", @@ -13,7 +13,8 @@ "project_repo": "https://github.com/YosefLab/scvi-hub-models", "license": "MIT License", "_copy_without_render": [ - ".github/workflows/**.yaml", + ".github/workflows/build.yaml", + ".github/workflows/test.yaml", "docs/_templates/autosummary/**.rst" ], "_render_devdocs": false, diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index bd82eb5..f36faa6 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest environment: name: pypi - url: https://pypi.org/p/{{ cookiecutter.package_name }} + url: https://pypi.org/p/scvi_hub_models permissions: id-token: write # IMPORTANT: this permission is mandatory for trusted publishing steps: diff --git a/.pre-commit-config.yaml.rej b/.pre-commit-config.yaml.rej new file mode 100644 index 0000000..831fbdc --- /dev/null +++ b/.pre-commit-config.yaml.rej @@ -0,0 +1,34 @@ +diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml (rejected hunks) +@@ -6,29 +6,18 @@ default_stages: + - push + minimum_pre_commit_version: 2.16.0 + repos: +- - repo: https://github.com/psf/black +- rev: "24.2.0" +- hooks: +- - id: black +- - repo: https://github.com/asottile/blacken-docs +- rev: 1.16.0 +- hooks: +- - id: blacken-docs + - repo: https://github.com/pre-commit/mirrors-prettier + rev: v4.0.0-alpha.8 + hooks: + - id: prettier +- # Newer versions of node don't work on systems that have an older version of GLIBC +- # (in particular Ubuntu 18.04 and Centos 7) +- # EOL of Centos 7 is in 2024-06, we can probably get rid of this then. +- # See https://github.com/scverse/cookiecutter-scverse/issues/143 and +- # https://github.com/jupyterlab/jupyterlab/issues/12675 +- language_version: "17.9.1" + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.2.2 + hooks: + - id: ruff ++ types_or: [python, pyi, jupyter] + args: [--fix, --exit-non-zero-on-fix] ++ - id: ruff-format ++ types_or: [python, pyi, jupyter] + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.5.0 + hooks: diff --git a/docs/contributing.md b/docs/contributing.md index 63f6174..8152502 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -93,7 +93,7 @@ Before making a release, you need to update the version number in the `pyproject > Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format. Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub. -Specify `vX.X.X` as a tag name and create a release. For more information, see [managing Github releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI. +Specify `vX.X.X` as a tag name and create a release. For more information, see [managing GitHub releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI. ## Writing documentation @@ -157,3 +157,4 @@ open _build/html/index.html [numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html [sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints [pypi]: https://pypi.org/ +[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository diff --git a/pyproject.toml b/pyproject.toml index 05358a0..c4a699b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,13 +21,13 @@ urls.Home-page = "https://github.com/YosefLab/scvi-hub-models" dependencies = [ "anndata", # for debug logging (referenced from the issue template) - "session-info" + "session-info", ] [project.optional-dependencies] dev = [ "pre-commit", - "twine>=4.0.2" + "twine>=4.0.2", ] doc = [ "docutils>=0.8,!=0.18.*,!=0.19.*", @@ -61,12 +61,15 @@ addopts = [ "--import-mode=importlib", # allow using test files with same name ] -[tool.black] -line-length = 120 - [tool.ruff] -src = ["src"] line-length = 120 +src = ["src"] +extend-include = ["*.ipynb"] + +[tool.ruff.format] +docstring-code-format = true + +[tool.ruff.lint] select = [ "F", # Errors detected by Pyflakes "E", # Error detected by Pycodestyle @@ -81,7 +84,7 @@ select = [ "RUF100", # Report unused noqa directives ] ignore = [ - # line too long -> we accept long comment lines; black gets rid of long code lines + # line too long -> we accept long comment lines; formatter gets rid of long code lines "E501", # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient "E731", @@ -108,10 +111,10 @@ ignore = [ "D213", ] -[tool.ruff.pydocstyle] +[tool.ruff.lint.pydocstyle] convention = "numpy" -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] "docs/*" = ["I"] "tests/*" = ["D"] "*/__init__.py" = ["F401"] @@ -125,5 +128,5 @@ skip = [ "docs/changelog.md", "docs/references.bib", "docs/references.md", - "docs/notebooks/example.ipynb" + "docs/notebooks/example.ipynb", ]