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Update template to v0.3.1 #5

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7 changes: 4 additions & 3 deletions .cruft.json
Original file line number Diff line number Diff line change
@@ -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",
Expand All @@ -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,
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/release.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down
34 changes: 34 additions & 0 deletions .pre-commit-config.yaml.rej
Original file line number Diff line number Diff line change
@@ -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:
3 changes: 2 additions & 1 deletion docs/contributing.md
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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
23 changes: 13 additions & 10 deletions pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -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.*",
Expand Down Expand Up @@ -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
Expand All @@ -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",
Expand All @@ -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"]
Expand All @@ -125,5 +128,5 @@ skip = [
"docs/changelog.md",
"docs/references.bib",
"docs/references.md",
"docs/notebooks/example.ipynb"
"docs/notebooks/example.ipynb",
]
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