From 2f9eee479c11f5c3986e19f90c9367219d3bd731 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Tue, 21 May 2024 13:38:22 +0000 Subject: [PATCH] Update template to v0.4.0 --- .cruft.json | 7 ++++--- .gitignore | 1 + .pre-commit-config.yaml.rej | 34 ++++++++++++++++++++++++++++++++++ README.md.rej | 10 ++++++++++ docs/conf.py | 10 +++++----- docs/contributing.md | 5 +++-- pyproject.toml | 21 ++++++++++++--------- pyproject.toml.rej | 33 +++++++++++++++++++++++++++++++++ 8 files changed, 102 insertions(+), 19 deletions(-) create mode 100644 .pre-commit-config.yaml.rej create mode 100644 README.md.rej create mode 100644 pyproject.toml.rej diff --git a/.cruft.json b/.cruft.json index 38c173e..0f6f474 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,7 +1,7 @@ { "template": "https://github.com/scverse/cookiecutter-scverse", - "commit": "8e96abb5c3e2d5078c44713958da672711cf2a48", - "checkout": null, + "commit": "87a407a65408d75a949c0b54b19fd287475a56f8", + "checkout": "v0.4.0", "context": { "cookiecutter": { "project_name": "PopV", @@ -13,7 +13,8 @@ "project_repo": "https://github.com/YosefLab/PopV.git", "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/.gitignore b/.gitignore index de87789..c0f512d 100644 --- a/.gitignore +++ b/.gitignore @@ -19,6 +19,7 @@ __pycache__/ /.pytest_cache/ /.cache/ /data/ +/node_modules/ # docs /docs/generated/ diff --git a/.pre-commit-config.yaml.rej b/.pre-commit-config.yaml.rej new file mode 100644 index 0000000..5f9ac18 --- /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: "24.4.2" +- 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: v0.4.4 + 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: v4.6.0 + hooks: diff --git a/README.md.rej b/README.md.rej new file mode 100644 index 0000000..1446723 --- /dev/null +++ b/README.md.rej @@ -0,0 +1,10 @@ +diff a/README.md b/README.md (rejected hunks) +@@ -17,7 +17,7 @@ Please refer to the [documentation][link-docs]. In particular, the + + ## Installation + +-You need to have Python 3.9 or newer installed on your system. If you don't have ++You need to have Python 3.10 or newer installed on your system. If you don't have + Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge). + + There are several alternative options to install PopV: diff --git a/docs/conf.py b/docs/conf.py index 7274633..82dff57 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,5 +1,5 @@ # Configuration file for the Sphinx documentation builder. -# + # This file only contains a selection of the most common options. For a full # list see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html @@ -36,10 +36,10 @@ html_context = { "display_github": True, # Integrate GitHub - "github_user": "cane11", # Username - "github_repo": project_name, # Repo name - "github_version": "main", # Version - "conf_py_path": "/docs/", # Path in the checkout to the docs root + "github_user": "cane11", + "github_repo": "https://github.com/YosefLab/PopV.git", + "github_version": "main", + "conf_py_path": "/docs/", } # -- General configuration --------------------------------------------------- diff --git a/docs/contributing.md b/docs/contributing.md index 0f210e3..9fc2252 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -51,7 +51,7 @@ and [prettier][prettier-editors]. ## Writing tests ```{note} -Remember to first install the package with `pip install '-e[dev,test]'` +Remember to first install the package with `pip install -e '.[dev,test]'` ``` This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added @@ -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 77f3bd4..363c8c9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -82,12 +82,15 @@ 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 @@ -102,7 +105,7 @@ 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", @@ -116,7 +119,7 @@ ignore = [ "D107", # Errors from function calls in argument defaults. These are fine when the result is immutable. "B008", - # __magic__ methods are are often self-explanatory, allow missing docstrings + # __magic__ methods are often self-explanatory, allow missing docstrings "D105", # first line should end with a period [Bug: doesn't work with single-line docstrings] "D400", @@ -129,10 +132,10 @@ 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"] @@ -146,5 +149,5 @@ skip = [ "docs/changelog.md", "docs/references.bib", "docs/references.md", - "docs/notebooks/example.ipynb" + "docs/notebooks/example.ipynb", ] diff --git a/pyproject.toml.rej b/pyproject.toml.rej new file mode 100644 index 0000000..7aa2c8e --- /dev/null +++ b/pyproject.toml.rej @@ -0,0 +1,33 @@ +diff a/pyproject.toml b/pyproject.toml (rejected hunks) +@@ -7,7 +7,7 @@ name = "PopV" + version = "0.0.1" + description = "Consensus prediction of cell type labels with popV" + readme = "README.md" +-requires-python = ">=3.9" ++requires-python = ">=3.10" + license = {file = "LICENSE"} + authors = [ + {name = "Can Ergen"}, +@@ -21,19 +21,19 @@ urls.Home-page = "https://github.com/YosefLab/PopV.git" + 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.*", + "sphinx>=4", + "sphinx-book-theme>=1.0.0", +- "myst-nb", ++ "myst-nb>=1.1.0", + "sphinxcontrib-bibtex>=1.0.0", + "sphinx-autodoc-typehints", + "sphinxext-opengraph",