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some autofmt
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@flying-sheep
flying-sheep committed Jul 30, 2024
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5 changes: 5 additions & 0 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,11 @@ repos:
- id: biome-format
additional_dependencies: ["@biomejs/[email protected]"]
# Hooks that are run for scripts
- repo: https://github.com/tox-dev/pyproject-fmt
rev: "2.1.4"
hooks:
- id: pyproject-fmt
files: ^scripts/
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.5.5
hooks:
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184 changes: 95 additions & 89 deletions scripts/pyproject.toml
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@@ -1,44 +1,50 @@
[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"
requires = [
"hatch-vcs",
"hatchling",
]

[project]
name = "scverse-template-scripts"
dynamic = ["version"]
description = "scripts for ecosystem package data"
readme = "../README.md"
requires-python = ">=3.11"
license = "GPL-3.0"
authors = [
{ name = "Philipp A.", email = "[email protected]" },
{ name = "Philipp A.", email = "[email protected]" },
]
requires-python = ">=3.11"
classifiers = [
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]
dynamic = [
"version",
]
urls.Documentation = "https://github.com/scverse/cookiecutter-scverse#readme"
urls.Issues = "https://github.com/scverse/cookiecutter-scverse/issues"
urls.Source = "https://github.com/scverse/cookiecutter-scverse"
dependencies = [
"cruft",
"rich",
"typer",
"furl",
"GitPython",
"PyGitHub >= 2",
"PyYAML",
"pre-commit", # is ran by cruft
"cruft",
"furl",
"gitpython",
"pre-commit", # is ran by cruft
"pygithub>=2",
"pyyaml",
"rich",
"typer",
]

[project.optional-dependencies]
test = [
"pytest",
"pytest-socket",
"pytest-responsemock",
optional-dependencies.test = [
"pytest",
"pytest-responsemock",
"pytest-socket",
]

[project.scripts]
send-cruft-prs = "scverse_template_scripts.cruft_prs:cli"
make-rich-output = "scverse_template_scripts.make_rich_output:main"
urls.Documentation = "https://github.com/scverse/cookiecutter-scverse#readme"
urls.Issues = "https://github.com/scverse/cookiecutter-scverse/issues"
urls.Source = "https://github.com/scverse/cookiecutter-scverse"
scripts.make-rich-output = "scverse_template_scripts.make_rich_output:main"
scripts.send-cruft-prs = "scverse_template_scripts.cruft_prs:cli"

[tool.hatch.build.targets.wheel]
packages = ["src/testing", "src/scverse_template_scripts"]
packages = [ "src/testing", "src/scverse_template_scripts" ]

[tool.hatch.version]
source = "vcs"
Expand All @@ -48,75 +54,75 @@ fallback-version = "0.0"
python = "3.11"

[tool.hatch.envs.hatch-test]
features = ["test"]

[tool.pytest.ini_options]
addopts = [
"--import-mode=importlib",
"--disable-socket",
"-presponsemock",
"-ptesting.scverse_template_scripts._pytest"
]
filterwarnings = [
"error",
# https://github.com/man-group/pytest-plugins/issues/224
"ignore::DeprecationWarning:pytest_shutil",
]
features = [ "test" ]

[tool.ruff]
line-length = 120

[tool.ruff.format]
docstring-code-format = true
format.docstring-code-format = true

[tool.ruff.lint]
allowed-confusables = ["’", "×"]
select = [
"A",
"ARG",
"B",
"C",
"DTZ",
"E",
"EM",
"F",
"FBT",
"I",
"ICN",
"ISC",
"N",
"PLC",
"PLE",
"PLR",
"PLW",
"Q",
"RUF",
"S",
"T",
"TCH",
"TID",
"UP",
"W",
"YTT",
lint.select = [
"A",
"ARG",
"B",
"C",
"DTZ",
"E",
"EM",
"F",
"FBT",
"I",
"ICN",
"ISC",
"N",
"PLC",
"PLE",
"PLR",
"PLW",
"Q",
"RUF",
"S",
"T",
"TCH",
"TID",
"UP",
"W",
"YTT",
]
ignore = [
"S101", # assert should be allowed
"S603", # subprocess with shell=False should be allowed
"S311", # we don’t need cryptographically secure RNG
"ISC001", # conflicts with formatter
lint.ignore = [
"ISC001", # conflicts with formatter
"S101", # assert should be allowed
"S311", # we don’t need cryptographically secure RNG
"S603", # subprocess with shell=False should be allowed
]
lint.per-file-ignores."tests/*.py" = [
"ARG001", # pytest fixtures don’t need to be used
"PLR0913", # allow as many pytest fixtures being used as one likes
]
lint.unfixable = [
"RUF001", # never “fix” “confusables”
]
lint.allowed-confusables = [
"×",
"’",
]
lint.flake8-type-checking.exempt-modules = [
]
lint.flake8-type-checking.strict = true
lint.isort.known-first-party = [ "scverse_template_scripts", "testing.scverse_template_scripts" ]
lint.isort.required-imports = [
"from __future__ import annotations",
]
unfixable = ["RUF001"] # never “fix” “confusables”

[tool.ruff.lint.isort]
known-first-party = ["scverse_template_scripts", "testing.scverse_template_scripts"]
required-imports = ["from __future__ import annotations"]

[tool.ruff.lint.flake8-type-checking]
exempt-modules = []
strict = true

[tool.ruff.lint.per-file-ignores]
"tests/*.py" = [
"ARG001", # pytest fixtures don’t need to be used
"PLR0913", # allow as many pytest fixtures being used as one likes
[tool.pytest.ini_options]
addopts = [
"--import-mode=importlib",
"--disable-socket",
"-presponsemock",
"-ptesting.scverse_template_scripts._pytest",
]
filterwarnings = [
"error",
# https://github.com/man-group/pytest-plugins/issues/224
"ignore::DeprecationWarning:pytest_shutil",
]
128 changes: 64 additions & 64 deletions {{cookiecutter.project_name}}/pyproject.toml
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Expand Up @@ -10,39 +10,39 @@ readme = "README.md"
requires-python = ">=3.10"
license = {file = "LICENSE"}
authors = [
{name = "{{ cookiecutter.author_full_name }}"},
{name = "{{ cookiecutter.author_full_name }}"},
]
maintainers = [
{name = "{{ cookiecutter.author_full_name }}", email = "{{ cookiecutter.author_email }}"},
{name = "{{ cookiecutter.author_full_name }}", email = "{{ cookiecutter.author_email }}"},
]
urls.Documentation = "https://{{ cookiecutter.project_name }}.readthedocs.io/"
urls.Source = "{{ cookiecutter.project_repo }}"
urls.Home-page = "{{ cookiecutter.project_repo }}"
dependencies = [
"anndata",
# for debug logging (referenced from the issue template)
"session-info",
"anndata",
# for debug logging (referenced from the issue template)
"session-info",
]

[project.optional-dependencies]
dev = [
"pre-commit",
"twine>=4.0.2",
"pre-commit",
"twine>=4.0.2",
]
doc = [
"docutils>=0.8,!=0.18.*,!=0.19.*",
"sphinx>=4",
"sphinx-book-theme>=1.0.0",
"myst-nb>=1.1.0",
"sphinxcontrib-bibtex>=1.0.0",
"setuptools", # Until pybtex >0.23.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
"sphinx-autodoc-typehints",
"sphinxext-opengraph",
# For notebooks
"ipykernel",
"ipython",
"sphinx-copybutton",
"pandas",
"docutils>=0.8,!=0.18.*,!=0.19.*",
"sphinx>=4",
"sphinx-book-theme>=1.0.0",
"myst-nb>=1.1.0",
"sphinxcontrib-bibtex>=1.0.0",
"setuptools", # Until pybtex >0.23.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
"sphinx-autodoc-typehints",
"sphinxext-opengraph",
# For notebooks
"ipykernel",
"ipython",
"sphinx-copybutton",
"pandas",
]
test = [
"pytest",
Expand Down Expand Up @@ -78,44 +78,44 @@ docstring-code-format = true

[tool.ruff.lint]
select = [
"F", # Errors detected by Pyflakes
"E", # Error detected by Pycodestyle
"W", # Warning detected by Pycodestyle
"I", # isort
"D", # pydocstyle
"B", # flake8-bugbear
"TID", # flake8-tidy-imports
"C4", # flake8-comprehensions
"BLE", # flake8-blind-except
"UP", # pyupgrade
"RUF100", # Report unused noqa directives
"F", # Errors detected by Pyflakes
"E", # Error detected by Pycodestyle
"W", # Warning detected by Pycodestyle
"I", # isort
"D", # pydocstyle
"B", # flake8-bugbear
"TID", # flake8-tidy-imports
"C4", # flake8-comprehensions
"BLE", # flake8-blind-except
"UP", # pyupgrade
"RUF100", # Report unused noqa directives
]
ignore = [
# 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",
# allow I, O, l as variable names -> I is the identity matrix
"E741",
# Missing docstring in public package
"D104",
# Missing docstring in public module
"D100",
# Missing docstring in __init__
"D107",
# Errors from function calls in argument defaults. These are fine when the result is immutable.
"B008",
# __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",
# First line should be in imperative mood; try rephrasing
"D401",
## Disable one in each pair of mutually incompatible rules
# We don’t want a blank line before a class docstring
"D203",
# We want docstrings to start immediately after the opening triple quote
"D213",
# 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",
# allow I, O, l as variable names -> I is the identity matrix
"E741",
# Missing docstring in public package
"D104",
# Missing docstring in public module
"D100",
# Missing docstring in __init__
"D107",
# Errors from function calls in argument defaults. These are fine when the result is immutable.
"B008",
# __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",
# First line should be in imperative mood; try rephrasing
"D401",
## Disable one in each pair of mutually incompatible rules
# We don’t want a blank line before a class docstring
"D203",
# We want docstrings to start immediately after the opening triple quote
"D213",
]

[tool.ruff.lint.pydocstyle]
Expand All @@ -128,12 +128,12 @@ convention = "numpy"

[tool.cruft]
skip = [
"tests",
"src/**/__init__.py",
"src/**/basic.py",
"docs/api.md",
"docs/changelog.md",
"docs/references.bib",
"docs/references.md",
"docs/notebooks/example.ipynb",
"tests",
"src/**/__init__.py",
"src/**/basic.py",
"docs/api.md",
"docs/changelog.md",
"docs/references.bib",
"docs/references.md",
"docs/notebooks/example.ipynb",
]

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