Update instance repo from cookiecutter template

.editorconfig

@@ -8,10 +8,7 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
-[*.{yml,yaml}]
-indent_size = 2
-
-[.cruft.json]
+[{*.{yml,yaml,toml},.cruft.json}]
 indent_size = 2
 
 [Makefile]

.pre-commit-config.yaml

@@ -10,6 +10,10 @@ repos:
     rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: "2.2.1"
+    hooks:
+      - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.6.3
     hooks:

pyproject.toml

@@ -1,134 +1,120 @@
 [build-system]
 build-backend = "hatchling.build"
-requires = ["hatchling"]
+requires = [ "hatchling" ]
 
 [project]
 name = "cookiecutter-scverse-instance"
 version = "0.0.1"
 description = "An example repo generated from the `cookiecutter-scverse` template. Feel free to look around this repo and check out the docs to find out if the template works for you!"
 readme = "README.md"
-requires-python = ">=3.10"
-license = {file = "LICENSE"}
-authors = [
-    {name = "scverse community"},
-]
+license = { file = "LICENSE" }
 maintainers = [
-    {name = "scverse community", email = "core-team@scverse.org"},
+  { name = "scverse community", email = "core-team@scverse.org" },
 ]
-# https://docs.pypi.org/project_metadata/#project-urls
-urls.Documentation = "https://cookiecutter-scverse-instance.readthedocs.io/"
-urls.Source = "https://github.com/scverse/cookiecutter-scverse-instance"
-urls.Homepage = "https://github.com/scverse/cookiecutter-scverse-instance"
-dependencies = [
-    "anndata",
-    # for debug logging (referenced from the issue template)
-    "session-info",
+authors = [
+  { name = "scverse community" },
 ]
-
-[project.optional-dependencies]
-dev = [
-    "pre-commit",
-    "twine>=4.0.2",
+requires-python = ">=3.10"
+classifiers = [
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
 ]
-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",
+dependencies = [
+  "anndata",
+  # for debug logging (referenced from the issue template)
+  "session-info",
 ]
-test = [
-    "pytest",
-    "coverage",
+optional-dependencies.dev = [
+  "pre-commit",
+  "twine>=4.0.2",
 ]
-
-[tool.coverage.run]
-source = ["cookiecutter_scverse_instance"]
-omit = [
-    "**/test_*.py",
+optional-dependencies.doc = [
+  "docutils>=0.8,!=0.18.*,!=0.19.*",
+  "ipykernel",
+  "ipython",
+  "myst-nb>=1.1",
+  "pandas",
+  # Until pybtex >0.23.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
+  "setuptools",
+  "sphinx>=4",
+  "sphinx-autodoc-typehints",
+  "sphinx-book-theme>=1",
+  "sphinx-copybutton",
+  "sphinxcontrib-bibtex>=1",
+  "sphinxext-opengraph",
 ]
-
-[tool.pytest.ini_options]
-testpaths = ["tests"]
-xfail_strict = true
-addopts = [
-    "--import-mode=importlib",  # allow using test files with same name
+optional-dependencies.test = [
+  "coverage",
+  "pytest",
 ]
+# https://docs.pypi.org/project_metadata/#project-urls
+urls.Documentation = "https://cookiecutter-scverse-instance.readthedocs.io/"
+urls.Homepage = "https://github.com/scverse/cookiecutter-scverse-instance"
+urls.Source = "https://github.com/scverse/cookiecutter-scverse-instance"
 
 [tool.ruff]
 line-length = 120
-src = ["src"]
-extend-include = ["*.ipynb"]
+src = [ "src" ]
+extend-include = [ "*.ipynb" ]
 
-[tool.ruff.format]
-docstring-code-format = true
+format.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
+lint.select = [
+  "B",      # flake8-bugbear
+  "BLE",    # flake8-blind-except
+  "C4",     # flake8-comprehensions
+  "D",      # pydocstyle
+  "E",      # Error detected by Pycodestyle
+  "F",      # Errors detected by Pyflakes
+  "I",      # isort
+  "RUF100", # Report unused noqa directives
+  "TID",    # flake8-tidy-imports
+  "UP",     # pyupgrade
+  "W",      # Warning detected by Pycodestyle
 ]
-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",
+lint.ignore = [
+  "B008", # Errors from function calls in argument defaults. These are fine when the result is immutable.
+  "D100", # Missing docstring in public module
+  "D104", # Missing docstring in public package
+  "D105", # __magic__ methods are often self-explanatory, allow missing docstrings
+  "D107", # Missing docstring in __init__
+  # Disable one in each pair of mutually incompatible rules
+  "D203", # We don’t want a blank line before a class docstring
+  "D213", # <> We want docstrings to start immediately after the opening triple quote
+  "D400", # first line should end with a period [Bug: doesn’t work with single-line docstrings]
+  "D401", # First line should be in imperative mood; try rephrasing
+  "E501", # line too long -> we accept long comment lines; formatter gets rid of long code lines
+  "E731", # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
+  "E741", # allow I, O, l as variable names -> I is the identity matrix
 ]
+lint.per-file-ignores."*/__init__.py" = [ "F401" ]
+lint.per-file-ignores."docs/*" = [ "I" ]
+lint.per-file-ignores."tests/*" = [ "D" ]
+lint.pydocstyle.convention = "numpy"
 
-[tool.ruff.lint.pydocstyle]
-convention = "numpy"
+[tool.pytest.ini_options]
+testpaths = [ "tests" ]
+xfail_strict = true
+addopts = [
+  "--import-mode=importlib", # allow using test files with same name
+]
 
-[tool.ruff.lint.per-file-ignores]
-"docs/*" = ["I"]
-"tests/*" = ["D"]
-"*/__init__.py" = ["F401"]
+[tool.coverage.run]
+source = [ "cookiecutter_scverse_instance" ]
+omit = [
+  "**/test_*.py",
+]
 
 [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",
 ]