Merge pull request #167 from StingraySoftware/new_package_infra

Replace setup.cfg with pyproject.toml

.github/workflows/ci_test.yml

@@ -73,6 +73,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install tox
+          pip install -e ".[docs]"
       - name: Install system dependencies
         run: sudo apt-get -y install graphviz pandoc
       - name: Print Python, pip, setuptools, and tox versions
@@ -121,8 +122,8 @@ jobs:
             use_remote_data: true
             continue-on-error: true
           - os: ubuntu-latest
-            python: '3.8'
-            tox_env: 'py38-test-oldestdeps-cov'
+            python: '3.9'
+            tox_env: 'py39-test-oldestdeps-cov'
             use_remote_data: true
           - os: macos-latest
             python: '3.11'

.gitignore

@@ -11,6 +11,7 @@ __pycache__
 
 # Other generated files
 */version.py
+*/_version.py
 */cython_version.py
 htmlcov
 .coverage

.pre-commit-config.yaml

@@ -0,0 +1,117 @@
+ci:
+  autofix_prs: false
+  autoupdate_schedule: 'monthly'
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+        args: ["--enforce-all", "--maxkb=300"]
+        exclude: "^(\
+            .*.svg|\
+            notebooks/.*.ipynb|\
+            .*.jpe?g|\
+            .*logo.png|\
+            .*test.rmf|\
+        )$"
+        # Prevent giant files from being committed.
+      - id: check-case-conflict
+        # Check for files with names that would conflict on a case-insensitive
+        # filesystem like MacOS HFS+ or Windows FAT.
+      - id: check-json
+        # Attempts to load all json files to verify syntax.
+      - id: check-merge-conflict
+        # Check for files that contain merge conflict strings.
+      - id: check-symlinks
+        # Checks for symlinks which do not point to anything.
+      - id: check-toml
+        # Attempts to load all TOML files to verify syntax.
+      - id: check-xml
+        # Attempts to load all xml files to verify syntax.
+      - id: check-yaml
+        # Attempts to load all yaml files to verify syntax.
+        exclude: ".*(.github.*)$"
+      - id: detect-private-key
+        # Checks for the existence of private keys.
+      - id: end-of-file-fixer
+        # Makes sure files end in a newline and only a newline.
+        exclude: ".*(.*.svg|data.*|extern.*|_templates.*|licenses.*|_static.*|_parsetab.py|cli.rst)$"
+      # - id: fix-encoding-pragma  # covered by pyupgrade
+      - id: trailing-whitespace
+        # Trims trailing whitespace.
+        exclude_types: [python]  # Covered by Ruff W291.
+        exclude: ".*(data.*|extern.*|licenses.*|_static.*)$"
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: rst-directive-colons
+        # Detect mistake of rst directive not ending with double colon.
+      - id: rst-inline-touching-normal
+        # Detect mistake of inline code touching normal text in rst.
+      - id: text-unicode-replacement-char
+        # Forbid files which have a UTF-8 Unicode replacement character.
+        exclude: "^(\
+            .*.rmf|\
+        )$"
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        args: ["--write-changes"]
+        additional_dependencies:
+          - tomli
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.9
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  # - repo: https://github.com/scientific-python/cookie
+  #   rev: 2024.08.19
+  #   hooks:
+  #     - id: sp-repo-review
+
+  - repo: https://github.com/PyCQA/docformatter
+    # using an untagged rev for forward compatibility with pre-commit 4.0
+    # see https://github.com/PyCQA/docformatter/issues/289
+    # This should be changed back to a tag when (>1.7.5) is released
+    rev: 06907d0267368b49b9180eed423fae5697c1e909
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --config, ./pyproject.toml]
+        exclude: |
+          (?x)(
+              test.*\.py |
+              hendrics/__init__\.py |
+              hendrics/_dev/ |
+              hendrics/conftest\.py |
+              astropy/version\.py |
+              docs/ |
+              examples/
+          )
+
+  # - repo: local
+  #   hooks:
+  #     - id: changelogs-rst
+  #       name: changelog filenames
+  #       language: fail
+  #       entry: >-
+  #         changelog files must be named <sub-package>/####.(bugfix|feature|api|perf).rst
+  #         or ####.other.rst (in the root directory only)
+  #       exclude: >-
+  #         ^docs/changes/[\w\.]+/(\d+\.(bugfix|feature|api|perf)(\.\d)?.rst|.gitkeep)
+  #       files: ^docs/changes/[\w\.]+/
+  #     - id: changelogs-rst-other
+  #       name: changelog filenames for other category
+  #       language: fail
+  #       entry: >-
+  #         only "other" changelog files must be placed in the root directory
+  #       exclude: >-
+  #         ^docs/changes/(\d+\.other.rst|README.rst|template.rst)
+  #       files: ^docs/changes/\d+.\w+.rst

.ruff.toml

@@ -0,0 +1,211 @@
+extend = "pyproject.toml"
+lint.ignore = [
+    # NOTE: to find a good code to fix, run:
+    # ruff --select="ALL" --statistics astropy/<subpackage>
+
+    # flake8-annotations (ANN) : static typing
+    "ANN001",  # Function argument without type annotation
+    "ANN003",  # `**kwargs` without type annotation
+    "ANN202",  # Private function without return type annotation
+    "ANN401",  # Use of `Any` type
+
+    # flake8-unused-arguments (ARG)
+    "ARG001",  # unused-function-argument
+    "ARG002",  # unused-method-argument
+    "ARG003",  # unused-class-method-argument
+    "ARG004",  # unused-static-method-argument
+    "ARG005",  # unused-lambda-argument
+
+    # flake8-bugbear (B)
+    "B006",  # MutableArgumentDefault
+    "B007",  # UnusedLoopControlVariable
+    "B023",  # FunctionUsesLoopVariable
+    "B028",  # No-explicit-stacklevel
+    "B904",  # RaiseWithoutFromInsideExcept
+    "B905",  # ZipWithoutExplicitStrict
+
+    # flake8-blind-except (BLE)
+    "BLE001",  # blind-except
+
+    # mccabe (C90) : code complexity
+    # TODO: configure maximum allowed complexity.
+    "C901",  # McCabeComplexity
+
+    # pydocstyle (D)
+    # Missing Docstrings
+    "D100",  # undocumented-public-module
+    "D101",  # undocumented-public-class
+    "D103",  # undocumented-public-function
+    "D104",  # undocumented-public-package
+    "D205",  # blank-line-after-summary
+    # Quotes Issues
+    "D300",  # triple-single-quotes
+    "D301",  # escape-sequence-in-docstring
+    # Docstring Content Issues
+    "D403",  # first-line-capitalized
+    "D404",  # docstring-starts-with-this
+    "D401",  # non-imperative-mood.
+    "D414",  # empty-docstring-section
+    "D419",  # docstring is empty
+
+    # flake8-datetimez (DTZ)
+    "DTZ001",  # call-datetime-without-tzinfo
+    "DTZ005",  # call-datetime-now-without-tzinfo
+
+    # pycodestyle (E, W)
+    "E501",  # line-too-long
+    "E721",  # type-comparison
+    "E731",  # lambda-assignment
+
+    # flake8-errmsg (EM)  : nicer error tracebacks
+    "EM101",   # raw-string-in-exception
+    "EM102",   # f-string-in-exception
+    "EM103",   # dot-format-in-exception
+
+    # eradicate (ERA)
+    # NOTE: be careful that developer notes are kept.
+    "ERA001",  # commented-out-code
+
+    # flake8-executable (EXE)
+    "EXE002",  # shebang-missing-executable-file
+
+    # Pyflakes (F)
+    "F841",  # unused-variable
+
+    # flake8-boolean-trap (FBT)  : boolean flags should be kwargs, not args
+    # NOTE: a good thing to fix, but changes API.
+    "FBT001",  # boolean-positional-arg-in-function-definition
+    "FBT002",  # boolean-default-value-in-function-definition
+    "FBT003",  # boolean-positional-value-in-function-call
+
+    # flake8-fixme (FIX)
+    "FIX001",  # Line contains FIXME.  this should be fixed or at least FIXME replaced with TODO
+    "FIX004",  # Line contains HACK. replace HACK with NOTE.
+
+    # pep8-naming (N)
+    # NOTE: some of these can/should be fixed, but this changes the API.
+    "N801",  # invalid-class-name
+    "N802",  # invalid-function-name
+    "N803",  # invalid-argument-name
+    "N804",  # invalid-first-argument-name-for-class-method
+    "N805",  # invalid-first-argument-name-for-method
+    "N807",  # dunder-function-name
+    "N813",  # camelcase-imported-as-lowercase
+    "N815",  # mixed-case-variable-in-class-scope
+    "N816",  # mixed-case-variable-in-global-scope
+    "N818",  # error-suffix-on-exception-name
+
+    # NumPy-specific rules (NPY)
+    "NPY002", # Replace legacy `np.random.rand` call with `np.random.Generator`  (2023-05-03)
+
+    # Perflint (PERF)
+    "PERF203",  # `try`-`except` within a loop incurs performance overhead
+    "PERF401",  # Use a list comprehension to create a transformed list
+
+    # Pylint (PLC, PLE, PLR, PLW)
+    "PLE0101",  # return-in-init
+    "PLR0124",  # Name compared with itself
+    "PLR0402",  # ConsiderUsingFromImport
+    "PLR0912",  # too-many-branches
+    "PLR0913",  # too-many-args
+    "PLR0915",  # too-many-statements
+    "PLR1714",  # Consider merging multiple comparisons
+    "PLR2004",  # MagicValueComparison
+    "PLR5501",  # collapsible-else-if
+    "PLW0603",  # global-statement
+    "PLW2901",  # redefined-loop-name
+
+    # flake8-pytest-style (PT)
+    "PT003",   # pytest-extraneous-scope-function
+    "PT004",   # pytest-missing-fixture-name-underscore # deprecated in ruff 0.6.0
+    "PT006",   # pytest-parametrize-names-wrong-type
+    "PT007",   # pytest-parametrize-values-wrong-type
+    "PT011",   # pytest-raises-too-broad
+    "PT012",   # pytest-raises-with-multiple-statements
+    "PT017",   # pytest-assert-in-exceptinstead
+    "PT018",   # pytest-composite-assertion
+    "PT022",   # pytest-useless-yield-fixture
+
+    # flake8-return (RET)
+    "RET501",  # unnecessary-return-none
+    "RET502",  # implicit-return-value
+    "RET503",  # implicit-return
+    "RET504",  # unnecessary-assign
+    "RET507",  # superfluous-else-continue
+
+    # flake8-raise (RSE)
+    "RSE102",  # unnecessary-paren-on-raise-exception
+
+    # Ruff-specific rules (RUF)
+    "RUF001",  # ambiguous-unicode-character-string
+    "RUF002",  # ambiguous-unicode-character-docstring
+    "RUF010",  # use conversion in f-string
+    "RUF012",  # Mutable class attributes should be annotated with `typing.ClassVar`
+
+    # flake8-bandit (S)
+    "S101",  # Use of `assert` detected
+    "S105",  # hardcoded-password-string
+    "S110",  # try-except-pass
+    "S112",  # try-except-continue
+    "S301",  # suspicious-pickle-usage
+    "S307",  # Use of possibly insecure function; consider using `ast.literal_eval`
+    "S311",  # suspicious-non-cryptographic-randomness
+    "S324",  # hashlib-insecure-hash-function
+    "S506",  # UnsafeYAMLLoad
+    "S310",  # Suspicious-url-open-usage
+    "S603",  # `subprocess` call: check for execution of untrusted input
+    "S607",  # Starting a process with a partial executable path
+
+    # flake8-simplify (SIM)
+    "SIM102",  # NestedIfStatements
+    "SIM105",  # UseContextlibSuppress
+    "SIM108",  # UseTernaryOperator
+    "SIM114",  # if-with-same-arms
+    "SIM115",  # OpenFileWithContextHandler
+    "SIM117",  # MultipleWithStatements
+    "SIM118",  # KeyInDict
+    "SIM201",  # NegateEqualOp
+    "SIM300",  # yoda condition
+
+    # flake8-print (T20)
+    "T201",  # PrintUsed
+
+    # flake8-todos (TD)
+    "TD001",  # Invalid TODO tag
+    "TD003",  # Missing issue link on the line following this TODO
+    "TD004",  # Missing colon in TODO
+    "TD007",  # Missing space after colon in TODO
+
+    # tryceratops (TRY)
+    "TRY002",  # raise-vanilla-class
+    "TRY003",  # raise-vanilla-args
+    "TRY004",  # prefer-type-error
+    "TRY201",  # verbose-raise
+    "TRY301",  # raise-within-try
+
+    # pyupgrade (UP)
+    "UP038",  # isinstance using union separators. The code is slower as of Python 3.11-3.12
+
+    # flake8-quotes (Q)
+    "Q000",  # use double quotes
+]
+lint.unfixable = [
+    "E711"  # NoneComparison. Hard to fix b/c numpy has it's own None.
+]
+
+[lint.extend-per-file-ignores]
+"__init__.py" = ["E402", "F401", "F403"]
+"test_*.py" = [
+    "PTH", # all flake8-use-pathlib
+    "RUF015",  # Prefer next({iterable}) over single element slice
+    "F401",
+]
+# TODO: fix these, on a per-subpackage basis.
+# When a general exclusion is being fixed, but it affects many subpackages, it
+# is better to fix for subpackages individually. The general exclusion should be
+# copied to these subpackage sections and fixed there.
+# "astropy/config/*" = []
+# "astropy/constants/*" = [
+#     "N817",    # camelcase-imported-as-acronym
+#     "RET505",  # superfluous-else-return
+# ]

CITATION

@@ -42,4 +42,3 @@ archivePrefix = "arXiv",
    adsurl = {https://adsabs.harvard.edu/abs/2015ApJ...800..109B},
   adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
-