Updates from new config

.pre-commit-config.yaml

@@ -2,41 +2,47 @@ default_language_version:
   python: python3.10
 
 ci:
-  autoupdate_commit_msg: "chore: update pre-commit hooks"
-  autofix_commit_msg: "style: pre-commit fixes"
+  autoupdate_commit_msg: 'chore: update pre-commit hooks'
+  autofix_commit_msg: 'style: pre-commit fixes'
 
 repos:
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.6.0
+  rev: v2.13.0
   hooks:
   - id: pretty-format-ini
     args: [--autofix]
   - id: pretty-format-toml
-    args: [--autofix]
+    args: [--autofix, --indent, '2', --trailing-commas]
     additional_dependencies:
     - setuptools>=69.2.0
   - id: pretty-format-yaml
-    args: [--autofix, --preserve-quotes, --indent, "2"]
+    args: [--autofix, --indent, '2', --line-width, '100']
     additional_dependencies:
     - setuptools>=69.2.0
 
-- repo: https://github.com/pre-commit/mirrors-prettier
-  rev: "v3.1.0"
+- repo: https://github.com/executablebooks/mdformat
+  rev: 0.7.17
   hooks:
-  - id: prettier
-    types_or: [markdown, html, css, scss, javascript, json]
-    args: [--prose-wrap=preserve]
+  - id: mdformat
+    args: [--number]
+    additional_dependencies:
+    - mdformat-gfm
+    - mdformat-black
 
 - repo: https://github.com/Lucas-C/pre-commit-hooks
-  rev: v1.1.9
+  rev: v1.5.5
   hooks:
   - id: insert-license
-    exclude: ^\..*$
+    exclude: |
+      (?x)^(
+          ^\..*$ |
+          noxfile.py
+      )$
     types: [python]
-    args: [--comment-style, "|#|", --license-filepath, ./LICENSE_HEADER.txt]
+    args: [--comment-style, '|#|', --license-filepath, ./LICENSE_HEADER.txt]
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: "v4.6.0"
+  rev: v4.6.0
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
@@ -46,15 +52,13 @@ repos:
   - id: debug-statements
   - id: end-of-file-fixer
   - id: mixed-line-ending
-  - id: name-tests-test
-    args: ["--pytest-test-first"]
   - id: trailing-whitespace
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   rev: v0.4.8
   hooks:
   - id: ruff
-    args: ["--fix", "--show-fixes", "--preview"]
+    args: [--fix, --show-fixes]
   - id: ruff-format
 
 - repo: https://github.com/pre-commit/mirrors-mypy
@@ -67,15 +71,14 @@ repos:
     - dace==0.15.1
     - jax[cpu]==0.4.28
     - numpy==1.26.4
-    - pytest==8.2.2
-    - typing-extensions==4.12.2
+    - pytest==8.2.1
 - repo: https://github.com/codespell-project/codespell
-  rev: "v2.2.6"
+  rev: v2.3.0
   hooks:
   - id: codespell
 
 - repo: https://github.com/shellcheck-py/shellcheck-py
-  rev: "v0.10.0.1"
+  rev: v0.10.0.1
   hooks:
   - id: shellcheck
 
@@ -88,13 +91,13 @@ repos:
     exclude: .pre-commit-config.yaml
 
 - repo: https://github.com/abravalheri/validate-pyproject
-  rev: "v0.16"
+  rev: v0.18
   hooks:
   - id: validate-pyproject
-    additional_dependencies: ["validate-pyproject-schema-store[all]"]
+    additional_dependencies: ['validate-pyproject-schema-store[all]']
 
 - repo: https://github.com/python-jsonschema/check-jsonschema
-  rev: "0.28.1"
+  rev: 0.28.5
   hooks:
   - id: check-dependabot
   - id: check-github-workflows

pyproject.toml

@@ -1,9 +1,13 @@
 [build-system]
 build-backend = "setuptools.build_meta"
-requires = ["setuptools>=61"]
+requires = [
+  "setuptools>=61",
+]
 
 [project]
-authors = [{name = "ETH Zurich", email = "gridtools@cscs.ch"}]
+authors = [
+  {name = "ETH Zurich", email = "gridtools@cscs.ch"},
+]
 classifiers = [
   "Development Status :: 1 - Planning",
   "Intended Audience :: Science/Research",
@@ -17,9 +21,13 @@ classifiers = [
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Topic :: Scientific/Engineering",
-  "Typing :: Typed"
+  "Typing :: Typed",
+]
+dependencies = [
+  "dace>=0.15",
+  "jax[cpu]>=0.4.24",
+  "numpy>=1.26.0",
 ]
-dependencies = ["dace>=0.15", "jax[cpu]>=0.4.24", "numpy>=1.26.0"]
 description = "JAX jit using DaCe (Data Centric Parallel Programming)"
 name = "JaCe"
 readme = "README.md"
@@ -28,17 +36,44 @@ version = "0.1.0"
 license.file = "LICENSE"
 
 [project.optional-dependencies]
-cuda12 = ["cupy-cuda12x>=12.1.0", "jax[cuda12]>=0.4.24", "optuna>=3.4.0"]
+cuda12 = [
+  "cupy-cuda12x>=12.1.0",
+  "jax[cuda12]>=0.4.24",
+  "optuna>=3.4.0",
+]
 
 [project.urls]
 "Bug Tracker" = "https://github.com/GridTools/JaCe/issues"
 Changelog = "https://github.com/GridTools/JaCe/releases"
 Discussions = "https://github.com/GridTools/JaCe/discussions"
 Homepage = "https://github.com/GridTools/JaCe"
 
+# -- coverage --
 [tool.coverage]
-report.exclude_also = ['\.\.\.', 'if typing.TYPE_CHECKING:']
-run.source = ["jace"]
+
+[tool.coverage.html]
+show_contexts = true
+
+[tool.coverage.report]
+exclude_also = [
+  '\.\.\.',
+  'if TYPE_CHECKING:',
+  'if typing.TYPE_CHECKING:',
+  'def __repr__',
+  '@overload',
+  'raise AssertionError',
+  'raise NotImplementedError',
+  'if 0:',
+  'if __name__ == .__main__.:',
+  '@(abc\\.)?abstractmethod',
+  '@(abc\\.)?abstract',
+  'class .*\bProtocol\):',
+]
+
+[tool.coverage.run]
+branch = true
+dynamic_context = "test_function"
+source = ["jace"]
 
 # -- mypy  --
 [tool.mypy]
@@ -63,7 +98,12 @@ warn_unused_ignores = true
 disallow_incomplete_defs = false
 disallow_untyped_defs = false
 ignore_missing_imports = true
-module = ["tests.*", "dace.*", "jax.*", "jaxlib.*"]
+module = [
+  "tests.*",
+  "dace.*",
+  "jax.*",
+  "jaxlib.*",
+]
 
 # -- pytest  --
 [tool.pytest]
@@ -79,6 +119,7 @@ xfail_strict = true
 # -- ruff --
 [tool.ruff]
 line-length = 100
+preview = true
 respect-gitignore = true
 show-fixes = true
 src = ["src"]
@@ -87,72 +128,115 @@ src = ["src"]
 docstring-code-format = true
 
 [tool.ruff.lint]
+extend-safe-fixes = ["D", "TCH"]
 extend-select = [
   "A",  # flake8-builtins
   "B",  # flake8-bugbear
   "I",  # isort
   "G",  # flake8-logging-format
+  "N",  # pep8-naming
   "W",  # pycodestyle-warning
   "C4",  # flake8-comprehensions
   "C90",  # mccabe
+  "D",  # pydocstyle
+  "D213",  # multi-line-summary-second-line (off by default in pydocstyle "google' convention)
   "PT",  # flake8-pytest-style
-  "UP",  # pyupgrade       # TODO: in evaluation
+  "TD",  # flake8-todo
+  "UP",  # pyupgrade
   "ARG",  # flake8-unused-arguments
   "ERA",  # eradicate
+  "FLY",  # flynt
   "ICN",  # flake8-import-conventions
+  "NPY",  # NumPy specific rules
+  "PERF",  # Perflint
   "PGH",  # pygrep-hooks
   "PIE",  # flake8-pie
+  "PL",  # pylint
   "PTH",  # flake8-use-pathlib
-  "RET",  # flake8-return   # TODO: in evaluation
+  "RET",  # flake8-return
   "RUF",  # Ruff-specific
-  "SIM",  # flake8-simplify # TODO: in evaluation
+  "SIM",  # flake8-simplify
+  "SLOT",  # flake8-slots
   "T10",  # flake8-debugger
-  "T20",  # flake8-print    # TODO: in evaluation
-  "TCH",  # flake8-type-checking  # TODO: in evaluation
-  "NPY"  # NumPy specific rules
+  "T20",  # flake8-print
+  "TCH",  # flake8-type-checking
+  "TRY",  # tryceratops
 ]
 ignore = [
-  'B905',  # [zip-without-explicit-strict]
-  'E501',  # [line-too-long]
-  'TCH003',  # [typing-only-standard-library-import]
-  'UP038'  # [non-pep604-isinstance]
+  "B905",  # [zip-without-explicit-strict]
+  "D105",  # [undocumented-magic-method]
+  "D107",  # [undocumented-public-init]
+  "D212",  # [multi-line-summary-first-line]
+  "D402",  # [no-signature]
+  "E501",  # [line-too-long]
+  "TCH003",  # [typing-only-standard-library-import]
+  "TD003",  # [missing-todo-link]
+  "TRY003",  # [raise-vanilla-args]  # TODO(egparedes): reevaluate if it should be activated
+  "UP038",  # [non-pep604-isinstance]
 ]
+task-tags = ["TODO"]
 # ignore-init-module-imports = true  # deprecated in preview mode
 unfixable = []
 
 [tool.ruff.lint.isort]
 combine-as-imports = true
-known-first-party = ['jace']
+known-first-party = ["jace"]
 known-third-party = [
-  'cupy',
-  'dace',
-  'jax',
-  'numpy',
-  'pytest',
-  'typing_extensions'
+  "cupy",
+  "dace",
+  "jax",
+  "numpy",
+  "pytest",
+  "typing_extensions",
 ]
 lines-after-imports = 2
 order-by-type = true
 required-imports = ["from __future__ import annotations"]
 section-order = [
-  'future',
-  'standard-library',
-  'third-party',
-  'first-party',
-  'tests',
-  'local-folder'
+  "future",
+  "standard-library",
+  "third-party",
+  "first-party",
+  "tests",
+  "local-folder",
 ]
 
 [tool.ruff.lint.isort.sections]
-tests = ["tests", "unit_tests", "integration_tests"]
+tests = [
+  "tests",
+  "unit_tests",
+  "integration_tests",
+]
 
 [tool.ruff.lint.mccabe]
 max-complexity = 12
 
 [tool.ruff.lint.per-file-ignores]
-"!tests/**.py" = ["PT"]  # Ignore `flake8-pytest-style` everywhere except in `tests/`
-"noxfile.py" = ["T20"]  # Ignore `flake8-print`
-"tests/**" = ["T10", "T20"]  # Ignore `flake8-debugger` and `flake8-print`
+"!tests/**.py" = ["PT"]  # Ignore flake8-pytest-style outside 'tests/'
+"docs/**" = [
+  "D",  # pydocstyle
+  "T10",  # flake8-debugger
+  "T20",  # flake8-print
+]
+"noxfile.py" = [
+  "D",  # pydocstyle
+  "T20",  # flake8-print
+]
+"tests/**" = [
+  "D",  # pydocstyle
+  "N",  # TODO(egparedes): remove ignore as soon as all tests are properly named
+  "PLR2004",  # [magic-value-comparison]
+  "T10",  # flake8-debugger
+  "T20",  # flake8-print
+]
 
 [tool.ruff.lint.pycodestyle]
-max-doc-length = 85
+ignore-overlong-task-comments = true
+max-doc-length = 88
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+ignore-decorators = ["typing.overload"]
+
+[tool.ruff.lint.pylint]
+max-positional-args = 6