Replace linter and formatter with ruff and mypy (#392)

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ exclude: src\/msg_database.c
 fail_fast: false
 repos:
   - repo: https://github.com/Takishima/cmake-pre-commit-hooks
-    rev: v1.5.3
+    rev: v1.9.5
     hooks:
       - id: clang-format
         additional_dependencies: [ clang-format >= 16 ]
@@ -23,40 +23,27 @@ repos:
           - '-DSPGLIB_WITH_TESTS=ON'
         stages: [ manual ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
       - id: check-added-large-files
-  - repo: https://github.com/pycqa/flake8
-    rev: 5.0.4
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.13
     hooks:
-      - id: flake8
-        files: python\/.*
-        args:
-          - "--max-line-length=88"
-          - "--ignore=E203,W503"
-  - repo: https://github.com/psf/black
-    rev: 22.6.0
-    hooks:
-      - id: black
-        files: python\/.*
-        args: [ "--line-length=88" ]
-  - repo: https://github.com/pycqa/pydocstyle
-    rev: 6.1.1
-    hooks:
-      - id: pydocstyle
-        files: python/spglib
-        additional_dependencies: [ "toml" ]
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+      - id: ruff
+        args: [ "--fix", "--show-fixes" ]
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
     hooks:
-      - id: isort
-        files: python\/.*
-        args: [ "--profile", "black" ]
+    - id: mypy
+      pass_filenames: false
+      additional_dependencies:
+        - types-PyYAML
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.16
+    rev: 0.7.17
     hooks:
       - id: mdformat
         additional_dependencies:
@@ -66,14 +53,14 @@ repos:
     # TODO: Temporarily separate docs formatiing
     # https://github.com/executablebooks/mdformat/issues/234
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.16
+    rev: 0.7.17
     hooks:
       - id: mdformat
         additional_dependencies:
           - mdformat-myst
         files: doc\/(?!README).*\.md$
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.21.0
+    rev: 0.27.3
     hooks:
       - id: check-github-workflows
       - id: check-readthedocs

doc/conf.py

@@ -1,13 +1,10 @@
-from importlib.metadata import version
+from spglib import __version__ as version
 
 project = "Spglib"
 copyright = "2009, Atsushi Togo"
-release = version("spglib")  # e.g. "v.1.16.5"
-# The short X.Y version.
-version = ".".join(release.split(".")[:3])  # e.g. "v.1.16"
 
 extensions = [
-    'sphinx.ext.mathjax',
+    "sphinx.ext.mathjax",
     "sphinx.ext.viewcode",
     "sphinxcontrib.bibtex",
     "myst_parser",
@@ -54,7 +51,7 @@
 # -----------------------------------------------------------------------------
 
 html_theme = "sphinx_book_theme"
-html_title = f"Spglib v{release}"
+html_title = f"Spglib v{version}"
 html_theme_options = {
     # https://sphinx-book-theme.readthedocs.io/en/latest/reference.html
     "repository_url": "https://github.com/spglib/spglib",
@@ -77,9 +74,9 @@
     {
         "path": "../python/spglib/spglib.py",
         "module": "spglib",
-    }
+    },
 ]
-autodoc2_hidden_objects = ['undoc', 'dunder', 'private', 'inherited']
+autodoc2_hidden_objects = ["undoc", "dunder", "private", "inherited"]
 autodoc2_hidden_regexes = [
     "spglib.get_pointgroup",
     # Layer group

example/python_api/example_full.py

@@ -27,7 +27,7 @@ def _show_lattice(lattice):
                     axis,
                 )
                 + tuple(vec)
-            )
+            ),
         )
 
 
@@ -144,16 +144,15 @@ def main():
     print("")
     print("[get_pointgroup]")
     print(
-        "  Pointgroup of MgB2 is %s."
-        % spglib.get_pointgroup(symmetry["rotations"])[0]
+        "  Pointgroup of MgB2 is %s." % spglib.get_pointgroup(symmetry["rotations"])[0],
     )
     print("")
 
     dataset = spglib.get_symmetry_dataset(rutile)
     print("[get_symmetry_dataset] ['international']")
     print(
         "  Spacegroup of Rutile is %s (%d)."
-        % (dataset["international"], dataset["number"])
+        % (dataset["international"], dataset["number"]),
     )
     print("")
     print("[get_symmetry_dataset] ['pointgroup']")
@@ -162,7 +161,7 @@ def main():
     print("[get_symmetry_dataset] ['hall']")
     print(
         "  Hall symbol of Rutile is %s (%d)."
-        % (dataset["hall"], dataset["hall_number"])
+        % (dataset["hall"], dataset["hall_number"]),
     )
     print("")
     print("[get_symmetry_dataset] ['wyckoffs']")
@@ -176,7 +175,7 @@ def main():
     print("[get_symmetry_dataset] ['rotations'], ['translations']")
     print("  Symmetry operations of Rutile unitcell are:")
     for i, (rot, trans) in enumerate(
-        zip(dataset["rotations"], dataset["translations"])
+        zip(dataset["rotations"], dataset["translations"]),
     ):
         print("  --------------- %4d ---------------" % (i + 1))
         print("  rotation:")
@@ -202,7 +201,10 @@ def main():
     print(" Standardize distorted rutile structure:")
     print(" (to_primitive=0 and no_idealize=0)")
     lattice, positions, numbers = spglib.standardize_cell(
-        rutile_dist, to_primitive=0, no_idealize=0, symprec=1e-1
+        rutile_dist,
+        to_primitive=0,
+        no_idealize=0,
+        symprec=1e-1,
     )
     _show_cell(lattice, positions, numbers)
     print("")
@@ -211,7 +213,10 @@ def main():
     print(" Standardize distorted rutile structure:")
     print(" (to_primitive=0 and no_idealize=1)")
     lattice, positions, numbers = spglib.standardize_cell(
-        rutile_dist, to_primitive=0, no_idealize=1, symprec=1e-1
+        rutile_dist,
+        to_primitive=0,
+        no_idealize=1,
+        symprec=1e-1,
     )
     _show_cell(lattice, positions, numbers)
     print("")
@@ -220,7 +225,10 @@ def main():
     print(" Standardize distorted silicon structure:")
     print(" (to_primitive=1 and no_idealize=0)")
     lattice, positions, numbers = spglib.standardize_cell(
-        silicon_dist, to_primitive=1, no_idealize=0, symprec=1e-1
+        silicon_dist,
+        to_primitive=1,
+        no_idealize=0,
+        symprec=1e-1,
     )
     _show_cell(lattice, positions, numbers)
     print("")
@@ -229,7 +237,10 @@ def main():
     print(" Standardize distorted silicon structure:")
     print(" (to_primitive=1 and no_idealize=1)")
     lattice, positions, numbers = spglib.standardize_cell(
-        silicon_dist, to_primitive=1, no_idealize=1, symprec=1e-1
+        silicon_dist,
+        to_primitive=1,
+        no_idealize=1,
+        symprec=1e-1,
     )
     _show_cell(lattice, positions, numbers)
     print("")
@@ -257,7 +268,9 @@ def main():
     print("")
 
     mapping, grid = spglib.get_ir_reciprocal_mesh(
-        [11, 11, 11], silicon_prim, is_shift=[0, 0, 0]
+        [11, 11, 11],
+        silicon_prim,
+        is_shift=[0, 0, 0],
     )
     num_ir_kpt = len(np.unique(mapping))
     print("[get_ir_reciprocal_mesh]")

pyproject.toml

@@ -122,3 +122,78 @@ command_line = '-m pytest'
 # TODO: Cannot report relative to project path because we cannot do editable installs yet
 #source = ['python/spglib']
 source = ['spglib']
+
+[tool.ruff]
+line-length = 88
+extend-select = [
+    "F",           # pyflakes
+    # "W",           # pycodestyle-warnings
+    "E",           # pycodestyle-errors
+    # "C90",         # mccabe
+    "I",           # isort
+    # "N",           # pep8-naming
+    "D",           # pydocstyle
+    # "UP",          # pyupgrade
+    # "YTT",         # flake8-2020
+    # "ANN",         # flake8-annotations
+    # "S",           # flake8-bandit
+    # "BLE",         # flake8-blind-except
+    # "FBT",         # flake8-boolean-trap
+    # "B",           # flake8-bugbear
+    # "A",           # flake8-builtins
+    # "COM",         # flake8-comma
+    # "C4",          # flake8-comprehensions
+    # "T10",         # flake8-debugger
+    # "EM",          # flake8-errmsg
+    # "FA",          # flake8-future-annotations
+    # "ISC",         # flake8-implicit-str-concat
+    # "ICN",         # flake8-import-conventions
+    # "G",           # flake8-logging-format
+    # "PIE",         # flake8-pie
+    # "T20",         # flake8-print
+    # "PYI",         # flake8-pyi
+    # "PT",          # flake8-pytest-style
+    # "Q",           # flake8-quotes
+    # "RSE",         # flake8-raise
+    # "RET",         # flake8-return
+    # "SLF",         # flake8-self
+    # "SIM",         # flake8-simplify
+    # "TID",         # flake8-tidy-imports
+    # "TCH",         # flake8-type-checking
+    # "ARG",         # flake8-unused-arguments
+    # "PTH",         # flake8-use-pathlib
+    # "TD",          # flake8-todos
+    # "ERA",         # eradicate
+    # "PD",          # pandas-vet
+    # "PGH",         # pygrep-hooks
+    # "PL",          # pylint
+    # "TRY",         # tryceratops
+    # "FLY",         # flynt
+    # "NPY",         # NumPy
+    # "PERF",        # perflint
+    # "FURB",        # refurb
+    # "RUF",         # Ruff-specific
+]
+extend-ignore = [
+    "D100",
+    "D101",
+    "D102",
+    "D103",
+    "D203",  # Confilct with D211
+    "D205",
+    "D213",  # Conflict with D212
+]
+exclude = [
+    "database",
+]
+
+[tool.mypy]
+mypy_path = ["python"]
+files = ["python", "test/functional/python", "example/python_api"]
+python_version = "3.12"
+warn_unused_configs = true
+show_error_codes = true
+# TODO: Enable strict mode once we clean up type annotations
+# strict = true
+enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
+no_strict_optional = true