dev: Migrate from flake8 to ruff

.pre-commit-config.yaml

@@ -35,20 +35,13 @@ repos:
     rev: 5.12.0
     hooks:
     -   id: isort
-        args: ["--profile", "black", "--filter-files"]
 -   repo: https://github.com/asottile/pyupgrade
     rev: v3.10.1
     hooks:
     -   id: pyupgrade
--   repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.282
     hooks:
-    -   id: flake8
-        args: ["--max-line-length", "88", "--extend-ignore", "E203,E501,E722,W503"]
-        exclude: |  # https://pre-commit.com/#regular-expressions
-            (?x)^(
-                src/initial_implementation/AlternativeFunctions.py|
-                src/pydrex/__init__.py
-            )$
+    -   id: ruff
 
-exclude: \.vtu$
+exclude: \.*vtu$

pyproject.toml

@@ -44,7 +44,8 @@ dependencies = [
 [project.optional-dependencies]
 test = ["pytest", "matplotlib"]
 doc = ["pdoc"]
-dev = ["pytest", "matplotlib", "pdoc", "flake8", "black", "h5py", "isort", "ipython"]
+dev = ["pytest", "matplotlib", "pdoc", "ruff", "black", "h5py", "isort", "ipython"]
+lsp = ["python-lsp-server", "pyls-isort", "python-lsp-black", "python-lsp-ruff"]
 
 [project.urls]
 repository = "https://github.com/Patol75/PyDRex/"
@@ -72,3 +73,19 @@ testpaths = ["tests"]
 # --show-capture=no : Don't show captured output (stdout/stderr/logs) for failed tests.
 # --doctest-modules : Run doctest snippets in docstrings
 addopts = "--tb=short --show-capture=no --doctest-modules"
+
+# Global linter and devtools settings.
+[tool.isort]
+profile = "black"
+filter_files = true
+# Ruff is faster than flake8 and supports pyproject.toml config, line length is 88 by default.
+[tool.ruff]
+exclude = [
+    "src/initial_implementation",
+    ".scsv",
+    ".npz",
+    ".vtu",
+]
+[tool.ruff.per-file-ignores]
+"src/pydrex/__init__.py" = ["F401", "E501"]  # Don't complain about unused imports or long lines in __init__.py file.
+"tests/test_scsv.py" = ["E501"]  # Don't complain about long lines here.

src/pydrex/diagnostics.py

@@ -156,7 +156,7 @@ def finite_strain(deformation_gradient, **kwargs):
 
 
 def symmetry(orientations, axis="a"):
-    r"""Compute texture symmetry eigenvalue diagnostics from olivine orientation matrices.
+    r"""Compute texture symmetry eigenvalue diagnostics from grain orientation matrices.
 
     Compute Point, Girdle and Random symmetry diagnostics
     for ternary texture classification.

src/pydrex/minerals.py

@@ -27,7 +27,8 @@
 """Stiffness tensor for olivine (Voigt representation), with units of GPa.
 
 The source of the values used here is unknown, but they are copied
-from the original DRex code: <http://www.ipgp.fr/~kaminski/web_doudoud/DRex.tar.gz> [88K download]
+from the original DRex code: <http://www.ipgp.fr/~kaminski/web_doudoud/DRex.tar.gz>
+[88K download]
 
 """
 
@@ -45,7 +46,8 @@
 """Stiffness tensor for enstatite (Voigt representation), with units of GPa.
 
 The source of the values used here is unknown, but they are copied
-from the original DRex code: <http://www.ipgp.fr/~kaminski/web_doudoud/DRex.tar.gz> [88K download]
+from the original DRex code: <http://www.ipgp.fr/~kaminski/web_doudoud/DRex.tar.gz>
+[88K download]
 
 """
 
@@ -83,7 +85,8 @@ def voigt_averages(minerals, weights):
     - `minerals` — list of `pydrex.minerals.Mineral` instances storing orientations and
       fractional volumes of the grains within each distinct mineral phase
     - `weights` (dict) — dictionary containing weights of each mineral
-      phase, as a fraction of 1, in keys named "<phase>_fraction", e.g. "olivine_fraction"
+      phase, as a fraction of 1, in keys named "<phase>_fraction",
+      e.g. "olivine_fraction"
 
     Raises a ValueError if the minerals contain an unequal number of grains or stored
     texture results.
@@ -176,7 +179,7 @@ class Mineral:
     >>>     regime=pydrex.DeformationRegime.dislocation,
     >>>     n_grains=2000,
     >>> )
-    Mineral(phase=0, fabric=0, regime=1, n_grains=2000, fractions=<list of ndarray (2000,)>, orientations=<list of ndarray (2000, 3, 3)>)
+    Mineral(phase=0, fabric=0, regime=1, n_grains=2000, ...)
 
     Mineral with specified initial texture and default phase, fabric and regime settings
     which are for an olivine A-type mineral in the dislocation creep regime.
@@ -190,18 +193,22 @@ class Mineral:
     >>>     n_grains=n_grains,
     >>>     fractions_init=np.full(n_grains, 1 / n_grains),
     >>>     orientations_init=Rotation.from_euler(
-    >>>         "zxz", [[x * np.pi / 2, np.pi / /2, np.pi / 2] for x in rng.random(n_grains)]
+    >>>         "zxz", [
+    >>>             [x * np.pi / 2, np.pi / /2, np.pi / 2] for x in rng.random(n_grains)
+    >>>         ]
     >>>     ).inv().as_matrix(),
     >>> )
-    Mineral(phase=0, fabric=0, regime=1, n_grains=2000, fractions=<list of ndarray (2000,)>, orientations=<list of ndarray (2000, 3, 3)>)
+    Mineral(phase=0, fabric=0, regime=1, n_grains=2000, ...)
 
     **Attributes:**
     - `phase` (`pydrex.core.MineralPhase`) — ordinal number of the mineral phase
     - `fabric` (`pydrex.core.MineralFabric`) — ordinal number of the fabric type
-    - `regime` (`pydrex.core.DeformationRegime`) — ordinal number of the deformation regime
+    - `regime` (`pydrex.core.DeformationRegime`) — ordinal number of the deformation
+      regime
     - `n_grains` (int) — number of grains in the aggregate
     - `fractions` (list of arrays) — grain volume fractions for each texture snapshot
-    - `orientations` (list of arrays) — grain orientation matrices for each texture snapshot
+    - `orientations` (list of arrays) — grain orientation matrices for each texture
+      snapshot
     - `seed` (`int`) — seed used by the random number generator to set up the isotropic
       initial condition when `fractions_init` or `orientations_init` are not provided
 
@@ -241,7 +248,8 @@ def __str__(self):
             + f"fractions=<{self.fractions.__class__.__qualname__}"
             + f" of {self.fractions[0].__class__.__qualname__} {shape_of_fractions}>, "
             + f"orientations=<{self.orientations.__class__.__qualname__}"
-            + f" of {self.orientations[0].__class__.__qualname__} {shape_of_orientations}>)"
+            + f" of {self.orientations[0].__class__.__qualname__}"
+            + f" {shape_of_orientations}>)"
         )
 
     def _repr_pretty_(self, p, cycle):

src/pydrex/stats.py

@@ -157,7 +157,8 @@ def point_density(
     - `gridsteps` (int) — the number of steps, i.e. number of points along a diameter of
         the spherical counting grid
     - `weights` (array) — auxiliary weights for each data point
-    - `kernel` (string) — the name of the kernel function to use, see `SPHERICAL_COUNTING_KERNELS`
+    - `kernel` (string) — the name of the kernel function to use, see
+      `SPHERICAL_COUNTING_KERNELS`
     - `axial` (bool) — toggle axial versions of the kernel functions
         (for crystallographic data this should normally be kept as `True`)