use ruff as linter and formatter

jcapriot · jcapriot · commit b7e37e00a055 · 2025-10-08T09:03:59.000-06:00
diff --git a/.ci/azure/style.yml b/.ci/azure/style.yml
@@ -1,6 +1,6 @@
 jobs:
   - job:
-    displayName: Run style checks with Black
+    displayName: Run style checks with ruff
     pool:
       vmImage: ubuntu-latest
     steps:
@@ -9,18 +9,5 @@ jobs:
           versionSpec: "3.11"
       - bash: .ci/install_style.sh
         displayName: "Install dependencies to run the checks"
-      - script: black --check .
-        displayName: "Run black"
-
-  - job:
-    displayName: Run (permissive) style checks with flake8
-    pool:
-      vmImage: ubuntu-latest
-    steps:
-      - task: UsePythonVersion@0
-        inputs:
-          versionSpec: "3.11"
-      - bash: .ci/install_style.sh
-        displayName: "Install dependencies to run the checks"
-      - script: flake8
-        displayName: "Run flake8"
+      - script: ruff --check .
+        displayName: "Run black"
diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
@@ -0,0 +1,8 @@
+name: Ruff
+on: [ push, pull_request ]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v3
diff --git a/.gitignore b/.gitignore
@@ -72,3 +72,5 @@ discretize/version.py
 .idea/
 
 docs/sg_execution_times.rst
+
+.vscode/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,18 +1,10 @@
 repos:
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.3.0
-    hooks:
-      - id: black
-        language_version: python3.11
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
-    hooks:
-      - id: flake8
-        language_version: python3.11
-        additional_dependencies:
-          - flake8-bugbear==23.12.2
-          - flake8-builtins==2.2.0
-          - flake8-mutable==1.2.0
-          - flake8-rst-docstrings==0.3.0
-          - flake8-docstrings==1.7.0
-          - flake8-pyproject==1.2.3
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.14.0
+  hooks:
+    # Run the linter.
+    - id: ruff-check
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
diff --git a/discretize/base/base_mesh.py b/discretize/base/base_mesh.py
@@ -2796,7 +2796,7 @@ def get_face_inner_product_surface_deriv(
             elif invert_model:
                 dMdprop = A * sdiag(-1.0 / model**2)
             elif invert_matrix:
-                dMdprop = sdiag(-MI.diagonal() ** 2) * A
+                dMdprop = sdiag(-(MI.diagonal() ** 2)) * A
 
         elif tensorType == 1:  # isotropic, variable in space
             if not invert_matrix and not invert_model:
@@ -2806,7 +2806,7 @@ def get_face_inner_product_surface_deriv(
             elif invert_model:
                 dMdprop = A * sdiag(-1.0 / model**2)
             elif invert_matrix:
-                dMdprop = sdiag(-MI.diagonal() ** 2) * A
+                dMdprop = sdiag(-(MI.diagonal() ** 2)) * A
 
         if dMdprop is not None:
 
@@ -2901,7 +2901,7 @@ def get_edge_inner_product_line_deriv(
             elif invert_model:
                 dMdprop = L * sdiag(-1.0 / model**2)
             elif invert_matrix:
-                dMdprop = sdiag(-MI.diagonal() ** 2) * L
+                dMdprop = sdiag(-(MI.diagonal() ** 2)) * L
 
         elif tensorType == 1:  # isotropic, variable in space
             if not invert_matrix and not invert_model:
@@ -2911,7 +2911,7 @@ def get_edge_inner_product_line_deriv(
             elif invert_model:
                 dMdprop = L * sdiag(-1.0 / model**2)
             elif invert_matrix:
-                dMdprop = sdiag(-MI.diagonal() ** 2) * L
+                dMdprop = sdiag(-(MI.diagonal() ** 2)) * L
 
         if dMdprop is not None:
 
diff --git a/discretize/base/base_regular_mesh.py b/discretize/base/base_regular_mesh.py
@@ -955,8 +955,9 @@ def switchKernal(xx):
                     if dimName in out_type:
                         if self.dim <= dim:
                             raise ValueError(
-                                "Dimensions of mesh not great enough for "
-                                "{}_{}".format(x_type, dimName)
+                                "Dimensions of mesh not great enough for {}_{}".format(
+                                    x_type, dimName
+                                )
                             )
                         if xx.size != np.sum(nn):
                             raise ValueError("Vector is not the right size.")
diff --git a/discretize/base/base_tensor_mesh.py b/discretize/base/base_tensor_mesh.py
@@ -924,7 +924,7 @@ def _fastInnerProductDeriv(
             elif invert_model:
                 dMdprop = n_elements * Av.T * V * sdiag(-1.0 / model**2)
             elif invert_matrix:
-                dMdprop = n_elements * (sdiag(-MI.diagonal() ** 2) * Av.T * V)
+                dMdprop = n_elements * (sdiag(-(MI.diagonal() ** 2)) * Av.T * V)
 
         elif tensorType == 1:  # isotropic, variable in space
             Av = getattr(self, "ave" + projection_type + "2CC")
@@ -938,7 +938,7 @@ def _fastInnerProductDeriv(
             elif invert_model:
                 dMdprop = n_elements * Av.T * V * sdiag(-1.0 / model**2)
             elif invert_matrix:
-                dMdprop = n_elements * (sdiag(-MI.diagonal() ** 2) * Av.T * V)
+                dMdprop = n_elements * (sdiag(-(MI.diagonal() ** 2)) * Av.T * V)
 
         elif tensorType == 2:  # anisotropic
             Av = getattr(self, "ave" + projection_type + "2CCV")
@@ -967,7 +967,7 @@ def _fastInnerProductDeriv(
             elif invert_model:
                 dMdprop = Av.T * P * V * sdiag(-1.0 / model**2)
             elif invert_matrix:
-                dMdprop = sdiag(-MI.diagonal() ** 2) * Av.T * P * V
+                dMdprop = sdiag(-(MI.diagonal() ** 2)) * Av.T * P * V
 
         if dMdprop is not None:
 
diff --git a/discretize/mixins/mesh_io.py b/discretize/mixins/mesh_io.py
@@ -194,9 +194,7 @@ def _readModelUBC_2D(mesh, file_name):
         if not len(model) == mesh.nC:
             raise Exception(
                 """Something is not right, expected size is {:d}
-                but unwrap vector is size {:d}""".format(
-                    mesh.nC, len(model)
-                )
+                but unwrap vector is size {:d}""".format(mesh.nC, len(model))
             )
 
         return model.reshape(mesh.vnC, order="F")[:, ::-1].reshape(-1, order="F")
diff --git a/discretize/operators/differential_operators.py b/discretize/operators/differential_operators.py
@@ -2318,7 +2318,7 @@ def get_BC_projections(self, BC, discretization="CC"):
         """
         if discretization != "CC":
             raise NotImplementedError(
-                "Boundary conditions only implemented" "for CC discretization."
+                "Boundary conditions only implemented for CC discretization."
             )
 
         if isinstance(BC, str):
@@ -2411,7 +2411,7 @@ def get_BC_projections_simple(self, discretization="CC"):
         """Create weak form boundary condition projection matrices for mixed boundary condition."""
         if discretization != "CC":
             raise NotImplementedError(
-                "Boundary conditions only implemented" "for CC discretization."
+                "Boundary conditions only implemented for CC discretization."
             )
 
         def projBC(n):
diff --git a/discretize/operators/inner_products.py b/discretize/operators/inner_products.py
@@ -379,7 +379,7 @@ def get_edge_inner_product_surface_deriv(  # NOQA D102
             elif invert_model:
                 dMdprop = n_elements * Av.T * A * sdiag(-1.0 / model**2)
             elif invert_matrix:
-                dMdprop = n_elements * (sdiag(-MI.diagonal() ** 2) * Av.T * A)
+                dMdprop = n_elements * (sdiag(-(MI.diagonal() ** 2)) * Av.T * A)
 
         elif tensorType == 1:  # isotropic, variable in space
             if not invert_matrix and not invert_model:
@@ -391,7 +391,7 @@ def get_edge_inner_product_surface_deriv(  # NOQA D102
             elif invert_model:
                 dMdprop = n_elements * Av.T * A * sdiag(-1.0 / model**2)
             elif invert_matrix:
-                dMdprop = n_elements * (sdiag(-MI.diagonal() ** 2) * Av.T * A)
+                dMdprop = n_elements * (sdiag(-(MI.diagonal() ** 2)) * Av.T * A)
 
         if dMdprop is not None:
 
@@ -819,17 +819,29 @@ def Pxxx(xEdge, yEdge, zEdge):
             posX = (
                 [0, 0]
                 if xEdge == "eX0"
-                else [1, 0] if xEdge == "eX1" else [0, 1] if xEdge == "eX2" else [1, 1]
+                else [1, 0]
+                if xEdge == "eX1"
+                else [0, 1]
+                if xEdge == "eX2"
+                else [1, 1]
             )
             posY = (
                 [0, 0]
                 if yEdge == "eY0"
-                else [1, 0] if yEdge == "eY1" else [0, 1] if yEdge == "eY2" else [1, 1]
+                else [1, 0]
+                if yEdge == "eY1"
+                else [0, 1]
+                if yEdge == "eY2"
+                else [1, 1]
             )
             posZ = (
                 [0, 0]
                 if zEdge == "eZ0"
-                else [1, 0] if zEdge == "eZ1" else [0, 1] if zEdge == "eZ2" else [1, 1]
+                else [1, 0]
+                if zEdge == "eZ1"
+                else [0, 1]
+                if zEdge == "eZ2"
+                else [1, 1]
             )
 
             ind1 = sub2ind(M.vnEx, np.c_[ii, jj + posX[0], kk + posX[1]])
diff --git a/discretize/tests.py b/discretize/tests.py
@@ -926,7 +926,7 @@ def random(size, iscomplex):
 
         print(
             f"Adjoint test {'PASSED' if passed else 'FAILED'} ::  "
-            f"{abs(rhs-lhs):.3e} < {atol+rtol*abs(lhs):.3e}  :: "
+            f"{abs(rhs - lhs):.3e} < {atol + rtol * abs(lhs):.3e}  :: "
             f"|rhs-lhs| < atol + rtol|lhs|"
         )
 
diff --git a/discretize/utils/mesh_utils.py b/discretize/utils/mesh_utils.py
@@ -931,7 +931,7 @@ def refine_tree_xyz(
 
     else:
         raise NotImplementedError(
-            "Only method= 'radial', 'surface'" " or 'box' have been implemented"
+            "Only method= 'radial', 'surface' or 'box' have been implemented"
         )
 
     return mesh
diff --git a/docs/conf.py b/docs/conf.py
@@ -13,12 +13,13 @@
 
 import os
 import sys
-from pathlib import Path
 from datetime import datetime
 from packaging.version import parse
 import discretize
 import shutil
 from importlib.metadata import version
+import math
+import pyvista
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -218,8 +219,6 @@ def linkcode_resolve(domain, info):
 plot_include_source = True
 plot_formats = [("png", 100), "pdf"]
 
-import math
-
 phi = (math.sqrt(5) + 1) / 2
 
 plot_rcparams = {
@@ -457,7 +456,7 @@ def linkcode_resolve(domain, info):
 ]
 
 # -- pyvista configuration ---------------------------------------------------
-import pyvista
+
 
 # Manage errors
 pyvista.set_error_output_file("errors.txt")
diff --git a/examples/plot_slicer_demo.py b/examples/plot_slicer_demo.py
@@ -117,8 +117,7 @@ def beautify(title, fig=None):
 
 mesh.plot_3d_slicer(Lpout, 370000, 6002500, -2500, transparent=[[-0.02, 0.1]])
 beautify(
-    "mesh.plot_3d_slicer("
-    "\nLpout, 370000, 6002500, -2500, transparent=[[-0.02, 0.1]])"
+    "mesh.plot_3d_slicer(\nLpout, 370000, 6002500, -2500, transparent=[[-0.02, 0.1]])"
 )
 plt.show()
 
diff --git a/pyproject.toml b/pyproject.toml
@@ -79,14 +79,7 @@ test = [
 ]
 # when changing these, make sure to keep it consistent with .pre-commit-config.
 style = [
-    "black==24.3.0",
-    "flake8==7.0.0",
-    "flake8-bugbear==23.12.2",
-    "flake8-builtins==2.2.0",
-    "flake8-mutable==1.2.0",
-    "flake8-rst-docstrings==0.3.0",
-    "flake8-docstrings==1.7.0",
-    "flake8-pyproject==1.2.3",
+    "ruff=0.14.0",
 ]
 build = [
     "meson-python>=0.14.0",
@@ -150,74 +143,23 @@ exclude_also = [
     # Don't complain about abstract methods, they aren't run:
     "@(abc\\.)?abstractmethod",
 ]
+[tool.ruff]
+required-version='0.14.0'
+target-version = 'py311'
+#extend-exclude = [
+#    'docs/examples/*',
+#    'docs/tutorials/*',
+#]
 
-[tool.black]
-required-version = '24.3.0'
-target-version = ['py38', 'py39', 'py310', 'py311']
-
-[tool.flake8]
+[tool.ruff.lint]
 extend-ignore = [
-    # Too many leading '#' for block comment
-    'E266',
-    # Line too long (82 > 79 characters)
-    'E501',
     # Do not use variables named 'I', 'O', or 'l'
     'E741',
-    # Line break before binary operator (conflicts with black)
-    'W503',
-    # Ignore spaces before a colon (Black handles it)
-    'E203',
-    # Ignore spaces around an operator (Black handles it)
-    'E225',
-    # Ignore rst warnings for start and end, due to *args and **kwargs being invalid rst, but good for numpydoc
-    'RST210',
-    'RST213',
-    # ignore undocced __init__
-    'D107',
-]
-exclude = [
-    '.git',
-    '.eggs',
-    '__pycache__',
-    '.ipynb_checkpoints',
-    'docs/examples/*',
-    'docs/tutorials/*',
-    'docs/*',
-    'discretize/_extensions/*.py',
-    '.ci/*'
-]
-per-file-ignores = [
-    # disable unused-imports errors on __init__.py
-    # Automodule used for __init__ scripts' description
-    '__init__.py: F401, D204, D205, D400',
-    # do not check for assigned lambdas in tests
-    # do not check for missing docstrings in tests
-    'tests/*: E731, D',
-    'tutorials/*: D',
-    'examples/*: D',
-]
-exclude-from-doctest = [
-    # Only check discretize for docstring style
-    'tests',
-    'tutorials',
-    'examples',
 ]
 
-rst-roles = [
-    'class',
-    'func',
-    'mod',
-    'meth',
-    'attr',
-    'ref',
-    'data',
-    # Python programming language:
-    'py:func','py:mod','py:attr','py:meth',
-]
+[tool.ruff.lint.extend-per-file-ignores]
+"tests/*" = ["E731"]  # Ignore assigning lambdas in tests
+"__init__.py" = ["F401"]  # Ignore unused import in __init__.py
 
-rst-directives = [
-    # These are sorted alphabetically - but that does not matter
-    'autosummary',
-    'currentmodule',
-    'deprecated',
-]
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
diff --git a/tests/base/test_operators.py b/tests/base/test_operators.py
diff --git a/tests/base/test_tests.py b/tests/base/test_tests.py
diff --git a/tests/cyl/test_cylOperators.py b/tests/cyl/test_cylOperators.py
diff --git a/tests/cyl/test_cyl_innerproducts.py b/tests/cyl/test_cyl_innerproducts.py
diff --git a/tests/tree/test_safeguards.py b/tests/tree/test_safeguards.py
diff --git a/tutorials/pde/1_poisson.py b/tutorials/pde/1_poisson.py
