Merge pull request #22 from finsberg/formatting

Update hooks and build docs settings

.github/workflows/build_docs.yml

@@ -29,9 +29,10 @@ jobs:
 
   build:
     runs-on: ubuntu-22.04
-    container: ghcr.io/fenics/dolfinx/lab:nightly
+    container: ghcr.io/fenics/dolfinx/lab:v0.8.0
     env:
       PUBLISH_DIR: ./_build/html
+      DISPLAY: ":99.0"
       PYVISTA_TRAME_SERVER_PROXY_PREFIX: "/proxy/"
       PYVISTA_TRAME_SERVER_PROXY_ENABLED: "True"
       PYVISTA_OFF_SCREEN: false

.pre-commit-config.yaml

@@ -9,16 +9,17 @@ repos:
       - id: debug-statements
       - id: requirements-txt-fixer
 
-  - repo: https://github.com/psf/black
-    rev: 23.7.0
-    hooks:
-      - id: black
 
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
+  - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.0.278'
+    rev: 'v0.3.7'
     hooks:
+       # Run the linter.
       - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+        exclude: 'demos/.*.py$'
 
 
   - repo: https://github.com/asottile/add-trailing-comma

Dockerfile

@@ -1,19 +1,16 @@
-# Use github pages for docker image
-FROM ghcr.io/finsberg/fenicsx-pulse:v0.1.5
+# We choose ubuntu 22.04 as our base docker image
+FROM ghcr.io/fenics/dolfinx/dolfinx:v0.8.0
 
-# Create user with a home directory
-ARG NB_USER
-ARG NB_UID=1000
-ENV USER ${NB_USER}
-ENV HOME /home/${NB_USER}
+ENV PYVISTA_JUPYTER_BACKEND="html"
 
-# Copy current directory
-WORKDIR ${HOME}
-COPY . ${HOME}
+# Requirements for pyvista
+RUN apt-get update && apt-get install -y libgl1-mesa-glx libxrender1 xvfb nodejs
 
-# Change ownership of home directory
-USER root
-RUN chown -R ${NB_UID} ${HOME}
+COPY . /repo
+WORKDIR /repo
 
-USER ${NB_USER}
-ENTRYPOINT []
+ARG TARGETPLATFORM
+RUN echo "Building for $TARGETPLATFORM"
+RUN if [ "$TARGETPLATFORM" = "linux/arm64" ]; then python3 -m pip install "https://github.com/finsberg/vtk-aarch64/releases/download/vtk-9.2.6-cp310/vtk-9.2.6.dev0-cp310-cp310-linux_aarch64.whl"; fi
+
+RUN python3 -m pip install ".[docs]"

demo/unit_cube.py

@@ -5,12 +5,12 @@
 #
 # First let us do the necessary imports
 
-import dolfinx
-import numpy as np
-import fenicsx_pulse
 from mpi4py import MPI
 from petsc4py import PETSc
 
+import dolfinx
+import fenicsx_pulse
+import numpy as np
 
 # Then we can create unit cube mesh
 

pyproject.toml

@@ -25,7 +25,11 @@ dev = [
 docs = [
    "jupyter-book",
    "jupytext",
-   "pyvista"
+   "jupyter",
+   "cardiac-geometriesx",
+   "pyvista[all]>=0.43.0",
+   "trame-vuetify",
+   "ipywidgets",
 ]
 
 all = [
@@ -46,23 +50,8 @@ testpaths = [
     "tests"
 ]
 
-[tool.coverage.report]
-exclude_lines = [
-    "pragma: no cover",
-    "pass",
-    "raise NotImplementedError",
-    "def __str__"
-]
 
 [tool.ruff]
-# Enable pycodestyle (`E`) and Pyflakes (`F`) codes by default.
-select = ["E", "F"]
-ignore = ["E402", "E741", "E731"]
-
-# Allow autofix for all enabled rules (when `--fix`) is provided.
-fixable = ["A", "B", "C", "D", "E", "F"]
-unfixable = []
-
 # Exclude a variety of commonly ignored directories.
 exclude = [
     ".bzr",
@@ -85,17 +74,52 @@ exclude = [
     "dist",
     "node_modules",
     "venv",
+    "demos",
 ]
 
 # Same as Black.
 line-length = 100
 
 # Allow unused variables when underscore-prefixed.
-dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 
 # Assume Python 3.10.
 target-version = "py310"
 
-[tool.ruff.mccabe]
+
+[tool.ruff.lint]
+# Enable pycodestyle (`E`) and Pyflakes (`F`) codes by default.
+select = ["E", "F", "I"]
+ignore = ["E402", "E741", "E743", "E731"]
+
+# Allow autofix for all enabled rules (when `--fix`) is provided.
+fixable = ["A", "B", "C", "D", "E", "F", "I"]
+unfixable = []
+
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[tool.ruff.lint.mccabe]
 # Unlike Flake8, default to a complexity level of 10.
 max-complexity = 10
+
+
+[tool.ruff.lint.isort]
+known-first-party = ["cardiac_geometries"]
+known-third-party = [
+    "basix",
+    "dolfinx",
+    "ffcx",
+    "ufl",
+    "gmsh",
+    "numpy",
+    "pytest",
+]
+section-order = [
+    "future",
+    "standard-library",
+    "mpi",
+    "third-party",
+    "first-party",
+    "local-folder",
+]
+[tool.ruff.lint.isort.sections]
+"mpi" = ["mpi4py", "petsc4py"]

src/fenicsx_pulse/__init__.py

@@ -1,4 +1,5 @@
 """Top-level package for fenicsx_pulse."""
+
 from importlib.metadata import metadata
 
 meta = metadata("fenicsx_pulse")
@@ -8,26 +9,28 @@
 __email__ = meta["Author-email"]
 __program_name__ = meta["Name"]
 
-from . import kinematics
-from . import invariants
-from . import material_model
-from .material_model import HyperElasticMaterial
-from . import compressibility
-from .compressibility import Compressible, Incompressible
-from . import exceptions
-from . import cardiac_model
-from .cardiac_model import CardiacModel
-from . import active_model
-from . import active_stress
+from . import (
+    active_model,
+    active_stress,
+    boundary_conditions,
+    cardiac_model,
+    compressibility,
+    exceptions,
+    geometry,
+    invariants,
+    kinematics,
+    material_model,
+    mechanicsproblem,
+)
 from .active_stress import ActiveStress
-from . import geometry
+from .boundary_conditions import BoundaryConditions, NeumannBC, RobinBC
+from .cardiac_model import CardiacModel
+from .compressibility import Compressible, Incompressible
 from .geometry import Geometry, Marker
-from . import boundary_conditions
-from .boundary_conditions import NeumannBC, RobinBC, BoundaryConditions
-from . import mechanicsproblem
-from .mechanicsproblem import MechanicsProblem
-from .linear_elastic import LinearElastic
 from .holzapfelogden import HolzapfelOgden
+from .linear_elastic import LinearElastic
+from .material_model import HyperElasticMaterial
+from .mechanicsproblem import MechanicsProblem
 
 __all__ = [
     "kinematics",

src/fenicsx_pulse/active_stress.py

@@ -44,13 +44,16 @@ class ActiveStress(ActiveModel):
     activation: dolfinx.fem.Function | dolfinx.fem.Constant = None
     s0: dolfinx.fem.Function | dolfinx.fem.Constant | None = None
     n0: dolfinx.fem.Function | dolfinx.fem.Constant | None = None
-    T_ref: dolfinx.fem.Constant = 1.0
-    eta: dolfinx.fem.Constant = 0.0
+    T_ref: dolfinx.fem.Constant = dolfinx.default_scalar_type(1.0)
+    eta: dolfinx.fem.Constant = dolfinx.default_scalar_type(0.0)
     isotropy: ActiveStressModels = ActiveStressModels.transversely
 
     def __post_init__(self) -> None:
         if self.activation is None:
-            self.activation = dolfinx.fem.Constant(self.f0.ufl_domain(), 0.0)
+            self.activation = dolfinx.fem.Constant(
+                self.f0.ufl_domain(),
+                dolfinx.default_scalar_type(0.0),
+            )
 
         self.T_ref = dolfinx.fem.Constant(self.f0.ufl_domain(), self.T_ref)
         self.eta = dolfinx.fem.Constant(self.f0.ufl_domain(), self.eta)

src/fenicsx_pulse/boundary_conditions.py

@@ -22,6 +22,4 @@ class BoundaryConditions(typing.NamedTuple):
         ]
     ] = ()
     robin: typing.Sequence[RobinBC] = ()
-    body_force: typing.Sequence[
-        float | dolfinx.fem.Constant | dolfinx.fem.Function
-    ] = ()
+    body_force: typing.Sequence[float | dolfinx.fem.Constant | dolfinx.fem.Function] = ()

src/fenicsx_pulse/compressibility.py

@@ -1,6 +1,5 @@
 import abc
-from dataclasses import dataclass
-from dataclasses import field
+from dataclasses import dataclass, field
 
 import dolfinx
 import ufl

src/fenicsx_pulse/exceptions.py

@@ -1,9 +1,10 @@
 import operator
 from dataclasses import dataclass
 
+from mpi4py import MPI
+
 import dolfinx
 import numpy as np
-from mpi4py import MPI
 
 
 def check_value_greater_than(

src/fenicsx_pulse/geometry.py

@@ -1,6 +1,5 @@
 import typing
-from dataclasses import dataclass
-from dataclasses import field
+from dataclasses import dataclass, field
 from pathlib import Path
 from typing import NamedTuple
 
@@ -43,16 +42,8 @@ def __post_init__(self) -> None:
         self._facet_indices = hstack(facet_indices)
         self._facet_markers = hstack(facet_markers)
         self._sorted_facets = np.argsort(self._facet_indices)
-        entities = (
-            []
-            if len(self._sorted_facets) == 0
-            else self._facet_indices[self._sorted_facets]
-        )
-        values = (
-            []
-            if len(self._sorted_facets) == 0
-            else self._facet_markers[self._sorted_facets]
-        )
+        entities = [] if len(self._sorted_facets) == 0 else self._facet_indices[self._sorted_facets]
+        values = [] if len(self._sorted_facets) == 0 else self._facet_markers[self._sorted_facets]
         self.facet_tags = dolfinx.mesh.meshtags(
             self.mesh,
             self.facet_dimension,

src/fenicsx_pulse/holzapfelogden.py

@@ -1,15 +1,12 @@
 import typing
-from dataclasses import dataclass
-from dataclasses import field
+from dataclasses import dataclass, field
 from functools import partial
 
 import dolfinx
 import numpy as np
 import ufl
 
-from . import exceptions
-from . import functions
-from . import invariants
+from . import exceptions, functions, invariants
 from .material_model import HyperElasticMaterial
 
 
@@ -85,16 +82,17 @@ class HolzapfelOgden(HyperElasticMaterial):
         3445-3475.
 
     """
+
     f0: dolfinx.fem.Function | dolfinx.fem.Constant | None = None
     s0: dolfinx.fem.Function | dolfinx.fem.Constant | None = None
-    a: float | dolfinx.fem.Function | dolfinx.fem.Constant = 0.0
-    b: float | dolfinx.fem.Function | dolfinx.fem.Constant = 0.0
-    a_f: float | dolfinx.fem.Function | dolfinx.fem.Constant = 0.0
-    b_f: float | dolfinx.fem.Function | dolfinx.fem.Constant = 0.0
-    a_s: float | dolfinx.fem.Function | dolfinx.fem.Constant = 0.0
-    b_s: float | dolfinx.fem.Function | dolfinx.fem.Constant = 0.0
-    a_fs: float | dolfinx.fem.Function | dolfinx.fem.Constant = 0.0
-    b_fs: float | dolfinx.fem.Function | dolfinx.fem.Constant = 0.0
+    a: float | dolfinx.fem.Function | dolfinx.fem.Constant = dolfinx.default_scalar_type(0.0)
+    b: float | dolfinx.fem.Function | dolfinx.fem.Constant = dolfinx.default_scalar_type(0.0)
+    a_f: float | dolfinx.fem.Function | dolfinx.fem.Constant = dolfinx.default_scalar_type(0.0)
+    b_f: float | dolfinx.fem.Function | dolfinx.fem.Constant = dolfinx.default_scalar_type(0.0)
+    a_s: float | dolfinx.fem.Function | dolfinx.fem.Constant = dolfinx.default_scalar_type(0.0)
+    b_s: float | dolfinx.fem.Function | dolfinx.fem.Constant = dolfinx.default_scalar_type(0.0)
+    a_fs: float | dolfinx.fem.Function | dolfinx.fem.Constant = dolfinx.default_scalar_type(0.0)
+    b_fs: float | dolfinx.fem.Function | dolfinx.fem.Constant = dolfinx.default_scalar_type(0.0)
     use_subplus: bool = field(default=True, repr=False)
     use_heaviside: bool = field(default=True, repr=False)
 
@@ -163,9 +161,7 @@ def __post_init__(self):
     def _resolve_W1(self):
         if exceptions.check_value_greater_than(self.a, 1e-10):
             if exceptions.check_value_greater_than(self.b, 1e-10):
-                return lambda I1: (self.a / (2.0 * self.b)) * (
-                    ufl.exp(self.b * (I1 - 3)) - 1.0
-                )
+                return lambda I1: (self.a / (2.0 * self.b)) * (ufl.exp(self.b * (I1 - 3)) - 1.0)
             else:
                 return lambda I1: (self.a / 2.0) * (I1 - 3)
         else:
@@ -200,11 +196,7 @@ def _resolve_W8fs(self):
                     model=type(self).__name__,
                 )
             if exceptions.check_value_greater_than(self.b_fs, 1e-10):
-                return (
-                    lambda I8: self.a_fs
-                    / (2.0 * self.b_fs)
-                    * (ufl.exp(self.b_fs * I8**2) - 1.0)
-                )
+                return lambda I8: self.a_fs / (2.0 * self.b_fs) * (ufl.exp(self.b_fs * I8**2) - 1.0)
             else:
                 return lambda I8: self.a_fs / 2.0 * I8**2
         else: