Merge pull request #52 from firedrakeproject/ksagiyam/merge_upstream

Merge upstream

.github/dependabot.yml

@@ -0,0 +1,15 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/build-wheels.yml

@@ -11,11 +11,11 @@ on:
         default: "main"
         type: string
       test_pypi_publish:
-        description: "Publish to Test PyPi (true | false)"
+        description: "Publish to Test PyPi"
         default: false
         type: boolean
       pypi_publish:
-        description: "Publish to PyPi (true | false)"
+        description: "Publish to PyPi"
         default: false
         type: boolean
 
@@ -26,11 +26,11 @@ on:
         default: "main"
         type: string
       test_pypi_publish:
-        description: "Publish to Test PyPi (true | false)"
+        description: "Publish to Test PyPi"
         default: false
         type: boolean
       pypi_publish:
-        description: "Publish to PyPi (true | false))"
+        description: "Publish to PyPi"
         default: false
         type: boolean
 
@@ -54,28 +54,44 @@ jobs:
         with:
           path: dist/*
 
-  upload_pypi:
-    name: Upload to PyPI (optional)
+  upload_test_pypi:
+    name: Upload to test PyPI (optional)
+    if: ${{ github.event.inputs.test_pypi_publish == 'true' }}
     needs: [build]
     runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/fenics-ufl
+    permissions:
+      id-token: write
+
     steps:
       - uses: actions/download-artifact@v4
         with:
           name: artifact
           path: dist
 
-      - name: Push to PyPI
+      - name: Push to test PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
-        if: ${{ github.event.inputs.pypi_publish == 'true' }}
         with:
-          user: __token__
-          password: ${{ secrets.PYPI_TOKEN }}
-          repository_url: https://upload.pypi.org/legacy/
+          repository-url: https://test.pypi.org/legacy/
+
+  upload_pypi:
+    name: Upload to PyPI (optional)
+    if: ${{ github.event.inputs.pypi_publish == 'true' }}
+    needs: [build]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/fenics-ufl
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: artifact
+          path: dist
 
-      - name: Push to Test PyPI
+      - name: Push to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
-        if: ${{ github.event.inputs.test_pypi_publish == 'true' }}
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_TEST_TOKEN }}
-          repository_url: https://test.pypi.org/legacy/

.github/workflows/fenicsx-tests.yml

@@ -22,15 +22,15 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.12
 
       - name: Install test dependencies
         run: |
           sudo apt-get install -y graphviz libgraphviz-dev ninja-build pkg-config
 
       - name: Install UFL
         run: |
-          pip3 install .
+          pip3 install --break-system-packages .
 
       - name: Install Basix
         run: |
@@ -65,12 +65,12 @@ jobs:
 
       - name: Install UFL
         run: |
-          pip3 install .
+          pip3 install --break-system-packages .
 
       - name: Install Basix and FFCx
         run: |
-          python3 -m pip install git+https://github.com/FEniCS/basix.git
-          python3 -m pip install git+https://github.com/FEniCS/ffcx.git
+          python3 -m pip install --break-system-packages  git+https://github.com/FEniCS/basix.git
+          python3 -m pip install --break-system-packages  git+https://github.com/FEniCS/ffcx.git
 
       - name: Clone DOLFINx
         uses: actions/checkout@v4
@@ -83,6 +83,7 @@ jobs:
           cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build -S dolfinx/cpp/
           cmake --build build
           cmake --install build
-          python3 -m pip -v install --no-build-isolation --check-build-dependencies --config-settings=cmake.build-type="Developer" dolfinx/python/
+          python3 -m pip install --break-system-packages -r dolfinx/python/build-requirements.txt
+          python3 -m pip -v install --break-system-packages --no-build-isolation --check-build-dependencies --config-settings=cmake.build-type="Developer" dolfinx/python/[ci]
       - name: Run DOLFINx unit tests
         run: python3 -m pytest -n auto dolfinx/python/test/unit

.github/workflows/pythonapp.yml

@@ -21,29 +21,35 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest]
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        exclude:
+          - os: macos-latest
+            python-version: '3.8'
+          - os: macos-latest
+            python-version: '3.9'
+        include:
+          - os: windows-latest
+            python-version: '3.11'
 
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Lint with flake8
+      - name: Lint with ruff
         run: |
-          python -m pip install flake8
-          flake8 --statistics .
-      - name: Check documentation style
-        run: |
-          python -m pip install pydocstyle[toml]
-          python -m pydocstyle ufl/
+          pip install ruff
+          ruff check .
+          ruff format --check .
       - name: Install UFL
         run: python -m pip install .[ci]
       - name: Run unit tests
         run: |
           python -m pytest -n auto --cov=ufl/ --junitxml=junit/test-results-${{ matrix.os }}-${{ matrix.python-version }}.xml test/
       - name: Upload to Coveralls
-        if: ${{ github.repository == 'FEniCS/ufl' && github.head_ref == '' && matrix.os == 'ubuntu-latest' && matrix.python-version == '3.8' }}
+        if: ${{ github.repository == 'FEniCS/ufl' && github.head_ref == '' && matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' }}
         env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
         run: coveralls
 
@@ -61,25 +67,25 @@ jobs:
           if-no-files-found: error
 
       - name: Checkout FEniCS/docs
-        if: ${{ github.repository == 'FEniCS/ufl' && ( github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/') ) && runner.os == 'Linux' && matrix.python-version == 3.8 }}
+        if: ${{ github.repository == 'FEniCS/ufl' && ( github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/') ) && runner.os == 'Linux' && matrix.python-version == 3.12 }}
         uses: actions/checkout@v4
         with:
           repository: "FEniCS/docs"
           path: "docs"
           ssh-key: "${{ secrets.SSH_GITHUB_DOCS_PRIVATE_KEY }}"
       - name: Set version name
-        if: ${{ github.repository == 'FEniCS/ufl' && ( github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/') ) && runner.os == 'Linux' && matrix.python-version == 3.8 }}
+        if: ${{ github.repository == 'FEniCS/ufl' && ( github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/') ) && runner.os == 'Linux' && matrix.python-version == 3.12 }}
         run: |
           echo "VERSION_NAME=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
       - name: Copy documentation into repository
-        if: ${{ github.repository == 'FEniCS/ufl' && ( github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/') ) && runner.os == 'Linux' && matrix.python-version == 3.8 }}
+        if: ${{ github.repository == 'FEniCS/ufl' && ( github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/') ) && runner.os == 'Linux' && matrix.python-version == 3.12 }}
         run: |
           cd docs
           git rm -r --ignore-unmatch ufl/${{ env.VERSION_NAME }}
           mkdir -p ufl/${{ env.VERSION_NAME }}
           cp -r ../doc/sphinx/build/html/* ufl/${{ env.VERSION_NAME }}
       - name: Commit and push documentation to FEniCS/docs
-        if: ${{ github.repository == 'FEniCS/ufl' && ( github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/') ) && runner.os == 'Linux' && matrix.python-version == 3.8 }}
+        if: ${{ github.repository == 'FEniCS/ufl' && ( github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/') ) && runner.os == 'Linux' && matrix.python-version == 3.12 }}
         run: |
           cd docs
           git config --global user.email "[email protected]"

.github/workflows/tsfc-tests.yml

@@ -17,9 +17,9 @@ jobs:
       CXX: g++-10
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: 3.9
 
@@ -28,7 +28,7 @@ jobs:
           pip3 install .
 
       - name: Clone tsfc
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: ./tsfc
           repository: firedrakeproject/tsfc

README.md

@@ -11,12 +11,10 @@ https://www.fenicsproject.org
 
 [![UFL CI](https://github.com/FEniCS/ufl/workflows/UFL%20CI/badge.svg)](https://github.com/FEniCS/ufl/workflows/UFL%20CI)
 [![Coverage Status](https://coveralls.io/repos/github/FEniCS/ufl/badge.svg?branch=master)](https://coveralls.io/github/FEniCS/ufl?branch=master)
-[![Documentation Status](https://readthedocs.org/projects/fenics-ufl/badge/?version=latest)](https://fenics.readthedocs.io/projects/ufl/en/latest/?badge=latest)
 
 ## Documentation
 
-Documentation can be viewed at https://fenics-ufl.readthedocs.org/.
-
+Documentation can be viewed at https://docs.fenicsproject.org
 
 ## License
 

demo/Constant.py

@@ -18,15 +18,27 @@
 # Modified by Martin Sandve Alnes, 2009
 #
 # Test form for scalar and vector constants.
-from ufl import (Coefficient, Constant, FunctionSpace, Mesh, TestFunction, TrialFunction, VectorConstant, dot, dx, grad,
-                 inner, triangle)
+from ufl import (
+    Coefficient,
+    Constant,
+    FunctionSpace,
+    Mesh,
+    TestFunction,
+    TrialFunction,
+    VectorConstant,
+    dot,
+    dx,
+    grad,
+    inner,
+    triangle,
+)
 from ufl.finiteelement import FiniteElement
 from ufl.pullback import identity_pullback
 from ufl.sobolevspace import H1
 
 cell = triangle
 element = FiniteElement("Lagrange", cell, 1, (), identity_pullback, H1)
-domain = Mesh(FiniteElement("Lagrange", cell, 1, (2, ), identity_pullback, H1))
+domain = Mesh(FiniteElement("Lagrange", cell, 1, (2,), identity_pullback, H1))
 space = FunctionSpace(domain, element)
 
 v = TestFunction(space)

demo/ConvectionJacobi.py

@@ -2,13 +2,23 @@
 # Author: Martin Sandve Alnes
 # Date: 2008-10-03
 #
-from ufl import Coefficient, FunctionSpace, Mesh, TestFunction, TrialFunction, dot, dx, grad, triangle
+from ufl import (
+    Coefficient,
+    FunctionSpace,
+    Mesh,
+    TestFunction,
+    TrialFunction,
+    dot,
+    dx,
+    grad,
+    triangle,
+)
 from ufl.finiteelement import FiniteElement
 from ufl.pullback import identity_pullback
 from ufl.sobolevspace import H1
 
-element = FiniteElement("Lagrange", triangle, 1, (2, ), identity_pullback, H1)
-domain = Mesh(FiniteElement("Lagrange", triangle, 1, (2, ), identity_pullback, H1))
+element = FiniteElement("Lagrange", triangle, 1, (2,), identity_pullback, H1)
+domain = Mesh(FiniteElement("Lagrange", triangle, 1, (2,), identity_pullback, H1))
 space = FunctionSpace(domain, element)
 
 u = TrialFunction(space)

demo/ConvectionJacobi2.py

@@ -7,8 +7,8 @@
 from ufl.pullback import identity_pullback
 from ufl.sobolevspace import H1
 
-element = FiniteElement("Lagrange", triangle, 1, (2, ), identity_pullback, H1)
-domain = Mesh(FiniteElement("Lagrange", triangle, 1, (2, ), identity_pullback, H1))
+element = FiniteElement("Lagrange", triangle, 1, (2,), identity_pullback, H1)
+domain = Mesh(FiniteElement("Lagrange", triangle, 1, (2,), identity_pullback, H1))
 space = FunctionSpace(domain, element)
 
 u = TrialFunction(space)

demo/ConvectionVector.py

@@ -7,8 +7,8 @@
 from ufl.pullback import identity_pullback
 from ufl.sobolevspace import H1
 
-element = FiniteElement("Lagrange", triangle, 1, (2, ), identity_pullback, H1)
-domain = Mesh(FiniteElement("Lagrange", triangle, 1, (2, ), identity_pullback, H1))
+element = FiniteElement("Lagrange", triangle, 1, (2,), identity_pullback, H1)
+domain = Mesh(FiniteElement("Lagrange", triangle, 1, (2,), identity_pullback, H1))
 space = FunctionSpace(domain, element)
 
 v = TestFunction(space)

demo/Elasticity.py

@@ -8,8 +8,8 @@
 from ufl.pullback import identity_pullback
 from ufl.sobolevspace import H1
 
-element = FiniteElement("Lagrange", tetrahedron, 1, (3, ), identity_pullback, H1)
-domain = Mesh(FiniteElement("Lagrange", tetrahedron, 1, (3, ), identity_pullback, H1))
+element = FiniteElement("Lagrange", tetrahedron, 1, (3,), identity_pullback, H1)
+domain = Mesh(FiniteElement("Lagrange", tetrahedron, 1, (3,), identity_pullback, H1))
 space = FunctionSpace(domain, element)
 
 v = TestFunction(space)

demo/EnergyNorm.py

@@ -23,7 +23,7 @@
 from ufl.sobolevspace import H1
 
 element = FiniteElement("Lagrange", tetrahedron, 1, (), identity_pullback, H1)
-domain = Mesh(FiniteElement("Lagrange", tetrahedron, 1, (3, ), identity_pullback, H1))
+domain = Mesh(FiniteElement("Lagrange", tetrahedron, 1, (3,), identity_pullback, H1))
 space = FunctionSpace(domain, element)
 
 v = Coefficient(space)

demo/Equation.py

@@ -34,13 +34,25 @@
 # the unknown u to the right-hand side, all terms may
 # be listed on one line and left- and right-hand sides
 # extracted by lhs() and rhs().
-from ufl import Coefficient, FunctionSpace, Mesh, TestFunction, TrialFunction, dot, dx, grad, lhs, rhs, triangle
+from ufl import (
+    Coefficient,
+    FunctionSpace,
+    Mesh,
+    TestFunction,
+    TrialFunction,
+    dot,
+    dx,
+    grad,
+    lhs,
+    rhs,
+    triangle,
+)
 from ufl.finiteelement import FiniteElement
 from ufl.pullback import identity_pullback
 from ufl.sobolevspace import H1
 
 element = FiniteElement("Lagrange", triangle, 1, (), identity_pullback, H1)
-domain = Mesh(FiniteElement("Lagrange", triangle, 1, (2, ), identity_pullback, H1))
+domain = Mesh(FiniteElement("Lagrange", triangle, 1, (2,), identity_pullback, H1))
 space = FunctionSpace(domain, element)
 
 k = 0.1