Merge branch 'JHopeCollins/fdv-saddle-pc' into JHopeCollins/fdv-saddle-pc-arf

Author: JHopeCollins

.github/workflows/core.yml

@@ -8,7 +8,7 @@ on:
         type: string
         required: true
       target_branch:
-        description: The target branch (usually 'master' or 'release')
+        description: The target branch (usually 'main' or 'release')
         type: string
         required: true
       run_tests:
@@ -39,7 +39,7 @@ on:
         type: string
         required: true
       target_branch:
-        description: The target branch (usually 'master' or 'release')
+        description: The target branch (usually 'main' or 'release')
         type: string
         required: true
       run_tests:
@@ -93,7 +93,9 @@ jobs:
       FIREDRAKE_CI: 1
       PYOP2_CI_TESTS: 1
       PYOP2_SPMD_STRICT: 1
-      EXTRA_PYTEST_ARGS: --splitting-algorithm least_duration --timeout=600 --timeout-method=thread -o faulthandler_timeout=660
+      # NOTE: One should occasionally update test_durations.json by running
+      # 'make test_durations' inside a 'firedrake:latest' Docker image.
+      EXTRA_PYTEST_ARGS: --splitting-algorithm least_duration --timeout=600 --timeout-method=thread -o faulthandler_timeout=660 --durations-path=./firedrake-repo/tests/test_durations.json
       PYTEST_MPI_MAX_NPROCS: 8
     steps:
       - name: Fix HOME
@@ -144,7 +146,7 @@ jobs:
             $(python3 ./firedrake-repo/scripts/firedrake-configure --arch ${{ matrix.arch }} --show-system-packages)
           apt-get -y install python3-venv
           : # Dependencies needed to run the test suite
-          apt-get -y install parallel
+          apt-get -y install fonts-dejavu graphviz graphviz-dev parallel poppler-utils
 
       - name: Install PETSc
         run: |
@@ -191,7 +193,7 @@ jobs:
             : # because they rely on non-PyPI versions of petsc4py.
             pip install --no-build-isolation --no-deps \
               "$PETSC_DIR"/"$PETSC_ARCH"/externalpackages/git.slepc/src/binding/slepc4py
-            pip install --no-deps ngsPETSc netgen-mesher netgen-occt
+            pip install --no-deps git+https://github.com/NGSolve/ngsPETSc.git netgen-mesher netgen-occt
 
             : # We have to pass '--no-build-isolation' to use a custom petsc4py
             EXTRA_BUILD_ARGS='--no-isolation'
@@ -205,9 +207,13 @@ jobs:
           pip install --verbose $EXTRA_PIP_FLAGS \
             --no-binary h5py \
             --extra-index-url https://download.pytorch.org/whl/cpu \
-            "$(echo ./firedrake-repo/dist/firedrake-*.tar.gz)[ci,docs]"
+            "$(echo ./firedrake-repo/dist/firedrake-*.tar.gz)"
+
+          pip install -U pip
+          pip install --group ./firedrake-repo/pyproject.toml:ci
+
           : # TODO: Remove before merge
-          pip install --verbose --editable git+https://github.com/dolfin-adjoint/pyadjoint.git@JHopeCollins/tlm#egg=pyadjoint-ad
+          pip install --verbose --editable git+https://github.com/dolfin-adjoint/pyadjoint.git@dham/abstract_reduced_functional#egg=pyadjoint-ad
 
           firedrake-clean
           pip list
@@ -237,7 +243,7 @@ jobs:
           : # Use pytest-xdist here so we can have a single collated output (not possible
           : # for parallel tests)
           firedrake-run-split-tests 1 1 -n 8 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/tsfc
-        timeout-minutes: 60
+        timeout-minutes: 10
 
       - name: Run PyOP2 tests
         if: inputs.run_tests && (success() || steps.install.conclusion == 'success')
@@ -249,7 +255,7 @@ jobs:
           firedrake-run-split-tests 2 4 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/pyop2
           firedrake-run-split-tests 3 2 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/pyop2
           firedrake-run-split-tests 4 2 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/pyop2
-        timeout-minutes: 15
+        timeout-minutes: 10
 
 
       - name: Run Firedrake tests (nprocs = 1)
@@ -259,14 +265,14 @@ jobs:
           : # Use pytest-xdist here so we can have a single collated output (not possible
           : # for parallel tests)
           firedrake-run-split-tests 1 1 -n 8 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
-        timeout-minutes: 60
+        timeout-minutes: 90
 
       - name: Run tests (nprocs = 2)
         if: inputs.run_tests && (success() || steps.install.conclusion == 'success')
         run: |
           . venv/bin/activate
           firedrake-run-split-tests 2 4 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
-        timeout-minutes: 30
+        timeout-minutes: 60
 
       - name: Run tests (nprocs = 3)
         if: inputs.run_tests && (success() || steps.install.conclusion == 'success')
@@ -425,6 +431,8 @@ jobs:
             echo Error: there are untracked files in the repository
             echo The output from 'git status' is:
             git status
+            echo The output from 'git diff' is:
+            git diff
             exit 1
           fi
 
@@ -544,12 +552,12 @@ jobs:
   deploy_website:
     name: Deploy GitHub pages (optional)
     needs: test_linux
-    # Only deploy the website for master here, the release branch is managed
+    # Only deploy the website for main here, the release branch is managed
     # by https://github.com/firedrakeproject/firedrakeproject.github.io
     if: |
       always() &&
       inputs.deploy_website &&
-      inputs.target_branch == 'master' &&
+      inputs.target_branch == 'main' &&
       needs.test_linux.outputs.docs_conclusion == 'success'
     permissions:
       pages: write
@@ -573,15 +581,15 @@ jobs:
     runs-on: ubuntu-latest
     environment:
       name: pypi
-    permissions:
-      id-token: write
     steps:
       - uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist
       - name: Push to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
 
   upload_testpypi:
     name: Upload to TestPyPI (optional)

.github/workflows/push.yml

@@ -3,7 +3,7 @@ name: Deploy after push
 on:
   push:
     branches:
-      - master
+      - main
       - release
 
 jobs:

.gitignore

@@ -15,10 +15,12 @@ __pycache__/
 /demos/immersed_fem/immersed_domain.msh
 /docs/build/
 /docs/notebooks/.ipynb_checkpoints/
+/docs/notebooks/tape.pdf
 /docs/source/apt_deps.txt
 /docs/source/firedrake.rst
 /docs/source/firedrake.*.rst
 /docs/source/homebrew_deps.txt
+/docs/source/minimal_apt_deps.txt
 /docs/source/obtaining_pyop2.rst
 /docs/source/petsc_configure_options.txt
 /docs/source/team.rst