Merge branch 'master' into pbrubeck/zany-point-evaluation

Author: pbrubeck

.github/workflows/build.yml

@@ -39,7 +39,7 @@ 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 firedrake-repo/tests/firedrake
+      EXTRA_PYTEST_ARGS: --splitting-algorithm least_duration --timeout=600 --timeout-method=thread -o faulthandler_timeout=660
       PYTEST_MPI_MAX_NPROCS: 8
     steps:
       - name: Fix HOME
@@ -72,8 +72,11 @@ jobs:
             xargs -L1 ./configure --with-make-np=8 --download-slepc
           make PETSC_DIR=/__w/firedrake/firedrake/petsc PETSC_ARCH=arch-firedrake-${{ matrix.arch }}
           make check
-          echo "PETSC_DIR=/__w/firedrake/firedrake/petsc" >> "$GITHUB_ENV"
-          echo "PETSC_ARCH=arch-firedrake-${{ matrix.arch }}" >> "$GITHUB_ENV"
+          {
+            echo "PETSC_DIR=/__w/firedrake/firedrake/petsc"
+            echo "PETSC_ARCH=arch-firedrake-${{ matrix.arch }}"
+            echo "SLEPC_DIR=/__w/firedrake/firedrake/petsc/arch-firedrake-${{ matrix.arch }}"
+          } >> "$GITHUB_ENV"
 
       - name: Install Firedrake
         id: install
@@ -98,63 +101,85 @@ jobs:
           firedrake-check
         timeout-minutes: 5
 
-      - name: Run tests (nprocs = 1)
+      - name: Run TSFC tests
         # Run even if earlier tests failed
-        if: ${{ success() || steps.install.conclusion == 'success' }}
+        if: success() || steps.install.conclusion == 'success'
         run: |
           . venv/bin/activate
           : # 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 $EXTRA_PYTEST_ARGS"
+          firedrake-run-split-tests 1 1 -n 8 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/tsfc
+        timeout-minutes: 60
+
+      - name: Run PyOP2 tests
+        if: success() || steps.install.conclusion == 'success'
+        run: |
+          . venv/bin/activate
+          : # 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 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/pyop2
+          firedrake-run-split-tests 2 4 "$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
+
+
+      - name: Run Firedrake tests (nprocs = 1)
+        if: success() || steps.install.conclusion == 'success'
+        run: |
+          . venv/bin/activate
+          : # 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
 
       - name: Run tests (nprocs = 2)
-        if: ${{ success() || steps.install.conclusion == 'success' }}
+        if: success() || steps.install.conclusion == 'success'
         run: |
           . venv/bin/activate
-          firedrake-run-split-tests 2 4 "$EXTRA_PYTEST_ARGS"
+          firedrake-run-split-tests 2 4 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
         timeout-minutes: 30
 
       - name: Run tests (nprocs = 3)
-        if: ${{ success() || steps.install.conclusion == 'success' }}
+        if: success() || steps.install.conclusion == 'success'
         run: |
           . venv/bin/activate
-          firedrake-run-split-tests 3 2 "$EXTRA_PYTEST_ARGS"
+          firedrake-run-split-tests 3 2 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
         timeout-minutes: 60
 
       - name: Run tests (nprocs = 4)
-        if: ${{ success() || steps.install.conclusion == 'success' }}
+        if: success() || steps.install.conclusion == 'success'
         run: |
           . venv/bin/activate
-          firedrake-run-split-tests 4 2 "$EXTRA_PYTEST_ARGS"
+          firedrake-run-split-tests 4 2 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
         timeout-minutes: 15
 
       - name: Run tests (nprocs = 5)
-        if: ${{ success() || steps.install.conclusion == 'success' }}
+        if: success() || steps.install.conclusion == 'success'
         run: |
           . venv/bin/activate
-          firedrake-run-split-tests 5 1 "$EXTRA_PYTEST_ARGS"
+          firedrake-run-split-tests 5 1 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
         timeout-minutes: 15
 
       - name: Run tests (nprocs = 6)
-        if: ${{ success() || steps.install.conclusion == 'success' }}
+        if: success() || steps.install.conclusion == 'success'
         run: |
           . venv/bin/activate
-          firedrake-run-split-tests 6 1 "$EXTRA_PYTEST_ARGS"
+          firedrake-run-split-tests 6 1 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
         timeout-minutes: 15
 
       - name: Run tests (nprocs = 7)
-        if: ${{ success() || steps.install.conclusion == 'success' }}
+        if: success() || steps.install.conclusion == 'success'
         run: |
           . venv/bin/activate
-          firedrake-run-split-tests 7 1 "$EXTRA_PYTEST_ARGS"
+          firedrake-run-split-tests 7 1 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
         timeout-minutes: 15
 
       - name: Run tests (nprocs = 8)
-        if: ${{ success() || steps.install.conclusion == 'success' }}
+        if: success() || steps.install.conclusion == 'success'
         run: |
           . venv/bin/activate
-          firedrake-run-split-tests 8 1 "$EXTRA_PYTEST_ARGS"
+          firedrake-run-split-tests 8 1 "$EXTRA_PYTEST_ARGS" firedrake-repo/tests/firedrake
         timeout-minutes: 15
 
       - name: Run Gusto smoke tests
@@ -260,7 +285,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: "3.12"
       - name: Install deps
         run: pip install requests packaging
       - name: Zenodo API canary
@@ -269,5 +294,5 @@ jobs:
         uses: actions/upload-artifact@v4
         if: failure()
         with:
-          name: "zenodo-canary"
+          name: zenodo-canary
           path: firedrake-install.log

demos/eigenvalues_QG_basinmodes/qgbasinmodes.py.rst

@@ -18,10 +18,8 @@ dissipative forces. Unlike the other demo that integrated the equations forward
 in time, in this problem it is necessary to compute the eigenvalues and
 eigenfunctions for a particular differential operator.
 
-This demo requires SLEPc and slepc4py to be installed.  This is most easily
-achieved by providing the optional `--slepc` flag to either `firedrake-install`
-(for a new installation), or `firedrake-update` (to add SLEPc to an existing
-installation).
+This demo requires SLEPc and slepc4py to be installed. For instructions on how
+to install them please follow `these instructions <https://www.firedrakeproject.org/install#slepc>`_.
 
 
 Governing PDE

demos/netgen/netgen_mesh.py.rst

@@ -11,7 +11,7 @@ Finally we will show how to use mesh refinement features included in Netgen to c
 
 Installing Netgen
 ------------------
-This demo requires the NGSolve/Netgen suite to be installed. This is most easily achieved by providing the optional `--netgen` flag to either `firedrake-install` (for a new installation), or `firedrake-update` (to add the NGSolve/Netgen suite to an existing installation). ::
+This demo requires the NGSolve/Netgen suite to be installed. This can be done by running ``pip install ngsPETSc``. ::
 
    from firedrake import *
    try:

docs/source/aims_25.rst

@@ -1,6 +1,6 @@
 :orphan: true
 
-.. title:: Finite Element Course at AIMS Rwanda
+.. title:: Finite Element Course at AIMS Research and Innovation Centre Rwanda
 
 Finite Element Course at AIMS Rwanda
 ------------------------------------
@@ -50,7 +50,7 @@ reading is available on the links above.
     - Firedrake practical 2: `Dirichlet boundary conditions <https://colab.research.google.com/github/firedrakeproject/notebooks/blob/aims/02-poisson.ipynb>`__
     - Firedrake practical 4: `mixed Poisson <https://colab.research.google.com/github/firedrakeproject/notebooks/blob/aims/05-mixed-poisson.ipynb>`__
     - Firedrake practical 6: `solvers <https://colab.research.google.com/github/firedrakeproject/notebooks/blob/aims/08-composable-solvers.ipynb>`__
-    - Adjoint practical 1: Burgers again
+    - Adjoint practical 1: `Burgers again <https://colab.research.google.com/github/firedrakeproject/notebooks/blob/aims/13_adjoint_calculations.ipynb#scrollTo=e7b5808f-f0ae-4e40-bcca-eff67f251fc9>`__
     - `Scientific machine learning <https://github.com/NBoulle/physics-driven-ml/raw/main/tutorials/sciml_intro.pdf>`__, `practical <https://colab.research.google.com/github/NBoulle/physics-driven-ml/blob/main/tutorials/Tutorial_2_ex.ipynb>`__
 
 

docs/source/checkpointing.rst

@@ -617,9 +617,9 @@ Firedrake uses the PETSc_ HDF5 Viewer_ object to write and read state.
 As such, writing data is collective across processes.  h5py_ is used
 for attribute manipulation.  To this end, h5py_ *must* be linked
 against the same version of the HDF5 library that PETSc was built
-with.  The ``firedrake-install`` script automates this, however, if
-you build PETSc manually, you will need to ensure that h5py_ is linked
-correctly following the instructions for custom installation here_.
+with. If you have a custom installation of Firedrake then it may be
+necessary to manually ensure that h5py is linked correctly.
+Instructions for how to do this can be found here_.
 
 .. warning::