Merge branch 'master' into pbrubeck/interpolate-mixed

Author: pbrubeck

.github/workflows/core.yml

@@ -169,6 +169,7 @@ jobs:
           pip cache remove slepc4py
 
           if [ ${{ inputs.target_branch }} = 'release' ]; then
+            EXTRA_BUILD_ARGS=''
             EXTRA_PIP_FLAGS=''
           else
             : # Install build dependencies
@@ -182,18 +183,34 @@ jobs:
             pip install --no-deps ngsPETSc netgen-mesher netgen-occt
 
             : # We have to pass '--no-build-isolation' to use a custom petsc4py
+            EXTRA_BUILD_ARGS='--no-isolation'
             EXTRA_PIP_FLAGS='--no-build-isolation'
           fi
 
+          : # Install from an sdist so we can make sure that it is not ill-formed
+          pip install build
+          python -m build ./firedrake-repo --sdist "$EXTRA_BUILD_ARGS"
+
           pip install --verbose $EXTRA_PIP_FLAGS \
             --no-binary h5py \
             --extra-index-url https://download.pytorch.org/whl/cpu \
-            './firedrake-repo[ci,docs]'
+            "$(echo ./firedrake-repo/dist/firedrake-*.tar.gz)[ci,docs]"
 
           pip install -I "fenics-ufl @ git+https://github.com/firedrakeproject/ufl.git@pbrubeck/fix/baseform"
           firedrake-clean
           pip list
 
+      - name: Upload sdist (default ARCH only)
+        if: matrix.arch == 'default'
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: firedrake-repo/dist/*
+
+      - name: Report sdist build status
+        id: report_sdist
+        run: echo "conclusion=success" >> "$GITHUB_OUTPUT"
+
       - name: Run firedrake-check
         run: |
           . venv/bin/activate
@@ -340,32 +357,6 @@ jobs:
           name: firedrake-logs-${{ matrix.arch }}
           path: pytest_*.log
 
-      - name: Build sdist (release only)
-        if: |
-          inputs.target_branch == 'release' &&
-          matrix.arch == 'default' &&
-          (success() || steps.install.conclusion == 'success')
-        run: |
-          . venv/bin/activate
-          pip install build
-          python -m build ./firedrake-repo --sdist
-
-      - name: Upload sdist (release only)
-        id: upload_sdist
-        if: |
-          inputs.target_branch == 'release' &&
-          matrix.arch == 'default' &&
-          (success() || steps.install.conclusion == 'success')
-        uses: actions/upload-artifact@v4
-        with:
-          name: dist
-          path: firedrake-repo/dist/*
-
-      - name: Report sdist build status
-        id: report_sdist
-        if: success() || steps.upload_sdist.conclusion == 'success'
-        run: echo "conclusion=success" >> "$GITHUB_OUTPUT"
-
       - name: Check bibtex
         if: (success() || steps.install.conclusion == 'success') && matrix.arch == 'default'
         run: |

.gitignore

@@ -27,7 +27,8 @@ __pycache__/
 /docs/source/demos
 /firedrake/cython/*.c
 /firedrake.egg-info
-/firedrake_check/
+/firedrake/_check/Makefile
+/firedrake/_check/tests
 /docs/source/element_list.csv
 
 

MANIFEST.in

@@ -0,0 +1,5 @@
+# This file contains all the non-standard files that need to be included
+# in the source distribution.
+
+recursive-include firedrake/cython *.pyx *.pxi
+recursive-exclude firedrake/cython *.c

Makefile

@@ -88,12 +88,13 @@ clean:
 	@echo "    RM tinyasm/*.so"
 	-@rm -f tinyasm/*.so > /dev/null 2>&1
 
-# Do verbose checking if running on CI
+# Do verbose checking if running on CI and always set no:cacheprovider because
+# we don't want to generate any cache files in $VIRTUAL_ENV/lib/.../firedrake/_check
 check_flags =
 ifeq ($(FIREDRAKE_CI), 1)
-	check_flags = --verbose
+	check_flags = --verbose -p no:cacheprovider
 else
-	check_flags = --quiet
+	check_flags = --quiet -p no:cacheprovider
 endif
 
 CHECK_PYTEST_ARGS =

docs/source/conf.py

@@ -162,7 +162,7 @@
     r'https://www.tuomaskarna.com',
     r'https://www.crosscountrytrains.co.uk/',
     r'https://www.siam.org/',
-    r'https://aims.ac.rw/',
+    r'https://aims.ac.rw',
 ]
 linkcheck_timeout = 30
 

docs/source/install.rst

@@ -180,7 +180,7 @@ install Firedrake. To do this perform the following steps:
 #. Install Firedrake::
 
       $ pip cache remove petsc4py
-      $ pip install --no-binary h5py "firedrake @ git+https://github.com/firedrakeproject/firedrake.git@release#[check]"
+      $ pip install --no-binary h5py 'firedrake[check]'
 
    .. note::
       Though not strictly necessary to install Firedrake's optional
@@ -219,7 +219,7 @@ Updating Firedrake involves following the same steps as above when
 :ref:`installing Firedrake<install_firedrake>`. First, use ``firedrake-configure``
 to set the right environment variables and then run::
 
-     $ pip install --upgrade git+https://github.com/firedrakeproject/firedrake.git@release
+     $ pip install --upgrade firedrake
 
 Updating PETSc
 ~~~~~~~~~~~~~~
@@ -326,15 +326,15 @@ To install Firedrake with SLEPc support you should:
    and install Firedrake with the ``slepc`` optional dependency. For example::
 
    $ pip cache remove slepc4py
-   $ pip install --no-binary h5py "firedrake @ git+https://github.com/firedrakeproject/firedrake.git@release#[check,slepc]"
+   $ pip install --no-binary h5py 'firedrake[check,slepc]'
 
 VTK
 ~~~
 
 To install Firedrake with VTK, it should be installed using the ``vtk`` optional
 dependency. For example::
 
-   $ pip install --no-binary h5py "firedrake @ git+https://github.com/firedrakeproject/firedrake.git@release#[check,vtk]"
+   $ pip install --no-binary h5py 'firedrake[check,vtk]'
 
 At present VTK wheels are not available for ARM Linux machines. Depending on your
 Python version you may be able to work around this by downloading and pip installing
@@ -348,7 +348,7 @@ PyTorch
 To install Firedrake with `PyTorch <https://pytorch.org/>`_, it should be installed
 using the ``torch`` optional dependency. For example::
 
-   $ pip install --no-binary h5py "firedrake @ git+https://github.com/firedrakeproject/firedrake.git@release#[check,torch]" --extra-index-url https://download.pytorch.org/whl/cpu
+   $ pip install --no-binary h5py 'firedrake[check,torch]' --extra-index-url https://download.pytorch.org/whl/cpu
 
 Observe that, in addition to specifying ``torch``, an additional
 argument (``--extra-index-url``) is needed. More information on installing
@@ -361,7 +361,7 @@ JAX
 To install Firedrake with JAX, it should be installed using the ``jax`` optional
 dependency. For example::
 
-   $ pip install --no-binary h5py "firedrake @ git+https://github.com/firedrakeproject/firedrake.git@release#[check,jax]"
+   $ pip install --no-binary h5py 'firedrake[check,jax]'
 
 
 Netgen
@@ -370,7 +370,7 @@ Netgen
 To install Firedrake with `Netgen <https://ngsolve.org/>`_ support, it should be
 installed with the ``netgen`` optional dependency. For example::
 
-   $ pip install --no-binary h5py "firedrake @ git+https://github.com/firedrakeproject/firedrake.git@release#[check,netgen]"
+   $ pip install --no-binary h5py 'firedrake[check,netgen]'
 
 
 Customising PETSc

firedrake/_check/__init__.py

@@ -0,0 +1,9 @@
+"""Run the Firedrake smoke tests."""
+
+import pathlib
+import subprocess
+
+
+def main() -> None:
+    dir = pathlib.Path(__file__).parent
+    subprocess.run(f"make -C {dir} check".split(), errors=True)

pyproject.toml

@@ -60,7 +60,7 @@ Repository = "https://github.com/firedrakeproject/firedrake"
 Issues = "https://github.com/firedrakeproject/firedrake/issues/new/choose"
 
 [project.scripts]
-firedrake-check = "firedrake_check:main"
+firedrake-check = "firedrake._check:main"
 firedrake-clean = "firedrake.scripts.firedrake_clean:main"
 firedrake-preprocess-bibtex = "firedrake.scripts.firedrake_preprocess_bibtex:main"
 firedrake-status = "firedrake.scripts.firedrake_status:main"
@@ -168,11 +168,7 @@ firedrake = [
   "evaluate.h",
   "locate.c",
   "icons/*.png",
-]
-firedrake_check = [
-  "Makefile",
-  "tests/firedrake/conftest.py",
-  "tests/*/*/*.py",
+  "_check/**",
 ]
 pyop2 = [
   "*.h",

setup.py

@@ -12,6 +12,7 @@
 import pkgconfig
 from dataclasses import dataclass, field
 from setuptools import setup, find_packages, Extension
+from setuptools.command.sdist import sdist as _sdist
 from glob import glob
 from pathlib import Path
 from Cython.Build import cythonize
@@ -236,7 +237,9 @@ def extensions():
 
 
 # TODO: It would be good to have a single source of truth for these files
-FIREDRAKE_CHECK_TEST_FILES = (
+FIREDRAKE_CHECK_FILES = (
+    "Makefile",
+    "tests/firedrake/conftest.py",
     "tests/firedrake/regression/test_stokes_mini.py",
     "tests/firedrake/regression/test_locate_cell.py",
     "tests/firedrake/supermesh/test_assemble_mixed_mass_matrix.py",
@@ -247,46 +250,21 @@ def extensions():
 )
 
 
-# This diabolical function is needed to allow 'firedrake-check' to work. Since
-# installed packages are not allowed to contain files from outside that Python
-# package we cannot access the Makefile or test files once installation is
-# complete. Therefore, before we install, we create a dummy package, called
-# 'firedrake-check' containing said Makefile and tests.
-def make_firedrake_check_package():
-    package_dir = "firedrake_check"
-    logging.info(f"Creating '{package_dir}' package")
-    if os.path.exists(package_dir):
-        logging.info(f"'{package_dir}' already found, removing")
-        shutil.rmtree(package_dir)
+class sdist(_sdist):
+    def run(self):
+        self._copy_check_files()
+        super().run()
 
-    os.mkdir(package_dir)
-    with open(f"{package_dir}/__init__.py", "w") as f:
-        # set 'errors=True' to make sure that we propagate failures to the
-        # outer process
-        f.write("""import pathlib
-import subprocess
-
-def main():
-    dir = pathlib.Path(__file__).parent
-    subprocess.run(f'make -C {dir} check'.split(), errors=True)
-""")
-
-    # copy Makefile and tests into dummy package
-    shutil.copy("Makefile", package_dir)
-    for test_file in FIREDRAKE_CHECK_TEST_FILES:
-        package_test_dir = os.path.join(package_dir, Path(test_file).parent)
-        os.makedirs(package_test_dir, exist_ok=True)
-        shutil.copy(test_file, package_test_dir)
-
-    # Also copy conftest.py so any markers are recognised
-    conftest_dir = os.path.join(package_dir, "tests", "firedrake")
-    shutil.copy("tests/firedrake/conftest.py", conftest_dir)
-
-
-make_firedrake_check_package()
+    def _copy_check_files(self):
+        """Copy Makefile and tests into firedrake/_check."""
+        dest_dir = Path("firedrake/_check")
+        for check_file in map(Path, FIREDRAKE_CHECK_FILES ):
+            os.makedirs(dest_dir / check_file.parent, exist_ok=True)
+            shutil.copy(check_file, dest_dir / check_file.parent)
 
 
 setup(
+    cmdclass={"sdist": sdist},
     packages=find_packages(),
-    ext_modules=extensions()
+    ext_modules=extensions(),
 )