MKL build updates

.github/make_ci_environ.py

@@ -15,6 +15,9 @@ def parse_pyproject(path: str, optional_sections_to_skip=None):
             # numpy is also listed in build requirements with a higher version number
             # so we skip it here to avoid conflicts.
             continue
+        if "mkl" in dep:
+            # mkl is pinned to the exact version under test below instead.
+            continue
         deps.add(dep)
 
     # optional dependencies (PEP 621)
@@ -26,10 +29,6 @@ def parse_pyproject(path: str, optional_sections_to_skip=None):
             continue
         deps.update(group_deps)
 
-    deps.discard("geoana[all]")
-    deps.discard("geoana[doc,all]")
-    deps.discard("geoana[plot,extras,jittable]")
-
     if "matplotlib" in deps:
         deps.remove("matplotlib")
         deps.add("matplotlib-base")
@@ -77,7 +76,7 @@ def create_env_yaml(deps, name="env", python_version=None, free_threaded=False):
 
     deps = parse_pyproject(pyproject_path, optional_sections_to_skip=optional_to_skip)
     deps.add("mkl-devel")
-    deps.add("pkg-config")
+    deps.add("cmake")
     deps.add(f"mkl={mkl_vers}")
     env_data = create_env_yaml(deps, name=env_name, python_version=py_vers, free_threaded=is_free_threaded)
 

.github/strip_wheel_dependency.py

@@ -0,0 +1,85 @@
+"""Remove a dependency from every wheel in a directory, in place.
+
+These wheels statically link MKL (see [tool.cibuildwheel] in
+pyproject.toml), so they have no runtime dependency on the `mkl`
+package - but `dependencies` is static and shared with the source
+build, which does need it. Strips it from these wheels after the fact,
+since meson-python can't make it conditional on how a wheel was built.
+
+Invoked from `repair-wheel-command` (pyproject.toml) as the last step
+after auditwheel/delvewheel, directly on cibuildwheel's own
+`{dest_dir}` - takes a directory rather than explicit wheel paths so
+the same invocation works from both sh (Linux) and cmd.exe (Windows),
+which doesn't glob `*.whl` itself.
+"""
+
+import argparse
+import re
+import subprocess
+import sys
+import tempfile
+from pathlib import Path
+
+
+def strip_dependency(wheel_path: Path, dependency_name: str) -> None:
+    dest_dir = wheel_path.parent
+
+    with tempfile.TemporaryDirectory() as tmp:
+        tmp = Path(tmp)
+        # Shell out to `wheel`'s CLI rather than importing wheel.cli.unpack/
+        # pack directly: wheel 0.46 made that package private with no
+        # compat shim (it's wheel._commands now, and could move again) -
+        # `python -m wheel unpack`/`pack` is the interface it actually
+        # keeps stable across versions.
+        subprocess.run(
+            [sys.executable, "-m", "wheel", "unpack", str(wheel_path), "--dest", str(tmp)],
+            check=True,
+        )
+        (unpacked_dir,) = tmp.iterdir()
+
+        dist_info = next(unpacked_dir.glob("*.dist-info"))
+        metadata_path = dist_info / "METADATA"
+        text = metadata_path.read_text(encoding="utf-8")
+
+        pattern = re.compile(rf"^Requires-Dist: {re.escape(dependency_name)}(\W.*)?$\n", re.MULTILINE)
+        new_text, count = pattern.subn("", text)
+        if count == 0:
+            raise SystemExit(f"'{dependency_name}' Requires-Dist not found in {wheel_path.name}; nothing to strip")
+
+        metadata_path.write_text(new_text, encoding="utf-8")
+
+        # Repacking to the same directory overwrites wheel_path in place:
+        # name/version/tags are unchanged, so the output filename matches,
+        # and by this point everything's already been read out of it.
+        result = subprocess.run(
+            [sys.executable, "-m", "wheel", "pack", str(unpacked_dir), "--dest-dir", str(dest_dir)],
+            check=True,
+            capture_output=True,
+            text=True,
+        )
+        print(result.stdout, end="")
+
+    # Sanity-check the output path wheel pack reports against wheel_path
+    # (parsed from its own report, not re-globbed: dest_dir may hold other
+    # wheels sharing this filename prefix, e.g. one per Python version).
+    match = re.search(r"^Repacking wheel as (?P<path>.+)\.\.\.", result.stdout, re.MULTILINE)
+    if match is None:
+        raise SystemExit(f"Couldn't parse the output wheel path from `wheel pack`'s output: {result.stdout!r}")
+    out_path = Path(match.group("path"))
+    if out_path != wheel_path:
+        raise SystemExit(f"Expected repacking to overwrite {wheel_path}, but it wrote {out_path} instead")
+
+
+def main():
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("wheel_dir", type=Path, help="Directory of wheel(s) to process in place")
+    parser.add_argument("--dependency", default="mkl", help="Dependency name to strip (default: mkl)")
+    args = parser.parse_args()
+
+    for wheel_path in sorted(args.wheel_dir.glob("*.whl")):
+        strip_dependency(wheel_path, args.dependency)
+        print(f"stripped '{args.dependency}' from {wheel_path.name}", file=sys.stderr)
+
+
+if __name__ == "__main__":
+    main()

.github/workflows/python-package-conda.yml

@@ -16,130 +16,115 @@ jobs:
       fail-fast: False
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: ["3.11", "3.12", "3.13", "3.14"]
-        mkl-version: ['2024', '2025']
+        python-version: ["3.12", "3.13", "3.14"]
+        mkl-version: ["2025", "2026"]
         free-threaded: [true, false]
         include:
           - os: ubuntu-latest
             python-version: "3.12"
-            mkl-version: "2024"
+            mkl-version: "2025"
             coverage: true
           - os: macos-15-intel
-            python-version: "3.11"
+            python-version: "3.12"
+            # Intel has not published MKL for macOS past 2023.2.
             mkl-version: "2023"
             free-threaded:
           - os: macos-15-intel
-            python-version: "3.12"
+            python-version: "3.13"
             mkl-version: "2023"
             free-threaded:
         exclude:
-          - python-version: "3.11"
-            free-threaded: true
+          # Free-threaded builds don't exist prior to Python 3.13.
           - python-version: "3.12"
             free-threaded: true
+          # Don't build free-threaded versions for experimental Python 3.13.
           - python-version: "3.13"
             free-threaded: true
-            mkl-version: "2025"
-          - python-version: "3.14"
-            mkl-version: "2025"
 
     steps:
-    - uses: actions/checkout@v5
-      with:
-        fetch-depth: 0
-
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: "3.13"
-
-    - name: Create Conda environment file
-      run: |
-        python -m pip install pyyaml
-        python .github/make_ci_environ.py
-      env:
-        PYTHON_VERSION: ${{ matrix.python-version}}
-        MKL_VERSION: ${{ matrix.mkl-version }}
-        FREE_THREADED: ${{ matrix.free-threaded && 'true' || 'false' }}
-        DO_COVERAGE: ${{ matrix.coverage && 'true' || 'false' }}
-        ENV_NAME: pydiso-ci
-
-    - name: Setup Conda
-      uses: conda-incubator/setup-miniconda@v3
-      with:
-        auto-update-conda: true
-        environment-file: environment_ci.yml
-        activate-environment: pydiso-ci
-
-    - name: Conda information
-      run: |
-        conda info
-        conda list
-        conda config --show
-
-    - name: Install Our Package
-      run: |
-        python -m pip install --no-build-isolation --verbose --editable . \
-          --config-setting=compile-args=-v \
-          ${{ matrix.coverage && '--config-settings=setup-args="-Db_coverage=true"' || ''}} \
-          ${{ matrix.os == 'windows-latest' && '--config-settings=setup-args="-Dvsenv=true"' || ''}}
+      - uses: actions/checkout@v7
+        with:
+          fetch-depth: 0
 
-    - name: Run Tests
-      run: |
-        ${{ matrix.coverage && 'coverage run -m' || '' }} pytest -s -v
-        ${{ matrix.coverage && 'coverage xml' || '' }}
+      - name: Set up Python
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+
+      - name: Create Conda environment file
+        run: |
+          python -m pip install pyyaml
+          python .github/make_ci_environ.py
+        env:
+          PYTHON_VERSION: ${{ matrix.python-version}}
+          MKL_VERSION: ${{ matrix.mkl-version }}
+          FREE_THREADED: ${{ matrix.free-threaded && 'true' || 'false' }}
+          DO_COVERAGE: ${{ matrix.coverage && 'true' || 'false' }}
+          ENV_NAME: pydiso-ci
+
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v4
+        with:
+          auto-update-conda: true
+          environment-file: environment_ci.yml
+          activate-environment: pydiso-ci
+
+      - name: Conda information
+        run: |
+          conda info
+          conda list
+          conda config --show
+
+      - name: Install Our Package
+        run: |
+          # --no-deps: deps come from the conda env above, as conda-forge
+          # would. Opt out of [tool.meson-python]'s unconditional
+          # limited-API target for 3.14t specifically (no stable ABI
+          # exists before 3.15) - checked by version, not just
+          # free-threaded, so a future 3.15t entry isn't caught too.
+          python -m pip install --no-build-isolation --no-deps --verbose --editable . \
+            --config-setting=compile-args=-v \
+            ${{ matrix.coverage && '--config-settings=setup-args="-Db_coverage=true"' || ''}} \
+            ${{ matrix.os == 'windows-latest' && '--config-settings=setup-args="-Dvsenv=true"' || ''}} \
+            ${{ matrix.python-version == '3.14' && matrix.free-threaded && '--config-settings=setup-args="-Dpython.allow_limited_api=false"' || ''}}
+
+      - name: Run Tests
+        run: |
+          ${{ matrix.coverage && 'coverage run -m' || '' }} pytest -s -v
+          ${{ matrix.coverage && 'coverage xml' || '' }}
+
+      - name: Upload coverage
+        if: ${{ matrix.coverage }}
+        uses: codecov/codecov-action@v7
+        with:
+          verbose: true # optional (default = false)
+          token: ${{ secrets.CODECOV_TOKEN }} # required
 
-    - name: Upload coverage
-      if: ${{ matrix.coverage }}
-      uses: codecov/codecov-action@v4
-      with:
-        verbose: true # optional (default = false)
-        token: ${{ secrets.CODECOV_TOKEN }} # required
+  build-and-test-pypi-mkl:
+    name: Testing (Python ${{ matrix.python-version }}, on ${{ matrix.os }}, with PyPI MKL)
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: False
+      matrix:
+        # macOS excluded: Intel's PyPI mkl-devel wheel (frozen at 2023.2)
+        # is missing a symlink CMake needs, so MKL fails to import. See README.
+        os: [ubuntu-latest, windows-latest]
+        python-version: ["3.12", "3.13", "3.14"]
 
-  build_sdist:
-    name: Build source distribution
-    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
 
-      - name: Build sdist
-        run: pipx run build --sdist -Csetup-args="-Ddist_ignore_mkl_dep=true"
-
-      - uses: actions/upload-artifact@v4
+      - name: Set up Python
+        uses: actions/setup-python@v7
         with:
-          name: cibw-sdist
-          path: dist/*.tar.gz
-
-  release:
-    needs: [
-      build_sdist
-    ]
-    runs-on: ubuntu-latest
-    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-    - uses: actions/download-artifact@v4
-      with:
-        # unpacks all CIBW artifacts into dist/
-        pattern: cibw-*
-        path: dist
-        merge-multiple: true
+          python-version: ${{ matrix.python-version }}
 
-    - name: Release to github
-      uses: softprops/action-gh-release@v2
-      with:
-        files: dist/*
-        generate_release_notes: true
-        prerelease: false
+      - name: Install our package against PyPI MKL
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --verbose ".[test]"
 
-    - name: Upload wheels to pypi
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
-        skip-existing: true
-        packages-dir: ./dist/
+      - name: Run Tests
+        run: pytest -s -v