Use Pixi in macOS-intel CI

.github/workflows/scheduled_updates.yml

@@ -75,6 +75,14 @@ jobs:
             echo "dirty=true" >> $GITHUB_OUTPUT
           fi
         id: status
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.9.4
+        if: steps.status.outputs.dirty == 'true'
+      - name: Update pixi.toml and pixi.lock for macos-intel CI job
+        run: |
+          pixi run python tools/write-pixi-toml.py
+          pixi lock --no-install --manifest-path tools/ci/macos-intel/
+        if: steps.status.outputs.dirty == 'true'
       - uses: j178/prek-action@v3.0.0
         if: steps.status.outputs.dirty == 'true'
       - name: Create PR

.github/workflows/tests.yml

@@ -61,7 +61,7 @@ jobs:
             kind: pip
           - os: macos-15-intel  # Intel
             python: '3.13'
-            kind: pip
+            kind: pixi
           - os: ubuntu-latest
             python: '3.12'
             kind: minimal
@@ -104,9 +104,26 @@ jobs:
           python-version: ${{ matrix.python }}
         if: startswith(matrix.kind, 'pip') || matrix.kind == 'minimal'
         id: setup-python
+      # Python (if pixi)
+      - uses: prefix-dev/setup-pixi@v0.10.0
+        with:
+          manifest-path: tools/ci/macos-intel/pixi.toml
+          # https://github.com/prefix-dev/setup-pixi/issues/139
+          activate-environment: true
+          frozen: true
+        if: matrix.kind == 'pixi'
       # Workaround macOS path behavior with login shells (which puts system Python first)
-      - run: echo "export PATH=\"$(dirname ${{ steps.setup-python.outputs.python-path }}):$PATH\"" | tee -a ~/.bash_profile  # zizmor: ignore[template-injection]
-        if: startswith(matrix.kind, 'pip') && startswith(matrix.os, 'macos')
+      - run: |  # zizmor: ignore[template-injection]
+          if [[ $MNE_CI_KIND == "pip" ]]; then
+            prepend_path="$(dirname ${{ steps.setup-python.outputs.python-path }})"
+          elif [[ $MNE_CI_KIND == "pixi" ]]; then
+            prepend_path="${{ github.workspace }}/tools/ci/macos-intel/.pixi/envs/default/bin"
+          else
+            echo "Unsupported CI Kind: $MNE_CI_KIND"
+            exit 1
+          fi
+          echo "export PATH=\"$prepend_path:$PATH\"" | tee -a ~/.bash_profile
+        if: (startswith(matrix.kind, 'pip') || matrix.kind == 'pixi') && startswith(matrix.os, 'macos')
       # Python (if conda)
       - uses: mamba-org/setup-micromamba@v3
         with:
@@ -130,6 +147,7 @@ jobs:
       - run: bash ./tools/github_actions_verify_python.sh "${{ matrix.python }}"
       - run: bash ./tools/github_actions_dependencies.sh
         timeout-minutes: 10
+        if: matrix.kind != 'pixi'
       - name: Check 'old' CI environment
         uses: mne-tools/mne-tools/actions/check-environment@main
         with:

tools/ci/macos-intel/pixi.toml

@@ -0,0 +1,91 @@
+# THIS FILE IS AUTO-GENERATED BY tools/write_pixi_toml.py AND WILL BE OVERWRITTEN
+
+[workspace]
+authors = ["MNE-Python contributors"]
+channels = ["conda-forge"]
+name = "mne"
+platforms = ["osx-64"]
+version = "0.1.0"
+
+[dependencies]
+antio = ">=0.5.0"
+codespell = "*"
+curryreader = ">=0.1.2"
+darkdetect = "*"
+decorator = ">=5.1"
+defusedxml = "*"
+dipy = ">=1.9"
+edfio = ">=0.4.10"
+eeglabio = "*"
+filelock = ">=3.18.0"
+h5io = ">=0.2.4"
+h5py = ">=2.4"
+imageio = ">=2.6.1"
+imageio-ffmpeg = ">=0.4.1"
+ipyevents = "*"
+ipympl = "*"
+ipython = ">=8.20"
+ipywidgets = "*"
+jinja2 = ">=3.1"
+joblib = ">=0.8"
+jupyter = "*"
+jupyter_client = "*"
+lazy_loader = ">=0.3"
+matplotlib = ">=3.9"
+mffpy = ">=0.11.0"
+nbclient = "*"
+nest-asyncio2 = "*"
+nibabel = ">=5.2"
+nilearn = ">=0.10"
+nitime = ">=0.7"
+numba = ">=0.60"
+numpy = "<3,>=2.0"
+numpydoc = ">=1.6"
+openmeeg = ">=2.5.7"
+packaging = "*"
+pandas = "!=3.0.4,>=2.2"
+pillow = ">=10.2"
+pip = ">=25.1"
+pooch = ">=1.5"
+pre-commit = "*"
+pyarrow = "*"
+pybv = "*"
+pymatreader = "*"
+pyobjc-framework-Cocoa = ">=5.2.0"
+pyside6 = ">=6.11.1"
+pytest = "!=9.1.0,>=8.0"
+pytest-cov = ">=4.1"
+pytest-qt = ">=4.3"
+pytest-rerunfailures = "*"
+pytest-timeout = ">=2.2"
+pytest-xdist = ">=3.6.1"
+python-neo = "*"
+python-picard = ">=0.4"
+pyvista = ">=0.44"
+pyvistaqt = ">=0.11"
+qdarkstyle = "!=3.2.2"
+qtpy = "*"
+rcssmin = ">=1.1"
+refleak = ">=0.2.1"
+ruff = ">=0.1"
+scikit-learn = ">=1.5"
+scipy = ">=1.14"
+sip = "*"
+snirf = "*"
+statsmodels = ">=0.6"
+threadpoolctl = "*"
+tqdm = ">=4.66"
+traitlets = "*"
+trame = "*"
+trame-pyvista = "*"
+trame-vtk = "*"
+trame-vuetify = "!=3.2.3"
+twine = "*"
+vtk = ">=9.2"
+vulture = "*"
+xlrd = "*"
+python = "3.13.*"
+
+[pypi-dependencies]
+mne-qt-browser = "*"
+pymef = "*"

tools/github_actions_env_vars.sh

@@ -61,6 +61,14 @@ elif [[ "$MNE_CI_KIND" == "conda" ]]; then
     echo "MNE_LOGGING_LEVEL=warning" | tee -a $GITHUB_ENV
     echo "MNE_TEST_ALLOW_SKIP=.*(on conda|Requires (spm|brainstorm|misc) dataset|CUDA not|Flakey verbose behavior|PySide6 causes segfaults|SCIPY_ARRAY_API).*" | tee -a $GITHUB_ENV
     echo "MNE_QT_BACKEND=PySide6" | tee -a $GITHUB_ENV
+elif [[ "$MNE_CI_KIND" == "pixi" ]]; then
+    echo "Setting env vars for $MNE_CI_KIND"
+    echo "MNE_LOGGING_LEVEL=warning" | tee -a $GITHUB_ENV
+    echo "MNE_QT_BACKEND=PySide6" | tee -a $GITHUB_ENV
+    # Our cache_dir test has problems when the path is too long, so prevent it from getting too long
+    if [[ "$RUNNER_OS" == "macOS" ]]; then
+        echo "PYTEST_DEBUG_TEMPROOT=/tmp" | tee -a $GITHUB_ENV
+    fi
 else
     echo "✕ ERROR: Unrecognized MNE_CI_KIND=${MNE_CI_KIND}"
     exit 1

tools/github_actions_verify_python.sh

@@ -29,6 +29,8 @@ elif [[ "${MNE_CI_KIND}" == "old" ]]; then
 	WANT="mne-python/mne-python/.venv/bin"
 elif [[ "${MNE_CI_KIND}" == 'pip'* ]] || [[ "${MNE_CI_KIND}" == "minimal" ]]; then
 	WANT="/hostedtoolcache/"
+elif [[ "${MNE_CI_KIND}" == "pixi" ]]; then
+	WANT="mne-python/mne-python/tools/ci/macos-intel/.pixi/"
 else
 	echo "✕ ERROR: Unrecognized MNE_CI_KIND=${MNE_CI_KIND}"
 	exit 1

tools/write-pixi-toml.py

@@ -0,0 +1,102 @@
+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+from pathlib import Path
+
+import tomlkit
+import yaml
+from packaging.requirements import Requirement
+
+
+def pip_to_pixi(dependencies_list):
+    """Convert pip dependency specifier strings to a pixi-style dict."""
+    out = dict()
+    for dep in dependencies_list:
+        out[dep.name] = str(dep.specifier) if str(dep.specifier) != "" else "*"
+    return out
+
+
+pypi_dependencies = sorted(["mne-qt-browser", "pymef"])
+
+repo_root = Path(__file__).resolve().parent.parent
+tests_yaml_fpath = repo_root / ".github" / "workflows" / "tests.yml"
+pyproject_fpath = repo_root / "pyproject.toml"
+pyproject = tomlkit.loads(pyproject_fpath.read_bytes())
+outfile = repo_root / "tools" / "ci" / "macos-intel" / "pixi.toml"
+
+# handle naming differences between PyPI and conda-forge
+remapping = dict(neo="python-neo")
+
+# Specify the python version that our pixi job wants
+with open(tests_yaml_fpath) as fid:
+    test_yaml = yaml.safe_load(fid)
+
+foo = test_yaml["jobs"]["pytest"]["strategy"]["matrix"]["include"]
+for job in foo:
+    if job["os"] == "macos-15-intel":
+        python_version = job["python"]
+        # Pixi complains if we don't specify a patch version
+        if len(python_version.split(".")) <= 2:
+            python_version += ".*"
+        break
+
+# in keys: build-system, dependency-groups, project, tool
+# out keys: workspace, dependencies, pypi-dependencies (may need tasks)
+out = dict()
+workspace = dict(
+    authors=["MNE-Python contributors"],
+    channels=["conda-forge"],
+    name=pyproject["project"]["name"],
+    platforms=["osx-64"],
+    version="0.1.0",
+)
+dependencies = pyproject["project"]["dependencies"]
+dependencies.extend(pyproject["dependency-groups"]["dev"])
+dependencies.extend(pyproject["dependency-groups"]["test"])
+dependencies.extend(pyproject["dependency-groups"]["test_extra"])
+dependencies.extend(pyproject["project"]["optional-dependencies"]["hdf5"])
+dependencies.extend(pyproject["project"]["optional-dependencies"]["full-no-qt"])
+dependencies.extend(pyproject["project"]["optional-dependencies"]["full-pyside6"])
+# exclude recursive MNE deps
+dependencies = list(
+    filter(lambda x: isinstance(x, str) and "mne[" not in x, dependencies)
+)
+# strip out platform specifiers; for now this affects only pyobj-framework-cocoa, and
+# since this pixi.toml is destined for macos-intel job, we want it in there so we're
+# skipping writing the logic to parse the platform spec.
+for ix, dep in enumerate(dependencies):
+    if (split_ix := dep.find(";")) >= 0:
+        dependencies[ix] = dep[:split_ix].strip()
+# handle mismatch between names on PyPI and conda-forge
+dependencies = [remapping.get(dep, dep) for dep in dependencies]
+dependencies.sort()
+
+# exclude pypi-only deps
+dependencies = [Requirement(dep) for dep in dependencies]
+pypi_dependencies = [Requirement(dep) for dep in pypi_dependencies]
+
+dependencies = [
+    dep
+    for dep in dependencies
+    if dep.name not in {pdep.name for pdep in pypi_dependencies}
+]
+
+out = {
+    "workspace": workspace,
+    "dependencies": pip_to_pixi(dependencies),
+    "pypi-dependencies": pip_to_pixi(pypi_dependencies),
+}
+out["dependencies"].update(python=python_version)
+
+doc = tomlkit.document()
+doc.add(
+    tomlkit.comment(
+        "THIS FILE IS AUTO-GENERATED BY tools/write_pixi_toml.py AND WILL BE OVERWRITTEN"  # noqa E501
+    )
+)
+doc.update(out)
+# write the file
+outfile.parent.mkdir(parents=True, exist_ok=True)
+with open(outfile, "w") as fid:
+    tomlkit.dump(doc, fid, sort_keys=False)