Use Pixi in macOS-intel CI

.github/workflows/tests.yml

@@ -81,7 +81,7 @@ jobs:
             kind: pip
           - os: macos-15-intel  # Intel
             python: '3.13'
-            kind: pip
+            kind: pixi
           - os: ubuntu-latest
             python: '3.12'
             kind: minimal
@@ -121,9 +121,26 @@ jobs:
           python-version: ${{ matrix.python }}
         if: startswith(matrix.kind, 'pip') || matrix.kind == 'minimal'
         id: setup-python
+      # Python (if pixi)
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          manifest-path: tools/ci/macos-intel/pixi.toml
+          # https://github.com/prefix-dev/setup-pixi/issues/139
+          activate-environment: true
+          frozen: true
+        if: matrix.kind == 'pixi'
       # Workaround macOS path behavior with login shells (which puts system Python first)
-      - run: echo "export PATH=\"$(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:

tools/ci/macos-intel/pixi.toml

@@ -0,0 +1,76 @@
+# THIS FILE IS AUTO-GENERATED BY tools/hooks/update_environment_file.py AND WILL BE OVERWRITTEN
+[workspace]
+authors = ["Scott Huberty <seh33@uw.edu>"] # TODO: fix this
+channels = ["conda-forge"]
+name = "mne"
+platforms = ["osx-64"]
+version = "0.1.0"
+
+[tasks]
+
+[dependencies]
+python = "3.13.*"
+antio = ">=0.5.0"
+curryreader = ">=0.1.2"
+darkdetect = "*"
+decorator = "*"
+defusedxml = "*"
+dipy = "*"
+edfio = ">=0.4.10"
+eeglabio = "*"
+filelock = ">=3.18.0"
+h5io = ">=0.2.4"
+h5py = "*"
+imageio = ">=2.6.1"
+imageio-ffmpeg = ">=0.4.1"
+ipyevents = "*"
+ipympl = "*"
+ipython = "!=8.7.0"
+ipywidgets = "*"
+jinja2 = "*"
+joblib = "*"
+jupyter = "*"
+lazy_loader = ">=0.3"
+mamba = "*"
+matplotlib = ">=3.8"
+mffpy = ">=0.5.7"
+mne-qt-browser = "*"
+nibabel = "*"
+nilearn = "*"
+nomkl = "*"
+numba = "*"
+numpy = ">=1.26,<3"
+openmeeg = ">=2.5.7"
+packaging = "*"
+pandas = ">=2.2"
+pillow = "*"
+pip = "*"
+pooch = ">=1.5"
+pyarrow = "*"
+pybv = "*"
+pymatreader = "*"
+pyside6 = "==6.9.2"
+python-neo = "*"
+python-picard = "*"
+pyvista = ">=0.43"
+pyvistaqt = ">=0.11"
+qdarkstyle = "!=3.2.2"
+qtpy = "*"
+scikit-learn = ">=1.4"
+scipy = ">=1.12"
+sip = "*"
+snirf = "*"
+statsmodels = "*"
+threadpoolctl = "*"
+tqdm = "*"
+traitlets = "*"
+trame = "*"
+trame-vtk = "*"
+trame-vuetify = "*"
+vtk = "==9.5.1"
+xlrd = "*"
+
+[pypi-dependencies]
+nest-asyncio2 = "*"
+pymef = "*"
+pyobjc-framework-cocoa = ">=5.2.0"

tools/github_actions_dependencies.sh

@@ -36,6 +36,10 @@ elif [[ "${MNE_CI_KIND}" == "pip" ]]; then
 	GROUP="test_extra"
 	EXTRAS="[full-pyside6]"
 	python -m pip install --upgrade pip setuptools
+elif [[ "${MNE_CI_KIND}" == "pixi" ]]; then
+	GROUP="test_extra"
+	EXTRAS="[hdf5]"
+	INSTALL_ARGS=""
 else
 	test "${MNE_CI_KIND}" == "pip-pre"
 	python -m pip install $STD_ARGS pip setuptools

tools/github_actions_download.sh

@@ -1,5 +1,6 @@
 #!/bin/bash -ef
 
+# TODO: I think that DEPS is cruft. Its not set anywhere??
 if [ "${MNE_CI_KIND}" != "minimal" ]; then
 	python -c 'import mne; mne.datasets.testing.data_path(verbose=True)';
 	python -c "import mne; mne.datasets.misc.data_path(verbose=True)";

tools/github_actions_env_vars.sh

@@ -25,6 +25,16 @@ elif [[ "$MNE_CI_KIND" == "conda" ]]; then
         echo "PYTEST_DEBUG_TEMPROOT=/tmp" | tee -a $GITHUB_ENV
     fi
     echo "MNE_QT_BACKEND=PySide6" | tee -a $GITHUB_ENV
+# NON-DRY but just gonna get it working and then refactor.
+elif [[ "$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
+    echo "MNE_TEST_ALLOW_SKIP=.*(Requires (spm|brainstorm) dataset|CUDA not|PySide6 causes segfaults|Accelerate|Flakey verbose behavior).*" | 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_test.sh

@@ -2,6 +2,7 @@
 
 set -eo pipefail
 
+
 if [[ "${CI_OS_NAME}" == "ubuntu"* ]]; then
   CONDITION="not (ultraslowtest or pgtest)"
 elif [[ "${CI_OS_NAME}" == "macos"* ]]; then

tools/github_actions_verify_python.sh

@@ -21,6 +21,8 @@ elif [[ "${MNE_CI_KIND}" == "old" ]]; then
 	WANT="mne-python/mne-python/.venv/bin"
 elif [[ "${MNE_CI_KIND}" == "pip" ]] || [[ "${MNE_CI_KIND}" == "pip-pre" ]] || [[ "${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 +1,36 @@
+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+import tomlkit
+import tomllib
+
+with open("../pyproject.toml", "rb") as fid:
+    foo = tomllib.load(fid)
+
+# 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=foo["project"]["name"],
+    platforms=["osx-64"],
+    version="0.1.0",
+)
+dependencies = foo["project"]["dependencies"]
+dependencies.extend(foo["dependency-groups"]["test"])
+dependencies.extend(foo["dependency-groups"]["test_extra"])
+dependencies.extend(foo["project"]["optional-dependencies"]["hdf5"])
+dependencies.extend(foo["project"]["optional-dependencies"]["full-no-qt"])
+dependencies.extend(foo["project"]["optional-dependencies"]["full-pyside6"])
+dependencies = list(
+    filter(lambda x: isinstance(x, str) and "mne[" not in x, dependencies)
+)
+dependencies = sorted(set(dependencies))
+
+out = {"workspace": workspace, "dependencies": dependencies, "pypi-dependencies": []}
+
+with open("pixi-new.toml", "w") as fid:
+    tomlkit.dump(out, fid, sort_keys=True)