FIX: Test environments with only torch or onnxruntime installed (#271)

* Drop torch and onnx variants from text extras

* Test CI's in environments with either torch or onnxruntime installed

* TST: import or skip

* FIX: oops need to capture output of importorskip

* FIX: dep

* DOC: Note for Megnet users

* FIX, DOC: flaky link

* Revert "FIX, DOC: flaky link"

This reverts commit 49d678f.

* TST: Add backend job

* Update doc/install.rst

Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

* FIX, STY: Flakes

---------

Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

Author: scott-huberty

.github/workflows/pytest.yaml

@@ -34,7 +34,7 @@ jobs:
       - name: Install package
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools
-          python -m pip install --progress-bar off .[test]
+          python -m pip install --progress-bar off ".[test,torch,onnx]"
       - run: mne_icalabel-sys_info --developer
       - run: pytest mne_icalabel --cov=mne_icalabel --cov-report=xml --cov-config=pyproject.toml
       - uses: codecov/codecov-action@v5
@@ -64,7 +64,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools
-          python -m pip install --progress-bar off .[test]
+          python -m pip install --progress-bar off ".[test,torch,onnx]"
           python -m pip install --progress-bar off --upgrade git+https://github.com/mne-tools/mne-python
           python -m pip install --progress-bar off --upgrade git+https://github.com/mne-tools/mne-bids
           python -m pip install --progress-bar off --upgrade --pre --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --timeout=180 numpy scipy matplotlib
@@ -77,3 +77,35 @@ jobs:
           name: codecov-umbrella  # optional
           token: ${{ secrets.CODECOV_TOKEN }}
           verbose: true  # optional (default = false)
+
+  pytest-backend:
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu]
+        backend: ["torch", "onnx"]
+        python-version: ["3.12"]
+    name: ${{ matrix.os }} - ${{ matrix.backend }} backend - py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}-latest
+    steps:
+      - uses: actions/checkout@v5
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: pyvista/setup-headless-display-action@main
+        with:
+          qt: true
+      - name: Install package
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools
+          python -m pip install --progress-bar off ".[test,${{ matrix.backend }}]";
+      - run: mne_icalabel-sys_info --developer
+      - run: pytest mne_icalabel --cov=mne_icalabel --cov-report=xml --cov-config=pyproject.toml
+      - uses: codecov/codecov-action@v5
+        with:
+          files: ./coverage.xml
+          flags: unittests  # optional
+          name: codecov-umbrella  # optional
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true  # optional (default = false)

doc/install.rst

@@ -43,6 +43,12 @@ Methods
 
             pip install torch
             pip install onnxruntime
+        
+        .. note::
+
+            If you are working with MEG data and plan to use the MEGnet model, e.g.
+            :func:`mne_icalabel.megnet.megnet_label_components`, you *must* install
+            ``onnxruntime``, and do not need to install ``torch``.
 
         Additional dependencies can be installed with different keywords:
 

mne_icalabel/iclabel/network/tests/test_network.py

@@ -2,13 +2,14 @@
 
 import numpy as np
 import pytest
-import torch
 from scipy.io import loadmat
 
 from mne_icalabel.datasets import icalabel
 from mne_icalabel.iclabel.network.utils import _format_input
 from mne_icalabel.utils._tests import requires_module
 
+torch = pytest.importorskip("torch")
+
 dataset_path = icalabel.data_path() / "iclabel"
 
 

mne_icalabel/megnet/label_components.py

@@ -4,13 +4,14 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-import onnxruntime as ort
 from mne.io import BaseRaw
 from mne.preprocessing import ICA
 
+from ..utils._imports import import_optional_dependency
 from .features import get_megnet_features
 
 if TYPE_CHECKING:
+    import onnxruntime as ort
     from numpy.typing import NDArray
 
 _MODEL_PATH: str = files("mne_icalabel.megnet") / "assets" / "megnet.onnx"
@@ -43,6 +44,7 @@ def megnet_label_components(raw: BaseRaw, ica: ICA) -> NDArray:
     ----------
     .. footbibliography::
     """
+    ort = import_optional_dependency("onnxruntime")
     time_series, topomaps = get_megnet_features(raw, ica)
 
     # sanity-checks

mne_icalabel/megnet/tests/test_label_components.py

@@ -5,7 +5,6 @@
 
 import mne
 import numpy as np
-import onnxruntime as ort
 import pytest
 from mne.io.base import BaseRaw
 from mne.preprocessing.ica import ICA
@@ -17,6 +16,8 @@
     megnet_label_components,
 )
 
+ort = pytest.importorskip("onnxruntime")
+
 if TYPE_CHECKING:
     from mne.io import BaseRaw
     from mne.preprocessing import ICA

pyproject.toml

@@ -113,8 +113,6 @@ test = [
   'mne-bids>=0.14',
   'mne-icalabel[gui]',
   'mne-icalabel[ica]',
-  'mne-icalabel[onnx]',
-  'mne-icalabel[torch]',
   'pandas',
   'pymatreader',
   'PyQt6',