Maint fixes (#164)

* FIX: workaround for torch FutureWarning

- MNE-ICALabel causes triggers a warning by Pytorch
- I submitted a fix to icalabel, but...
- in the meantime let's filter the warning in our tests. Which can be removed once mne-icalabe v0.7 is released

* FIX: catch warning that is rightfully thrown by pipeline

- since we are downsampling our test file that has a non-integer sfreq, a warning is thrown and that's okay. If it isn't thrown in the future this test will fail to notify us

* FIX: don't manually install packages in CI's. rely on requirements files

* FIX: Skip failing test_TopoViz for now.

- We have marked this test for failure for a while now, and the failing test causes our CI's to hang for a long time (over ten minutes sometimes). I am makring for skip so that our CI's aren't dramatically slowed down, until we fix it.

* FIX: flake

* FIX: more torch warning fixes

* FIX: try another variation of glob in FutureWarning

* FIX: try again...

* MAINT: update GHA

* FIX: try to ignore the warning globally

.github/workflows/test_pipeline.yml

@@ -12,9 +12,9 @@ jobs:
   test:
     runs-on: macos-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.9"
       - name: Install Pylossless & Deps
@@ -23,10 +23,6 @@ jobs:
         run: pip install -r requirements_testing.txt
       - name: Install QC depedencies
         run: pip install -r requirements_qc.txt
-      - name: install openneuro
-        run: pip install openneuro-py
-      - name: install pytorch
-        run: pip install torch
       - name: Test Pipeline
         run: |
           coverage run -m pytest

pylossless/conftest.py

@@ -14,6 +14,9 @@
 import pytest
 
 
+# XXX: This is a temporary fix to suppress a warning from MNE-ICAlabel
+# This can be removed once MNE-ICAlabel 0.7 is released
+@pytest.mark.filterwarnings("ignore::FutureWarning")
 @pytest.fixture(scope="session")
 def pipeline_fixture():
     """Return a namedTuple containing MNE eyetracking raw data and events."""

pylossless/dash/tests/test_topo_viz.py

@@ -68,7 +68,7 @@ def test_GridTopoPlot():
 
 # chromedriver: https://chromedriver.storage.googleapis.com/
 #               index.html?path=114.0.5735.90/
-@pytest.mark.xfail(reason="an issue with chromedriver causes failure. Need to debug.")
+@pytest.mark.skip(reason="an issue with chromedriver causes failure. Need to debug.")
 def test_TopoViz(dash_duo):
     """Test TopoViz."""
     raw, ica = get_raw_ica()

pylossless/tests/test_rejection.py

@@ -7,6 +7,8 @@
 import pylossless as ll
 
 
+# XXX: This filter can be removed once MNE-ICAlabel 0.7 is released
+@pytest.mark.filterwarnings("ignore::FutureWarning")
 @pytest.mark.parametrize("clean_ch_mode", [None, "drop", "interpolate"])
 def test_rejection_policy(clean_ch_mode, pipeline_fixture):
     """Test the rejection policy."""

pylossless/tests/test_simulated.py

@@ -26,7 +26,8 @@
 @pytest.mark.parametrize("pipeline", [(pipeline)])
 def test_simulated_raw(pipeline):
     """Test pipeline on simulated EEG."""
-    pipeline._check_sfreq()
+    with pytest.warns(RuntimeWarning, match="sampling frequency"):
+        pipeline._check_sfreq()
     # This file should have been downsampled
     assert pipeline.raw.info["sfreq"] == 600
     # FIND NOISY EPOCHS

pyproject.toml

@@ -27,4 +27,6 @@ filterwarnings = ["error",
  # deprecation in dash-testing that needs to be reported
 "ignore::DeprecationWarning",
 # TODO MNE deprecation that wont effect us. remove if we ever bump to mne 1.7
-"ignore:The current default of copy=False will change to copy=True in 1.7.",]
+"ignore:The current default of copy=False will change to copy=True in 1.7.",
+"ignore:You are using",
+]