[MAINT] Fix failing unit tests & update CI packages (mne-tools#157)

* [MAINT] Specify data copy behaviour * [MAINT] Updated required MNE version * Revert "[MAINT] Updated required MNE version" This reverts commit bfb175e. * [MAINT] Specify data copy behaviour for MNE>1.5 * [MAINT] Add missing PyQt6 * Revert "[MAINT] Add missing PyQt6" This reverts commit 5836037. * [MAINT] Add missing PyQt6 to CircleCI * [MAINT] Add missing pyvistaqt to CircleCI * [MAINT] Switch unit tests Python 3.8 to 3.9 * [MAINT] Add missing sphinx extension to CircleCI * [MAINT] Add missing sphinx extension to CircleCI * [MAINT] Add missing sphinx extensions to CircleCI * [MAINT] Add missing sphinx extensions to CircleCI * [MAINT] Add missing doc requirements to CircleCI
tsbinns · Nov 25, 2023 · 1b64fc1 · 1b64fc1
1 parent 8bebc62
commit 1b64fc1
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Showing 7 changed files with 34 additions and 8 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -81,6 +81,7 @@ jobs:
               curl https://raw.githubusercontent.com/mne-tools/mne-python/main/tools/circleci_dependencies.sh -o circleci_dependencies.sh
               chmod +x circleci_dependencies.sh
               ./circleci_dependencies.sh
+              pip install -r requirements_doc.txt
 
         - save_cache:
             key: pip-cache

diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
@@ -44,7 +44,7 @@ jobs:
         include:
           # An old one
           - os: ubuntu-latest
-            python-version: "3.8"
+            python-version: "3.9"
     steps:
       - uses: actions/checkout@v4
       - uses: pyvista/setup-headless-display-action@main
@@ -103,7 +103,7 @@ jobs:
       matrix:
         include:
           - os: ubuntu-latest
-            python-version: "3.8"
+            python-version: "3.9"
             mne-version: mne-main
           - os: ubuntu-latest
             python-version: "3.11"

diff --git a/mne_connectivity/envelope.py b/mne_connectivity/envelope.py
@@ -5,6 +5,8 @@
 #
 # License: BSD (3-clause)
 
+import inspect
+
 import numpy as np
 from mne import BaseEpochs
 from mne.filter import next_fast_len
@@ -100,7 +102,11 @@ def envelope_correlation(data, names=None,
             data.add_annotations_to_metadata(overwrite=True)
         metadata = data.metadata
         # get the actual data in numpy
-        data = data.get_data()
+        # XXX: remove logic once support for mne<1.6 is dropped
+        kwargs = dict()
+        if "copy" in inspect.getfullargspec(data.get_data).kwonlyargs:
+            kwargs["copy"] = False
+        data = data.get_data(**kwargs)
     else:
         metadata = None
 

diff --git a/mne_connectivity/spectral/epochs.py b/mne_connectivity/spectral/epochs.py
@@ -201,7 +201,11 @@ def _check_rank_input(rank, data, indices):
         rank = np.zeros((2, len(indices[0])), dtype=int)
 
         if isinstance(data, BaseEpochs):
-            data_arr = data.get_data()
+            # XXX: remove logic once support for mne<1.6 is dropped
+            kwargs = dict()
+            if "copy" in inspect.getfullargspec(data.get_data).kwonlyargs:
+                kwargs["copy"] = False
+            data_arr = data.get_data(**kwargs)
         else:
             data_arr = data
 

diff --git a/mne_connectivity/spectral/time.py b/mne_connectivity/spectral/time.py
@@ -4,6 +4,8 @@
 #
 # License: BSD (3-clause)
 
+import inspect
+
 import numpy as np
 import xarray as xr
 from mne.epochs import BaseEpochs
@@ -325,7 +327,6 @@ def spectral_connectivity_time(data, freqs, method='coh', average=False,
         sfreq = data.info['sfreq']
         events = data.events
         event_id = data.event_id
-        n_epochs, n_signals, n_times = data.get_data().shape
         # Extract metadata from the Epochs data structure.
         # Make Annotations persist through by adding them to the metadata.
         metadata = data.metadata
@@ -338,7 +339,12 @@ def spectral_connectivity_time(data, freqs, method='coh', average=False,
         if hasattr(data, 'annotations') and not annots_in_metadata:
             data.add_annotations_to_metadata(overwrite=True)
         metadata = data.metadata
-        data = data.get_data()
+        # XXX: remove logic once support for mne<1.6 is dropped
+        kwargs = dict()
+        if "copy" in inspect.getfullargspec(data.get_data).kwonlyargs:
+            kwargs["copy"] = False
+        data = data.get_data(**kwargs)
+        n_epochs, n_signals, n_times = data.shape
     else:
         data = np.asarray(data)
         n_epochs, n_signals, n_times = data.shape

diff --git a/mne_connectivity/vector_ar/var.py b/mne_connectivity/vector_ar/var.py
@@ -1,3 +1,5 @@
+import inspect
+
 import numpy as np
 import scipy
 from scipy.linalg import sqrtm
@@ -144,7 +146,12 @@ def vector_auto_regression(
         metadata = data.metadata
 
         # get the actual data in numpy
-        data = data.get_data()
+        # get the actual data in numpy
+        # XXX: remove logic once support for mne<1.6 is dropped
+        kwargs = dict()
+        if "copy" in inspect.getfullargspec(data.get_data).kwonlyargs:
+            kwargs["copy"] = False
+        data = data.get_data(**kwargs)
     else:
         metadata = None
 

diff --git a/requirements_doc.txt b/requirements_doc.txt
@@ -12,4 +12,6 @@ sphinx-autodoc-typehints
 sphinxcontrib-bibtex
 git+https://github.com/mne-tools/mne-bids@main
 pooch
-mne-qt-browser
+mne-qt-browser
+PyQt6
+pyvistaqt