Merge pull request #118 from coganlab/mac-port

Mac port

.github/workflows/Package.yml

@@ -4,17 +4,15 @@ on:
     branches: [ main ]
 
 jobs:
-  packaging:
+  build:
     runs-on: ubuntu-latest
-    permissions:
-      id-token: write  # IMPORTANT: mandatory for trusted publishing
     environment: release
     steps:
       - uses: actions/checkout@v4
       # Python
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.10'
           cache: 'pip'
       # Publish (moved to end of document later)
       - name: Build source distribution
@@ -27,10 +25,46 @@ jobs:
         with:
           name: python-package-distributions
           path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
       - name: Download all the dists
         uses: actions/download-artifact@v3
         with:
           name: python-package-distributions
           path: dist/
       - name: Publish package distributions to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  publish-to-testpypi:
+    name: Publish Python 🐍 distribution 📦 to TestPyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/ieeg
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/

.github/workflows/Python-CI.yml

@@ -24,12 +24,15 @@ jobs:
     strategy:
       matrix:
         include:
-        - os: ubuntu-latest
+        - os: windows-latest
           python: '3.12'
           kind: pip
-        - os: windows-latest
+        - os: macos-latest
           python: '3.11'
           kind: pip
+        - os: ubuntu-latest
+          python: '3.10'
+          kind: pip
     environment: release
     steps:
       - uses: actions/checkout@v4

envs/requirements.txt

@@ -1,5 +1,4 @@
 bids>=0.0
-EDFlib-Python
 mne
 mne-bids
 numpy

ieeg/calc/mat.py

@@ -627,7 +627,7 @@ def combine(self, levels: tuple[int, int]) -> 'LabeledArray':
         all_idx = ([slice(None) if i != levels[0] else sl for i in
                     range(self.ndim)] for sl in range(self.shape[levels[0]]))
 
-        arrs = [self.__array__()[*idx] for idx in all_idx]
+        arrs = [self.__array__()[tuple(idx)] for idx in all_idx]
         new_array = concatenate_arrays(arrs, axis=levels[1] - 1)
 
         return LabeledArray(new_array, new_labels, dtype=self.dtype)

ieeg/calc/scaling.py

@@ -6,8 +6,6 @@
 from mne.time_frequency import AverageTFR, EpochsTFR
 from mne.utils import logger, verbose
 
-TFR = EpochsTFR | AverageTFR
-
 
 def _log_rescale(baseline, mode='mean'):
     """Log the rescaling method."""
@@ -126,7 +124,7 @@ def _(line: BaseEpochs, baseline: BaseEpochs,
 
 @rescale.register
 @verbose
-def _(line: TFR, baseline: TFR,
+def _(line: EpochsTFR, baseline: EpochsTFR,
       mode: str = 'mean', copy: bool = False, picks: list = 'data',
       verbose=None) -> Epochs:
     """Rescale (baseline correct) Epochs"""
@@ -138,18 +136,32 @@ def _(line: TFR, baseline: TFR,
 
     # Average the baseline across epochs
     basedata = baseline.pick(picks)._data
-    axes = list(range(basedata.ndim))
 
-    # within channels
-    axes.pop(1)
+    # If time frequency then within frequency
+    axes = (0, 3)
+
+    line.pick(picks)._data = rescale(line.pick(picks)._data, basedata, mode,
+                                     False, axes)
+    return line
+
+
+@rescale.register
+@verbose
+def _(line: AverageTFR, baseline: AverageTFR,
+      mode: str = 'mean', copy: bool = False, picks: list = 'data',
+      verbose=None) -> Epochs:
+    """Rescale (baseline correct) Epochs"""
+    if copy:
+        line: Epochs = line.copy()
+    if verbose is not False:
+        msg = _log_rescale(baseline, mode)
+        logger.info(msg)
+
+    # Average the baseline across epochs
+    basedata = baseline.pick(picks)._data
 
     # If time frequency then within frequency
-    if isinstance(line, EpochsTFR):
-        axes = (0, 3)
-    elif isinstance(line, AverageTFR):
-        axes = 2
-    else:
-        axes = tuple(axes)
+    axes = 2
 
     line.pick(picks)._data = rescale(line.pick(picks)._data, basedata, mode,
                                      False, axes)

pyproject.toml

@@ -11,7 +11,7 @@ authors = [
 ]
 dynamic = ["dependencies", "version"]
 readme = "README.md"
-requires-python = ">=3.11"
+requires-python = ">=3.10"
 
 [tool.setuptools.packages.find]
 where = ["."]

setup.py

@@ -24,6 +24,8 @@ def get_file_list(path, ext):
     compile_args = ["/O2"]
 elif sys.platform == 'linux':
     compile_args = ["-O3"]
+elif sys.platform == 'darwin':
+    compile_args = ["-O3"]
 else:
     raise NotImplementedError(f"Platform {sys.platform} not supported.")
 
@@ -77,7 +79,7 @@ def get_file_list(path, ext):
 
 setup(
     name='ieeg',
-    version='0.4',
+    version='0.5',
     packages=find_packages(
         where='.',
         include=['ieeg*'],