Merge with master

alejoe91 · alejoe91 · commit 33e8bfb884e5 · 2024-01-26T15:56:48.000+01:00
diff --git a/.github/workflows/publish-to-pypi-test.yml b/.github/workflows/publish-to-pypi-test.yml
@@ -0,0 +1,46 @@
+name: Release to Test PyPI
+
+on:
+  push:
+    tags:
+       - '*'
+jobs:
+  release:
+    environment: TEST_PYPI_API_TOKEN
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - name: Install Tools
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine build
+        pip install .
+    - name: Test version/tag correspondence
+      id: version-check
+      run: |
+        neo_version=$(python -c "import neo; print(neo.__version__)")
+        echo $neo_version
+        TAG=${{ github.event.release.tag_name }}
+        echo $TAG
+        if [[ $TAG == $neo_version ]]; then
+            echo "VERSION_TAG_MATCH=true" >> $GITHUB_OUTPUT
+            echo "Version matches tag, proceeding with release to Test PyPI"
+        else
+            echo "VERSION_TAG_MATCH=false" >> $GITHUB_OUTPUT
+            echo "Version does not match tag! Fix this before proceeding."
+            exit 1
+        fi
+    - name: Package and Upload
+      env:
+        STACKMANAGER_VERSION: ${{ github.event.release.tag_name }}
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.TEST_PYPI_API_TOKEN }}
+      if: ${{ steps.version-check.outputs.VERSION_TAG_MATCH == 'true' }}
+      run: |
+        python -m build --sdist --wheel
+        twine upload --repository testpypi dist/*
diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -0,0 +1,28 @@
+name: Release to PyPI
+
+on:
+  workflow_dispatch:
+
+jobs:
+  release:
+    environment: PYPI_API_TOKEN
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - name: Install Tools
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine build
+    - name: Package and Upload
+      env:
+        STACKMANAGER_VERSION: ${{ github.event.release.tag_name }}
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+      run: |
+        python -m build --sdist --wheel
+        twine upload dist/*
diff --git a/neo/rawio/biocamrawio.py b/neo/rawio/biocamrawio.py
@@ -148,14 +148,14 @@ def open_biocam_file_header(filename):
         if format_100:
             if signal_inv == 1:
                 read_function = readHDF5t_100
-            elif signal_inv == 1:
+            elif signal_inv == -1:
                 read_function = readHDF5t_100_i
             else:
                 raise Exception("Unknown signal inversion")
         else:
             if signal_inv == 1:
                 read_function = readHDF5t_101
-            elif signal_inv == 1:
+            elif signal_inv == -1:
                 read_function = readHDF5t_101_i
             else:
                 raise Exception("Unknown signal inversion")
diff --git a/neo/rawio/openephysrawio.py b/neo/rawio/openephysrawio.py
@@ -171,27 +171,31 @@ def _parse_header(self):
             self._sig_length[seg_index] = all_sigs_length[0]
             self._sig_timestamp0[seg_index] = all_first_timestamps[0]
 
-        signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
-        self._sig_sampling_rate = signal_channels['sampling_rate'][0]  # unique for channel
-
-        # split channels in stream depending the name CHxxx ADCxxx
-        chan_stream_ids = [name[:2] if name.startswith('CH') else name[:3]
-                      for name in signal_channels['name']]
-        signal_channels['stream_id'] = chan_stream_ids
-
-        # and create streams channels (keep natural order 'CH' first)
-        stream_ids, order = np.unique(chan_stream_ids, return_index=True)
-        stream_ids = stream_ids[np.argsort(order)]
-        signal_streams = [(f'Signals {stream_id}', f'{stream_id}') for stream_id in stream_ids]
-        signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)
-
+        if len(signal_channels) > 0:
+            signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
+            self._sig_sampling_rate = signal_channels['sampling_rate'][0]  # unique for channel
+
+            # split channels in stream depending the name CHxxx ADCxxx
+            chan_stream_ids = [name[:2] if name.startswith('CH') else name[:3]
+                        for name in signal_channels['name']]
+            signal_channels['stream_id'] = chan_stream_ids
+
+            # and create streams channels (keep natural order 'CH' first)
+            stream_ids, order = np.unique(chan_stream_ids, return_index=True)
+            stream_ids = stream_ids[np.argsort(order)]
+            signal_streams = [(f'Signals {stream_id}', f'{stream_id}') for stream_id in stream_ids]
+            signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)
+        else:
+            signal_streams = np.array([])
         # scan for spikes files
         spike_channels = []
 
         if len(info['spikes']) > 0:
-
+            self._first_spk_timestamps = []
+            self._last_spk_timestamps = []
             self._spikes_memmap = {}
-            for seg_index, oe_index in enumerate(oe_indices):
+            oe_indices_spk = sorted(list(info['spikes'].keys()))
+            for seg_index, oe_index in enumerate(oe_indices_spk):
                 self._spikes_memmap[seg_index] = {}
                 for spike_filename in info['spikes'][oe_index]:
                     fullname = os.path.join(self.dirname, spike_filename)
@@ -207,6 +211,9 @@ def _parse_header(self):
                                         dtype=spikes_dtype)
                     self._spikes_memmap[seg_index][name] = data_spike
 
+                    self._first_spk_timestamps.append(data_spike[0]['timestamp'])
+                    self._last_spk_timestamps.append(data_spike[-1]['timestamp'])
+
             # In each file 'sorted_id' indicate the number of cluster so number of units
             # so need to scan file for all segment to get units
             self._spike_sampling_rate = None
@@ -335,9 +342,9 @@ def _get_spike_slice(self, seg_index, unit_index, t_start, t_stop):
         data_spike = self._spikes_memmap[seg_index][name]
 
         if t_start is None:
-            t_start = self._segment_t_start(0, seg_index)
+            t_start = self._first_spk_timestamps[seg_index]
         if t_stop is None:
-            t_stop = self._segment_t_stop(0, seg_index)
+            t_stop = self._last_spk_timestamps[seg_index]
         ts0 = int(t_start * self._spike_sampling_rate)
         ts1 = int(t_stop * self._spike_sampling_rate)
 
@@ -489,11 +496,11 @@ def explore_folder(dirname):
             if (seg_index + 1) > info['nb_segment']:
                 info['nb_segment'] += 1
         elif filename.endswith('.spikes'):
-            s = filename.replace('.spikes', '').split('_')
-            if len(s) == 1:
-                seg_index = 0
+            s = re.findall(r"(_\d+)$", filename.replace('.spikes', ''))
+            if s:
+                seg_index = int(s[0][1:]) - 1
             else:
-                seg_index = int(s[1]) - 1
+                seg_index = 0
             if seg_index not in info['spikes'].keys():
                 info['spikes'][seg_index] = []
             info['spikes'][seg_index].append(filename)
