Merge branch 'master' into add_brw_4.x_sparse

Author: b-grimaud

.github/workflows/io-test.yml

@@ -76,10 +76,25 @@ jobs:
         # restore-key hits should result in `cache-hit` == 'false'
         #if: steps.cache-conda-env.outputs.cache-hit != 'true'
         run: |
-          conda install datalad pip numpy=${{ matrix.numpy-version }} -c conda-forge
+          conda install pip numpy=${{ matrix.numpy-version }} -c conda-forge
         # this command is for updating cache. We are resting removal.
         # conda env update --name neo-test-env-${{ matrix.python-version }} --file environment_testing.yml --prune
 
+      - name: Install git-annex
+        # this is the trick from the spikeinterface repo for getting git-annex to work with datalad
+        shell: bash
+        run: |
+          pip install datalad-installer
+          wget https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz
+          mkdir /home/runner/work/installation
+          mv git-annex-standalone-amd64.tar.gz /home/runner/work/installation/
+          workdir=$(pwd)
+          cd /home/runner/work/installation
+          tar xvzf git-annex-standalone-amd64.tar.gz
+          echo "$(pwd)/git-annex.linux" >> $GITHUB_PATH
+          cd $workdir
+          git config --global filter.annex.process "git-annex filter-process"  # recommended for efficiency
+
       - name: Configure git
         run: |
           git config --global user.email "neo_ci@fake_mail.com"

doc/source/authors.rst

@@ -90,8 +90,11 @@ and may not be the current affiliation of a contributor.
 * Xin Niu
 * Nikhil Chandra [40]
 * Luigi Petrucco [42]
+* Tommaso Lambresa [43]
+* Nina Kudryashova [37]
+* Rémi Proville [44]
 
-1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Universite Claude Bernard Lyon 1
+1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Université Claude Bernard Lyon 1
 2. Unité de Neuroscience, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France
 3. University of California, Berkeley
 4. Laboratoire de Neurosciences Intégratives et Adaptatives, CNRS UMR 6149 - Université de Provence, Marseille, France
@@ -133,6 +136,8 @@ and may not be the current affiliation of a contributor.
 40. Plexon Inc.
 41. Paris Brain Institute
 42. Istituto Italiano di Tecnologia (IIT), Italy
+43. University of Genoa, Italy
+44. AquiNeuro, SAS
 
 
 

neo/io/__init__.py

@@ -167,7 +167,7 @@
 .. autoclass:: neo.io.MaxwellIO
 
     .. autoattribute:: extensions
-    
+
 .. autoclass:: neo.io.MedIO
 
     .. autoattribute:: extensions
@@ -280,24 +280,17 @@
 
 import pathlib
 from collections import Counter
+import importlib.util
 
-# try to import the neuroshare library.
+# check if neuroshare library exists
 # if it is present, use the neuroshareapiio to load neuroshare files
 # if it is not present, use the neurosharectypesio to load files
-try:
-    import neuroshare as ns
-except ModuleNotFoundError as err:
-    from neo.io.neurosharectypesio import NeurosharectypesIO as NeuroshareIO
 
-    # print("\n neuroshare library not found, loading data with ctypes" )
-    # print("\n to use the API be sure to install the library found at:")
-    # print("\n www.http://pythonhosted.org/neuroshare/")
-
-else:
+neuroshare_spec = importlib.util.find_spec("neuroshare")
+if neuroshare_spec is not None:
     from neo.io.neuroshareapiio import NeuroshareapiIO as NeuroshareIO
-
-    # print("neuroshare library successfully imported")
-    # print("\n loading with API...")
+else:
+    from neo.io.neurosharectypesio import NeurosharectypesIO as NeuroshareIO
 
 from neo.io.alphaomegaio import AlphaOmegaIO
 from neo.io.asciiimageio import AsciiImageIO

neo/io/baseio.py

@@ -13,11 +13,7 @@
 
 from __future__ import annotations
 from pathlib import Path
-
-try:
-    from collections.abc import Sequence
-except ImportError:
-    from collections import Sequence
+from collections.abc import Sequence
 import logging
 
 from neo import logging_handler

neo/io/nixio.py

@@ -27,6 +27,8 @@
 from uuid import uuid4
 import warnings
 from packaging.version import Version
+import importlib.util
+import importlib.metadata
 
 import quantities as pq
 import numpy as np
@@ -122,17 +124,15 @@ def dt_from_nix(nixdt, annotype):
 
 
 def check_nix_version():
-    try:
-        import nixio
-    except ImportError:
-        raise Exception(
+    nixio_spec = importlib.util.find_spec("nixio")
+    if nixio_spec is None:
+        raise ImportError(
             "Failed to import NIX. "
             "The NixIO requires the Python package for NIX "
             "(nixio on PyPi). Try `pip install nixio`."
         )
 
-    # nixio version numbers have a 'v' prefix which breaks the comparison
-    nixverstr = nixio.__version__.lstrip("v")
+    nixverstr = importlib.metadata.version("nixio")
     try:
         nixver = Version(nixverstr)
     except ValueError:

neo/io/stimfitio.py

@@ -26,6 +26,8 @@
 08 Feb 2014, C. Schmidt-Hieber, University College London
 """
 
+import importlib.util
+
 import numpy as np
 import quantities as pq
 
@@ -92,7 +94,9 @@ def __init__(self, filename=None):
         """
         # We need this module, so try importing now so that it fails on
         # instantiation rather than read_block
-        import stfio  # noqa
+        stfio_spec = importlib.util.find_spec("stfio")
+        if stfio_spec is None:
+            raise ImportError("stfio must be installed to use StimfitIO")
 
         BaseIO.__init__(self)
 

neo/rawio/axonrawio.py

@@ -23,7 +23,7 @@
 strings section:
 [uModifierNameIndex, uCreatorNameIndex, uProtocolPathIndex, lFileComment, lADCCChannelNames, lADCUnitsIndex
 lDACChannelNameIndex, lDACUnitIndex, lDACFilePath, nLeakSubtractADC]
-['', 'Clampex', '', 'C:/path/protocol.pro', 'some comment', 'IN 0', 'mV', 'IN 1', 'mV', 'Cmd 0', 'pA', 
+['', 'Clampex', '', 'C:/path/protocol.pro', 'some comment', 'IN 0', 'mV', 'IN 1', 'mV', 'Cmd 0', 'pA',
 'Cmd 1', 'pA', 'Cmd 2', 'mV', 'Cmd 3', 'mV']
 
 Information on abf 1 and 2 formats is available here:

neo/rawio/baserawio.py

@@ -239,6 +239,184 @@ def __repr__(self):
 
         return txt
 
+    def _repr_html_(self):
+        """
+        HTML representation for the raw recording base.
+
+        Returns
+        -------
+        html : str
+            The HTML representation as a string.
+        """
+        html = []
+        html.append('<div style="font-family: Arial, sans-serif; max-width: 1000px; margin: 0 auto;">')
+
+        # Header
+        html.append(f'<h3 style="color: #2c3e50;">{self.__class__.__name__}: {self.source_name()}</h3>')
+
+        if self.is_header_parsed:
+            # Basic info
+            nb_block = self.block_count()
+            html.append(f"<p><strong>nb_block:</strong> {nb_block}</p>")
+            nb_seg = [self.segment_count(i) for i in range(nb_block)]
+            html.append(f"<p><strong>nb_segment:</strong> {nb_seg}</p>")
+
+            # CSS for tables - using only black, white, and gray colors
+            html.append(
+                """
+            <style>
+                #{unique_id} table.neo-table {{
+                    border-collapse: collapse;
+                    width: 100%;
+                    margin-bottom: 20px;
+                    font-size: 14px;
+                    color: inherit;
+                    background-color: transparent;
+                }}
+                #{unique_id} table.neo-table th,
+                #{unique_id} table.neo-table td {{
+                    border: 1px solid #888;
+                    padding: 8px;
+                    text-align: left;
+                }}
+                #{unique_id} table.neo-table th {{
+                    background-color: rgba(128,128,128,0.2);
+                }}
+                #{unique_id} table.neo-table tr:nth-child(even) {{
+                    background-color: rgba(128,128,128,0.1);
+                }}
+                #{unique_id} details {{
+                    margin-bottom: 15px;
+                    border: 1px solid rgba(128,128,128,0.3);
+                    border-radius: 4px;
+                    overflow: hidden;
+                    background-color: transparent;
+                }}
+                #{unique_id} summary {{
+                    padding: 10px;
+                    background-color: rgba(128,128,128,0.2);
+                    cursor: pointer;
+                    font-weight: bold;
+                    color: inherit;
+                }}
+                #{unique_id} details[open] summary {{
+                    border-bottom: 1px solid rgba(128,128,128,0.3);
+                }}
+                #{unique_id} .table-container {{
+                    padding: 10px;
+                    overflow-x: auto;
+                    background-color: transparent;
+                }}
+            </style>
+            """
+            )
+
+            # Signal Streams
+            signal_streams = self.header["signal_streams"]
+            if signal_streams.size > 0:
+                html.append("<details>")
+                html.append("<summary>Signal Streams</summary>")
+                html.append('<div class="table-container">')
+                html.append('<table class="neo-table">')
+                html.append("<thead><tr><th>Name</th><th>ID</th><th>Buffer ID</th><th>Channel Count</th></tr></thead>")
+                html.append("<tbody>")
+
+                for i, stream in enumerate(signal_streams):
+                    html.append("<tr>")
+                    html.append(f'<td>{stream["name"]}</td>')
+                    html.append(f'<td>{stream["id"]}</td>')
+                    html.append(f'<td>{stream["buffer_id"]}</td>')
+                    html.append(f"<td>{self.signal_channels_count(i)}</td>")
+                    html.append("</tr>")
+
+                html.append("</tbody></table>")
+                html.append("</div>")
+                html.append("</details>")
+
+            # Signal Channels
+            signal_channels = self.header["signal_channels"]
+            if signal_channels.size > 0:
+                html.append("<details>")
+                html.append("<summary>Signal Channels</summary>")
+                html.append('<div class="table-container">')
+                html.append('<table class="neo-table">')
+                html.append(
+                    "<thead><tr><th>Name</th><th>ID</th><th>Sampling Rate</th><th>Data Type</th><th>Units</th><th>Gain</th><th>Offset</th><th>Stream ID</th><th>Buffer ID</th></tr></thead>"
+                )
+                html.append("<tbody>")
+
+                for channel in signal_channels:
+                    html.append("<tr>")
+                    html.append(f'<td>{channel["name"]}</td>')
+                    html.append(f'<td>{channel["id"]}</td>')
+                    html.append(f'<td>{channel["sampling_rate"]}</td>')
+                    html.append(f'<td>{channel["dtype"]}</td>')
+                    html.append(f'<td>{channel["units"]}</td>')
+                    html.append(f'<td>{channel["gain"]}</td>')
+                    html.append(f'<td>{channel["offset"]}</td>')
+                    html.append(f'<td>{channel["stream_id"]}</td>')
+                    html.append(f'<td>{channel["buffer_id"]}</td>')
+                    html.append("</tr>")
+
+                html.append("</tbody></table>")
+                html.append("</div>")
+                html.append("</details>")
+
+            # Spike Channels
+            spike_channels = self.header["spike_channels"]
+            if spike_channels.size > 0:
+                html.append("<details>")
+                html.append("<summary>Spike Channels</summary>")
+                html.append('<div class="table-container">')
+                html.append('<table class="neo-table">')
+                html.append(
+                    "<thead><tr><th>Name</th><th>ID</th><th>WF Units</th><th>WF Gain</th><th>WF Offset</th><th>WF Left Sweep</th><th>WF Sampling Rate</th></tr></thead>"
+                )
+                html.append("<tbody>")
+
+                for channel in spike_channels:
+                    html.append("<tr>")
+                    html.append(f'<td>{channel["name"]}</td>')
+                    html.append(f'<td>{channel["id"]}</td>')
+                    html.append(f'<td>{channel["wf_units"]}</td>')
+                    html.append(f'<td>{channel["wf_gain"]}</td>')
+                    html.append(f'<td>{channel["wf_offset"]}</td>')
+                    html.append(f'<td>{channel["wf_left_sweep"]}</td>')
+                    html.append(f'<td>{channel["wf_sampling_rate"]}</td>')
+                    html.append("</tr>")
+
+                html.append("</tbody></table>")
+                html.append("</div>")
+                html.append("</details>")
+
+            # Event Channels
+            event_channels = self.header["event_channels"]
+            if event_channels.size > 0:
+                html.append("<details>")
+                html.append("<summary>Event Channels</summary>")
+                html.append('<div class="table-container">')
+                html.append('<table class="neo-table">')
+                html.append("<thead><tr><th>Name</th><th>ID</th><th>Type</th></tr></thead>")
+                html.append("<tbody>")
+
+                for channel in event_channels:
+                    html.append("<tr>")
+                    html.append(f'<td>{channel["name"]}</td>')
+                    html.append(f'<td>{channel["id"]}</td>')
+                    html.append(
+                        f'<td>{channel["type"].decode("utf-8") if isinstance(channel["type"], bytes) else channel["type"]}</td>'
+                    )
+                    html.append("</tr>")
+
+                html.append("</tbody></table>")
+                html.append("</div>")
+                html.append("</details>")
+        else:
+            html.append("<p><em>Call <code>parse_header()</code> to load the reader data.</p>")
+
+        html.append("</div>")
+        return "\n".join(html)
+
     def _generate_minimal_annotations(self):
         """
         Helper function that generates a nested dict for annotations.

neo/rawio/blackrockrawio.py

@@ -979,7 +979,7 @@ def __read_nsx_dataheader_variant_b(
             # use of `int` avoids overflow problem
             data_size = int(dh["nb_data_points"]) * int(self.__nsx_basic_header[nsx_nb]["channel_count"]) * 2
             # define new offset (to possible next data block)
-            offset = data_header[index]["offset_to_data_block"] + data_size
+            offset = int(data_header[index]["offset_to_data_block"]) + data_size
 
             index += 1