merge with main and resolve conflicts

Author: samuelgarcia

.github/workflows/core-test.yml

@@ -26,24 +26,9 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
-        numpy-version: ['1.20.3', '1.21.6', '1.22.4', '1.23.5', '1.24.1', '1.25.1', '1.26.4']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+        numpy-version: ['1.22.4', '1.23.5', '1.24.1', '1.25.1', '1.26.4']
         exclude:
-           - python-version: '3.8'
-             numpy-version: '1.25.1'
-           - python-version: '3.8'
-             numpy-version: '1.26.4'
-           - python-version: '3.10'
-             numpy-version: '1.20.3'
-           - python-version: '3.11'
-             numpy-version: '1.20.3'
-           - python-version: '3.11'
-             numpy-version: '1.21.6'
-           - python-version: '3.12'
-             numpy-version: '1.20.3'
-           # python 3.12 only works on latest numpy
-           - python-version: '3.12'
-             numpy-version: '1.21.6'
            - python-version: '3.12'
              numpy-version: '1.22.4'
            - python-version: '3.12'

codemeta.json

@@ -4,15 +4,15 @@
   "license": "https://spdx.org/licenses/BSD-3-Clause",
   "codeRepository": "https://github.com/NeuralEnsemble/python-neo",
   "contIntegration": "https://github.com/NeuralEnsemble/python-neo/actions",
-  "dateModified": "2024-08-01",
-  "downloadUrl": "https://files.pythonhosted.org/packages/0f/16/4e22eb38621183d56acde0abbe591f15e79c6332e9ec360fc5db171b39ab/neo-0.13.2.tar.gz",
+  "dateModified": "2024-08-28",
+  "downloadUrl": "https://files.pythonhosted.org/packages/08/4b/c863c6bff783e94c92cb814f6ae821b35e6463c5a66e809b6864d0c66b4e/neo-0.13.3.tar.gz",
   "issueTracker": "https://github.com/NeuralEnsemble/python-neo/issues",
   "name": "Neo",
-  "version": "0.13.2",
+  "version": "0.13.3",
   "identifier": "RRID:SCR_000634",
   "description": "Neo is a Python package for working with electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5.\n\nThe goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysiology data by providing a common, shared object model. In order to be as lightweight a dependency as possible, Neo is deliberately limited to represention of data, with no functions for data analysis or visualization.\n\nNeo is used by a number of other software tools, including SpykeViewer (data analysis and visualization), Elephant (data analysis), the G-node suite (databasing), PyNN (simulations), tridesclous_ (spike sorting) and ephyviewer (data visualization).\n\nNeo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes (for example tetrodes). Neo's data objects build on the quantities package, which in turn builds on NumPy by adding support for physical dimensions. Thus Neo objects behave just like normal NumPy arrays, but with additional metadata, checks for dimensional consistency and automatic unit conversion.",
   "applicationCategory": "neuroscience",
-  "releaseNotes": "https://neo.readthedocs.io/en/stable/releases/0.13.2.html",
+  "releaseNotes": "https://neo.readthedocs.io/en/stable/releases/0.13.3.html",
   "funding": "https://cordis.europa.eu/project/id/945539",
   "developmentStatus": "active",
   "referencePublication": "https://doi.org/10.3389/fninf.2014.00010",

neo/io/__init__.py

@@ -45,6 +45,7 @@
 * :attr:`NestIO`
 * :attr:`NeuralynxIO`
 * :attr:`NeuroExplorerIO`
+* :attr:`NeuroNexusIO
 * :attr:`NeuroScopeIO`
 * :attr:`NeuroshareIO`
 * :attr:`NixIO`
@@ -191,6 +192,9 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.io.NeuroNexusIO
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.io.NeuroScopeIO
 
     .. autoattribute:: extensions
@@ -326,6 +330,7 @@
 from neo.io.nestio import NestIO
 from neo.io.neuralynxio import NeuralynxIO
 from neo.io.neuroexplorerio import NeuroExplorerIO
+from neo.io.neuronexusio import NeuroNexusIO
 from neo.io.neuroscopeio import NeuroScopeIO
 from neo.io.nixio import NixIO
 from neo.io.nixio_fr import NixIO as NixIOFr
@@ -382,6 +387,7 @@
     NestIO,
     NeuralynxIO,
     NeuroExplorerIO,
+    NeuroNexusIO,
     NeuroScopeIO,
     NeuroshareIO,
     NWBIO,

neo/io/neuronexusio.py

@@ -0,0 +1,11 @@
+from neo.io.basefromrawio import BaseFromRaw
+from neo.rawio.neuronexusrawio import NeuroNexusRawIO
+
+
+class NeuroNexusIO(NeuroNexusRawIO, BaseFromRaw):
+    __doc__ = NeuroNexusRawIO.__doc__
+    _prefered_signal_group_mode = "group-by-same-units"
+
+    def __init__(self, filename):
+        NeuroNexusRawIO.__init__(self, filename=filename)
+        BaseFromRaw.__init__(self, filename)

neo/rawio/__init__.py

@@ -29,6 +29,7 @@
 * :attr:`MicromedRawIO`
 * :attr:`NeuralynxRawIO`
 * :attr:`NeuroExplorerRawIO`
+* :attr:`NeuroNexusRawIO
 * :attr:`NeuroScopeRawIO`
 * :attr:`NIXRawIO`
 * :attr:`OpenEphysRawIO`
@@ -114,6 +115,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.rawio.NeuroNexusRawIO
+
+    .. autoattributes:: extensions
+
 .. autoclass:: neo.rawio.NeuroScopeRawIO
 
     .. autoattribute:: extensions
@@ -197,6 +202,7 @@
 from neo.rawio.micromedrawio import MicromedRawIO
 from neo.rawio.neuralynxrawio import NeuralynxRawIO
 from neo.rawio.neuroexplorerrawio import NeuroExplorerRawIO
+from neo.rawio.neuronexusrawio import NeuroNexusRawIO
 from neo.rawio.neuroscoperawio import NeuroScopeRawIO
 from neo.rawio.nixrawio import NIXRawIO
 from neo.rawio.openephysrawio import OpenEphysRawIO
@@ -231,6 +237,7 @@
     MedRawIO,
     NeuralynxRawIO,
     NeuroExplorerRawIO,
+    NeuroNexusRawIO,
     NeuroScopeRawIO,
     NIXRawIO,
     OpenEphysRawIO,

neo/rawio/brainvisionrawio.py

@@ -94,8 +94,22 @@ def _parse_header(self):
                 channel_desc = channel_infos[f"Ch{c+1}"]
             except KeyError:
                 channel_desc = channel_infos[f"ch{c + 1}"]
-            name, ref, res, units = channel_desc.split(",")
-            units = units.replace("µ", "u")
+            # split up channel description, handling default values
+            cds = channel_desc.split(",")
+            name = cds[0]
+            if len(cds) >= 2:
+                ref = cds[1]
+            else:
+                ref = ""
+            if len(cds) >= 3:
+                res = cds[2]
+            else:
+                res = "1.0"
+            if len(cds) == 4:
+                units = cds[3]
+            else:
+                units = "u"
+            units = units.replace("µ", "u")  # Brainvision spec for specific unicode
             chan_id = str(c + 1)
             if sig_dtype == np.int16 or sig_dtype == np.int32:
                 gain = float(res)

neo/rawio/intanrawio.py

@@ -180,6 +180,7 @@ def _parse_header(self):
             self._raw_data = np.memmap(self.filename, dtype=memmap_data_dtype, mode="r", offset=header_size)
 
         # for 'one-file-per-signal' we have one memory map / neo stream
+        # based on https://github.com/NeuralEnsemble/python-neo/issues/1556 bug in versions 0.13.1, .2, .3
         elif self.file_format == "one-file-per-signal":
             self._raw_data = {}
             for stream_index, (stream_index_key, stream_datatype) in enumerate(memmap_data_dtype.items()):
@@ -189,8 +190,12 @@ def _parse_header(self):
                 dtype_size = np.dtype(stream_datatype).itemsize
                 n_samples = size_in_bytes // (dtype_size * num_channels)
                 signal_stream_memmap = np.memmap(
-                    file_path, dtype=stream_datatype, mode="r", shape=(num_channels, n_samples)
-                ).T
+                    file_path,
+                    dtype=stream_datatype,
+                    mode="r",
+                    shape=(n_samples, num_channels),
+                    order="C",
+                )
                 self._raw_data[stream_index] = signal_stream_memmap
 
         # for one-file-per-channel we have one memory map / channel stored as a list / neo stream