Merge branch 'master' into issue1530

Author: zm711

.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'

README.rst

@@ -64,7 +64,8 @@ grant agreement FETPI-015879 (FACETS), by the European Union Seventh Framework P
 under grant agreements no. 269921 (BrainScaleS) and no. 604102 (HBP),
 and by the European Union’s Horizon 2020 Framework Programme for
 Research and Innovation under the Specific Grant Agreements No. 720270 (Human Brain Project SGA1),
-No. 785907 (Human Brain Project SGA2) and No. 945539 (Human Brain Project SGA3).
+No. 785907 (Human Brain Project SGA2) and No. 945539 (Human Brain Project SGA3),
+and by the European Union's Research and Innovation Program Horizon Europe Grant Agreement No. 101147319 (EBRAINS 2.0).
 
 .. _OpenElectrophy: https://github.com/OpenElectrophy/OpenElectrophy
 .. _Elephant: http://neuralensemble.org/elephant

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",

doc/source/releases.rst

@@ -6,6 +6,7 @@ Release notes
 .. toctree::
    :maxdepth: 1
 
+   releases/0.13.3.rst
    releases/0.13.2.rst
    releases/0.13.1.rst
    releases/0.13.0.rst

doc/source/releases/0.13.3.rst

@@ -0,0 +1,33 @@
+========================
+Neo 0.13.3 release notes
+========================
+
+28 August 2024
+
+This release of Neo contains bug fixes, still with a focus on the planned 1.0 release,
+and will be the last release not to support NumPy 2.0.
+
+See all `pull requests`_ included in this release and the `list of closed issues`_.
+
+
+Updated dependencies
+--------------------
+
+Neo has a limit of NumPy >= 1.19.5, < 2.0.0 and Quantities >= 14.0.1, < 0.16.0
+
+
+Bug fixes and improvements in IO modules
+----------------------------------------
+
+Bug fixes and/or improvements have been made to :class:`PlexonIO`, :class:`SpikeGLXIO`,
+:class:`BiocamIO`.
+
+Acknowledgements
+----------------
+
+Thanks to Zach McKenzie, Heberto Mayorquin, and Alessio Buccino for their contributions to this release.
+
+
+.. _`pull requests`: https://github.com/NeuralEnsemble/python-neo/pulls?q=is%3Apr+is%3Aclosed+milestone%3A0.13.3
+
+.. _`list of closed issues`: https://github.com/NeuralEnsemble/python-neo/issues?q=is%3Aissue+is%3Aclosed+milestone%3A0.13.3

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/biocamrawio.py

@@ -136,28 +136,36 @@ def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop, strea
 
         # newer style data returns an initial flat array (n_samples * n_channels)
         # we iterate through channels rather than slicing
+        # Due to the fact that Neo and SpikeInterface tend to prefer slices we need to add
+        # some careful checks around slicing of None in the case we need to iterate through
+        # channels. First check if None. Then check if slice and only if slice check that it is slice(None)
         else:
             if channel_indexes is None:
                 channel_indexes = [ch for ch in range(self._num_channels)]
+            elif isinstance(channel_indexes, slice):
+                start = channel_indexes.start or 0
+                stop = channel_indexes.stop or self._num_channels
+                step = channel_indexes.step or 1
+                channel_indexes = [ch for ch in range(start, stop, step)]
 
-            sig_chunk = np.zeros((i_stop-i_start, len(channel_indexes)))
+            sig_chunk = np.zeros((i_stop - i_start, len(channel_indexes)), dtype=data.dtype)
             # iterate through channels to prevent loading all channels into memory which can cause
             # memory exhaustion. See https://github.com/SpikeInterface/spikeinterface/issues/3303
             for index, channel_index in enumerate(channel_indexes):
-                sig_chunk[:, index] = data[channel_index::self._num_channels]
+                sig_chunk[:, index] = data[channel_index :: self._num_channels]
 
         return sig_chunk
 
 
-def open_biocam_file_header(filename)-> dict:
+def open_biocam_file_header(filename) -> dict:
     """Open a Biocam hdf5 file, read and return the recording info, pick the correct method to access raw data,
     and return this to the caller
-    
+
     Parameters
     ----------
     filename: str
         The file to be parsed
-    
+
     Returns
     -------
     dict
@@ -244,7 +252,7 @@ def open_biocam_file_header(filename)-> dict:
             num_channels_x = num_channels_y = int(np.sqrt(num_channels))
         else:
             raise NeoReadWriteError("No Well found in the file")
-        
+
         if num_channels_x * num_channels_y != num_channels:
             raise NeoReadWriteError(f"Cannot determine structure of the MEA plate with {num_channels} channels")
         channels = 1 + np.concatenate(np.transpose(np.meshgrid(range(num_channels_x), range(num_channels_y))))
@@ -268,6 +276,7 @@ def open_biocam_file_header(filename)-> dict:
 ######################################################################
 # Helper functions to obtain the raw data split by Biocam version.
 
+
 # return the full array for the old datasets
 def readHDF5t_100(rf, t0, t1, nch):
     return rf["3BData/Raw"][t0:t1]

neo/rawio/blackrockrawio.py

@@ -986,7 +986,8 @@ def __read_nsx_dataheader_variant_c(
         index = 0
 
         if offset is None:
-            offset = self.__nsx_basic_header[nsx_nb]["bytes_in_headers"]
+            # This is read as an uint32 numpy scalar from the header so we transform it to python int
+            offset = int(self.__nsx_basic_header[nsx_nb]["bytes_in_headers"])
 
         ptp_dt = [
             ("reserved", "uint8"),