Merge branch 'master' into fix_axonarawio

Author: zm711

.github/workflows/core-test.yml

@@ -26,17 +26,13 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "windows-latest", "macos-latest"]
         python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
-        numpy-version: ['1.22.4', '1.23.5', '1.24.4', '1.25.1', '1.26.4', '2.0.2','2.1']
-        # numpy 1.22: 3.10, 1.23: 3.11, 1.24: 3.11, 1.25: 3.11, 1.26: 3.12
+        numpy-version: ['1.24.4', '1.25.1', '1.26.4', '2.0.2','2.1.3', '2.2.4']
+        # 1.24: 3.11, 1.25: 3.11, 1.26: 3.12
         exclude:
            - python-version: '3.9'
-             numpy-version: '2.1'
-           - python-version: '3.11'
-             numpy-version: '1.22.4'
-           - python-version: '3.12'
-             numpy-version: '1.22.4'
-           - python-version: '3.12'
-             numpy-version: '1.23.5'
+             numpy-version: '2.1.3'
+           - python-version: '3.9'
+             numpy-version: '2.2.4'
            - python-version: '3.12'
              numpy-version: '1.24.4'
            - python-version: '3.12'

.github/workflows/io-test.yml

@@ -82,17 +82,11 @@ jobs:
 
       - name: Install git-annex
         # this is the trick from the spikeinterface repo for getting git-annex to work with datalad
+        # see https://github.com/SpikeInterface/spikeinterface/pull/3877 for more info
         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
+          datalad-installer --sudo ok git-annex --method datalad/packages
           git config --global filter.annex.process "git-annex filter-process"  # recommended for efficiency
 
       - name: Configure git
@@ -120,13 +114,6 @@ jobs:
       #  run: |
       #    pip install --no-dependencies -e .
 
-      - name: Install wine
-        run: |
-          sudo rm -f /etc/apt/sources.list.d/microsoft-prod.list
-          sudo dpkg --add-architecture i386
-          sudo apt-get update -qq
-          sudo apt-get install -yqq --allow-downgrades libc6:i386 libgcc-s1:i386 libstdc++6:i386 wine
-
       - name: Pip list
         run: |
           pip list

.github/workflows/plexon2-testing.yml

@@ -0,0 +1,109 @@
+name: NeoPlexon2Test
+
+on:
+  workflow_dispatch:
+    schedule:
+      - cron: "0 12 * * 0" # weekly at noon UTC on Sundays
+
+
+jobs:
+  build-and-test:
+    name: Test on (${{ inputs.os }}) (${{ matrix.python-version}}) (${{ matrix.numpy-version }})
+    runs-on: ${{ inputs.os }}
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: ['3.9', '3.12']
+        numpy-version: ['1.26', '2.0']
+    defaults:
+      # by default run in bash mode (required for conda usage)
+      run:
+        shell: bash -l {0}
+    steps:
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Get current year-month
+        id: date
+        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
+
+      - name: Get ephy_testing_data current head hash
+        # the key depend on the last commit repo https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git
+        id: ephy_testing_data
+        run: |
+          echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
+
+      - uses: actions/cache/restore@v4
+        # Loading cache of ephys_testing_dataset
+        id: cache-datasets
+        with:
+          path: ~/ephy_testing_data
+          key: ${{ runner.os }}-datasets-${{ steps.ephy_testing_data.outputs.dataset_hash }}
+          restore-keys: ${{ runner.os }}-datasets-
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: neo-test-env-${{ matrix.python-version }}
+          python-version: "${{ matrix.python-version }}"
+
+      - name: Install testing dependencies
+        # testing environment is only created from yml if no cache was found
+        # restore-key hits should result in `cache-hit` == 'false'
+        #if: steps.cache-conda-env.outputs.cache-hit != 'true'
+        run: |
+          conda install pip numpy=${{ 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
+        # see https://github.com/SpikeInterface/spikeinterface/pull/3877 for more info
+        shell: bash
+        run: |
+          pip install datalad-installer
+          datalad-installer --sudo ok git-annex --method datalad/packages
+          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"
+          git config --global user.name "neo CI"
+
+      - name: Python version
+        run: |
+          which python
+          python --version
+
+      - name: Install neo including dependencies
+        # installation with dependencies is only required if no cache was found
+        # restore-key hits should result in `cache-hit` == 'false'
+        # if: steps.cache-conda-env.outputs.cache-hit != 'true'
+        run: |
+          pip install --upgrade -e .
+          pip install .[test]
+
+
+      - name: Install wine
+        run: |
+          sudo rm -f /etc/apt/sources.list.d/microsoft-prod.list
+          sudo dpkg --add-architecture i386
+          sudo apt-get update -qq
+          sudo apt-get install -yqq --allow-downgrades libc6:i386 libgcc-s1:i386 libstdc++6:i386 wine
+
+      - name: Pip list
+        run: |
+          pip list
+
+      - name: Conda list
+        run: |
+          conda list
+
+      - name: Test with pytest
+        env:
+          HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_local_plugin_path
+          PLEXON2_TEST: true
+        run: |
+          # only neo.rawio and neo.io
+          pytest --cov=neo neo/test/rawiotest
+          pytest --cov=neo neo/test/iotest

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": "2025-01-20",
-  "downloadUrl": "https://files.pythonhosted.org/packages/3b/91/c3630d766b3b959f8e604d8d41580c78973ece5f1e070b13bd9755dba60b/neo-0.14.0.tar.gz",
+  "dateModified": "2025-04-14",
+  "downloadUrl": "https://files.pythonhosted.org/packages/f1/81/618538a70b0a7db16a174da9a7b5e8aec65462ebcd8f1120cd41b583a8dd/neo-0.14.1.tar.gz",
   "issueTracker": "https://github.com/NeuralEnsemble/python-neo/issues",
   "name": "Neo",
-  "version": "0.14.0",
+  "version": "0.14.1",
   "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/latest/releases/0.14.0.html",
+  "releaseNotes": "https://neo.readthedocs.io/en/latest/releases/0.14.1.html",
   "funding": "https://cordis.europa.eu/project/id/945539",
   "developmentStatus": "active",
   "referencePublication": "https://doi.org/10.3389/fninf.2014.00010",
@@ -114,6 +114,10 @@
     { "@type": "Person", "givenName": "Anthony", "familyName": "Pinto"},
     { "@type": "Person", "givenName": "Chris", "familyName": "Heydrick"},
     {"@type": "Person", "givenName": "Nikhil", "familyName": "Chandra"},
-    {"@type": "Person", "givenName": "Luigi", "familyName": "Petrucco"}
+    {"@type": "Person", "givenName": "Luigi", "familyName": "Petrucco"},
+    {"@type": "Person", "givenName": "Tommaso", "familyName": "Lambresa"},
+    {"@type": "Person", "givenName": "Rémi", "familyName": "Proville"},
+    {"@type": "Person", "givenName": "Nina", "familyName": "Kudryashova"},
+    {"@type": "Person", "givenName": "Paul", "familyName": "Adkisson"}
   ]
 }

doc/source/authors.rst

@@ -71,8 +71,8 @@ and may not be the current affiliation of a contributor.
 * Daniel P. Crepeau [30]
 * Divyansh Gupta [31]
 * Nate Dolensek [3]
-* Philipp Hornauer [32]
-* Robert Wolff
+* Philipp Hornauer [32, 45]
+* Robert Wolff [42]
 * Jules Lebert [33]
 * Benjamin Heasly
 * Baptiste Grimaud [34]
@@ -93,7 +93,10 @@ and may not be the current affiliation of a contributor.
 * Tommaso Lambresa [43]
 * Nina Kudryashova [37]
 * Rémi Proville [44]
-* Letizia Signorelli [45]
+* Paul Adkisson [24]
+* Luiz Tauffer [24]
+* Akshaj Verma [46]
+* Letizia Signorelli [47]
 
 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
@@ -136,10 +139,12 @@ and may not be the current affiliation of a contributor.
 39. Massachusetts General Hospital, Department of Molecular Biology
 40. Plexon Inc.
 41. Paris Brain Institute
-42. Istituto Italiano di Tecnologia (IIT), Italy
+42. Istituto Italiano di Tecnologia (IIT), Genoa, Italy
 43. University of Genoa, Italy
 44. AquiNeuro, SAS
-45. Centre for Molecular Medicine Norway (NCMM), University of Oslo, Norway
+45. Maxwell Biosystems AG
+46. Brain Center, University Medical Center Utrecht, Utrecht University, The Netherlands
+47. Centre for Molecular Medicine Norway (NCMM), University of Oslo, Norway
 
 
 

doc/source/conf.py

@@ -60,7 +60,7 @@
 
 # General information about the project.
 project = "Neo"
-copyright = "2010-2024, " + AUTHORS
+copyright = "2010-2025, " + AUTHORS
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/source/governance.rst

@@ -38,6 +38,7 @@ The current maintainers are:
 - Julia Sprenger (`@JuliaSprenger`_)
 - Michael Denker (`@mdenker`_)
 - Alessio Buccino (`@alejoe91`_)
+- Zach McKenzie (`@zm711`_)
 
 
 .. _`Neo maintainers team`: https://github.com/orgs/NeuralEnsemble/teams/neo-maintainers
@@ -47,3 +48,4 @@ The current maintainers are:
 .. _`@JuliaSprenger`: https://github.com/JuliaSprenger
 .. _`@mdenker`: https://github.com/mdenker
 .. _`@alejoe91`: https://github.com/alejoe91
+.. _`@zm711`: https://github.com/zm711

doc/source/releases.rst

@@ -6,6 +6,7 @@ Release notes
 .. toctree::
    :maxdepth: 1
 
+   releases/0.14.1.rst
    releases/0.14.0.rst
    releases/0.13.4.rst
    releases/0.13.3.rst

doc/source/releases/0.14.1.rst

@@ -0,0 +1,56 @@
+========================
+Neo 0.14.1 release notes
+========================
+
+14 April 25
+
+This release of Neo includes many bug fixes in various IOs, a new HTML based repr, and fixes to the CI all with an eye toward our 1.0 release.
+
+See all `pull requests`_ included in this release and the `list of closed issues`_.
+
+
+Updated dependencies
+--------------------
+
+setuptools >= 78.0.2
+numpy >= 1.24.4
+
+Import improvements
+-------------------
+
+As part of our ongoing effort to improve the speed of importing Neo we have moved the library over to using :code:`importlib.util.find_spec`
+rather than eagerly importing packages in :code:`try-except` blocks.
+
+CI Improvements
+---------------
+
+The install for datalad/git-annex in the CI was fixed for our Python 3.12 tests allowing for all IOs to be tested on Python 3.9 and Python 3.12.
+The buidling of documentation was improved by fixing code style errors.
+
+
+HTML repr
+---------
+
+Thanks to the work of Heberto Mayorquin Neo now supports an html based repr. To see an example check out `html repr`_.
+
+
+Bug fixes and improvements in IO modules
+----------------------------------------
+
+Bug fixes and/or improvements have been made to :code:`BlackRockIO`, :code:`SpikeGLXIO`, :code:`MaxwellIO`, :code:`IntanIO`, :code:`TdtIO`,
+:code:`OpenEphysBinaryIO`, :code:`NeoMatlabIO`, :code:`EdfIO`, :code:`Neuralynx`, and :code:`SpikeGadgetsIO`.
+
+
+Acknowledgements
+----------------
+
+Thanks to Heberto Mayorquin, Zach McKenzie, Andrew Davison, Alessio Buccino, Rémi Proville, Paul Adkisson, Baptiste Grimaud, 
+Robert Wolff, Tommaso Lambresa, and Nina Kudryashova.
+
+
+
+.. _`html repr` : https://github.com/NeuralEnsemble/python-neo/pull/1651
+
+.. _`pull requests` : https://github.com/NeuralEnsemble/python-neo/pulls?q=is%3Apr+is%3Aclosed+milestone%3A0.14.1
+
+.. _`list of closed issues` : https://github.com/NeuralEnsemble/python-neo/issues?q=is%3Aissue%20state%3Aclosed%20milestone%3A0.14.1

neo/core/spiketrainlist.py

@@ -113,8 +113,11 @@ def __init__(self, items=None, parent=None):
         self._channel_id_array = None
         self._all_channel_ids = None
         self._spiketrain_metadata = {}
-        if parent is not None and parent.__class__.__name__ != "Segment":
-            raise AttributeError("The parent class must be a Segment")
+
+        from .segment import Segment  # import here rather than at the top to avoid circular import
+
+        if parent is not None and not isinstance(parent, Segment):
+            raise AttributeError("If provided, the parent class must be a Segment")
         self.segment = parent
 
     @property