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theairbend3rtheairbend3r
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Merge branch 'NeuralEnsemble:master' into master
2 parents ee1c6fc + 361d313 commit 37cea06

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‎.github/workflows/io-test.yml‎

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@@ -114,13 +114,6 @@ jobs:
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# run: |
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# pip install --no-dependencies -e .
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- name: Install wine
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run: |
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sudo rm -f /etc/apt/sources.list.d/microsoft-prod.list
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sudo dpkg --add-architecture i386
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sudo apt-get update -qq
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sudo apt-get install -yqq --allow-downgrades libc6:i386 libgcc-s1:i386 libstdc++6:i386 wine
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- name: Pip list
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run: |
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pip list

‎.github/workflows/plexon2-testing.yml‎

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

‎neo/core/spiketrainlist.py‎

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@@ -113,8 +113,10 @@ def __init__(self, items=None, parent=None):
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self._channel_id_array = None
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self._all_channel_ids = None
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self._spiketrain_metadata = {}
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if parent is not None and parent.__class__.__name__ != "Segment":
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raise AttributeError("The parent class must be a Segment")
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from .segment import Segment # import here rather than at the top to avoid circular import
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if parent is not None and not isinstance(parent, Segment):
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raise AttributeError("If provided, the parent class must be a Segment")
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self.segment = parent
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@property

‎neo/test/iotest/test_plexon2io.py‎

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"""
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import unittest
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import os
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from neo.io import Plexon2IO
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from neo.test.iotest.common_io_test import BaseTestIO
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except (ImportError, TimeoutError):
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HAVE_PYPL2 = False
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TEST_PLEXON2 = bool(os.getenv("PLEXON2_TEST"))
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@unittest.skipUnless(HAVE_PYPL2, "requires pypl package and all its dependencies")
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@unittest.skipUnless(HAVE_PYPL2 and TEST_PLEXON2, "requires pypl package and all its dependencies")
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class TestPlexon2IO(BaseTestIO, unittest.TestCase):
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entities_to_download = TestPlexon2RawIO.entities_to_download
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entities_to_test = TestPlexon2RawIO.entities_to_test

‎neo/test/rawiotest/test_plexon2rawio.py‎

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"""
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Tests of neo.rawio.mearecrawio
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Tests of neo.rawio.plexon2
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"""
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import unittest
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import os
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from neo.rawio.plexon2rawio import Plexon2RawIO
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from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
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from numpy.testing import assert_equal
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try:
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except (ImportError, TimeoutError):
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HAVE_PYPL2 = False
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TEST_PLEXON2 = bool(os.getenv("PLEXON2_TEST"))
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@unittest.skipUnless(HAVE_PYPL2, "requires pypl package and all its dependencies")
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@unittest.skipUnless(HAVE_PYPL2 and TEST_PLEXON2, "requires pypl package and all its dependencies")
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class TestPlexon2RawIO(
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BaseTestRawIO,
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unittest.TestCase,

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