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Merge remote-tracking branch 'refs/remotes/origin/add_one_box_reading' into add_one_box_reading
2 parents ceec396 + fb1cb2d commit 8bc3087

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‎.github/workflows/io-test.yml‎

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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

‎doc/source/authors.rst‎

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@@ -71,7 +71,7 @@ and may not be the current affiliation of a contributor.
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* Daniel P. Crepeau [30]
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* Divyansh Gupta [31]
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* Nate Dolensek [3]
74-
* Philipp Hornauer [32]
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* Philipp Hornauer [32, 45]
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* Robert Wolff [42]
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* Jules Lebert [33]
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* Benjamin Heasly
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42. Istituto Italiano di Tecnologia (IIT), Genoa, Italy
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43. University of Genoa, Italy
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44. AquiNeuro, SAS
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45. Maxwell Biosystems AG
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‎neo/rawio/blackrockrawio.py‎

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@@ -607,7 +607,7 @@ def _parse_header(self):
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st_ann["unit_classification"] = "noise"
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else: # 17-254 are reserved
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st_ann["unit_classification"] = "reserved"
610-
st_ann['unit_tag'] = st_ann['unit_classification']
610+
st_ann["unit_tag"] = st_ann["unit_classification"]
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st_ann["description"] = f"SpikeTrain channel_id: {channel_id}, unit_id: {unit_id}"
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st_ann["file_origin"] = self._filenames["nev"] + ".nev"
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‎neo/rawio/maxwellrawio.py‎

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@@ -242,18 +242,20 @@ def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop, strea
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raise (e)
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_hdf_maxwell_error = """Maxwell file format is based on HDF5.
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The internal compression requires a custom plugin!!!
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This is a big pain for the end user.
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You, as a end user, should ask Maxwell company to change this.
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Please visit this page and install the missing decompression libraries:
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https://share.mxwbio.com/d/4742248b2e674a85be97/
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Then, link the decompression library by setting the `HDF5_PLUGIN_PATH` to your
252-
installation location, e.g. via
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_hdf_maxwell_error = """The MaxWell file compression requires a custom plugin.
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You can use the auto_install_maxwell_hdf5_compression_plugin() function or
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(if it fails) install it manually:
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Download the missing decompression library:
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https://share.mxwbio.com/d/7f2d1e98a1724a1b8b35
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Then, link the decompression library by setting the `HDF5_PLUGIN_PATH` to its location,
251+
e.g. directly in Python via:
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os.environ['HDF5_PLUGIN_PATH'] = '/path/to/custom/hdf5/plugin/'
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255-
Alternatively, you can use the auto_install_maxwell_hdf5_compression_plugin() below
256-
function that do it automagically.
253+
or in your shell via:
254+
export HDF5_PLUGIN_PATH=/path/to/custom/hdf5/plugin/
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You can also set the `HDF5_PLUGIN_PATH` environment variable in your shell
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configuration file (e.g. .bashrc, .bash_profile, .zshrc, etc.) to make it
257+
permanent.
258+
See https://mxw.bio/MxW_Doc_Installing_Decompression_Library_to_load_MaxLab_Live_Recordings for more details.
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"""
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hdf5_plugin_path.mkdir(exist_ok=True)
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269271
if platform.system() == "Linux":
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remote_lib = "https://share.mxwbio.com/d/4742248b2e674a85be97/files/?p=%2FLinux%2Flibcompression.so&dl=1"
272+
remote_lib = "https://share.mxwbio.com/d/7f2d1e98a1724a1b8b35/files/?p=%2FLinux%2Flibcompression.so&dl=1"
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local_lib = hdf5_plugin_path / "libcompression.so"
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elif platform.system() == "Darwin":
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remote_lib = "https://share.mxwbio.com/d/4742248b2e674a85be97/files/?p=%2FMacOS%2Flibcompression.dylib&dl=1"
275+
if platform.machine() == "arm64":
276+
remote_lib = "https://share.mxwbio.com/d/7f2d1e98a1724a1b8b35/files/?p=%2FMacOS%2FMac_arm64%2Flibcompression.dylib&dl=1"
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else:
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# Assuming x86_64 for MacOS
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remote_lib = "https://share.mxwbio.com/d/7f2d1e98a1724a1b8b35/files/?p=%2FMacOS%2FMac_x86_64%2Flibcompression.dylib&dl=1"
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local_lib = hdf5_plugin_path / "libcompression.dylib"
275281
elif platform.system() == "Windows":
276-
remote_lib = "https://share.mxwbio.com/d/4742248b2e674a85be97/files/?p=%2FWindows%2Fcompression.dll&dl=1"
282+
remote_lib = "https://share.mxwbio.com/d/7f2d1e98a1724a1b8b35/files/?p=%2FWindows%2Fcompression.dll&dl=1"
277283
local_lib = hdf5_plugin_path / "compression.dll"
278284

279285
if not force_download and local_lib.is_file():

‎neo/rawio/spikeglxrawio.py‎

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if (
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"imDatPrb_type" not in meta
611611
or meta["imDatPrb_type"] == "0"
612-
or meta["imDatPrb_type"] in ("1015", "1016", "1022", "1030", "1031", "1032", "1100", "1121", "1300")
612+
or meta["imDatPrb_type"] in ("1015", "1016", "1022", "1030", "1031", "1032", "1100", "1121", "1123","1300")
613613
):
614614
# This work with NP 1.0 case with different metadata versions
615615
# https://github.com/billkarsh/SpikeGLX/blob/15ec8898e17829f9f08c226bf04f46281f106e5f/Markdown/Metadata_30.md

‎neo/test/iotest/test_plexon2io.py‎

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33
"""
44

55
import unittest
6+
import os
67

78
from neo.io import Plexon2IO
89
from neo.test.iotest.common_io_test import BaseTestIO
@@ -17,8 +18,9 @@
1718
except (ImportError, TimeoutError):
1819
HAVE_PYPL2 = False
1920

21+
TEST_PLEXON2 = bool(os.getenv("PLEXON2_TEST"))
2022

21-
@unittest.skipUnless(HAVE_PYPL2, "requires pypl package and all its dependencies")
23+
@unittest.skipUnless(HAVE_PYPL2 and TEST_PLEXON2, "requires pypl package and all its dependencies")
2224
class TestPlexon2IO(BaseTestIO, unittest.TestCase):
2325
entities_to_download = TestPlexon2RawIO.entities_to_download
2426
entities_to_test = TestPlexon2RawIO.entities_to_test

‎neo/test/rawiotest/test_plexon2rawio.py‎

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11
"""
2-
Tests of neo.rawio.mearecrawio
2+
Tests of neo.rawio.plexon2
33
44
"""
55

66
import unittest
7+
import os
78

89
from neo.rawio.plexon2rawio import Plexon2RawIO
9-
1010
from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
11-
1211
from numpy.testing import assert_equal
1312

1413
try:
@@ -18,8 +17,9 @@
1817
except (ImportError, TimeoutError):
1918
HAVE_PYPL2 = False
2019

20+
TEST_PLEXON2 = bool(os.getenv("PLEXON2_TEST"))
2121

22-
@unittest.skipUnless(HAVE_PYPL2, "requires pypl package and all its dependencies")
22+
@unittest.skipUnless(HAVE_PYPL2 and TEST_PLEXON2, "requires pypl package and all its dependencies")
2323
class TestPlexon2RawIO(
2424
BaseTestRawIO,
2525
unittest.TestCase,

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