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Merge branch 'master' into micromed_segments
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14 files changed

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‎.github/workflows/core-test.yml‎

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@@ -25,28 +25,43 @@ jobs:
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fail-fast: true
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matrix:
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os: ["ubuntu-latest", "windows-latest", "macos-latest"]
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python-version: ['3.9', '3.10', '3.11', '3.12']
29-
numpy-version: ['1.22.4', '1.23.5', '1.24.1', '1.25.1', '1.26.4']
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python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
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numpy-version: ['1.22.4', '1.23.5', '1.24.4', '1.25.1', '1.26.4', '2.0.2','2.1']
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# numpy 1.22: 3.10, 1.23: 3.11, 1.24: 3.11, 1.25: 3.11, 1.26: 3.12
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exclude:
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- python-version: '3.9'
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numpy-version: '2.1'
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- python-version: '3.11'
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numpy-version: '1.22.4'
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- python-version: '3.12'
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numpy-version: '1.22.4'
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- python-version: '3.12'
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numpy-version: '1.23.5'
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- python-version: '3.12'
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numpy-version: '1.24.1'
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numpy-version: '1.24.4'
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- python-version: '3.12'
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numpy-version: '1.25.1'
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- python-version: '3.13'
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numpy-version: '1.22.4'
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- python-version: '3.13'
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numpy-version: '1.23.5'
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- python-version: '3.13'
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numpy-version: '1.24.4'
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- python-version: '3.13'
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numpy-version: '1.25.1'
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- python-version: '3.13'
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numpy-version: '1.26.4'
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- python-version: '3.13'
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numpy-version: '2.0.2'
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steps:
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Checkout repository
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Install numpy ${{ matrix.numpy-version }}
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run: |

‎.github/workflows/io-test.yml‎

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Original file line numberDiff line numberDiff line change
@@ -18,15 +18,15 @@ jobs:
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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', '3.11.9']
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python-version: ['3.9', '3.12']
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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@v3
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uses: actions/checkout@v4
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- name: Get current year-month
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id: date
@@ -38,7 +38,7 @@ jobs:
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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)" >> $GITHUB_OUTPUT
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- uses: actions/cache/restore@v3
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- uses: actions/cache/restore@v4
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# Loading cache of ephys_testing_dataset
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id: cache-datasets
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with:
@@ -48,7 +48,7 @@ jobs:
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- uses: conda-incubator/setup-miniconda@v3
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with:
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activate-environment: neo-test-env
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activate-environment: neo-test-env-${{ matrix.python-version }}
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python-version: "${{ matrix.python-version }}"
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- name: Get current dependencies hash
@@ -62,7 +62,7 @@ jobs:
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# * when package dependencies change
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id: cache-conda-env
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with:
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path: /usr/share/miniconda/envs/neo-test-env
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path: /usr/share/miniconda/envs/neo-test-env-${{ matrix.python-version }}
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key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
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# restore-keys match any key that starts with the restore-key
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restore-keys: |
@@ -74,8 +74,7 @@ jobs:
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# restore-key hits should result in `cache-hit` == 'false'
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if: steps.cache-conda-env.outputs.cache-hit != 'true'
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run: |
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conda env update --name neo-test-env --file environment_testing.yml --prune
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conda install python=${{ matrix.python-version }}
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conda env update --name neo-test-env-${{ matrix.python-version }} --file environment_testing.yml --prune
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- name: Configure git
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run: |

‎README.rst‎

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@@ -31,10 +31,13 @@ A project with similar aims but for neuroimaging file formats is `NiBabel`_.
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Code status
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-----------
3333

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.. image:: https://img.shields.io/pypi/v/neo.svg
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:target: https://pypi.python.org/pypi/neo
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:alt: PyPI Release Version
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.. image:: https://github.com/NeuralEnsemble/python-neo/actions/workflows/core-test.yml/badge.svg?event=push&branch=master
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:target: https://github.com/NeuralEnsemble/python-neo/actions?query=event%3Apush+branch%3Amaster
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:alt: Core Test Status (Github Actions)
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.. image:: https://github.com/NeuralEnsemble/python-neo/actions/workflows/io-test.yml/badge.svg?event=push&branch=master
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.. image:: https://github.com/NeuralEnsemble/python-neo/actions/workflows/io-test_trigger.yml/badge.svg?event=push&branch=master
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:target: https://github.com/NeuralEnsemble/python-neo/actions?query=event%3Apush+branch%3Amaster
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:alt: IO Test Status (Github Actions)
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.. image:: https://coveralls.io/repos/NeuralEnsemble/python-neo/badge.png

‎environment_testing.yml‎

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@@ -4,3 +4,6 @@ channels:
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dependencies:
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- datalad
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- pip
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# temporary have this here for IO testing while we decide how to deal with
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# external packages not 2.0 ready
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- numpy=1.26.4

‎neo/core/spiketrain.py‎

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Original file line numberDiff line numberDiff line change
@@ -979,7 +979,7 @@ def _merge_array_annotations(self, others, sorting=None):
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omitted_keys_other = [
981981
key
982-
for key in np.unique([key for other in others for key in other.array_annotations])
982+
for key in set([key for other in others for key in other.array_annotations])
983983
if key not in self.array_annotations
984984
]
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‎neo/io/nwbio.py‎

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Original file line numberDiff line numberDiff line change
@@ -495,7 +495,7 @@ def _write_block(self, block):
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if segment.block is not block:
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raise TypeError(f"segment.block must be block it is {segment.block}")
497497
if not segment.name:
498-
segment.name = f"{block.name} : segment{i}"
498+
segment.name = f"{block.name} segment{i}"
499499
self._write_segment(self._nwbfile, segment, electrodes)
500500
self.blocks_written += 1
501501

@@ -529,14 +529,14 @@ def _write_segment(self, nwbfile, segment, electrodes):
529529
signal.name = f"{segment.name} {signal.name} {i}"
530530
logging.warning(f"Warning signal name exists. New name: {signal.name}")
531531
else:
532-
signal.name = f"{segment.name} : analogsignal{signal.name} {i}"
532+
signal.name = f"{segment.name} analogsignal{signal.name} {i}"
533533
self._write_signal(self._nwbfile, signal, electrodes)
534534

535535
for i, train in enumerate(segment.spiketrains):
536536
if train.segment is not segment:
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raise TypeError(f"train.segment must be segment and is {train.segment}")
538538
if not train.name:
539-
train.name = f"{segment.name} : spiketrain{i}"
539+
train.name = f"{segment.name} spiketrain{i}"
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self._write_spiketrain(self._nwbfile, train)
541541

542542
for i, event in enumerate(segment.events):
@@ -546,12 +546,12 @@ def _write_segment(self, nwbfile, segment, electrodes):
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event.name = f"{segment.name} {event.name} {i}"
547547
logging.warning(f"Warning event name exists. New name: {event.name}")
548548
else:
549-
event.name = f"{segment.name} : event{event.name} {i}"
549+
event.name = f"{segment.name} event{event.name} {i}"
550550
self._write_event(self._nwbfile, event)
551551

552552
for i, epoch in enumerate(segment.epochs):
553553
if not epoch.name:
554-
epoch.name = f"{segment.name} : epoch{i}"
554+
epoch.name = f"{segment.name} epoch{i}"
555555
self._write_epoch(self._nwbfile, epoch)
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557557
def _write_signal(self, nwbfile, signal, electrodes):

‎neo/rawio/__init__.py‎

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@@ -29,7 +29,7 @@
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* :attr:`MicromedRawIO`
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* :attr:`NeuralynxRawIO`
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* :attr:`NeuroExplorerRawIO`
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* :attr:`NeuroNexusRawIO
32+
* :attr:`NeuroNexusRawIO`
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* :attr:`NeuroScopeRawIO`
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* :attr:`NIXRawIO`
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* :attr:`OpenEphysRawIO`

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