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‎.github/workflows/caches_cron_job.yml‎

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jobs:
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create-conda-env-cache-if-missing:
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name: Caching conda env
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runs-on: "ubuntu-latest"
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strategy:
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fail-fast: true
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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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- uses: actions/checkout@v3
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- name: Get current year-month
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id: date
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run: |
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echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
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- name: Get current dependencies hash
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id: dependencies
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run: |
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echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
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- uses: actions/cache@v3
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# the cache for python package is reset:
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# * every month
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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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key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
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- name: Cache found?
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run: echo "Cache-hit == ${{steps.cache-conda-env.outputs.cache-hit == 'true'}}"
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# activate environment if not restored from cache
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- uses: conda-incubator/[email protected]
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if: steps.cache-conda-env.outputs.cache-hit != 'true'
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with:
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activate-environment: neo-test-env
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environment-file: environment_testing.yml
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python-version: 3.9
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- name: Create the conda environment to be cached
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if: steps.cache-conda-env.outputs.cache-hit != 'true'
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# create conda env, configure git and install pip, neo and test dependencies from master
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# for PRs that change dependencies, this environment will be updated in the test workflow
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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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python -m pip install -U pip # Official recommended way
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pip install --upgrade -e .[test]
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# create-conda-env-cache-if-missing:
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# name: Caching conda env
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# runs-on: "ubuntu-latest"
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# strategy:
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# fail-fast: true
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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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# - uses: actions/checkout@v3
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# - name: Get current year-month
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# id: date
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# run: |
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# echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
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# - name: Get current dependencies hash
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# id: dependencies
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# run: |
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# echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
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# - uses: actions/cache@v3
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# # the cache for python package is reset:
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# # * every month
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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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# key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
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# - name: Cache found?
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# run: echo "Cache-hit == ${{steps.cache-conda-env.outputs.cache-hit == 'true'}}"
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# # activate environment if not restored from cache
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# - uses: conda-incubator/[email protected]
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# if: steps.cache-conda-env.outputs.cache-hit != 'true'
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# with:
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# activate-environment: neo-test-env
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# environment-file: environment_testing.yml
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# python-version: 3.9
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# - name: Create the conda environment to be cached
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# if: steps.cache-conda-env.outputs.cache-hit != 'true'
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# # create conda env, configure git and install pip, neo and test dependencies from master
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# # for PRs that change dependencies, this environment will be updated in the test workflow
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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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# python -m pip install -U pip # Official recommended way
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# pip install --upgrade -e .[test]
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create-data-cache-if-missing:
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name: Caching data env

‎.github/workflows/core-test.yml‎

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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']
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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 }}
44-
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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jobs:
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build-and-test:
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name: Test on (${{ inputs.os }}) (${{ matrix.python-version}})
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name: Test on (${{ inputs.os }}) (${{ matrix.python-version}}) (${{ matrix.numpy-version }})
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runs-on: ${{ inputs.os }}
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strategy:
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fail-fast: true
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matrix:
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python-version: ['3.9', '3.11.9']
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python-version: ['3.9', '3.12']
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numpy-version: ['1.26', '2.0']
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defaults:
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# by default run in bash mode (required for conda usage)
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run:
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shell: bash -l {0}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Get current year-month
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id: date
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run: |
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echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
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- uses: actions/cache/restore@v3
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- uses: actions/cache/restore@v4
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# Loading cache of ephys_testing_dataset
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id: cache-datasets
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with:
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- uses: conda-incubator/setup-miniconda@v3
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with:
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activate-environment: neo-test-env
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activate-environment: neo-test-env-${{ matrix.python-version }}
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python-version: "${{ matrix.python-version }}"
53-
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- name: Get current dependencies hash
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id: dependencies
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run: |
57-
echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
58-
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- uses: actions/cache/restore@v3
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# TEST NOT USING CACHE
56+
#- name: Get current dependencies hash
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# id: dependencies
58+
# run: |
59+
# echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
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#- uses: actions/cache/restore@v3
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# the cache for python package is reset:
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# * every month
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# * when package dependencies change
63-
id: cache-conda-env
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with:
65-
path: /usr/share/miniconda/envs/neo-test-env
66-
key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
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# id: cache-conda-env
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# with:
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# path: /usr/share/miniconda/envs/neo-test-env-${{ 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
68-
restore-keys: |
69-
${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-
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${{ runner.os }}-conda-env-
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# restore-keys: |
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# ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-
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# ${{ runner.os }}-conda-env-
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- name: Install testing dependencies
7375
# testing environment is only created from yml if no cache was found
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# restore-key hits should result in `cache-hit` == 'false'
75-
if: steps.cache-conda-env.outputs.cache-hit != 'true'
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#if: steps.cache-conda-env.outputs.cache-hit != 'true'
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run: |
77-
conda env update --name neo-test-env --file environment_testing.yml --prune
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conda install python=${{ matrix.python-version }}
79+
conda install pip numpy=${{ matrix.numpy-version }} -c conda-forge
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# this command is for updating cache. We are resting removal.
81+
# conda env update --name neo-test-env-${{ matrix.python-version }} --file environment_testing.yml --prune
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83+
- name: Install git-annex
84+
# this is the trick from the spikeinterface repo for getting git-annex to work with datalad
85+
shell: bash
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run: |
87+
pip install datalad-installer
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wget https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz
89+
mkdir /home/runner/work/installation
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mv git-annex-standalone-amd64.tar.gz /home/runner/work/installation/
91+
workdir=$(pwd)
92+
cd /home/runner/work/installation
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tar xvzf git-annex-standalone-amd64.tar.gz
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echo "$(pwd)/git-annex.linux" >> $GITHUB_PATH
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cd $workdir
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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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- 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'
93-
if: steps.cache-conda-env.outputs.cache-hit != 'true'
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# if: steps.cache-conda-env.outputs.cache-hit != 'true'
94112
run: |
95113
pip install --upgrade -e .
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pip install .[test]
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- name: Install neo without dependencies
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# TEST NOT USING CACHE
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#- name: Install neo without dependencies
99118
# only installing neo version to test as dependencies should be in cached conda env already
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if: steps.cache-conda-env.outputs.cache-hit == 'true'
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run: |
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pip install --no-dependencies -e .
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# if: steps.cache-conda-env.outputs.cache-hit == 'true'
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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: |

‎LICENSE.txt‎

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Copyright (c) 2010-2024, Neo authors and contributors
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Copyright (c) 2010-2025, Neo authors and contributors
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All rights reserved.
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Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

‎README.rst‎

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To cite Neo in publications, see CITATION.txt
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:copyright: Copyright 2010-2024 by the Neo team, see doc/source/authors.rst.
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:copyright: Copyright 2010-2025 by the Neo team, see doc/source/authors.rst.
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:license: 3-Clause Revised BSD License, see LICENSE.txt for details.
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Funding

‎codemeta.json‎

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"license": "https://spdx.org/licenses/BSD-3-Clause",
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"codeRepository": "https://github.com/NeuralEnsemble/python-neo",
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"contIntegration": "https://github.com/NeuralEnsemble/python-neo/actions",
7-
"dateModified": "2024-10-14",
8-
"downloadUrl": "https://files.pythonhosted.org/packages/e0/0d/e973b7e8464b6f1d88022c46040f203d93c0b080af0e33702bb11873dbbb/neo-0.13.4.tar.gz",
7+
"dateModified": "2025-01-20",
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"downloadUrl": "https://files.pythonhosted.org/packages/3b/91/c3630d766b3b959f8e604d8d41580c78973ece5f1e070b13bd9755dba60b/neo-0.14.0.tar.gz",
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"issueTracker": "https://github.com/NeuralEnsemble/python-neo/issues",
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"name": "Neo",
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"version": "0.13.4",
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"version": "0.14.0",
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"identifier": "RRID:SCR_000634",
1313
"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.",
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"applicationCategory": "neuroscience",
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"releaseNotes": "https://neo.readthedocs.io/en/latest/releases/0.13.4.html",
15+
"releaseNotes": "https://neo.readthedocs.io/en/latest/releases/0.14.0.html",
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"funding": "https://cordis.europa.eu/project/id/945539",
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"developmentStatus": "active",
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"referencePublication": "https://doi.org/10.3389/fninf.2014.00010",
@@ -113,6 +113,7 @@
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{ "@type": "Person", "givenName": "Xin", "familyName": "Niu"},
114114
{ "@type": "Person", "givenName": "Anthony", "familyName": "Pinto"},
115115
{ "@type": "Person", "givenName": "Chris", "familyName": "Heydrick"},
116-
{"@type": "Person", "givenName": "Nikhil", "familyName": "Chandra"}
116+
{"@type": "Person", "givenName": "Nikhil", "familyName": "Chandra"},
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{"@type": "Person", "givenName": "Luigi", "familyName": "Petrucco"}
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]
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}

‎doc/source/authors.rst‎

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* Anthony Pinto [41]
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* Xin Niu
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* Nikhil Chandra [40]
92-
* Letizia Signorelli [42]
92+
* Luigi Petrucco [42]
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* Tommaso Lambresa [43]
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* Nina Kudryashova [37]
95+
* Rémi Proville [44]
96+
* Letizia Signorelli [45]
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1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Universite Claude Bernard Lyon 1
98+
1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Université Claude Bernard Lyon 1
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2. Unité de Neuroscience, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France
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3. University of California, Berkeley
98101
4. Laboratoire de Neurosciences Intégratives et Adaptatives, CNRS UMR 6149 - Université de Provence, Marseille, France
@@ -133,7 +136,10 @@ and may not be the current affiliation of a contributor.
133136
39. Massachusetts General Hospital, Department of Molecular Biology
134137
40. Plexon Inc.
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41. Paris Brain Institute
136-
42. Centre for Molecular Medicine Norway (NCMM), University of Oslo, Norway
139+
42. Istituto Italiano di Tecnologia (IIT), Italy
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43. University of Genoa, Italy
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44. AquiNeuro, SAS
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45. Centre for Molecular Medicine Norway (NCMM), University of Oslo, Norway
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‎doc/source/releases.rst‎

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.. toctree::
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:maxdepth: 1
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releases/0.14.0.rst
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releases/0.13.4.rst
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releases/0.13.3.rst
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releases/0.13.2.rst

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