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JulesLebertJulesLebert
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Merge branch 'NeuralEnsemble:master' into tdt_neo_changes
2 parents 8649dc4 + 2670b7f commit 49e4338

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‎.github/workflows/caches_cron_job.yml‎

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name: Create caches for ephy_testing_data and conda env
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on:
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workflow_dispatch: # Workflow can be triggered manually via GH actions webinterface
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push: # When something is pushed into master this checks if caches need to re-created
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branches:
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- master
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schedule:
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- cron: "0 12 * * *" # Daily at noon UTC
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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 .
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pip install .[test]
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create-data-cache-if-missing:
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name: Caching data env
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runs-on: "ubuntu-latest"
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steps:
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- name: Get current hash (SHA) of the ephy_testing_data repo
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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@v3
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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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- name: Cache found?
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run: echo "Cache-hit == ${{steps.cache-datasets.outputs.cache-hit == 'true'}}"
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- name: Installing datalad and git-annex
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if: steps.cache-datasets.outputs.cache-hit != 'true'
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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 datalad-installer
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datalad-installer --sudo ok git-annex --method datalad/packages
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pip install datalad
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git config --global filter.annex.process "git-annex filter-process" # recommended for efficiency
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- name: Download dataset
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if: steps.cache-datasets.outputs.cache-hit != 'true'
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# Download repository and also fetch data
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run: |
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cd ~
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datalad install --recursive --get-data https://gin.g-node.org/NeuralEnsemble/ephy_testing_data
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- name: Show size of the cache to assert data is downloaded
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run: |
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cd ~
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pwd
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du -hs ephy_testing_data
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cd ephy_testing_data
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pwd

‎.github/workflows/core-test.yml‎

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pull_request:
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branches: [master]
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types: [synchronize, opened, reopened, ready_for_review]
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paths:
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- 'neo/core/**'
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- 'pyproject.toml'
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# run checks on any change of master, including merge of PRs
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push:
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branches: [master]
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concurrency: # Cancel previous workflows on the same pull request
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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multi-os-python-numpy:
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matrix:
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os: ["ubuntu-latest", "windows-latest"]
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# "macos-latest",
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python-version: ['3.7', '3.8', '3.9', '3.10']
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numpy-version: ['1.18.5', '1.19.5', '1.20.3', '1.21.6', '1.22.4', '1.23.0']
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python-version: ['3.8', '3.9', '3.10', '3.11']
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numpy-version: ['1.19.5', '1.20.3', '1.21.6', '1.22.4', '1.23.5', '1.24.1']
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exclude:
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- python-version: '3.7'
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numpy-version: '1.22.4'
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- python-version: '3.7'
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numpy-version: '1.23.0'
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- python-version: '3.10'
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numpy-version: '1.18.5'
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- python-version: '3.10'
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numpy-version: '1.19.5'
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- python-version: '3.10'
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numpy-version: '1.20.3'
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- python-version: '3.11'
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numpy-version: '1.19.5'
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- python-version: '3.11'
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numpy-version: '1.20.3'
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- python-version: '3.11'
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numpy-version: '1.21.6'
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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

‎.github/workflows/ebrains.yml‎

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name: Mirror to EBRAINS
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# Configure the events that are going to trigger tha automated update of the mirror
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on:
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push:
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branches: [ master ]
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# Configure what will be updated
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jobs:
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# set the job name
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to_ebrains:
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runs-on: ubuntu-latest
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steps:
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# this task will push the master branch of the source_repo (github) to the
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# destination_repo (ebrains gitlab)
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- name: syncmaster
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uses: wei/git-sync@v3
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with:
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source_repo: https://github.com/NeuralEnsemble/python-neo
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source_branch: "master"
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destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/NeuralEnsemble/neo.git"
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destination_branch: "main"
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# this task will push all tags from the source_repo to the destination_repo
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- name: synctags
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uses: wei/git-sync@v3
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with:
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source_repo: https://github.com/NeuralEnsemble/python-neo
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source_branch: "refs/tags/*"
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destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/NeuralEnsemble/neo.git"
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destination_branch: "refs/tags/*"

‎.github/workflows/io-test.yml‎

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push:
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branches: [master]
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concurrency: # Cancel previous workflows on the same pull request
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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build-and-test:
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matrix:
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# "macos-latest", "windows-latest"
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os: ["ubuntu-latest", ]
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python-version: ['3.8', ]
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python-version: ['3.9', ]
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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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- 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_hash
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id: ephy_testing_data
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run: |
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echo "latest_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> GITHUB_OUTPUT
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echo "dataset_hash=$(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@v3
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- uses: actions/cache/restore@v3
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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_hash.outputs.latest_hash }}
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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@v2
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with:
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activate-environment: neo-test-env
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python-version: ${{ matrix.python-version }}
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clean-patched-environment-file: false
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- uses: actions/cache@v3
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- name: Get current dependencies hash
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id: dependencies
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run: |
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echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
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- uses: actions/cache/restore@v3
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# the cache for python package is reset:
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# * every month
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# * when requirements/requirements_testing change
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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: ${{ runner.os }}-conda-env-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements_testing.txt') }}-${{ hashFiles('**/environment_testing.txt') }}-${{ steps.date.outputs.date }}
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key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
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# restore-keys match any key that starts with the restore-key
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restore-keys: |
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${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-
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${{ runner.os }}-conda-env-
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- name: Install testing dependencies
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# testing environment is only installed if no cache was found
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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 env update neo-test-env --file environment_testing.yml
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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: Install neo
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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 neo without dependencies
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# 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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- name: Test with pytest
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run: |

‎.readthedocs.yaml‎

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install:
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- method: pip
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path: .
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- requirements: doc/requirements_docs.txt
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extra_requirements:
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- docs
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‎doc/requirements_docs.txt‎

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‎doc/source/conf.py‎

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import os
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import sys
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import re
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from packaging.version import Version
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with open("../../neo/version.py") as fp:
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d = {}
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exec(fp.read(), d)
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neo_release = d['version']
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with open('../../pyproject.toml', mode='r') as f:
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txt = f.read()
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neo_release = re.findall('version = "(\S+)"', txt)[0]
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neo_version = '.'.join((str(e) for e in Version(neo_release).release[:2]))
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AUTHORS = 'Neo authors and contributors <[email protected]>'
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# If extensions (or modules to document with autodoc) are in another directory,
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# General information about the project.
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project = 'Neo'
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copyright = '2010-2022, ' + AUTHORS
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copyright = '2010-2023, ' + AUTHORS
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# The version info for the project you're documenting, acts as replacement for
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# |version| and |release|, also used in various other places throughout the

‎doc/source/core.rst‎

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:download:`Click here for a better quality SVG diagram <./images/simple_generated_diagram.svg>`
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.. note:: This figure do not include :class:`ChannelView` and :class:`RegionOfInterest`.
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.. note:: This figure does not include :class:`ChannelView` and :class:`RegionOfInterest`.
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For more details, see the :doc:`api_reference`.
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