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Update repo to use latest template, black formatting
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‎.github/workflows/check_external_links.yml‎

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name: Check Sphinx external links
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on:
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push:
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branches:
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- main
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pull_request:
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schedule:
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- cron: '0 5 * * 0' # once every Sunday at midnight ET
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workflow_dispatch:
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jobs:
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check-external-links:
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name: Check for broken Sphinx external links
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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with:
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fetch-depth: 0 # tags are required to determine the version
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.13"
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- name: Install Sphinx dependencies and package
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run: |
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python -m pip install --upgrade pip
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python -m pip install -U ".[docs]"
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python -m pip list
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- name: Check Sphinx external links
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run: |
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cd docs # run_doc_autogen assumes spec is found in ../spec/
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sphinx-build -b linkcheck ./source ./test_build

‎.github/workflows/codespell.yml‎

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name: Codespell
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on:
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push:
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branches:
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- main
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pull_request:
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workflow_dispatch:
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jobs:
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codespell:
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name: Check for spelling errors
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Codespell
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uses: codespell-project/actions-codespell@v2

‎.github/workflows/ruff.yml‎

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name: Ruff
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on:
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push:
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branches:
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- main
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pull_request:
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workflow_dispatch:
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jobs:
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ruff:
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name: Check for style errors and common problems
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Ruff
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uses: astral-sh/ruff-action@v3

‎.github/workflows/run_all_tests.yml‎

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name: Run all tests
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on:
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push:
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branches:
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- main
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pull_request:
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schedule:
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- cron: '0 5 * * 0' # once every Sunday at midnight ET
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workflow_dispatch:
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jobs:
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run-all-tests:
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name: ${{ matrix.name }}
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runs-on: ${{ matrix.os }}
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defaults:
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run:
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shell: bash
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }}
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cancel-in-progress: true
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strategy:
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fail-fast: false
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matrix:
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include:
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- { name: linux-python3.9-minimum , requirements: minimum , python-ver: "3.9" , os: ubuntu-latest }
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- { name: linux-python3.9 , requirements: upgraded , python-ver: "3.9" , os: ubuntu-latest }
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- { name: linux-python3.10 , requirements: upgraded , python-ver: "3.10", os: ubuntu-latest }
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- { name: linux-python3.11 , requirements: upgraded , python-ver: "3.11", os: ubuntu-latest }
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- { name: linux-python3.12 , requirements: upgraded , python-ver: "3.12", os: ubuntu-latest }
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- { name: linux-python3.13 , requirements: upgraded , python-ver: "3.13", os: ubuntu-latest }
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- { name: windows-python3.9-minimum , requirements: minimum , python-ver: "3.9" , os: windows-latest }
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- { name: windows-python3.9 , requirements: upgraded , python-ver: "3.9" , os: windows-latest }
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- { name: windows-python3.10 , requirements: upgraded , python-ver: "3.10", os: windows-latest }
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- { name: windows-python3.11 , requirements: upgraded , python-ver: "3.11", os: windows-latest }
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- { name: windows-python3.12 , requirements: upgraded , python-ver: "3.12", os: windows-latest }
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- { name: windows-python3.13 , requirements: upgraded , python-ver: "3.13", os: windows-latest }
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- { name: macos-python3.9-minimum , requirements: minimum , python-ver: "3.9" , os: macos-latest }
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- { name: macos-python3.9 , requirements: upgraded , python-ver: "3.9" , os: macos-latest }
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- { name: macos-python3.10 , requirements: upgraded , python-ver: "3.10", os: macos-latest }
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- { name: macos-python3.11 , requirements: upgraded , python-ver: "3.11", os: macos-latest }
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- { name: macos-python3.12 , requirements: upgraded , python-ver: "3.12", os: macos-latest }
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- { name: macos-python3.13 , requirements: upgraded , python-ver: "3.13", os: macos-latest }
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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with:
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fetch-depth: 0 # tags are required to determine the version
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-ver }}
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- name: Install run requirements (minimum)
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if: ${{ matrix.requirements == 'minimum' }}
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run: |
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python -m pip install --upgrade pip
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python -m pip install ".[min-reqs,test]"
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python -m pip list
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python -m pip check
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- name: Install run requirements (upgraded)
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if: ${{ matrix.requirements == 'upgraded' }}
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run: |
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python -m pip install --upgrade pip
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# force upgrade of all dependencies to latest versions within allowed range
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python -m pip install -U ".[test]"
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python -m pip list
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python -m pip check
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- name: Run tests
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run: |
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pytest -v
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- name: Build wheel and source distribution
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run: |
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python -m pip install --upgrade build
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python -m build
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ls -1 dist
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- name: Test installation from a wheel (POSIX)
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if: ${{ matrix.os != 'windows-latest' }}
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run: |
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python -m venv test-wheel-env
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source test-wheel-env/bin/activate
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python -m pip install dist/*-none-any.whl
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python -c "import ndx_franklab_novela"
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- name: Test installation from a wheel (windows)
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if: ${{ matrix.os == 'windows-latest' }}
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run: |
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python -m venv test-wheel-env
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test-wheel-env/Scripts/activate.bat
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python -m pip install dist/*-none-any.whl
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python -c "import ndx_franklab_novela"

‎.github/workflows/run_coverage.yml‎

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name: Run code coverage
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on:
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push:
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branches:
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- main
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pull_request:
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workflow_dispatch:
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jobs:
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run-coverage:
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name: ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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# TODO handle forks
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# run pipeline on either a push event or a PR event on a fork
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# if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
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defaults:
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run:
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shell: bash
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.os }}
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cancel-in-progress: true
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strategy:
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matrix:
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os: [ubuntu-latest, windows-latest, macos-latest]
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env: # used by codecov-action
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OS: ${{ matrix.os }}
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PYTHON: '3.13'
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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with:
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fetch-depth: 0 # tags are required to determine the version
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ env.PYTHON }}
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- name: Install package and test dependencies
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run: |
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python -m pip install --upgrade pip
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# force upgrade of all dependencies to latest versions within allowed range
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python -m pip install -U ".[test]"
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python -m pip list
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python -m pip check
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- name: Run tests and generate coverage report
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run: |
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pytest --cov --cov-report=xml --cov-report=term # codecov uploader requires xml format
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# TODO uncomment after setting up repo on codecov.io and adding token
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# - name: Upload coverage to Codecov
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# uses: codecov/codecov-action@v4
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# with:
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# fail_ci_if_error: true
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# file: ./coverage.xml
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# env:
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# CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

‎.github/workflows/validate_schema.yml‎

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name: Validate schema
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on:
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push:
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branches:
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- main
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pull_request:
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workflow_dispatch:
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jobs:
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validate:
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name: Validate schema
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.13"
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- name: Install HDMF
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run: |
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pip install hdmf
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- name: Download latest nwb schema language specification
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run: |
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curl -L https://raw.githubusercontent.com/NeurodataWithoutBorders/nwb-schema/dev/nwb.schema.json -o nwb.schema.json
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- name: Validate schema specification
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run: |
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validate_hdmf_spec spec -m nwb.schema.json

‎.github/workflows/workflow.yml‎

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