Initial setup

.github/workflows/codespell.yml

@@ -0,0 +1,14 @@
+name: Codespell
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.github/workflows/run_all_tests.yml

@@ -0,0 +1,183 @@
+name: Run all tests
+on:
+  pull_request:
+  schedule:
+    - cron: '0 5 * * 0'  # once every Sunday at midnight ET
+  workflow_dispatch:
+
+jobs:
+  run-all-tests:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: linux-python3.8-minimum      , requirements: minimum    , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: linux-python3.8              , requirements: pinned     , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: linux-python3.9              , requirements: pinned     , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-python3.10             , requirements: pinned     , python-ver: "3.10", os: ubuntu-latest }
+          - { name: linux-python3.11             , requirements: pinned     , python-ver: "3.11", os: ubuntu-latest }
+          - { name: linux-python3.12             , requirements: pinned     , python-ver: "3.12", os: ubuntu-latest }
+          - { name: linux-python3.12-upgraded    , requirements: upgraded   , python-ver: "3.12", os: ubuntu-latest }
+          - { name: windows-python3.8-minimum    , requirements: minimum    , python-ver: "3.8" , os: windows-latest }
+          - { name: windows-python3.8            , requirements: pinned     , python-ver: "3.8" , os: windows-latest }
+          - { name: windows-python3.9            , requirements: pinned     , python-ver: "3.9" , os: windows-latest }
+          - { name: windows-python3.10           , requirements: pinned     , python-ver: "3.10", os: windows-latest }
+          - { name: windows-python3.11           , requirements: pinned     , python-ver: "3.11", os: windows-latest }
+          - { name: windows-python3.12           , requirements: pinned     , python-ver: "3.12", os: windows-latest }
+          - { name: windows-python3.12-upgraded  , requirements: upgraded   , python-ver: "3.12", os: windows-latest }
+          - { name: macos-python3.8-minimum      , requirements: minimum    , python-ver: "3.8" , os: macos-latest }
+          - { name: macos-python3.8              , requirements: pinned     , python-ver: "3.8" , os: macos-latest }
+          - { name: macos-python3.9              , requirements: pinned     , python-ver: "3.9" , os: macos-latest }
+          - { name: macos-python3.10             , requirements: pinned     , python-ver: "3.10", os: macos-latest }
+          - { name: macos-python3.11             , requirements: pinned     , python-ver: "3.11", os: macos-latest }
+          - { name: macos-python3.12             , requirements: pinned     , python-ver: "3.12", os: macos-latest }
+          - { name: macos-python3.12-upgraded    , requirements: upgraded   , python-ver: "3.12", os: macos-latest }
+    steps:
+      - name: Cancel non-latest runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          all_but_latest: true
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+          fetch-depth: 0  # fetch tags
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-ver }}
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip list
+          python -m pip check
+
+      - name: Install run requirements (minimum)
+        if: ${{ matrix.requirements == 'minimum' }}
+        run: |
+          python -m pip install -r requirements-min.txt -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (pinned)
+        if: ${{ matrix.requirements == 'pinned' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (upgraded)
+        if: ${{ matrix.requirements == 'upgraded' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install -U -e .
+
+      - name: Run tests
+        run: |
+          pytest -v
+
+      - name: Build wheel and source distribution
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+          ls -1 dist
+
+      - name: Test installation from a wheel (POSIX)
+        if: ${{ matrix.os != 'windows-latest' }}
+        run: |
+          python -m venv test-wheel-env
+          source test-wheel-env/bin/activate
+          python -m pip install dist/*-none-any.whl
+          python -c "import ndx_microscopy"
+
+      - name: Test installation from a wheel (windows)
+        if: ${{ matrix.os == 'windows-latest' }}
+        run: |
+          python -m venv test-wheel-env
+          test-wheel-env/Scripts/activate.bat
+          python -m pip install dist/*-none-any.whl
+          python -c "import ndx_microscopy"
+
+  run-all-tests-on-conda:
+    name: ${{ matrix.name }}
+    runs-on: ubuntu-latest
+    defaults:
+     run:
+       shell: bash -l {0}  # needed for conda environment to work
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: conda-linux-python3.8-minimum    , requirements: minimum    , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: conda-linux-python3.8            , requirements: pinned     , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: conda-linux-python3.9            , requirements: pinned     , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: conda-linux-python3.10           , requirements: pinned     , python-ver: "3.10", os: ubuntu-latest }
+          - { name: conda-linux-python3.11           , requirements: pinned     , python-ver: "3.11", os: ubuntu-latest }
+          - { name: conda-linux-python3.12           , requirements: pinned     , python-ver: "3.12", os: ubuntu-latest }
+          - { name: conda-linux-python3.12-upgraded  , requirements: upgraded   , python-ver: "3.12", os: ubuntu-latest }
+    steps:
+      - name: Cancel any previous incomplete runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+          fetch-depth: 0  # fetch tags
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          auto-activate-base: true
+          activate-environment: true
+          python-version: ${{ matrix.python-ver }}
+
+      - name: Install build dependencies
+        run: |
+          conda config --set always_yes yes --set changeps1 no
+          conda info
+          conda config --show-sources
+          conda list --show-channel-urls
+
+      - name: Install run requirements (minimum)
+        if: ${{ matrix.requirements == 'minimum' }}
+        run: |
+          python -m pip install -r requirements-min.txt -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (pinned)
+        if: ${{ matrix.requirements == 'pinned' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (upgraded)
+        if: ${{ matrix.requirements == 'upgraded' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install -U -e .
+
+      - name: Run tests
+        run: |
+          pytest -v
+
+      - name: Build wheel and source distribution
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+          ls -1 dist
+
+      - name: Test installation from a wheel (POSIX)
+        run: |
+          python -m venv test-wheel-env
+          source test-wheel-env/bin/activate
+          python -m pip install dist/*-none-any.whl
+          python -c "import ndx_microscopy"

.github/workflows/run_coverage.yml

@@ -0,0 +1,59 @@
+name: Run code coverage
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  run-coverage:
+    name: ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    # TODO handle forks
+    # run pipeline on either a push event or a PR event on a fork
+    # if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    defaults:
+      run:
+        shell: bash
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+    env:  # used by codecov-action
+      OS: ${{ matrix.os }}
+      PYTHON: '3.11'
+    steps:
+      - name: Cancel any previous incomplete runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          all_but_latest: true
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+          fetch-depth: 0  # fetch tags
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-dev.txt
+
+      - name: Install package
+        run: |
+          python -m pip install -e .  # must install in editable mode for coverage to find sources
+          python -m pip list
+
+      - name: Run tests and generate coverage report
+        run: |
+          pytest --cov
+          python -m coverage xml  # codecov uploader requires xml format
+          python -m coverage report -m
+
+      # TODO uncomment after setting up repo on codecov.io
+      # - name: Upload coverage to Codecov
+      #   uses: codecov/codecov-action@v3
+      #   with:
+      #     fail_ci_if_error: true

.gitignore

@@ -114,3 +114,6 @@ venv.bak/
 
 # Mac finder
 .DS_Store
+
+# PyCharm
+.idea/

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: check-yaml
+    -   id: check-toml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+    -   id: black
+-   repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort

NEXTSTEPS.md

@@ -107,7 +107,7 @@ with information on where to find your NWB extension.
       src: https://github.com/CodyCBakerPhD/ndx-microscopy
       pip: https://pypi.org/project/ndx-microscopy/
       license: MIT
-      maintainers: 
+      maintainers:
         - CodyCBakerPhD
       ```