Add base schema and classes (#3)

hed-standard · Oct 26, 2023 · 4b193bb · 4b193bb
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diff --git a/.github/workflows/check_external_links.yml b/.github/workflows/check_external_links.yml
@@ -0,0 +1,38 @@
+name: Check Sphinx external links
+on:
+  push:
+  schedule:
+    - cron: '0 5 * * *'  # once per day at midnight ET
+  workflow_dispatch:
+
+jobs:
+  check-external-links:
+    name: Check for broken Sphinx external links
+    runs-on: ubuntu-latest
+    steps:
+      - name: Cancel any previous incomplete runs
+        uses: styfle/[email protected]
+        with:
+          all_but_latest: true
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+          fetch-depth: 0  # tags are required for versioneer to determine the version
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install Sphinx dependencies and package
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-dev.txt
+          python -m pip install .
+
+      - name: Check Sphinx external links
+        run: |
+          cd docs  # run_doc_autogen assumes spec is found in ../spec/
+          sphinx-build -b linkcheck ./source ./test_build
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,14 @@
+name: Codespell
+on:
+  push:
+  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
diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
@@ -0,0 +1,14 @@
+name: Ruff
+on:
+  push:
+  workflow_dispatch:
+
+jobs:
+  ruff:
+    name: Check for style errors and common problems
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Ruff
+        uses: chartboost/ruff-action@v1
diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
@@ -0,0 +1,183 @@
+name: Run all tests
+on:
+  push:
+  schedule:
+    - cron: '0 5 * * *'  # once per day 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/[email protected]
+        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_hed"
+
+      - 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_hed"
+
+  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/[email protected]
+        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_hed"
diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
@@ -0,0 +1,59 @@
+name: Run code coverage
+on:
+  push:
+  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/[email protected]
+        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
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,9 @@
+# output NWB files
+*.nwb
+
+# generated docs
+docs/source/_format_auto_docs
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -50,6 +56,7 @@ coverage.xml
 .hypothesis/
 .pytest_cache/
 cover/
+.ruff_cache/
 
 # Translations
 *.mo
@@ -158,3 +165,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# Mac finder
+.DS_Store
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1 @@
+# Changelog for ndx-hed
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2023, Ryan Ly, Oliver Ruebel, Kay Robbins
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.