Fix Github worklfow/tox (#51)

* first/tox * Update setup.py * tox * Update requirements-dev.txt * Update requirements-dev.txt * Update requirements-dev.txt * Update requirements-dev.txt * Update requirements-dev.txt * Update nwb.py * Update requirements-min.txt * Update requirements-min.txt * Update requirements-min.txt * Update nwb.py * Update requirements-min.txt * Update requirements-min.txt * Update tox.ini * Update tox.ini * Update run_coverage.yml * Update run_coverage.yml * Update run_coverage.yml * workflows up to date with hdmf * Update requirements-min.txt * Update setup.py * Update run_coverage.yml * Update setup.py * Update setup.py * Update black.yml Co-authored-by: Ryan Ly <[email protected]>
hdmf-dev · Dec 20, 2022 · 439df57 · 439df57
1 parent 48ab39f
commit 439df57
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Showing 11 changed files with 99 additions and 83 deletions.
diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
@@ -6,8 +6,8 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
-    - uses: pre-commit/action@v2.0.3
+    - uses: actions/checkout@v3.2.0
+    - uses: actions/setup-python@v4
+    - uses: pre-commit/action@v3.0.0
       with:
         extra_args: black
diff --git a/.github/workflows/check_external_links.yml b/.github/workflows/check_external_links.yml
@@ -9,8 +9,8 @@ jobs:
   check-external-links:
     runs-on: ubuntu-latest
     steps:
-      - name: Cancel any previous incomplete runs
-        uses: styfle/cancel-workflow-action@0.9.1
+      - name: Cancel non-latest runs
+        uses: styfle/cancel-workflow-action@0.11.0
         with:
           all_but_latest: true
           access_token: ${{ github.token }}
@@ -20,7 +20,7 @@ jobs:
           submodules: 'recursive'
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: '3.10'
 

diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -16,7 +16,7 @@ jobs:
           fetch-depth: 0  # tags are required for versioneer to determine the version
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: '3.10'
 
@@ -25,22 +25,27 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install tox
           python -m pip list
+
       - name: Run tox tests
         run: |
           tox -e py310-upgraded
+
       - name: Build wheel and source distribution
         run: |
           tox -e build-py310-upgraded
           ls -1 dist
+
       - name: Test installation from a wheel
         run: |
           tox -e wheelinstall --recreate --installpkg dist/*-none-any.whl
+
       - name: Upload wheel and source distributions to PyPI
         run: |
           python -m pip install twine
           ls -1 dist
-          # twine upload --repository testpypi -u ${{ secrets.BOT_PYPI_USER }} -p ${{ secrets.BOT_PYPI_PASSWORD }} --skip-existing dist/*
+          # twine upload --repository-url https://test.pypi.org/legacy/ -u ${{ secrets.BOT_PYPI_USER }} -p ${{ secrets.BOT_PYPI_PASSWORD }} --skip-existing dist/*
           twine upload -u ${{ secrets.BOT_PYPI_USER }} -p ${{ secrets.BOT_PYPI_PASSWORD }} --skip-existing dist/*
+          
       - name: Publish wheel and source distributions as a GitHub release
         run: |
           python -m pip install "githubrelease>=1.5.9"

diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
@@ -23,36 +23,40 @@ jobs:
       matrix:
         include:
           - { name: linux-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
-          - { name: linux-python3.7              , test-tox-env: py37            , build-tox-env: build-py37            , python-ver: "3.7" , os: ubuntu-latest }
           - { name: linux-python3.8              , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: ubuntu-latest }
           - { name: linux-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: ubuntu-latest }
           - { name: linux-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
           - { name: linux-python3.10-optional    , test-tox-env: py310-optional  , build-tox-env: build-py310-optional  , python-ver: "3.10", os: ubuntu-latest }
           - { name: linux-python3.10-upgraded    , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: ubuntu-latest }
           - { name: linux-python3.10-prerelease  , test-tox-env: py310-prerelease, build-tox-env: build-py310-prerelease, python-ver: "3.10", os: ubuntu-latest }
           - { name: windows-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: windows-latest }
-          - { name: windows-python3.7            , test-tox-env: py37            , build-tox-env: build-py37            , python-ver: "3.7" , os: windows-latest }
           - { name: windows-python3.8            , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: windows-latest }
           - { name: windows-python3.9            , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: windows-latest }
           - { name: windows-python3.10           , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: windows-latest }
           - { name: windows-python3.10-optional  , test-tox-env: py310-optional  , build-tox-env: build-py310-optional  , python-ver: "3.10", os: windows-latest }
           - { name: windows-python3.10-upgraded  , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: windows-latest }
           - { name: windows-python3.10-prerelease, test-tox-env: py310-prerelease, build-tox-env: build-py310-prerelease, python-ver: "3.10", os: windows-latest }
           - { name: macos-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: macos-latest }
-          - { name: macos-python3.7              , test-tox-env: py37            , build-tox-env: build-py37            , python-ver: "3.7" , os: macos-latest }
           - { name: macos-python3.8              , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: macos-latest }
           - { name: macos-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: macos-latest }
           - { name: macos-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: macos-latest }
           - { name: macos-python3.10-optional    , test-tox-env: py310-optional  , build-tox-env: build-py310-optional  , python-ver: "3.10", os: macos-latest }
           - { name: macos-python3.10-upgraded    , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: macos-latest }
           - { name: macos-python3.10-prerelease  , test-tox-env: py310-prerelease, build-tox-env: build-py310-prerelease, python-ver: "3.10", 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  # tags are required for versioneer to determine the version
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-ver }}
 
@@ -91,17 +95,19 @@ jobs:
           - { name: macos-gallery-python3.10-upgraded    , test-tox-env: gallery-py310-upgraded  , python-ver: "3.10", os: macos-latest }
           - { name: macos-gallery-python3.10-prerelease  , test-tox-env: gallery-py310-prerelease, python-ver: "3.10", os: macos-latest }
     steps:
-      - name: Cancel any previous incomplete runs
-        uses: styfle/cancel-workflow-action@0.9.1
+      - 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  # tags are required for versioneer to determine the version
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-ver }}
 
@@ -123,38 +129,38 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
-          - { name: linux-python3.7            , test-tox-env: py37            , build-tox-env: build-py37            , python-ver: "3.7" , os: ubuntu-latest }
-          - { name: linux-python3.8            , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: ubuntu-latest }
-          - { name: linux-python3.9            , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: ubuntu-latest }
-          - { name: linux-python3.10           , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
-          - { name: linux-python3.10-optional  , test-tox-env: py310-optional  , build-tox-env: build-py310-optional  , python-ver: "3.10", os: ubuntu-latest }
-          - { name: linux-python3.10-upgraded  , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: ubuntu-latest }
-          - { name: linux-python3.10-prerelease, test-tox-env: py310-prerelease, build-tox-env: build-py310-prerelease, python-ver: "3.10", os: ubuntu-latest }
+          - { name: conda-linux-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
+          - { name: conda-linux-python3.8            , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: conda-linux-python3.9            , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: conda-linux-python3.10           , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
+          - { name: conda-linux-python3.10-optional  , test-tox-env: py310-optional  , build-tox-env: build-py310-optional  , python-ver: "3.10", os: ubuntu-latest }
+          - { name: conda-linux-python3.10-upgraded  , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: ubuntu-latest }
+          - { name: conda-linux-python3.10-prerelease, test-tox-env: py310-prerelease, build-tox-env: build-py310-prerelease, python-ver: "3.10", os: ubuntu-latest }
     steps:
-      - name: Cancel any previous incomplete runs
-        uses: styfle/cancel-workflow-action@0.9.1
+      - 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  # tags are required for versioneer to determine the version
 
       - name: Set up Conda
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           auto-activate-base: true
-          activate-environment: ""
+          activate-environment: true
+          python-version: ${{ matrix.python-ver }}
 
       - name: Install build dependencies
         run: |
-          conda update -n base -c defaults conda
           conda config --set always_yes yes --set changeps1 no
-          conda config --add channels conda-forge
-          conda install python=${{ matrix.python-ver }}
-          conda install tox
+          conda info
+          conda install -c conda-forge tox
           conda list
       - name: Run tox tests
         run: |

diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
@@ -30,8 +30,8 @@ jobs:
       OS: ${{ matrix.os }}
       PYTHON: '3.10'
     steps:
-      - name: Cancel any previous incomplete runs
-        uses: styfle/cancel-workflow-action@0.9.1
+      - name: Cancel non-latest runs
+        uses: styfle/cancel-workflow-action@0.11.0
         with:
           all_but_latest: true
           access_token: ${{ github.token }}
@@ -41,7 +41,7 @@ jobs:
           submodules: 'recursive'
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: '3.10'
 
@@ -56,7 +56,7 @@ jobs:
           python -m pip list
       - name: Run tests and generate coverage report
         run: |
-          python -m coverage run test.py -u
+          pytest --cov
           python -m coverage xml  # codecov uploader requires xml format
           python -m coverage report -m
       - name: Upload coverage to Codecov

diff --git a/.github/workflows/run_flake8.yml b/.github/workflows/run_flake8.yml
@@ -5,25 +5,26 @@ jobs:
   run-flake8:
     runs-on: ubuntu-latest
     steps:
-    - name: Cancel any previous incomplete runs
-      uses: styfle/cancel-workflow-action@0.9.1
-      with:
-        all_but_latest: true
-        access_token: ${{ github.token }}
+      - 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'
+      - 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@v3
-      with:
-        python-version: '3.10'
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
 
-    - name: Install flake8
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8
-        python -m pip list
-    - name: Run flake8
-      run: flake8
+      - name: Install flake8
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install flake8
+          python -m pip list
+      - name: Run flake8
+        run: flake8
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -20,7 +20,6 @@ jobs:
       matrix:
         include:
           - { name: linux-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
-          - { name: linux-python3.7              , test-tox-env: py37            , build-tox-env: build-py37            , python-ver: "3.7" , os: ubuntu-latest }
           - { name: linux-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
           # NOTE config below with "upload-wheels: true" specifies that wheels should be uploaded as an artifact
           - { name: linux-python3.10-upgraded    , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: ubuntu-latest , upload-wheels: true }
@@ -29,8 +28,8 @@ jobs:
           - { name: macos-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: macos-latest }
           - { name: macos-python3.10-upgraded    , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: macos-latest }
     steps:
-      - name: Cancel any previous incomplete runs
-        uses: styfle/cancel-workflow-action@0.9.1
+      - name: Cancel non-latest runs
+        uses: styfle/cancel-workflow-action@0.11.0
         with:
           all_but_latest: true
           access_token: ${{ github.token }}
@@ -41,7 +40,7 @@ jobs:
           fetch-depth: 0  # tags are required for versioneer to determine the version
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-ver }}
 
@@ -82,17 +81,18 @@ jobs:
           - { name: windows-gallery-python3.7-minimum  , test-tox-env: gallery-py37-minimum  , python-ver: "3.7" , os: windows-latest }
           - { name: windows-gallery-python3.10-upgraded, test-tox-env: gallery-py310-upgraded, python-ver: "3.10", os: windows-latest }
     steps:
-      - name: Cancel any previous incomplete runs
-        uses: styfle/cancel-workflow-action@0.9.1
+      - 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'
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-ver }}
 
@@ -117,9 +117,10 @@ jobs:
           - { name: conda-linux-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
           - { name: conda-linux-python3.10-upgraded  , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: ubuntu-latest }
     steps:
-      - name: Cancel any previous incomplete runs
-        uses: styfle/cancel-workflow-action@0.9.1
+      - 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
@@ -157,9 +158,10 @@ jobs:
     if: ${{ github.event_name == 'push' }}
     runs-on: ubuntu-latest
     steps:
-      - name: Cancel any previous incomplete runs
-        uses: styfle/cancel-workflow-action@0.9.1
+      - name: Cancel non-latest runs
+        uses: styfle/cancel-workflow-action@0.11.0
         with:
+          all_but_latest: true
           access_token: ${{ github.token }}
 
       - name: Checkout repo with submodules
@@ -168,7 +170,7 @@ jobs:
           submodules: 'recursive'
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: '3.10'
 
@@ -182,7 +184,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install scikit-ci-addons
-          ci_addons publish_github_release hdmf-dev/hdmf  \
+          ci_addons publish_github_release hdmf-dev/hdmf-zarr  \
               --prerelease-packages "dist/*" \
               --prerelease-sha $GITHUB_SHA \
               --prerelease-packages-clear-pattern "*" \

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -1,12 +1,11 @@
 # pinned dependencies to reproduce an entire development environment to use HDMF, run HDMF tests, check code style,
 # compute coverage, and create test environments
 codecov==2.1.12
-coverage==6.2
-flake8==4.0.1
-flake8-debugger==4.0.0
-flake8-print==4.0.0
-importlib-metadata==4.2.0
-pytest==6.2.5
+coverage==6.4.2
+flake8==5.0.4
+flake8-debugger==4.1.2
+flake8-print==5.0.0
+pytest==7.1.2
 pytest-cov==3.0.0
 python-dateutil==2.8.2
-tox==3.24.5
+tox==3.25.1
diff --git a/setup.py b/setup.py
@@ -20,8 +20,9 @@
     'hdmf>=3.4.0',
     'zarr>=2.11.0',
     'numcodecs>=0.9.1',
-    'pynwb>=2.0.0'
+    'pynwb>=2.0.0',
     'setuptools',
+    'numpy>=1.23; python_version >"3.7"'
 ]
 
 print(reqs)

diff --git a/src/hdmf_zarr/nwb.py b/src/hdmf_zarr/nwb.py
@@ -8,7 +8,6 @@
 from hdmf.backends.io import HDMFIO
 from hdmf.build import (BuildManager,
                         TypeMap)
-
 try:
     from pynwb import get_manager, get_type_map