Merge branch 'dev' into can_read

NeurodataWithoutBorders · Oct 4, 2023 · ba4fea1 · ba4fea1
2 parents a3d72ff + 734a6c4
commit ba4fea1
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diff --git a/.codespellrc b/.codespellrc
@@ -1,7 +1,8 @@
 [codespell]
 # in principle .ipynb can be corrected -- a good number of typos there
 # nwb-schema -- excluding since submodule, should have its own fixes/checks
-skip = .git,*.pdf,*.svg,venvs,env,*.ipynb,nwb-schema
+skip = .git,*.pdf,*.svg,venvs,env,nwb-schema
+ignore-regex = ^\s*"image/\S+": ".*
 # it is optin in a url
 # potatos - demanded to be left alone, autogenerated
 ignore-words-list = optin,potatos
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -60,7 +60,7 @@ body:
     attributes:
       label: Python Version
       options:
-        - "3.7"
+        - "lower version (unsupported)"
         - "3.8"
         - "3.9"
         - "3.10"

diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -16,4 +16,4 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v3
       - name: Codespell
-        uses: codespell-project/actions-codespell@v1
+        uses: codespell-project/actions-codespell@v2
diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
@@ -22,24 +22,21 @@ 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-python3.8              , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: linux-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , 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-python3.11             , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
           - { name: linux-python3.11-optional    , test-tox-env: py311-optional  , build-tox-env: build-py311-optional  , python-ver: "3.11", os: ubuntu-latest }
           - { name: linux-python3.11-upgraded    , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: ubuntu-latest }
           - { name: linux-python3.11-prerelease  , test-tox-env: py311-prerelease, build-tox-env: build-py311-prerelease, python-ver: "3.11", 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-python3.8            , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: windows-latest }
+          - { name: windows-python3.8-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , 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-python3.11           , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: windows-latest }
           - { name: windows-python3.11-optional  , test-tox-env: py311-optional  , build-tox-env: build-py311-optional  , python-ver: "3.11", os: windows-latest }
           - { name: windows-python3.11-upgraded  , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: windows-latest }
           - { name: windows-python3.11-prerelease, test-tox-env: py311-prerelease, build-tox-env: build-py311-prerelease, python-ver: "3.11", 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-python3.8              , test-tox-env: py38            , build-tox-env: build-py38            , python-ver: "3.8" , os: macos-latest }
+          - { name: macos-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , 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-python3.11             , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: macos-latest }
@@ -92,13 +89,13 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-gallery-python3.7-minimum      , test-tox-env: gallery-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
+          - { name: linux-gallery-python3.8-minimum      , test-tox-env: gallery-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
           - { name: linux-gallery-python3.11-upgraded    , test-tox-env: gallery-py311-upgraded  , python-ver: "3.11", os: ubuntu-latest }
           - { name: linux-gallery-python3.11-prerelease  , test-tox-env: gallery-py311-prerelease, python-ver: "3.11", os: ubuntu-latest }
-          - { name: windows-gallery-python3.7-minimum    , test-tox-env: gallery-py37-minimum    , python-ver: "3.7" , os: windows-latest }
+          - { name: windows-gallery-python3.8-minimum    , test-tox-env: gallery-py38-minimum    , python-ver: "3.8" , os: windows-latest }
           - { name: windows-gallery-python3.11-upgraded  , test-tox-env: gallery-py311-upgraded  , python-ver: "3.11", os: windows-latest }
           - { name: windows-gallery-python3.11-prerelease, test-tox-env: gallery-py311-prerelease, python-ver: "3.11", os: windows-latest }
-          - { name: macos-gallery-python3.7-minimum      , test-tox-env: gallery-py37-minimum    , python-ver: "3.7" , os: macos-latest }
+          - { name: macos-gallery-python3.8-minimum      , test-tox-env: gallery-py38-minimum    , python-ver: "3.8" , os: macos-latest }
           - { name: macos-gallery-python3.11-upgraded    , test-tox-env: gallery-py311-upgraded  , python-ver: "3.11", os: macos-latest }
           - { name: macos-gallery-python3.11-prerelease  , test-tox-env: gallery-py311-prerelease, python-ver: "3.11", os: macos-latest }
     steps:
@@ -111,6 +108,7 @@ jobs:
       - 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
@@ -137,8 +135,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { 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-python3.8-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , 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-python3.11           , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
@@ -155,6 +152,7 @@ jobs:
       - 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
@@ -166,8 +164,7 @@ jobs:
         run: |
           conda config --set always_yes yes --set changeps1 no
           conda info
-          # the conda dependency resolution for tox under python 3.7 can install the wrong importlib_metadata
-          conda install -c conda-forge tox "importlib_metadata>4"
+          conda install -c conda-forge tox
 
       - name: Conda reporting
         run: |
@@ -199,9 +196,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
-          - { name: windows-python3.11-ros3, python-ver: "3.11", os: windows-latest }
-          - { name: macos-python3.11-ros3  , python-ver: "3.11", os: macos-latest }
+          - { name: conda-linux-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
+          - { name: conda-windows-python3.11-ros3, python-ver: "3.11", os: windows-latest }
+          - { name: conda-macos-python3.11-ros3  , python-ver: "3.11", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -212,6 +209,7 @@ jobs:
       - 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
@@ -245,9 +243,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-gallery-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
-          - { name: windows-gallery-python3.11-ros3, python-ver: "3.11", os: windows-latest }
-          - { name: macos-gallery-python3.11-ros3  , python-ver: "3.11", os: macos-latest }
+          - { name: conda-linux-gallery-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
+          - { name: conda-windows-gallery-python3.11-ros3, python-ver: "3.11", os: windows-latest }
+          - { name: conda-macos-gallery-python3.11-ros3  , python-ver: "3.11", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -258,6 +256,7 @@ jobs:
       - 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
@@ -283,4 +282,4 @@ jobs:
 
       - name: Run gallery ros3 tests
         run: |
-          python test.py --example-ros3
+          python test.py --example-ros3
diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
@@ -71,7 +71,7 @@ jobs:
 
       - name: Run integration tests and generate coverage report
         run: |
-          python -m coverage run -p test.py --integration --backwards
+          python -m coverage run -p test.py --integration --validation-module --backwards
           # validation CLI tests generate separate .coverage files that need to be merged
           python -m coverage combine
           python -m coverage xml  # codecov uploader requires xml format

diff --git a/.github/workflows/run_dandi_read_tests.yml b/.github/workflows/run_dandi_read_tests.yml
@@ -47,4 +47,4 @@ jobs:
 
       - name: Run DANDI read tests
         run: |
-          pytest -rP tests/read_dandi/
+          python tests/read_dandi/test_read_dandi.py
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -19,12 +19,12 @@ 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-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum   , python-ver: "3.8" , os: ubuntu-latest }
           # NOTE config below with "upload-wheels: true" specifies that wheels should be uploaded as an artifact
-          - { name: linux-python3.11-upgraded    , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: ubuntu-latest , upload-wheels: true }
-          - { 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-python3.11-upgraded  , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", 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: linux-python3.11-upgraded    , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: ubuntu-latest , upload-wheels: true }
+          - { name: windows-python3.8-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum   , python-ver: "3.8" , os: windows-latest }
+          - { name: windows-python3.11-upgraded  , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: windows-latest }
+          - { name: macos-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum   , python-ver: "3.8" , os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -78,9 +78,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-gallery-python3.7-minimum    , test-tox-env: gallery-py37-minimum  , python-ver: "3.7" , os: ubuntu-latest }
+          - { name: linux-gallery-python3.8-minimum    , test-tox-env: gallery-py38-minimum  , python-ver: "3.8" , os: ubuntu-latest }
           - { name: linux-gallery-python3.11-upgraded  , test-tox-env: gallery-py311-upgraded, python-ver: "3.11", os: ubuntu-latest }
-          - { name: windows-gallery-python3.7-minimum  , test-tox-env: gallery-py37-minimum  , python-ver: "3.7" , os: windows-latest }
+          - { name: windows-gallery-python3.8-minimum  , test-tox-env: gallery-py38-minimum  , python-ver: "3.8" , os: windows-latest }
           - { name: windows-gallery-python3.11-upgraded, test-tox-env: gallery-py311-upgraded, python-ver: "3.11", os: windows-latest }
     steps:
       - name: Cancel non-latest runs
@@ -92,6 +92,7 @@ jobs:
       - 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
@@ -118,7 +119,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { 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-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
           - { name: conda-linux-python3.11-upgraded  , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: ubuntu-latest }
     steps:
       - name: Cancel non-latest runs
@@ -142,8 +143,7 @@ jobs:
         run: |
           conda config --set always_yes yes --set changeps1 no
           conda info
-          # the conda dependency resolution for tox under python 3.7 can install the wrong importlib_metadata
-          conda install -c conda-forge tox "importlib_metadata>4"
+          conda install -c conda-forge tox
 
       - name: Conda reporting
         run: |
@@ -174,7 +174,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
+          - { name: conda-linux-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -185,6 +185,7 @@ jobs:
       - 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
@@ -218,7 +219,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-gallery-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
+          - { name: conda-linux-gallery-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -229,6 +230,7 @@ jobs:
       - 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
@@ -272,6 +274,7 @@ jobs:
         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