Merge branch 'master' into gh-977

.gitattributes

@@ -0,0 +1 @@
+dandi/_version.py export-subst

.github/workflows/codeql.yml

@@ -24,19 +24,19 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v3
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
           config-file: codeql.yml
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v3
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3
         with:
           category: "/language:${{ matrix.language }}"

.github/workflows/docs.yml

@@ -13,20 +13,18 @@ jobs:
       fail-fast: false
       matrix:
         python:
-          - 3.8
-          #- 3.9
-          #- 3.10
+          - '3.10'
           #- 3.11
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         # Fetch all commits so that versioneer will return something compatible
         # with semantic-version
         fetch-depth: 0
 
     - name: Set up Python ${{ matrix.python }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python }}
 

.github/workflows/lint.yml

@@ -9,17 +9,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Set up environment
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install --upgrade tox
+    # Annotate codespell within PR
+    - uses: codespell-project/codespell-problem-matcher@v1
     - name: Run linters
       run: |
         tox -e lint

.github/workflows/release.yml

@@ -12,7 +12,7 @@ jobs:
     if: "!contains(github.event.head_commit.message, 'ci skip') && !contains(github.event.head_commit.message, 'skip ci')"
     steps:
       - name: Checkout source
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -23,9 +23,9 @@ jobs:
           chmod a+x ~/auto
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Install build & twine
         run: python -m pip install build twine

.github/workflows/test.yml

@@ -32,33 +32,37 @@ jobs:
           - ubuntu-latest
           - macos-latest
         python:
-          - 3.8
           - 3.9
           - '3.10'  # Needs quotes so YAML doesn't think it's 3.1
           - '3.11'
+          - '3.12'
+          - '3.13'
         mode:
           - normal
         include:
           - os: ubuntu-latest
-            python: 3.8
+            python: 3.9
             mode: dandi-api
           - os: ubuntu-latest
-            python: 3.8
+            python: 3.9
             mode: dev-deps
           - os: ubuntu-latest
-            python: 3.8
+            python: 3.13
+            mode: dev-deps
+          - os: ubuntu-latest
+            python: 3.9
             mode: nfs
 
     steps:
     - name: Set up environment
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         # Fetch all commits so that versioneer will return something compatible
         # with semantic-version
         fetch-depth: 0
 
     - name: Set up Python ${{ matrix.python }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python }}
 
@@ -72,7 +76,9 @@ jobs:
       run: |
         pip install git+https://github.com/jaraco/keyring
         pip install git+https://github.com/NeurodataWithoutBorders/nwbinspector
-        pip install git+https://github.com/NeurodataWithoutBorders/pynwb
+        pip install git+https://github.com/NeurodataWithoutBorders/pynwb \
+            git+https://github.com/hdmf-dev/hdmf \
+            git+https://github.com/hdmf-dev/hdmf-zarr
 
     - name: Create NFS filesystem
       if: matrix.mode == 'nfs'
@@ -87,6 +93,10 @@ jobs:
         echo HOME=/tmp/nfsmount/home >> "$GITHUB_ENV"
         echo DANDI_DEVEL_INSTRUMENT_REQUESTS_SUPERLEN=1 >> "$GITHUB_ENV"
 
+    - name: Use scheduled test configuration
+      if: github.event_name == 'schedule'
+      run: echo PYTEST_ADDOPTS=--scheduled >> "$GITHUB_ENV"
+
     - name: Run all tests
       if: matrix.mode != 'dandi-api'
       run: |
@@ -101,30 +111,40 @@ jobs:
         do python "$f"
         done
 
-    - name: Run Dandi API tests only
+    - name: Run DANDI API tests only
       if: matrix.mode == 'dandi-api'
       run: |
+        export DANDI_TESTS_AUDIT_CSV=/tmp/audit.csv
         python -m pytest -s -v --cov=dandi --cov-report=xml --dandi-api dandi
+        if [ ! -e /tmp/audit.csv ]
+        then echo Audit file not created
+             exit 1
+        fi
+        lines="$(wc -l /tmp/audit.csv | awk '{print $1}')"
+        if [ "$lines" -lt 100 ]
+        then echo Audit file shorter than expected - only "$lines" lines
+             exit 1
+        fi
 
     - name: Dump Docker Compose logs
       if: failure() && startsWith(matrix.os, 'ubuntu')
       run: |
-        docker-compose \
+        docker compose \
           -f dandi/tests/data/dandiarchive-docker/docker-compose.yml \
           logs --timestamps
 
     - name: Shut down Docker Compose
       if: startsWith(matrix.os, 'ubuntu')
       run: |
-        docker-compose \
+        docker compose \
           -f dandi/tests/data/dandiarchive-docker/docker-compose.yml \
           down -v
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.xml
+        files: ./coverage.xml
         flags: unittests
         # name: codecov-umbrella
         # yml: ./codecov.yml

.github/workflows/typing.yml

@@ -9,14 +9,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.8'
+          python-version: '3.9'
 
       - name: Install dependencies
         run: |

.github/workflows/update-year.yml

@@ -0,0 +1,21 @@
+name: Update year
+
+on:
+  # We would not trigger update until actual changes are done
+  # to our code, or we explicitly request
+  push:
+    branches:
+      - 'master'
+  workflow_dispatch:
+
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: FantasticFiasco/action-update-license-year@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -15,3 +15,4 @@ pip-wheel-metadata/
 sandbox/
 venv/
 venvs/
+.DS_Store

.pre-commit-config.yaml

@@ -24,7 +24,7 @@ repos:
     -   id: codespell
         exclude: ^(dandi/_version\.py|dandi/due\.py|versioneer\.py)$
 -   repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 7.0.0
     hooks:
       - id: flake8
         exclude: ^(dandi/_version\.py|dandi/due\.py|versioneer\.py)$

.readthedocs.yaml

@@ -2,7 +2,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.10"
 python:
     install:
         - requirements: docs/requirements.txt