Merge branch 'main' into the_ruffest_rule_of_all

catalystneuro · Dec 11, 2024 · fc3bfdb · fc3bfdb
2 parents be80b61 + 1032e15
commit fc3bfdb
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diff --git a/.github/workflows/all_os_versions.txt b/.github/workflows/all_os_versions.txt
@@ -0,0 +1 @@
+["ubuntu-latest", "macos-latest", "windows-latest", "macos-13"]
diff --git a/.github/workflows/all_python_versions.txt b/.github/workflows/all_python_versions.txt
@@ -0,0 +1 @@
+["3.9", "3.10", "3.11", "3.12"]
diff --git a/.github/workflows/build_and_upload_docker_image_yaml_variable.yml b/.github/workflows/build_and_upload_docker_image_yaml_variable.yml
@@ -31,7 +31,7 @@ jobs:
         uses: docker/build-push-action@v5
         with:
           push: true  # Push is a shorthand for --output=type=registry
-          tags: ghcr.io/catalystneuro/neuroconv:yaml_variable
+          tags: ghcr.io/catalystneuro/neuroconv_yaml_variable:latest
           context: .
           file: dockerfiles/neuroconv_latest_yaml_variable
           provenance: false
diff --git a/.github/workflows/dailies.yml b/.github/workflows/dailies.yml
@@ -6,32 +6,55 @@ on:
     - cron: "0 4 * * *" # Daily at 8PM PST, 11PM EST, 5AM CET to avoid working hours
 
 jobs:
+  load_python_and_os_versions:
+    runs-on: ubuntu-latest
+    outputs:
+      ALL_PYTHON_VERSIONS: ${{ steps.load_python_versions.outputs.python_versions }}
+      ALL_OS_VERSIONS: ${{ steps.load_os_versions.outputs.os_versions }}
+    steps:
+      - uses: actions/checkout@v4
+      - id: load_python_versions
+        run: echo "python_versions=$(cat ./.github/workflows/all_python_versions.txt)" >> "$GITHUB_OUTPUT"
+      - id: load_os_versions
+        run: echo "os_versions=$(cat ./.github/workflows/all_os_versions.txt)" >> "$GITHUB_OUTPUT"
+
   build-and-upload-docker-image-dev:
     uses: ./.github/workflows/build_and_upload_docker_image_dev.yml
     secrets:
       DOCKER_UPLOADER_USERNAME: ${{ secrets.DOCKER_UPLOADER_USERNAME }}
       DOCKER_UPLOADER_PASSWORD: ${{ secrets.DOCKER_UPLOADER_PASSWORD }}
 
   run-daily-tests:
+    needs: load_python_and_os_versions
     uses: ./.github/workflows/testing.yml
     secrets:
       AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
       AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
       S3_GIN_BUCKET: ${{ secrets.S3_GIN_BUCKET }}
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+    with:
+      python-versions: ${{ needs.load_python_and_os_versions.outputs.ALL_PYTHON_VERSIONS }}
+      os-versions: ${{ needs.load_python_and_os_versions.outputs.ALL_OS_VERSIONS }}
 
   run-daily-dev-tests:
+    needs: load_python_and_os_versions
     uses: ./.github/workflows/dev-testing.yml
     secrets:
       DANDI_API_KEY: ${{ secrets.DANDI_API_KEY }}
       AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
       AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
       S3_GIN_BUCKET: ${{ secrets.S3_GIN_BUCKET }}
+    with:
+      python-versions: ${{ needs.load_python_and_os_versions.outputs.ALL_PYTHON_VERSIONS }}
 
   run-daily-live-service-testing:
+    needs: load_python_and_os_versions
     uses: ./.github/workflows/live-service-testing.yml
     secrets:
       DANDI_API_KEY: ${{ secrets.DANDI_API_KEY }}
+    with:
+      python-versions: ${{ needs.load_python_and_os_versions.outputs.ALL_PYTHON_VERSIONS }}
+      os-versions: ${{ needs.load_python_and_os_versions.outputs.ALL_OS_VERSIONS }}
 
   run-daily-neuroconv-docker-testing:
     uses: ./.github/workflows/neuroconv_docker_testing.yml

diff --git a/.github/workflows/deploy-tests.yml b/.github/workflows/deploy-tests.yml
@@ -13,6 +13,17 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  load_python_and_os_versions:
+    runs-on: ubuntu-latest
+    outputs:
+      ALL_PYTHON_VERSIONS: ${{ steps.load_python_versions.outputs.python_versions }}
+      ALL_OS_VERSIONS: ${{ steps.load_os_versions.outputs.os_versions }}
+    steps:
+      - uses: actions/checkout@v4
+      - id: load_python_versions
+        run: echo "python_versions=$(cat ./.github/workflows/all_python_versions.txt)" >> "$GITHUB_OUTPUT"
+      - id: load_os_versions
+        run: echo "os_versions=$(cat ./.github/workflows/all_os_versions.txt)" >> "$GITHUB_OUTPUT"
 
   assess-file-changes:
     uses: ./.github/workflows/assess-file-changes.yml
@@ -31,7 +42,7 @@ jobs:
           0
 
   run-tests:
-    needs: assess-file-changes
+    needs: [assess-file-changes, load_python_and_os_versions]
     if: ${{ needs.assess-file-changes.outputs.SOURCE_CHANGED == 'true' }}
     uses: ./.github/workflows/testing.yml
     secrets:
@@ -40,28 +51,31 @@ jobs:
       S3_GIN_BUCKET: ${{ secrets.S3_GIN_BUCKET }}
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
     with:  #  Ternary operator: condition && value_if_true || value_if_false
-      python-versions: ${{ github.event.pull_request.draft == true && '["3.9"]' || '["3.9", "3.10", "3.11", "3.12"]' }}
-      os-versions: ${{ github.event.pull_request.draft == true && '["ubuntu-latest"]' || '["ubuntu-latest", "macos-latest", "macos-13", "windows-latest"]' }}
+      python-versions: ${{ github.event.pull_request.draft == true && '["3.9"]' || needs.load_python_and_os_versions.outputs.ALL_PYTHON_VERSIONS }}
+      os-versions: ${{ github.event.pull_request.draft == true && '["ubuntu-latest"]' || needs.load_python_and_os_versions.outputs.ALL_OS_VERSIONS }}
 
   # If the conversion gallery is the only thing that changed, run doctests only
   run-doctests-only:
-    needs: assess-file-changes
+    needs: [assess-file-changes, load_python_and_os_versions]
     if: ${{ needs.assess-file-changes.outputs.CONVERSION_GALLERY_CHANGED == 'true' && needs.assess-file-changes.outputs.SOURCE_CHANGED != 'true' }}
     uses: ./.github/workflows/doctests.yml
     with:  #  Ternary operator: condition && value_if_true || value_if_false
-      python-versions: ${{ github.event.pull_request.draft == true && '["3.9"]' || '["3.9", "3.10", "3.11", "3.12"]' }}
-      os-versions: ${{ github.event.pull_request.draft == true && '["ubuntu-latest"]' || '["ubuntu-latest", "macos-latest", "macos-13", "windows-latest"]' }}
+      python-versions: ${{ github.event.pull_request.draft == true && '["3.9"]' || needs.load_python_and_os_versions.outputs.ALL_PYTHON_VERSIONS }}
+      os-versions: ${{ github.event.pull_request.draft == true && '["ubuntu-latest"]' || needs.load_python_and_os_versions.outputs.ALL_OS_VERSIONS }}
 
 
   run-live-service-tests:
-    needs: assess-file-changes
+    needs: [assess-file-changes, load_python_and_os_versions]
     if: ${{ needs.assess-file-changes.outputs.SOURCE_CHANGED == 'true' }}
     uses: ./.github/workflows/live-service-testing.yml
     secrets:
+      AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+      AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+      S3_GIN_BUCKET: ${{ secrets.S3_GIN_BUCKET }}
       DANDI_API_KEY: ${{ secrets.DANDI_API_KEY }}
     with:  #  Ternary operator: condition && value_if_true || value_if_false
-      python-versions: ${{ github.event.pull_request.draft == true && '["3.9"]' || '["3.9", "3.10", "3.11", "3.12"]' }}
-      os-versions: ${{ github.event.pull_request.draft == true && '["ubuntu-latest"]' || '["ubuntu-latest", "macos-latest", "macos-13", "windows-latest"]' }}
+      python-versions: ${{ github.event.pull_request.draft == true && '["3.9"]' || needs.load_python_and_os_versions.outputs.ALL_PYTHON_VERSIONS }}
+      os-versions: ${{ github.event.pull_request.draft == true && '["ubuntu-latest"]' || needs.load_python_and_os_versions.outputs.ALL_OS_VERSIONS }}
 
 
   check-final-status:

diff --git a/.github/workflows/dev-testing.yml b/.github/workflows/dev-testing.yml
@@ -7,7 +7,6 @@ on:
         description: 'List of Python versions to use in matrix, as JSON string'
         required: true
         type: string
-        default: '["3.9", "3.10", "3.11", "3.12"]'
     secrets:
       DANDI_API_KEY:
         required: true

diff --git a/.github/workflows/doctests.yml b/.github/workflows/doctests.yml
@@ -6,12 +6,10 @@ on:
         description: 'List of Python versions to use in matrix, as JSON string'
         required: true
         type: string
-        default: '["3.9", "3.10", "3.11", "3.12"]'
       os-versions:
         description: 'List of OS versions to use in matrix, as JSON string'
         required: true
         type: string
-        default: '["ubuntu-latest", "macos-latest", "windows-latest"]'
 
 
 jobs:

diff --git a/.github/workflows/aws_tests.yml → .github/workflows/generic_aws_tests.yml b/.github/workflows/aws_tests.yml → .github/workflows/generic_aws_tests.yml
@@ -11,7 +11,6 @@ concurrency:  # Cancel previous workflows on the same pull request
 env:
   AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
   AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-  DANDI_API_KEY: ${{ secrets.DANDI_API_KEY }}
 
 jobs:
   run:
@@ -36,8 +35,8 @@ jobs:
           git config --global user.email "CI@example.com"
           git config --global user.name "CI Almighty"
 
-      - name: Install full requirements
+      - name: Install AWS requirements
         run: pip install .[aws,test]
 
-      - name: Run subset of tests that use S3 live services
-        run: pytest -rsx -n auto tests/test_minimal/test_tools/aws_tools.py
+      - name: Run generic AWS tests
+        run: pytest -rsx -n auto tests/test_minimal/test_tools/aws_tools_tests.py
diff --git a/.github/workflows/live-service-testing.yml b/.github/workflows/live-service-testing.yml
@@ -7,14 +7,18 @@ on:
         description: 'List of Python versions to use in matrix, as JSON string'
         required: true
         type: string
-        default: '["3.9", "3.10", "3.11", "3.12"]'
       os-versions:
         description: 'List of OS versions to use in matrix, as JSON string'
         required: true
         type: string
-        default: '["ubuntu-latest", "macos-latest", "windows-latest"]'
 
     secrets:
+      AWS_ACCESS_KEY_ID:
+        required: true
+      AWS_SECRET_ACCESS_KEY:
+        required: true
+      S3_GIN_BUCKET:
+        required: true
       DANDI_API_KEY:
         required: true
 
@@ -47,7 +51,17 @@ jobs:
       - name: Install full requirements
         run: pip install .[test,full]
 
+      - name: Prepare data for tests
+        uses: ./.github/actions/load-data
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          s3-gin-bucket: ${{ secrets.S3_GIN_BUCKET }}
+          os: ${{ matrix.os }}
+
       - name: Run subset of tests that use DANDI live services
         run: pytest -rsx -n auto tests/test_minimal/test_tools/dandi_transfer_tools.py
+      - name: Run subset of tests that use DANDI live services with YAML
+        run: pytest -rsx -n auto tests/test_on_data/test_yaml/yaml_dandi_transfer_tools.py
       - name: Run subset of tests that use Globus live services
         run: pytest -rsx -n auto tests/test_minimal/test_tools/globus_transfer_tools.py
diff --git a/.github/workflows/neuroconv_deployment_aws_tests.yml b/.github/workflows/neuroconv_deployment_aws_tests.yml
@@ -0,0 +1,46 @@
+name: NeuroConv Deployment AWS Tests
+on:
+  schedule:
+    - cron: "0 16 * * 3"  # Weekly at noon on Wednesday
+  workflow_dispatch:
+
+concurrency:  # Cancel previous workflows on the same pull request
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+  RCLONE_DRIVE_ACCESS_TOKEN: ${{ secrets.RCLONE_DRIVE_ACCESS_TOKEN }}
+  RCLONE_DRIVE_REFRESH_TOKEN: ${{ secrets.RCLONE_DRIVE_REFRESH_TOKEN }}
+  RCLONE_EXPIRY_TOKEN: ${{ secrets.RCLONE_EXPIRY_TOKEN }}
+  DANDI_API_KEY: ${{ secrets.DANDI_API_KEY }}
+
+jobs:
+  run:
+    name: ${{ matrix.os }} Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+        os: [ubuntu-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - run: git fetch --prune --unshallow --tags
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Global Setup
+        run: |
+          python -m pip install -U pip  # Official recommended way
+          git config --global user.email "CI@example.com"
+          git config --global user.name "CI Almighty"
+
+      - name: Install AWS requirements
+        run: pip install .[aws,test]
+
+      - name: Run NeuroConv Deployment on AWS tests
+        run: pytest -rsx -n auto tests/test_on_data/test_yaml/neuroconv_deployment_aws_tools_tests.py
diff --git a/.github/workflows/rclone_aws_tests.yml b/.github/workflows/rclone_aws_tests.yml
@@ -0,0 +1,46 @@
+name: Rclone AWS Tests
+on:
+  schedule:
+    - cron: "0 16 * * 2"  # Weekly at noon on Tuesday
+  workflow_dispatch:
+
+concurrency:  # Cancel previous workflows on the same pull request
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+  RCLONE_DRIVE_ACCESS_TOKEN: ${{ secrets.RCLONE_DRIVE_ACCESS_TOKEN }}
+  RCLONE_DRIVE_REFRESH_TOKEN: ${{ secrets.RCLONE_DRIVE_REFRESH_TOKEN }}
+  RCLONE_EXPIRY_TOKEN: ${{ secrets.RCLONE_EXPIRY_TOKEN }}
+  DANDI_API_KEY: ${{ secrets.DANDI_API_KEY }}
+
+jobs:
+  run:
+    name: ${{ matrix.os }} Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+        os: [ubuntu-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - run: git fetch --prune --unshallow --tags
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Global Setup
+        run: |
+          python -m pip install -U pip  # Official recommended way
+          git config --global user.email "CI@example.com"
+          git config --global user.name "CI Almighty"
+
+      - name: Install AWS requirements
+        run: pip install .[aws,test]
+
+      - name: Run RClone on AWS tests
+        run: pytest -rsx -n auto tests/test_on_data/test_yaml/yaml_aws_tools_tests.py
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -7,13 +7,10 @@ on:
         description: 'List of Python versions to use in matrix, as JSON string'
         required: true
         type: string
-        default: '["3.9", "3.10", "3.11", "3.12"]'
       os-versions:
         description: 'List of OS versions to use in matrix, as JSON string'
         required: true
         type: string
-        default: '["ubuntu-latest", "macos-latest", "windows-latest"]'
-
 
     secrets:
       AWS_ACCESS_KEY_ID:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,19 +1,19 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 
 -   repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
     -   id: black
         exclude: ^docs/
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.6.5
+  rev: v0.7.1
   hooks:
   - id: ruff
     args: [ --fix ]
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		["ubuntu-latest", "macos-latest", "windows-latest", "macos-13"]