Merge main into cellpack-analysis

.github/actions/dependencies/action.yml

@@ -3,8 +3,8 @@ description: Install UV and dependencies
 runs:
   using: composite
   steps:
-    - name: Install uv
-      uses: astral-sh/setup-uv@v4
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v7
 
     - name: Install dependencies
       shell: bash

.github/actions/uv/action.yml

@@ -3,7 +3,7 @@ description: Install UV
 runs:
   using: composite
   steps:
-    - name: Set up UV
-      uses: astral-sh/setup-uv@v3
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v7
       with:
         enable-cache: true

.github/dependabot.yml

@@ -16,4 +16,18 @@ updates:
     groups:
       actions:
         patterns:
-          - "github-actions"
+          - "*"
+
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    commit-message:
+      prefix: "deps(dependabot):"
+    open-pull-requests-limit: 1
+    rebase-strategy: "auto"
+    groups:
+      python-all:
+        patterns:
+          - "*"
+

.github/workflows/add-issue-to-project.yml

@@ -10,7 +10,7 @@ jobs:
     name: Add issue to project
     runs-on: ubuntu-latest
     steps:   
-      - uses: actions/add-to-project@v1.0.2
+      - uses: actions/add-to-project@v2.0.0
         with:
           project-url: https://github.com/orgs/mesoscope/projects/1
           github-token: ${{ secrets.PROJECT_PAT }}

.github/workflows/analyze.yml

@@ -15,7 +15,7 @@ jobs:
                 python-version: [3.11]
                 os: [ubuntu-latest]
         steps:
-            - uses: actions/checkout@v4.2.2
+            - uses: actions/checkout@v6
             - uses: ./.github/actions/dependencies
             - name: Pack test recipe
               run: |
@@ -27,49 +27,66 @@ jobs:
             - name: Run analysis code
               run: uv run analyze -r cellpack/tests/recipes/v2/test_spheres.json -a cellpack/tests/analysis-configs/PR_analysis_config.json -p cellpack/tests/outputs/test_spheres/spheresSST
             - name: Upload results
-              uses: actions/upload-artifact@v4
+              uses: actions/upload-artifact@v7
               with:
                   name: results
                   path: cellpack/tests/outputs/test_spheres/
     Comment:
         runs-on: ubuntu-latest
         needs: [Analyze]
         steps:
-            - uses: actions/checkout@v4.2.2
+            - uses: actions/checkout@v6
             - name: Configure AWS credentials for dependabot
               if: ${{ github.actor == 'dependabot[bot]' }}
-              uses: aws-actions/configure-aws-credentials@v4
+              uses: aws-actions/configure-aws-credentials@v6
               with:
                   aws-access-key-id: ${{ secrets.DEPENDABOT_AWS_ACCESS_KEY_ID }}
                   aws-secret-access-key: ${{ secrets.DEPENDABOT_AWS_SECRET_ACCESS_KEY }}
                   aws-region: us-west-2
             - name: Configure AWS credentials
               if: ${{ github.actor != 'dependabot[bot]' }}
-              uses: aws-actions/configure-aws-credentials@v4
+              uses: aws-actions/configure-aws-credentials@v6
               with:
                   aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
                   aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
                   aws-region: us-west-2
-            - uses: actions/download-artifact@v6
+            - uses: actions/download-artifact@v8
               with:
                   name: results
                   path: ./results
             - name: Copy files to results bucket
               run: aws s3 cp ./results s3://cellpack-results/${{  github.ref_name  }}/ --recursive --acl public-read
-            - uses: iterative/setup-cml@v2
-              with:
-                vega: false # we only use CML to post markdown reports, so disable vega to skip extra npm installs
             - name: Update comment for dependabot
-              if: ${{ github.actor == 'dependabot[bot]' }}
+              if: ${{ github.event_name == 'pull_request' && github.actor == 'dependabot[bot]' }}
               env:
-                  REPO_TOKEN: ${{ secrets.DEPENDABOT_TOKEN }}
+                  GH_TOKEN: ${{ secrets.DEPENDABOT_TOKEN }}
               run: |
-                  cml comment update --watermark-title="{workflow} report" ./results/analysis_report.md --target=pr
+                  MARKER="<!-- Analyze workflow report -->"
+                  COMMENT_BODY="${MARKER}
+                  $(cat ./results/analysis_report.md)"
+                  EXISTING_COMMENT_ID=$(gh api "/repos/${{ github.repository }}/issues/${{ github.event.pull_request.number }}/comments" --jq ".[] | select(.body | contains(\"${MARKER}\")) | .id" | head -1)
+                    if [ -n "$EXISTING_COMMENT_ID" ]; then
+                      echo "Updating existing comment with ID: $EXISTING_COMMENT_ID"
+                      echo "$COMMENT_BODY" | gh api -X PATCH "/repos/${{ github.repository }}/issues/comments/$EXISTING_COMMENT_ID" -F body=@-
+                    else
+                      echo "Creating new comment"
+                      echo "$COMMENT_BODY" | gh pr comment ${{ github.event.pull_request.number }} --body-file -
+                    fi
                   cat ./results/analysis_report.md
             - name: Update comment for PR
-              if: ${{ github.actor != 'dependabot[bot]' }}
+              if: ${{ github.event_name == 'pull_request' && github.actor != 'dependabot[bot]' }}
               env:
-                  REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+                  GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
               run: |
-                  cml comment update --watermark-title="{workflow} report" ./results/analysis_report.md --target=pr
+                  MARKER="<!-- Analyze workflow report -->"
+                  COMMENT_BODY="${MARKER}
+                  $(cat ./results/analysis_report.md)"
+                  EXISTING_COMMENT_ID=$(gh api "/repos/${{ github.repository }}/issues/${{ github.event.pull_request.number }}/comments" --jq ".[] | select(.body | contains(\"${MARKER}\")) | .id" | head -1)
+                  if [ -n "$EXISTING_COMMENT_ID" ]; then
+                    echo "Updating existing comment with ID: $EXISTING_COMMENT_ID"
+                    echo "$COMMENT_BODY" | gh api -X PATCH "/repos/${{ github.repository }}/issues/comments/$EXISTING_COMMENT_ID" -F body=@-
+                  else
+                    echo "Creating new comment"
+                    echo "$COMMENT_BODY" | gh pr comment ${{ github.event.pull_request.number }} --body-file -
+                  fi
                   cat ./results/analysis_report.md

.github/workflows/build-docs.yml

@@ -17,14 +17,14 @@ jobs:
     if: ${{ !contains(github.event.head_commit.message, 'Bump version') }}
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4.2.2
+    - uses: actions/checkout@v6
       with:
         persist-credentials: false
 
     - uses: ./.github/actions/dependencies
 
     - name: Setup Pages
-      uses: actions/configure-pages@v5
+      uses: actions/configure-pages@v6
 
     - name: Generate Docs
       run: |
@@ -33,7 +33,7 @@ jobs:
 
     - name: Upload artifact
       id: deployment
-      uses: actions/upload-pages-artifact@v4
+      uses: actions/upload-pages-artifact@v5
       with:
         path: docs/_build/html/
 
@@ -50,5 +50,5 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@v5
 

.github/workflows/cache-dependencies.yml

@@ -14,5 +14,5 @@ jobs:
   dependencies:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - uses: ./.github/actions/dependencies

.github/workflows/ci.yml

@@ -30,19 +30,19 @@ jobs:
         os: [ubuntu-latest, windows-latest, macOS-latest]
 
     steps:
-    - uses: actions/checkout@v4.2.2
+    - uses: actions/checkout@v6
     - uses: ./.github/actions/dependencies
     - name: Test with pytest
       run: |
         uv run pytest --cov cellpack/tests/
     - name: Upload codecov
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
 
   lint:
     runs-on: ubuntu-latest
     if: ${{ !contains(github.event.head_commit.message, 'Bump version') }}
     steps:
-    - uses: actions/checkout@v4.2.2
+    - uses: actions/checkout@v6
     - uses: ./.github/actions/dependencies
     - name: Lint with flake8
       run: |
@@ -62,7 +62,7 @@ jobs:
       id-token: write
 
     steps:
-    - uses: actions/checkout@v4.2.2
+    - uses: actions/checkout@v6
     - uses: ./.github/actions/dependencies
     - name: Publish to PyPI
       run: uv publish

.github/workflows/cleanup-aws.yml

@@ -9,9 +9,9 @@ jobs:
   cleanup:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4.2.2
+    - uses: actions/checkout@v6
     - name: Configure AWS credentials
-      uses: aws-actions/configure-aws-credentials@v4
+      uses: aws-actions/configure-aws-credentials@v6
       with:
         aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
         aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}