Merge origin/main

Author: cmdcolin

.github/workflows/push.yml

@@ -18,7 +18,7 @@ jobs:
       skip_jobs: ${{ steps.check_message.outputs.skip_jobs }}
     steps:
       - name: Checkout code
-        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           fetch-depth: 1
       - name: Check commit message
@@ -35,51 +35,27 @@ jobs:
             echo "Running regular push jobs"
           fi
 
-  # Conditionally run the buildwebsite job
-  buildwebsite:
-    name: Build website
+  main:
+    name: Build, deploy, lint, typecheck, and test
     needs: check_commit_message
     if: needs.check_commit_message.outputs.skip_jobs != 'true'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
-        with:
-          persist-credentials: false
-      - uses: actions/setup-node@2028fbc5c25fe9cf00d9f06a71cc4710d4507903 # v6.0.0
-        with:
-          node-version: '22'
-          cache: 'yarn'
-          cache-dependency-path: 'website/yarn.lock'
-      - name: Install dependencies
-        run: yarn install --frozen-lockfile
-        working-directory: website
-      - name: Build website
+      - name: Install system dependencies
         run: |
-          cd website/
-          yarn build
-          mkdir testing
-          mv build testing/jb2
-      - name: Check website links
-        uses: untitaker/hyperlink@fb5bb9c5011a3d143a54b4b30aedc30ec5bc0f89 # 0.2.0
-        with:
-          args: website/testing/ --check-anchors
-
-  # Conditionally run the buildjbrowseweb job
-  buildjbrowseweb:
-    name: Deploy jbrowse-web and storybooks to S3
-    needs: check_commit_message
-    if: needs.check_commit_message.outputs.skip_jobs != 'true'
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
+          sudo apt-get update
+          sudo apt-get -y install tabix libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           persist-credentials: false
-      - uses: actions/setup-node@2028fbc5c25fe9cf00d9f06a71cc4710d4507903 # v6.0.0
+      - uses: actions/setup-node@395ad3262231945c25e8478fd5baf05154b1d79f # v6.1.0
         with:
           node-version: '22'
           cache: 'yarn'
       - name: Install dependencies
         run: yarn install --frozen-lockfile
+
+      # Deploy jbrowse-web first
       - name: Validate branch/tag name for S3 path safety
         env:
           REF_NAME: ${{ github.ref_name }}
@@ -106,57 +82,7 @@ jobs:
           aws s3 sync --delete --exclude="*.map" build s3://jbrowse.org/code/jb2/${{ github.ref_name }}
           aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths "/code/jb2/${{ github.ref_name }}/*"
 
-      - name: Build LGV storybook
-        run: yarn storybook:build
-        working-directory: products/jbrowse-react-linear-genome-view
-
-      - name: Deploy LGV storybook
-        if: startsWith(github.ref, 'refs/tags/')
-        run: |
-          aws s3 sync --delete storybook-static s3://jbrowse.org/storybook/lgv/${{ github.ref_name }}
-          aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths "/storybook/lgv/${{ github.ref_name }}/*"
-        working-directory: products/jbrowse-react-linear-genome-view
-
-      - name: Build React App storybook
-        run: yarn storybook:build
-        working-directory: products/jbrowse-react-app
-
-      - name: Deploy React App storybook
-        if: startsWith(github.ref, 'refs/tags/')
-        run: |
-          aws s3 sync --delete storybook-static s3://jbrowse.org/storybook/app/${{ github.ref_name }}
-          aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths "/storybook/app/${{ github.ref_name }}/*"
-        working-directory: products/jbrowse-react-app
-
-      - name: Build CGV storybook
-        run: yarn storybook:build
-        working-directory: products/jbrowse-react-circular-genome-view
-
-      - name: Deploy CGV storybook
-        if: startsWith(github.ref, 'refs/tags/')
-        run: |
-          aws s3 sync --delete storybook-static s3://jbrowse.org/storybook/cgv/${{ github.ref_name }}
-          aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths "/storybook/cgv/${{ github.ref_name }}/*"
-        working-directory: products/jbrowse-react-circular-genome-view
-
-  # Conditionally run the main job
-  main:
-    name: Lint, typecheck, test, and build
-    needs: check_commit_message
-    if: needs.check_commit_message.outputs.skip_jobs != 'true'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Install tabix
-        run: sudo apt-get -y install tabix
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
-        with:
-          persist-credentials: false
-      - uses: actions/setup-node@2028fbc5c25fe9cf00d9f06a71cc4710d4507903 # v6.0.0
-        with:
-          node-version: '22'
-          cache: 'yarn'
-      - name: Install dependencies
-        run: yarn install --frozen-lockfile
+      # Lint, typecheck, test
       - name: Check code formatting
         run: yarn prettier --check .
       - name: Spellcheck
@@ -173,15 +99,11 @@ jobs:
         run: BUILT_TESTS=1 yarn built-test-ci
       - name: Run browser tests with Puppeteer
         id: browser-tests
-        run: yarn install --frozen-lockfile && yarn test
-        working-directory: products/jbrowse-web/browser-tests
+        run: node --experimental-strip-types browser-tests/runner.ts
+        working-directory: products/jbrowse-web
         continue-on-error: true
       - name: Upload snapshot diffs to S3
         if: steps.browser-tests.outcome == 'failure'
-        env:
-          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          AWS_DEFAULT_REGION: us-east-1
         run: |
           SNAPSHOTS_DIR="products/jbrowse-web/browser-tests/__snapshots__"
           S3_PATH="s3://jbrowse.org/demos/imagediff/${{ github.run_id }}"
@@ -205,13 +127,77 @@ jobs:
       - name: Fail if browser tests failed
         if: steps.browser-tests.outcome == 'failure'
         run: exit 1
+
+      # Deploy storybooks
+      - name: Build LGV storybook
+        run: yarn storybook:build
+        working-directory: products/jbrowse-react-linear-genome-view
+
+      - name: Deploy LGV storybook
+        if: startsWith(github.ref, 'refs/tags/')
+        run: |
+          aws s3 sync --delete storybook-static s3://jbrowse.org/storybook/lgv/${{ github.ref_name }}
+          aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths "/storybook/lgv/${{ github.ref_name }}/*"
+        working-directory: products/jbrowse-react-linear-genome-view
+
+      - name: Build React App storybook
+        run: yarn storybook:build
+        working-directory: products/jbrowse-react-app
+
+      - name: Deploy React App storybook
+        if: startsWith(github.ref, 'refs/tags/')
+        run: |
+          aws s3 sync --delete storybook-static s3://jbrowse.org/storybook/app/${{ github.ref_name }}
+          aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths "/storybook/app/${{ github.ref_name }}/*"
+        working-directory: products/jbrowse-react-app
+
+      - name: Build CGV storybook
+        run: yarn storybook:build
+        working-directory: products/jbrowse-react-circular-genome-view
+
+      - name: Deploy CGV storybook
+        if: startsWith(github.ref, 'refs/tags/')
+        run: |
+          aws s3 sync --delete storybook-static s3://jbrowse.org/storybook/cgv/${{ github.ref_name }}
+          aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths "/storybook/cgv/${{ github.ref_name }}/*"
+        working-directory: products/jbrowse-react-circular-genome-view
+
       - name: Upload packed artifacts for component tests
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6.0.0
         with:
           name: packed-artifacts
           path: component_tests/*/packed/
           retention-days: 1
 
+  # Conditionally run the buildwebsite job
+  buildwebsite:
+    name: Build website
+    needs: check_commit_message
+    if: needs.check_commit_message.outputs.skip_jobs != 'true'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
+        with:
+          persist-credentials: false
+      - uses: actions/setup-node@395ad3262231945c25e8478fd5baf05154b1d79f # v6.1.0
+        with:
+          node-version: '22'
+          cache: 'yarn'
+          cache-dependency-path: 'website/yarn.lock'
+      - name: Install dependencies
+        run: yarn install --frozen-lockfile
+        working-directory: website
+      - name: Build website
+        run: |
+          cd website/
+          yarn build
+          mkdir testing
+          mv build testing/jb2
+      - name: Check website links
+        uses: untitaker/hyperlink@fb5bb9c5011a3d143a54b4b30aedc30ec5bc0f89 # 0.2.0
+        with:
+          args: website/testing/ --check-anchors
+
   # Separate job for component_tests with no permissions.
   # These tests install npm packages without a yarn.lock, so untrusted
   # dependencies could potentially run malicious code. By isolating this
@@ -225,14 +211,14 @@ jobs:
     runs-on: ubuntu-latest
     permissions: {}
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           persist-credentials: false
-      - uses: actions/setup-node@2028fbc5c25fe9cf00d9f06a71cc4710d4507903 # v6.0.0
+      - uses: actions/setup-node@395ad3262231945c25e8478fd5baf05154b1d79f # v6.1.0
         with:
           node-version: '22'
       - name: Download packed artifacts
-        uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4.3.0
+        uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
         with:
           name: packed-artifacts
           path: component_tests/

.github/workflows/release.yml

@@ -14,10 +14,10 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           persist-credentials: false
-      - uses: actions/setup-node@2028fbc5c25fe9cf00d9f06a71cc4710d4507903 # v6.0.0
+      - uses: actions/setup-node@395ad3262231945c25e8478fd5baf05154b1d79f # v6.1.0
         with:
           node-version: '22'
           cache: 'yarn'
@@ -47,13 +47,13 @@ jobs:
     container:
       image: docker://node:22-bullseye
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           persist-credentials: false
       - name: Install dependencies
         run: yarn install --frozen-lockfile
       - name: Setup java
-        uses: actions/setup-java@dded0888837ed1f317902acf8a20df0ad188d165 # v5.0.0
+        uses: actions/setup-java@f2beeb24e141e01a676f977032f5a29d81c9e27e # v5.1.0
         with:
           # eclipse 'temurin' openjdk https://github.com/actions/setup-java/blob/main/docs/advanced-usage.md#Selecting-a-Java-distribution
           distribution: 'temurin'
@@ -95,11 +95,11 @@ jobs:
     name: Build Mac desktop app
     runs-on: macos-latest
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           persist-credentials: false
 
-      - uses: actions/setup-node@2028fbc5c25fe9cf00d9f06a71cc4710d4507903 # v6.0.0
+      - uses: actions/setup-node@395ad3262231945c25e8478fd5baf05154b1d79f # v6.1.0
         with:
           node-version: '22'
           cache: 'yarn'
@@ -123,11 +123,11 @@ jobs:
     name: Build Linux desktop app
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           persist-credentials: false
 
-      - uses: actions/setup-node@2028fbc5c25fe9cf00d9f06a71cc4710d4507903 # v6.0.0
+      - uses: actions/setup-node@395ad3262231945c25e8478fd5baf05154b1d79f # v6.1.0
         with:
           node-version: '22'
           cache: 'yarn'
@@ -148,10 +148,10 @@ jobs:
     name: Deploy jbrowse-web and storybooks to latest folder on tag
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           persist-credentials: false
-      - uses: actions/setup-node@2028fbc5c25fe9cf00d9f06a71cc4710d4507903 # v6.0.0
+      - uses: actions/setup-node@395ad3262231945c25e8478fd5baf05154b1d79f # v6.1.0
         with:
           node-version: '22'
           cache: 'yarn'

.github/workflows/update-docs.yml

@@ -15,10 +15,10 @@ jobs:
       ${{ contains(github.event.head_commit.message, 'update docs') ||
       contains(github.event.head_commit.message, '[update docs only]') }}
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           persist-credentials: false
-      - uses: actions/setup-node@2028fbc5c25fe9cf00d9f06a71cc4710d4507903 # v6.0.0
+      - uses: actions/setup-node@395ad3262231945c25e8478fd5baf05154b1d79f # v6.1.0
         with:
           node-version: '22'
           cache: 'yarn'

.gitignore

@@ -21,3 +21,4 @@ lerna-debug.log
 *.tsbuildinfo
 .aider*
 *.cpuprofile
+test_data/soa4

.ignore

@@ -23,3 +23,5 @@ test_data/config_demo.json
 docs/models/LinearGenomeView.md
 plugins/variants/src/d3-hierarchy2
 benchmarks
+products/jbrowse-web/src/tests/__file_snapshots__/save_track_data.sam
+products/jbrowse-web/src/tests/__file_snapshots__/save_track_data.cram.sam