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Sage-Bionetworks · Feb 6, 2024 · af29f24 · af29f24
2 parents 4986cf2 + 9b207d2
commit af29f24
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Showing 216 changed files with 8,418 additions and 5,372 deletions.
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -10,6 +10,7 @@
     "NX_HEAD": "${localEnv:NX_HEAD}",
     "NX_RUN_GROUP": "${localEnv:NX_RUN_GROUP}",
     "SONAR_TOKEN": "${localEnv:SONAR_TOKEN}",
+    "SONAR_PULL_REQUEST_NUMBER": "${localEnv:SONAR_PULL_REQUEST_NUMBER}",
     "DOCKER_USERNAME": "${localEnv:DOCKER_USERNAME}",
     "DOCKER_PASSWORD": "${localEnv:DOCKER_PASSWORD}"
   },
@@ -21,9 +22,7 @@
   },
   "customizations": {
     "codespaces": {
-      "openFiles": [
-        "README.md"
-      ]
+      "openFiles": ["README.md"]
     },
     "vscode": {
       "extensions": [
@@ -66,41 +65,9 @@
     }
   },
   "forwardPorts": [
-    2432,
-    3000,
-    3306,
-    4200,
-    4211,
-    5017,
-    5200,
-    5432,
-    5601,
-    7010,
-    7080,
-    7200,
-    7888,
-    8010,
-    8071,
-    8000,
-    8080,
-    8081,
-    8082,
-    8083,
-    8084,
-    8085,
-    8086,
-    8090,
-    8091,
-    8092,
-    8200,
-    8787,
-    8888,
-    8889,
-    9090,
-    9104,
-    9200,
-    9411,
-    27017
+    2432, 3000, 3306, 4200, 4211, 5017, 5200, 5432, 5601, 7010, 7080, 7200, 7888, 8010, 8071, 8000,
+    8080, 8081, 8082, 8083, 8084, 8085, 8086, 8090, 8091, 8092, 8200, 8787, 8888, 8889, 9090, 9104,
+    9200, 9411, 27017
   ],
   "portsAttributes": {
     "2432": {
@@ -250,8 +217,5 @@
   },
   "remoteUser": "vscode",
   "shutdownAction": "stopContainer",
-  "runArgs": [
-    "--name",
-    "sage_devcontainer"
-  ]
-}
+  "runArgs": ["--name", "sage_devcontainer"]
+}
diff --git a/.github/actions/setup-dev-container/action.yml b/.github/actions/setup-dev-container/action.yml
@@ -0,0 +1,80 @@
+name: 'Set up the dev container'
+description: 'Installs the dev container CLI, fetches caches (if exist), and starts the dev container'
+runs:
+  using: 'composite'
+  steps:
+    - name: Set up Yarn cache
+      uses: actions/cache@v3
+      with:
+        path: '/tmp/.yarn/cache'
+        key: ${{ runner.os }}-yarn-${{ hashFiles('**/yarn.lock') }}
+        restore-keys: |
+          ${{ runner.os }}-yarn-
+
+    - name: Set up Renv cache
+      uses: actions/cache@v3
+      with:
+        path: '/tmp/.cache/R/renv/cache'
+        key: ${{ runner.os }}-renv-cache-${{ hashFiles('**/renv.lock') }}
+        restore-keys: |
+          ${{ runner.os }}-renv-cache-
+
+    - name: Set up Poetry cache
+      uses: actions/cache@v3
+      with:
+        path: '/tmp/.cache/pypoetry'
+        key: ${{ runner.os }}-poetry-${{ hashFiles('**/poetry.lock') }}
+
+    - name: Set up venv cache
+      uses: actions/cache@v3
+      with:
+        path: |
+          /tmp/.local/share/virtualenv
+          **/.venv
+        key: ${{ runner.os }}-venv-${{ hashFiles('**/poetry.lock') }}
+
+    - name: Set up Gradle cache
+      uses: actions/cache@v3
+      with:
+        path: |
+          /tmp/.gradle/caches
+          /tmp/.gradle/wrapper
+        key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
+        restore-keys: |
+          ${{ runner.os }}-gradle-
+
+    - name: Install the Dev Container CLI
+      shell: bash
+      run: npm install -g @devcontainers/[email protected]
+
+    - name: Start the dev container
+      shell: bash
+      run: |
+        mkdir -p \
+          /tmp/.yarn/cache \
+          /tmp/.cache/R/renv/cache \
+          /tmp/.cache/pypoetry \
+          /tmp/.local/share/virtualenv \
+          /tmp/.gradle/caches \
+          /tmp/.gradle/wrapper
+
+        devcontainer up \
+          --mount type=bind,source=/tmp/.yarn/cache,target=/workspaces/sage-monorepo/.yarn/cache \
+          --mount type=bind,source=/tmp/.cache/R/renv/cache,target=/home/vscode/.cache/R/renv/cache \
+          --mount type=bind,source=/tmp/.cache/pypoetry,target=/home/vscode/.cache/pypoetry \
+          --mount type=bind,source=/tmp/.local/share/virtualenv,target=/home/vscode/.local/share/virtualenv \
+          --mount type=bind,source=/tmp/.gradle/caches,target=/home/vscode/.gradle/caches \
+          --mount type=bind,source=/tmp/.gradle/wrapper,target=/home/vscode/.gradle/wrapper \
+          --workspace-folder ../sage-monorepo
+
+    - name: Prepare the workspace
+      shell: bash
+      run: |
+        devcontainer exec --workspace-folder ../sage-monorepo bash -c "
+          sudo chown -R vscode:vscode \
+            /workspaces/sage-monorepo \
+            /home/vscode/.cache \
+            /home/vscode/.local \
+            /home/vscode/.gradle \
+          && . ./dev-env.sh \
+          && workspace-install-affected"
diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
@@ -0,0 +1,31 @@
+name: Build Docs
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'docs/**/*.md'
+      - 'docs/images/*'
+      - 'mkdocs.yml'
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV 
+      - uses: actions/cache@v3
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - run: pip install mkdocs-material mkdocstrings mkdocstrings-python termynal
+      - run: mkdocs gh-deploy --force
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -12,7 +12,7 @@ env:
   NX_CLOUD_AUTH_TOKEN: ${{ secrets.NX_CLOUD_AUTH_TOKEN }}
   NX_CLOUD_ENCRYPTION_KEY: ${{ secrets.NX_CLOUD_ENCRYPTION_KEY }}
   NX_CLOUD_ENV_NAME: 'linux'
-  SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+  # SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
   DOCKER_USERNAME: ${{ github.actor }}
   DOCKER_PASSWORD: ${{ secrets.GITHUB_TOKEN }}
 
@@ -31,78 +31,8 @@ jobs:
       - name: Derive appropriate SHAs for base and head for `nx affected` commands
         uses: nrwl/nx-set-shas@v3
 
-      - name: Set up Yarn cache
-        uses: actions/cache@v3
-        with:
-          path: '/tmp/.yarn/cache'
-          key: ${{ runner.os }}-yarn-${{ hashFiles('**/yarn.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-yarn-
-
-      - name: Set up Renv cache
-        uses: actions/cache@v3
-        with:
-          path: '/tmp/.cache/R/renv/cache'
-          key: ${{ runner.os }}-renv-cache-${{ hashFiles('**/renv.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-renv-cache-
-
-      - name: Set up Poetry cache
-        uses: actions/cache@v3
-        with:
-          path: '/tmp/.cache/pypoetry'
-          key: ${{ runner.os }}-poetry-${{ hashFiles('**/poetry.lock') }}
-
-      - name: Set up venv cache
-        uses: actions/cache@v3
-        with:
-          path: |
-            /tmp/.local/share/virtualenv
-            **/.venv
-          key: ${{ runner.os }}-venv-${{ hashFiles('**/poetry.lock') }}
-
-      - name: Set up Gradle cache
-        uses: actions/cache@v3
-        with:
-          path: |
-            /tmp/.gradle/caches
-            /tmp/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
-          restore-keys: |
-            ${{ runner.os }}-gradle-
-
-      - name: Install the Dev Container CLI
-        run: npm install -g @devcontainers/[email protected]
-
-      - name: Start the dev container
-        run: |
-          mkdir -p \
-            /tmp/.yarn/cache \
-            /tmp/.cache/R/renv/cache \
-            /tmp/.cache/pypoetry \
-            /tmp/.local/share/virtualenv \
-            /tmp/.gradle/caches \
-            /tmp/.gradle/wrapper
-
-          devcontainer up \
-            --mount type=bind,source=/tmp/.yarn/cache,target=/workspaces/sage-monorepo/.yarn/cache \
-            --mount type=bind,source=/tmp/.cache/R/renv/cache,target=/home/vscode/.cache/R/renv/cache \
-            --mount type=bind,source=/tmp/.cache/pypoetry,target=/home/vscode/.cache/pypoetry \
-            --mount type=bind,source=/tmp/.local/share/virtualenv,target=/home/vscode/.local/share/virtualenv \
-            --mount type=bind,source=/tmp/.gradle/caches,target=/home/vscode/.gradle/caches \
-            --mount type=bind,source=/tmp/.gradle/wrapper,target=/home/vscode/.gradle/wrapper \
-            --workspace-folder ../sage-monorepo
-
-      - name: Prepare the workspace
-        run: |
-          devcontainer exec --workspace-folder ../sage-monorepo bash -c "
-            sudo chown -R vscode:vscode \
-              /workspaces/sage-monorepo \
-              /home/vscode/.cache \
-              /home/vscode/.local \
-              /home/vscode/.gradle \
-            && . ./dev-env.sh \
-            && workspace-install-affected"
+      - name: Set up the dev container
+        uses: ./.github/actions/setup-dev-container
 
       - name: Lint the affected projects
         run: |
@@ -124,10 +54,10 @@ jobs:
           devcontainer exec --workspace-folder ../sage-monorepo bash -c ". ./dev-env.sh \
             && nx affected --target=integration-test"
 
-      - name: Scan the affected projects with Sonar
-        run: |
-          devcontainer exec --workspace-folder ../sage-monorepo bash -c ". ./dev-env.sh \
-            && nx affected --target=sonar"
+      # - name: Scan the affected projects with Sonar
+      #   run: |
+      #     devcontainer exec --workspace-folder ../sage-monorepo bash -c ". ./dev-env.sh \
+      #       && nx affected --target=sonar"
 
       - name: Publish the images of the affected projects
         run: |
@@ -161,78 +91,8 @@ jobs:
       - name: Derive appropriate SHAs for base and head for `nx affected` commands
         uses: nrwl/nx-set-shas@v3
 
-      - name: Set up Yarn cache
-        uses: actions/cache@v3
-        with:
-          path: '/tmp/.yarn/cache'
-          key: ${{ runner.os }}-yarn-${{ hashFiles('**/yarn.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-yarn-
-
-      - name: Set up Renv cache
-        uses: actions/cache@v3
-        with:
-          path: '/tmp/.cache/R/renv/cache'
-          key: ${{ runner.os }}-renv-cache-${{ hashFiles('**/renv.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-renv-cache-
-
-      - name: Set up Poetry cache
-        uses: actions/cache@v3
-        with:
-          path: '/tmp/.cache/pypoetry'
-          key: ${{ runner.os }}-poetry-${{ hashFiles('**/poetry.lock') }}
-
-      - name: Set up venv cache
-        uses: actions/cache@v3
-        with:
-          path: |
-            /tmp/.local/share/virtualenv
-            **/.venv
-          key: ${{ runner.os }}-venv-${{ hashFiles('**/poetry.lock') }}
-
-      - name: Set up Gradle cache
-        uses: actions/cache@v3
-        with:
-          path: |
-            /tmp/.gradle/caches
-            /tmp/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
-          restore-keys: |
-            ${{ runner.os }}-gradle-
-
-      - name: Install the Dev Container CLI
-        run: npm install -g @devcontainers/[email protected]
-
-      - name: Start the dev container
-        run: |
-          mkdir -p \
-            /tmp/.yarn/cache \
-            /tmp/.cache/R/renv/cache \
-            /tmp/.cache/pypoetry \
-            /tmp/.local/share/virtualenv \
-            /tmp/.gradle/caches \
-            /tmp/.gradle/wrapper
-
-          devcontainer up \
-            --mount type=bind,source=/tmp/.yarn/cache,target=/workspaces/sage-monorepo/.yarn/cache \
-            --mount type=bind,source=/tmp/.cache/R/renv/cache,target=/home/vscode/.cache/R/renv/cache \
-            --mount type=bind,source=/tmp/.cache/pypoetry,target=/home/vscode/.cache/pypoetry \
-            --mount type=bind,source=/tmp/.local/share/virtualenv,target=/home/vscode/.local/share/virtualenv \
-            --mount type=bind,source=/tmp/.gradle/caches,target=/home/vscode/.gradle/caches \
-            --mount type=bind,source=/tmp/.gradle/wrapper,target=/home/vscode/.gradle/wrapper \
-            --workspace-folder ../sage-monorepo
-
-      - name: Prepare the workspace
-        run: |
-          devcontainer exec --workspace-folder ../sage-monorepo bash -c "
-            sudo chown -R vscode:vscode \
-              /workspaces/sage-monorepo \
-              /home/vscode/.cache \
-              /home/vscode/.local \
-              /home/vscode/.gradle \
-            && . ./dev-env.sh \
-            && workspace-install"
+      - name: Set up the dev container
+        uses: ./.github/actions/setup-dev-container
 
       - name: Lint the affected projects
         run: |