Merge branch 'main' into agora/migration-toast

Sage-Bionetworks · Jan 28, 2025 · ec65823 · ec65823
2 parents 771af1e + 899e091
commit ec65823
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -1,6 +1,6 @@
 {
-  "name": "Sage Dev Container",
-  "image": "ghcr.io/sage-bionetworks/sage-devcontainer:fab0893",
+  "name": "Sage Monorepo Dev Container",
+  "image": "ghcr.io/sage-bionetworks/sage-monorepo-devcontainer:sha-c7e2cdbc88fb8cc4815dafedd92b105e4b9544f2",
   "containerEnv": {
     "NX_BASE": "${localEnv:NX_BASE}",
     "NX_BRANCH": "${localEnv:NX_BRANCH}",
@@ -14,61 +14,10 @@
     "DOCKER_USERNAME": "${localEnv:DOCKER_USERNAME}",
     "DOCKER_PASSWORD": "${localEnv:DOCKER_PASSWORD}"
   },
-  "features": {
-    "ghcr.io/devcontainers/features/docker-in-docker:2.11.0": {
-      "version": "27.0.3",
-      "moby": false
-    }
-  },
-  "customizations": {
-    "codespaces": {
-      "openFiles": ["README.md"]
-    },
-    "vscode": {
-      "extensions": [
-        "alefragnani.Bookmarks",
-        "Angular.ng-template",
-        "dbaeumer.vscode-eslint",
-        "donjayamanne.python-environment-manager",
-        "dorzey.vscode-sqlfluff",
-        "eamodio.gitlens",
-        "emeraldwalk.RunOnSave",
-        "esbenp.prettier-vscode",
-        "exiasr.hadolint",
-        "formulahendry.auto-rename-tag",
-        "github.vscode-github-actions",
-        "GitHub.vscode-pull-request-github",
-        "Gruntfuggly.todo-tree",
-        "humao.rest-client",
-        "mhutchie.git-graph",
-        "mongodb.mongodb-vscode",
-        "ms-playwright.playwright",
-        "ms-python.black-formatter",
-        "ms-python.python",
-        "ms-toolsai.jupyter",
-        "mtxr.sqltools-driver-mysql",
-        "mtxr.sqltools-driver-pg",
-        "mtxr.sqltools",
-        "njpwerner.autodocstring",
-        "Orta.vscode-jest",
-        "pranaygp.vscode-css-peek",
-        "ritwickdey.LiveServer",
-        "shengchen.vscode-checkstyle",
-        "SonarSource.sonarlint-vscode",
-        "stkb.rewrap",
-        "stylelint.vscode-stylelint",
-        "vmware.vscode-boot-dev-pack",
-        "vscjava.vscode-gradle",
-        "vscjava.vscode-java-pack"
-      ],
-      "settings": {
-        "workbench.startupEditor": "readme"
-      }
-    }
-  },
+  "features": {},
   "forwardPorts": [
-    2432, 3306, 3333, 4200, 4211, 5000, 5200, 5432, 5601, 7010, 7443, 7200, 7888, 8010, 8071, 8000,
-    8080, 8081, 8082, 8084, 8085, 8086, 8090, 8200, 8888, 8889, 9200, 9411, 27017
+    2432, 3306, 3333, 4200, 4211, 5000, 5200, 5432, 5601, 8010, 8071, 8000, 8080, 8081, 8082, 8084,
+    8085, 8086, 8090, 8200, 8888, 8889, 9200, 9411, 27017
   ],
   "portsAttributes": {
     "2432": {
@@ -107,22 +56,6 @@
       "label": "openchallenges-opensearch-dashboards",
       "onAutoForward": "silent"
     },
-    "7010": {
-      "label": "schematic-api-docs",
-      "onAutoForward": "silent"
-    },
-    "7443": {
-      "label": "schematic-api",
-      "onAutoForward": "silent"
-    },
-    "7200": {
-      "label": "schematic-app",
-      "onAutoForward": "silent"
-    },
-    "7888": {
-      "label": "schematic-notebook",
-      "onAutoForward": "silent"
-    },
     "8000": {
       "label": "openchallenges-apex",
       "onAutoForward": "silent"
@@ -180,7 +113,48 @@
       "onAutoForward": "silent"
     }
   },
-  "remoteUser": "vscode",
+  "otherPortsAttributes": {
+    "onAutoForward": "silent"
+  },
   "shutdownAction": "stopContainer",
-  "runArgs": ["--name", "sage_devcontainer"]
+  "runArgs": ["--name", "sage-monorepo-devcontainer"],
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "alefragnani.Bookmarks",
+        "Angular.ng-template",
+        "dbaeumer.vscode-eslint",
+        "donjayamanne.python-environment-manager",
+        "eamodio.gitlens",
+        "emeraldwalk.RunOnSave",
+        "esbenp.prettier-vscode",
+        "exiasr.hadolint",
+        "formulahendry.auto-rename-tag",
+        "github.vscode-github-actions",
+        "GitHub.vscode-pull-request-github",
+        "Gruntfuggly.todo-tree",
+        "humao.rest-client",
+        "mhutchie.git-graph",
+        "mongodb.mongodb-vscode",
+        "ms-playwright.playwright",
+        "ms-python.black-formatter",
+        "ms-python.python",
+        "ms-toolsai.jupyter",
+        "mtxr.sqltools-driver-mysql",
+        "mtxr.sqltools-driver-pg",
+        "mtxr.sqltools",
+        "njpwerner.autodocstring",
+        "Orta.vscode-jest",
+        "pranaygp.vscode-css-peek",
+        "ritwickdey.LiveServer",
+        "shengchen.vscode-checkstyle",
+        "SonarSource.sonarlint-vscode",
+        "stkb.rewrap",
+        "stylelint.vscode-stylelint",
+        "vmware.vscode-boot-dev-pack",
+        "vscjava.vscode-gradle",
+        "vscjava.vscode-java-pack"
+      ]
+    }
+  }
 }
diff --git a/.github/.devcontainer/Dockerfile b/.github/.devcontainer/Dockerfile
@@ -25,7 +25,7 @@ ARG nodeVersionMajor="22"
 # https://pypi.org/project/pipenv/
 ARG pipenvVersion="2024.4.0"
 # https://github.com/pnpm/pnpm/releases
-ARG pnpmVersion="9.15.2"
+ARG pnpmVersion="9.15.4"
 # List of Python versions separated by spaces
 ARG pyenvPythonVersions="3.13.1"
 # https://github.com/SonarSource/sonar-scanner-cli/releases

diff --git a/.github/.devcontainer/devcontainer.json b/.github/.devcontainer/devcontainer.json
@@ -10,16 +10,17 @@
   },
   "features": {
     "ghcr.io/devcontainers/features/docker-in-docker:2.12.0": {
-      "version": "27.4.1"
+      "version": "27.5.1",
+      "installDockerComposeSwitch": false
     },
     "ghcr.io/devcontainers/features/go:1.3.1": {
-      "version": "1.23",
+      "version": "1.23.5",
       "golangciLintVersion": "1.63.4"
     },
     "ghcr.io/devcontainers/features/kubectl-helm-minikube:1.2.0": {
-      "version": "1.32",
-      "helm": "3.16.4",
-      "minikube": "1.34.0"
+      "version": "1.32.1",
+      "helm": "3.17.0",
+      "minikube": "1.35.0"
     }
   },
   "remoteUser": "ubuntu",

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -21,11 +21,6 @@
 /apps/sage/ @tschaffter
 /libs/sage/ @tschaffter
 
-# Schematic
-/apps/schematic/ @andrewelamb @GiaJordan @linglp @milen-sage
-/libs/schematic/ @andrewelamb @GiaJordan @linglp @milen-sage
-/libs/schematic/api-client-r/ @andrewelamb @lakikowolfe @afwillia
-
 /apps/agora/ @Sage-Bionetworks/sage-monorepo-agora
 /libs/agora/ @Sage-Bionetworks/sage-monorepo-agora
 

diff --git a/.github/ISSUE_TEMPLATE/1-bug.yml b/.github/ISSUE_TEMPLATE/1-bug.yml
@@ -27,7 +27,6 @@ body:
         - Sage
         - Sage Monorepo
         - Sandbox
-        - Schematic
         - Synapse
         - Other
   - type: textarea

diff --git a/.github/ISSUE_TEMPLATE/2-feature.yml b/.github/ISSUE_TEMPLATE/2-feature.yml
@@ -16,7 +16,6 @@ body:
         - Sage
         - Sage Monorepo
         - Sandbox
-        - Schematic
         - Synapse
         - Other
   - type: textarea

diff --git a/.github/ISSUE_TEMPLATE/3-documentation.yml b/.github/ISSUE_TEMPLATE/3-documentation.yml
@@ -16,7 +16,6 @@ body:
         - Sage
         - Sage Monorepo
         - Sandbox
-        - Schematic
         - Synapse
         - Other
   - type: checkboxes

diff --git a/.github/ISSUE_TEMPLATE/4-story.yml b/.github/ISSUE_TEMPLATE/4-story.yml
@@ -16,7 +16,6 @@ body:
         - Sage
         - Sage Monorepo
         - Sandbox
-        - Schematic
         - Synapse
         - Other
   - type: textarea

diff --git a/.github/actions/setup-dev-container/action.yml b/.github/actions/setup-dev-container/action.yml
@@ -1,5 +1,10 @@
 name: 'Set up the dev container'
-description: 'Installs the dev container CLI, fetches caches (if exist), and starts the dev container'
+description: 'Installs the dev container CLI, fetches caches (if exist), and starts the dev container.'
+inputs:
+  devcontainer-user:
+    description: 'The dev container user.'
+    required: false
+    default: 'ubuntu'
 runs:
   using: 'composite'
   steps:
@@ -11,43 +16,45 @@ runs:
     #     restore-keys: |
     #       ${{ runner.os }}-pnpm-store-
 
-    - 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 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 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 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: 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/cli@0.69.0
+      run: npm install -g @devcontainers/cli@0.72.0
 
     - name: Start the dev container
+      env:
+        DEVCONTAINER_USER: ${{ inputs.devcontainer-user }}
       shell: bash
       run: |
         mkdir -p \
@@ -60,21 +67,23 @@ runs:
 
         devcontainer up \
           --mount type=bind,source=/tmp/.pnpm-store,target=/workspaces/sage-monorepo/.pnpm-store \
-          --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 \
+          --mount type=bind,source=/tmp/.cache/R/renv/cache,target=/home/${DEVCONTAINER_USER}/.cache/R/renv/cache \
+          --mount type=bind,source=/tmp/.cache/pypoetry,target=/home/${DEVCONTAINER_USER}/.cache/pypoetry \
+          --mount type=bind,source=/tmp/.local/share/virtualenv,target=/home/${DEVCONTAINER_USER}/.local/share/virtualenv \
+          --mount type=bind,source=/tmp/.gradle/caches,target=/home/${DEVCONTAINER_USER}/.gradle/caches \
+          --mount type=bind,source=/tmp/.gradle/wrapper,target=/home/${DEVCONTAINER_USER}/.gradle/wrapper \
           --workspace-folder ../sage-monorepo
 
     - name: Prepare the workspace
+      env:
+        DEVCONTAINER_USER: ${{ inputs.devcontainer-user }}
       shell: bash
       run: |
         devcontainer exec --workspace-folder ../sage-monorepo bash -c "
-          sudo chown -R vscode:vscode \
+          sudo chown -R ${DEVCONTAINER_USER}:${DEVCONTAINER_USER} \
             /workspaces/sage-monorepo \
-            /home/vscode/.cache \
-            /home/vscode/.local \
-            /home/vscode/.gradle \
+            /home/${DEVCONTAINER_USER}/.cache \
+            /home/${DEVCONTAINER_USER}/.local \
+            /home/${DEVCONTAINER_USER}/.gradle \
           && . ./dev-env.sh \
           && workspace-install-affected"
-Original file line number
+Diff line change
@@ Expand Up / @@ -27,7 +27,6 @@ body: @@
             - Sage
             - Sage Monorepo
             - Sandbox
-            - Schematic
             - Synapse
             - Other
       - type: textarea
@@ Expand Down @@