chore: update the Dev Container 24.01 Edition (#2975)

Sage-Bionetworks · Jan 28, 2025 · 899e091 · 899e091
1 parent dfc00d2
commit 899e091
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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}",
@@ -14,58 +14,7 @@
     "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, 8010, 8071, 8000, 8080, 8081, 8082, 8084,
     8085, 8086, 8090, 8200, 8888, 8889, 9200, 9411, 27017
@@ -164,7 +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/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"
diff --git a/apps/iatlas/api/poetry.lock b/apps/iatlas/api/poetry.lock
diff --git a/apps/iatlas/api/pyproject.toml b/apps/iatlas/api/pyproject.toml
@@ -9,21 +9,24 @@ authors = [
 ]
 readme = "README.md"
 
-[tool.poetry.dependencies]
-python = "3.8.20"
-ariadne = "0.13.0"
-click = "7.1.2"
-flask = "1.1.2"
-flask-sqlalchemy = "2.4.3"
-graphql-core = "3.1.0"
-itsdangerous = "1.1.0"
-jinja2 = "2.11.2"
-markupsafe = "1.1.1"
-psycopg2-binary = "2.8.5"
-sqlalchemy = "1.3.17"
-starlette = "0.13.4"
-typing-extensions = "3.7.4.2"
-werkzeug = "1.0.1"
+  [[tool.poetry.packages]]
+  include = "api"
+
+  [tool.poetry.dependencies]
+  python = "3.8.20"
+  ariadne = "0.13.0"
+  click = "7.1.2"
+  flask = "1.1.2"
+  flask-sqlalchemy = "2.4.3"
+  graphql-core = "3.1.0"
+  itsdangerous = "1.1.0"
+  jinja2 = "2.11.2"
+  markupsafe = "1.1.1"
+  psycopg2-binary = "2.8.5"
+  sqlalchemy = "1.3.17"
+  starlette = "0.13.4"
+  typing-extensions = "3.7.4.2"
+  werkzeug = "1.0.1"
 
 [tool.poetry.group.dev.dependencies]
 autopep8 = "1.5.4"
@@ -36,7 +39,7 @@ pytest-xdist = "2.1.0"
 snakeviz = "2.1.0"
 
 [tool.poetry.group.prod.dependencies]
-uWSGI = "2.0.19.1"
+uWSGI = "2.0.28"
 
 [tool.pytest.ini_options]
 log_cli = true

diff --git a/dev-env.sh b/dev-env.sh
@@ -42,8 +42,9 @@ function workspace-install-affected {
   workspace-install-nodejs-dependencies
   workspace-install-python-dependencies
   nx affected --target=create-config
-  nx affected --target=prepare --exclude '!tag:language:java' --parallel=1
-  nx affected --target=prepare --exclude 'tag:language:java'
+  nx affected --target=prepare --projects=tag:language:java --parallel=1
+  nx affected --target=prepare --projects=tag:language:python --parallel=1
+  nx affected --target=prepare --projects=tag:language:r
 }
 
 # Setup Python virtualenvs
@@ -176,6 +177,22 @@ function workspace-initialize-env {
   export COREPACK_ENABLE_DOWNLOAD_PROMPT="0"
 }
 
-function workspace-nuke-venv {
-  find . -name ".venv" -print0 | xargs -0 rm -fr
+function workspace-nuke {
+  rm -fr \
+    .angular \
+    .cache \
+    .nx \
+    .pnpm-store \
+    coverage \
+    playwright-report \
+    reports
+
+    # find . -name "build" -print0 | xargs -0 rm -fr  # but not OA build folders
+    find . -name ".coverage" -print0 | xargs -0 rm -fr
+    find . -name ".gradle" -print0 | xargs -0 rm -fr
+    find . -name ".pytest_cache" -print0 | xargs -0 rm -fr
+    find . -name ".venv" -print0 | xargs -0 rm -fr
+    find . -name "bin" -print0 | xargs -0 rm -fr
+    find . -name "dist" -print0 | xargs -0 rm -fr
+    find . -name "node_modules" -print0 | xargs -0 rm -fr
 }
diff --git a/libs/sandbox/py-lib/project.json b/libs/sandbox/py-lib/project.json
@@ -22,13 +22,10 @@
       }
     },
     "prepare": {
-      "executor": "@nxlv/python:install",
+      "executor": "nx:run-commands",
       "options": {
-        "silent": false,
-        "args": "",
-        "cacheDir": ".cache/pypoetry",
-        "verbose": false,
-        "debug": false
+        "command": "./install.sh",
+        "cwd": "{projectRoot}"
       }
     },
     "update": {