chore(sage-monorepo): update the dev container and Node.js

.github/actions/setup-dev-container/action.yml

@@ -45,7 +45,7 @@ runs:
 
     - name: Install the Dev Container CLI
       shell: bash
-      run: npm install -g @devcontainers/cli@0.49.0
+      run: npm install -g @devcontainers/cli@0.69.0
 
     - name: Start the dev container
       shell: bash

.github/workflows/build-devcontainer-image.yml

@@ -66,7 +66,7 @@ jobs:
           export DEVCONTAINER_VERSION=${{ steps.prep.outputs.devcontainer_version }}
 
           # Build the image
-          npm install -g @devcontainers/cli
+          npm install -g @devcontainers/cli@0.69.0
           devcontainer build \
             --image-name "${IMAGE_NAME}:${IMAGE_TAG}" \
             --workspace-folder "${WORKSPACE_FOLDER}"

.github/workflows/schematic-api-ci.yml

@@ -69,7 +69,7 @@ jobs:
             ${{ runner.os }}-gradle-
 
       - name: Install the Dev Container CLI
-        run: npm install -g @devcontainers/cli@0.49.0
+        run: npm install -g @devcontainers/cli@0.69.0
 
       - name: Start the dev container
         run: |

tools/devcontainers/sage/.devcontainer/Dockerfile

@@ -1,42 +1,50 @@
-ARG imageVersion=jammy-20240227
+# Base image
+ARG imageVersion=jammy-20240808
 FROM ubuntu:$imageVersion
 
-# Safer bash scripts with 'set -euxo pipefail'
+# Set safer bash scripts
 SHELL ["/bin/bash", "-euxo", "pipefail", "-c"]
 
-ARG devcontainerVersion=""
-ENV DEVCONTAINER_VERSION=${devcontainerVersion}
-
+# List of build arguments
 # https://github.com/nektos/act
-ARG actVersion="0.2.49"
+ARG actVersion="0.2.65"
 # https://github.com/sharkdp/hyperfine
-ARG hyperfineVersion="1.17.0"
-# https://github.com/yarnpkg/berry
-ARG yarnVersion="3.6.1"
+ARG hyperfineVersion="1.18.0"
 # https://www.npmjs.com/package/@devcontainers/cli
-ARG devcontainerCliVersion="0.50.2"
+ARG devcontainerCliVersion="0.69.0"
 # https://pypi.org/project/poetry
-ARG poetryVersion="1.8.2"
+ARG poetryVersion="1.8.3"
 # https://docs.posit.co/resources/install-r/#specify-r-version
 ARG rVersion="4.2.3"
 # https://aquasecurity.github.io/trivy
-ARG trivyVersion="0.44.1"
+ARG trivyVersion="0.54.1"
 # https://github.com/rstudio/renv
 ARG renvVersion="1.0.0"
-# https://www.npmjs.com/package/playwright
-ARG playwrightVersion="1.40.1"
+# https://nodejs.org/en/about/previous-releases
+ARG nodeVersionMajor="20"
+# https://pypi.org/project/pipenv/
+ARG pipenvVersion="2024.0.1"
 # https://github.com/pnpm/pnpm/releases
-ARG pnpmVersion="8.7.0"
+ARG pnpmVersion="9.9.0"
+# List of Python versions separated by spaces
+ARG pyenvPythonVersions="3.9.2 3.10.14 3.11.8"
 # https://github.com/SonarSource/sonar-scanner-cli/releases
 ARG sonarScannerVersion="5.0.1.3006"
 # https://github.com/hadolint/hadolint
 ARG hadolintVersion="2.12.0"
+# The version of this dev container image
+ARG devcontainerVersion=""
+# The username of the non-root user
+ARG user="vscode"
+
+# Set environment variables
+ENV DEVCONTAINER_VERSION=${devcontainerVersion} \
+  LANG=en_US.UTF-8 \
+  LC_ALL=en_US.UTF-8
 
-# Create the docker group so that we can assign it to the user.
-# This is to enable the non-root user to use the command `docker`.
-# hadolint ignore=DL3008,DL3013
-RUN groupadd docker \
-  && apt-get update -qq -y && export DEBIAN_FRONTEND=noninteractive \
+# Install system packages
+# hadolint ignore=DL3008
+RUN apt-get update -qq -y && export DEBIAN_FRONTEND=noninteractive \
   && apt-get install --no-install-recommends -qq -y \
     ca-certificates curl git bash-completion gnupg2 lsb-release ssh sudo \
     python3-pip python3-dev python-is-python3 openjdk-17-jdk \
@@ -53,16 +61,8 @@ RUN groupadd docker \
     # Required by Hadolint
     shellcheck \
   # Add Node.js repository
-  && mkdir -p /etc/apt/keyrings \
-  && curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key \
-    | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg \
-  && NODE_MAJOR=18 \
-  && echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_MAJOR.x nodistro main" \
-    | tee /etc/apt/sources.list.d/nodesource.list \
-  # Add Hadolint
-  && curl https://github.com/hadolint/hadolint/releases/download/v${hadolintVersion}/hadolint-Linux-x86_64 -o hadolint \
-  && mv hadolint /usr/local/bin/. \
-  && chmod +x /usr/local/bin/hadolint \
+  && curl -fsSL https://deb.nodesource.com/setup_${nodeVersionMajor}.x -o nodesource_setup.sh \
+  && bash nodesource_setup.sh \
   # Add GitHub CLI repository
   && curl -sSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | \
     gpg --dearmor -o /usr/share/keyrings/githubcli-archive-keyring.gpg \
@@ -74,69 +74,68 @@ RUN groupadd docker \
   # Add hashicorp repository
   && curl -fsSL https://apt.releases.hashicorp.com/gpg | apt-key add - \
   && echo "deb [arch=amd64] https://apt.releases.hashicorp.com $(lsb_release -cs) main" | tee /etc/apt/sources.list.d/hashicorp.list \
-  # Install extra packages
+  # Install additional packages
   && apt-get update -qq -y \
-  && apt-get install --no-install-recommends -qq -y \
-    nodejs gh ngrok \
-    terraform \
-    vault \
+  && apt-get install --no-install-recommends -qq -y nodejs gh ngrok terraform vault \
+  # Enable corepack
+  && corepack enable \
   # Fix Vault CLI
   # See https://github.com/hashicorp/vault/issues/10924
   && setcap -r /usr/bin/vault \
-  # Install Yarn
-  && corepack enable yarn \
-  && corepack prepare "yarn@${yarnVersion}" --activate \
-  # Instal pnpm
-  # && curl -fsSL https://get.pnpm.io/install.sh | env PNPM_VERSION=${pnpmVersion} bash - \
-  && corepack enable pnpm \
-  && corepack prepare "pnpm@${pnpmVersion}" --activate \
-  # Install @devcontainers/cli
-  && npm install -g "@devcontainers/cli@${devcontainerCliVersion}" \
-  # Install act
-  && curl "https://raw.githubusercontent.com/nektos/act/v${actVersion}/install.sh" | bash - \
-  # Install hyperfine
-  && curl -sSL "https://github.com/sharkdp/hyperfine/releases/download/v${hyperfineVersion}/hyperfine_${hyperfineVersion}_amd64.deb" \
-    -o /tmp/hyperfine.deb \
-  && apt-get install --no-install-recommends -qq -y /tmp/hyperfine.deb \
-  && rm -fr /tmp/hyperfine.deb \
-  # Install AWS CLI
-  && curl https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip -o awscliv2.zip \
+  # Set up UTF-8 locale
+  && echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && locale-gen \
+  # Install R (must be done before clearing the apt cache)
+  && curl "https://cdn.rstudio.com/r/ubuntu-2204/pkgs/r-${rVersion}_1_amd64.deb" -o /tmp/r_amd64.deb \
+    && gdebi --non-interactive /tmp/r_amd64.deb \
+    && rm -fr /tmp/r_amd64.deb \
+    && ln -s /opt/R/${rVersion}/bin/R /usr/local/bin/R \
+    && ln -s /opt/R/${rVersion}/bin/Rscript /usr/local/bin/Rscript \
+    && R -e "options(repos = c(POSIT = \"https://packagemanager.posit.co/all/__linux__/jammy/latest\", CRAN = \"https://mirror.las.iastate.edu/CRAN\")); install.packages(\"renv\", version = \"${renvVersion}\")" \
+  # Cleanup
+  && apt-get -y autoclean \
+  && apt-get -y autoremove \
+  && rm -rf /var/lib/apt/lists/*
+
+# Install Poetry
+RUN curl -sSL https://install.python-poetry.org | POETRY_HOME=/etc/poetry python3 - --version "${poetryVersion}" \
+  && ln -s /etc/poetry/bin/poetry /usr/local/bin/.
+
+# Install Trivy
+RUN curl -fsSL "https://github.com/aquasecurity/trivy/releases/download/v${trivyVersion}/trivy_${trivyVersion}_Linux-64bit.deb" -o /tmp/trivy.deb \
+  && dpkg -i /tmp/trivy.deb \
+  && rm -fr /tmp/trivy.deb
+
+# Install act
+RUN curl "https://raw.githubusercontent.com/nektos/act/v${actVersion}/install.sh" | bash -
+
+# Install AWS CLI
+RUN curl https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip -o awscliv2.zip \
   && unzip awscliv2.zip \
   && ./aws/install \
   && rm -fr awscliv2.zip ./aws \
   # Add AWS Session Manager plugin
   && curl -fsSL "https://s3.amazonaws.com/session-manager-downloads/plugin/latest/ubuntu_64bit/session-manager-plugin.deb" -o /tmp/session-manager-plugin.deb \
   && dpkg -i /tmp/session-manager-plugin.deb \
-  && rm -fr /tmp/session-manager-plugin.deb \
-  # Install Poetry
-  && curl -sSL https://install.python-poetry.org | POETRY_HOME=/etc/poetry python3 - --version "${poetryVersion}" \
-  && ln -s /etc/poetry/bin/poetry /usr/local/bin/. \
-  # Install R
-  && curl "https://cdn.rstudio.com/r/ubuntu-2204/pkgs/r-${rVersion}_1_amd64.deb" -o /tmp/r_amd64.deb \
-  && gdebi --non-interactive /tmp/r_amd64.deb \
-  && rm -fr /tmp/r_amd64.deb \
-  && ln -s /opt/R/${rVersion}/bin/R /usr/local/bin/R \
-  && ln -s /opt/R/${rVersion}/bin/Rscript /usr/local/bin/Rscript \
-  && R -e "options(repos = c(POSIT = \"https://packagemanager.posit.co/all/__linux__/jammy/latest\", CRAN = \"https://mirror.las.iastate.edu/CRAN\")); install.packages(\"renv\", version = \"${renvVersion}\")" \
-  # Install Trivy
-  && curl -fsSL "https://github.com/aquasecurity/trivy/releases/download/v${trivyVersion}/trivy_${trivyVersion}_Linux-64bit.deb" -o /tmp/trivy.deb \
-  && dpkg -i /tmp/trivy.deb \
-  && rm -fr /tmp/trivy.deb \
-  # Cleanup
-  && apt-get -y autoclean \
-  && apt-get -y autoremove \
-  && rm -rf /var/lib/apt/lists/* \
-  && pip install --no-cache-dir pipenv
+  && rm -fr /tmp/session-manager-plugin.deb
 
-# Setting up a UTF-8 locale
-RUN sed -i '/en_US.UTF-8/s/^# //g' /etc/locale.gen \
-  && locale-gen
-ENV LANG=en_US.UTF-8 \
-  LC_ALL=en_US.UTF-8
+# Install the devcontainer CLI
+RUN npm install -g "@devcontainers/cli@${devcontainerCliVersion}"
+
+# Install Hadolint
+RUN curl https://github.com/hadolint/hadolint/releases/download/v${hadolintVersion}/hadolint-Linux-x86_64 -o hadolint \
+  && mv hadolint /usr/local/bin/. \
+  && chmod +x /usr/local/bin/hadolint
+
+# Install hyperfine
+RUN curl -sSL "https://github.com/sharkdp/hyperfine/releases/download/v${hyperfineVersion}/hyperfine_${hyperfineVersion}_amd64.deb" \
+    -o /tmp/hyperfine.deb \
+  && apt-get install --no-install-recommends -qq -y /tmp/hyperfine.deb \
+  && rm -fr /tmp/hyperfine.deb
 
-ARG user=vscode
+# Create non-root user
 RUN useradd -m $user \
   && echo "$user:$user" | chpasswd \
+  && groupadd docker \
   && usermod -a --groups docker,sudo $user \
   && usermod --shell /bin/bash $user \
   && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers \
@@ -152,9 +151,7 @@ RUN useradd -m $user \
     "  . ./dev-env.sh" \
     "  workspace-initialize-env" \
     "fi" \
-    "" | tee -a "/home/$user/.bashrc" \
-  # Set the default version of Yarn
-  && corepack prepare "yarn@${yarnVersion}" --activate
+    "" | tee -a "/home/$user/.bashrc"
 
 # Install SonarScanner CLI
 ARG SONAR_SCANNER_HOME=/opt/sonar-scanner
@@ -168,23 +165,17 @@ RUN curl https://binaries.sonarsource.com/Distribution/sonar-scanner-cli/sonar-s
   && chown -R ${user}:${user} "${SONAR_SCANNER_HOME}" \
   && chmod -R 777 "${SONAR_USER_HOME}"
 
+# Switch to non-root user
 USER $user
 
-# Install browsers used for e2e testing with Playwright
-# Note: The version of Playwright should be the same as the one used by your project (package.json)
-RUN npx playwright@${playwrightVersion} install --with-deps \
-    chromium \
-    firefox \
-    webkit \
-  # Install pyenv as the user
-  && curl https://raw.githubusercontent.com/pyenv/pyenv-installer/master/bin/pyenv-installer | bash -
+# Install the global version of pnpm
+RUN corepack install --global "pnpm@${pnpmVersion}"
 
-# Install Python environments
+# Set up Python environments
 ENV PYENV_ROOT /home/${user}/.pyenv
 ENV PATH $PYENV_ROOT/shims:$PYENV_ROOT/bin:$PATH
-RUN pyenv install \
-  3.9.2 \
-  3.10.14 \
-  3.11.8
+RUN pip install --no-cache-dir pipenv==${pipenvVersion} \
+  && curl https://raw.githubusercontent.com/pyenv/pyenv-installer/master/bin/pyenv-installer | bash - \
+  && pyenv install ${pyenvPythonVersions}
 
 CMD ["bash"]

tools/devcontainers/sage/.devcontainer/devcontainer.json

@@ -1,13 +1,16 @@
 {
-  "name": "Sage Dev Container",
-	"build": {
-		"dockerfile": "Dockerfile",
-		"args": {
-			"imageVersion": "jammy-20230624",
+  "name": "Sage Dev Container (Test)",
+  "build": {
+    "dockerfile": "Dockerfile",
+    "args": {
+      "imageVersion": "jammy-20240808",
       "devcontainerVersion": "${localEnv:DEVCONTAINER_VERSION}"
-		}
-	},
-	"remoteUser": "vscode",
+    }
+  },
+  "remoteUser": "vscode",
   "shutdownAction": "stopContainer",
-  "runArgs": ["--name", "sage_devcontainer"]
+  "runArgs": [
+    "--name",
+    "sage_devcontainer_test"
+  ]
 }

tools/devcontainers/sage/README.md

@@ -0,0 +1,19 @@
+# Sage Dev Container
+
+Learn how to build and run dev containers with the devcontainer CLI:
+
+https://code.visualstudio.com/docs/remote/devcontainer-cli
+
+# Build the image with devcontainer
+
+```console
+devcontainer build \
+  --image-name ghcr.io/sage-bionetworks/sage-devcontainer:test \
+  --workspace-folder ../sage
+```
+
+# Build the image with Docker
+
+```console
+docker build -t ghcr.io/sage-bionetworks/sage-devcontainer:test .devcontainer/
+```