From b455d2bfeb42f6b0ab1d9f81daa08983f3a19c5e Mon Sep 17 00:00:00 2001
From: Thomas Schaffter <thomas.schaffter@gmail.com>
Date: Wed, 28 Aug 2024 16:45:50 +0000
Subject: [PATCH 01/10] remove yarn

---
 tools/devcontainers/sage/.devcontainer/Dockerfile | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/tools/devcontainers/sage/.devcontainer/Dockerfile b/tools/devcontainers/sage/.devcontainer/Dockerfile
index b3d23383ce..4ed326d07b 100644
--- a/tools/devcontainers/sage/.devcontainer/Dockerfile
+++ b/tools/devcontainers/sage/.devcontainer/Dockerfile
@@ -11,8 +11,6 @@ ENV DEVCONTAINER_VERSION=${devcontainerVersion}
 ARG actVersion="0.2.49"
 # https://github.com/sharkdp/hyperfine
 ARG hyperfineVersion="1.17.0"
-# https://github.com/yarnpkg/berry
-ARG yarnVersion="3.6.1"
 # https://www.npmjs.com/package/@devcontainers/cli
 ARG devcontainerCliVersion="0.50.2"
 # https://pypi.org/project/poetry
@@ -83,9 +81,6 @@ RUN groupadd docker \
   # Fix Vault CLI
   # See https://github.com/hashicorp/vault/issues/10924
   && setcap -r /usr/bin/vault \
-  # Install Yarn
-  && corepack enable yarn \
-  && corepack prepare "yarn@${yarnVersion}" --activate \
   # Instal pnpm
   # && curl -fsSL https://get.pnpm.io/install.sh | env PNPM_VERSION=${pnpmVersion} bash - \
   && corepack enable pnpm \
@@ -152,9 +147,7 @@ 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

From 980ad8d24676ac2dc988bf767be25427f6ae4ec9 Mon Sep 17 00:00:00 2001
From: Thomas Schaffter <thomas.schaffter@gmail.com>
Date: Wed, 28 Aug 2024 16:51:16 +0000
Subject: [PATCH 02/10] install pnpm globally

---
 tools/devcontainers/sage/.devcontainer/Dockerfile | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tools/devcontainers/sage/.devcontainer/Dockerfile b/tools/devcontainers/sage/.devcontainer/Dockerfile
index 4ed326d07b..f33b648010 100644
--- a/tools/devcontainers/sage/.devcontainer/Dockerfile
+++ b/tools/devcontainers/sage/.devcontainer/Dockerfile
@@ -24,7 +24,7 @@ ARG renvVersion="1.0.0"
 # https://www.npmjs.com/package/playwright
 ARG playwrightVersion="1.40.1"
 # https://github.com/pnpm/pnpm/releases
-ARG pnpmVersion="8.7.0"
+ARG pnpmVersion="9.9.0"
 # https://github.com/SonarSource/sonar-scanner-cli/releases
 ARG sonarScannerVersion="5.0.1.3006"
 # https://github.com/hadolint/hadolint
@@ -82,9 +82,7 @@ RUN groupadd docker \
   # See https://github.com/hashicorp/vault/issues/10924
   && setcap -r /usr/bin/vault \
   # Instal pnpm
-  # && curl -fsSL https://get.pnpm.io/install.sh | env PNPM_VERSION=${pnpmVersion} bash - \
-  && corepack enable pnpm \
-  && corepack prepare "pnpm@${pnpmVersion}" --activate \
+  && corepack install --global "pnpm@${pnpmVersion}" \
   # Install @devcontainers/cli
   && npm install -g "@devcontainers/cli@${devcontainerCliVersion}" \
   # Install act

From 940a8aacf69da984083764cea890a4045fec8c00 Mon Sep 17 00:00:00 2001
From: Thomas Schaffter <thomas.schaffter@gmail.com>
Date: Wed, 28 Aug 2024 18:03:03 +0000
Subject: [PATCH 03/10] update a few tools

---
 .../sage/.devcontainer/Dockerfile              | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/tools/devcontainers/sage/.devcontainer/Dockerfile b/tools/devcontainers/sage/.devcontainer/Dockerfile
index f33b648010..d57cd9fcaf 100644
--- a/tools/devcontainers/sage/.devcontainer/Dockerfile
+++ b/tools/devcontainers/sage/.devcontainer/Dockerfile
@@ -8,19 +8,21 @@ ARG devcontainerVersion=""
 ENV DEVCONTAINER_VERSION=${devcontainerVersion}
 
 # 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"
+ARG hyperfineVersion="1.18.0"
 # https://www.npmjs.com/package/@devcontainers/cli
 ARG devcontainerCliVersion="0.50.2"
 # 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://nodejs.org/en/about/previous-releases
+ARG nodeVersionMajor="20"
 # https://www.npmjs.com/package/playwright
 ARG playwrightVersion="1.40.1"
 # https://github.com/pnpm/pnpm/releases
@@ -51,12 +53,8 @@ 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_$NODE_MAJOR.x nodistro main" \
-    | tee /etc/apt/sources.list.d/nodesource.list \
+  && curl -fsSL https://deb.nodesource.com/setup_${nodeVersionMajor}.x -o nodesource_setup.sh \
+  && bash nodesource_setup.sh \
   # Add Hadolint
   && curl https://github.com/hadolint/hadolint/releases/download/v${hadolintVersion}/hadolint-Linux-x86_64 -o hadolint \
   && mv hadolint /usr/local/bin/. \

From cfb7e2f8cdc2de0ee1f0e80ed6103b8ab9ac1903 Mon Sep 17 00:00:00 2001
From: Thomas Schaffter <thomas.schaffter@gmail.com>
Date: Wed, 28 Aug 2024 21:52:05 +0000
Subject: [PATCH 04/10] update

---
 .../sage/.devcontainer/Dockerfile             | 14 ++++++++------
 .../sage/.devcontainer/devcontainer.json      | 19 +++++++++++--------
 2 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/tools/devcontainers/sage/.devcontainer/Dockerfile b/tools/devcontainers/sage/.devcontainer/Dockerfile
index d57cd9fcaf..107f9b6639 100644
--- a/tools/devcontainers/sage/.devcontainer/Dockerfile
+++ b/tools/devcontainers/sage/.devcontainer/Dockerfile
@@ -1,4 +1,4 @@
-ARG imageVersion=jammy-20240227
+ARG imageVersion=jammy-20240808
 FROM ubuntu:$imageVersion
 
 # Safer bash scripts with 'set -euxo pipefail'
@@ -52,7 +52,7 @@ RUN groupadd docker \
     xz-utils tk-dev libffi-dev liblzma-dev \
     # Required by Hadolint
     shellcheck \
-  # Add Node.js repository
+  # Add Node.js
   && curl -fsSL https://deb.nodesource.com/setup_${nodeVersionMajor}.x -o nodesource_setup.sh \
   && bash nodesource_setup.sh \
   # Add Hadolint
@@ -79,8 +79,8 @@ RUN groupadd docker \
   # Fix Vault CLI
   # See https://github.com/hashicorp/vault/issues/10924
   && setcap -r /usr/bin/vault \
-  # Instal pnpm
-  && corepack install --global "pnpm@${pnpmVersion}" \
+  # Enable corepack
+  && corepack enable \
   # Install @devcontainers/cli
   && npm install -g "@devcontainers/cli@${devcontainerCliVersion}" \
   # Install act
@@ -143,7 +143,9 @@ RUN useradd -m $user \
     "  . ./dev-env.sh" \
     "  workspace-initialize-env" \
     "fi" \
-    "" | tee -a "/home/$user/.bashrc"
+    "" | tee -a "/home/$user/.bashrc" \
+  # Install the default version of pnpm
+  && corepack install --global "pnpm@${pnpmVersion}"
 
 # Install SonarScanner CLI
 ARG SONAR_SCANNER_HOME=/opt/sonar-scanner
@@ -165,7 +167,7 @@ RUN npx playwright@${playwrightVersion} install --with-deps \
     chromium \
     firefox \
     webkit \
-  # Install pyenv as the user
+  # Install pyenv as the non-root user
   && curl https://raw.githubusercontent.com/pyenv/pyenv-installer/master/bin/pyenv-installer | bash -
 
 # Install Python environments
diff --git a/tools/devcontainers/sage/.devcontainer/devcontainer.json b/tools/devcontainers/sage/.devcontainer/devcontainer.json
index 209ea53e6a..98e4d0ddd9 100644
--- a/tools/devcontainers/sage/.devcontainer/devcontainer.json
+++ b/tools/devcontainers/sage/.devcontainer/devcontainer.json
@@ -1,13 +1,16 @@
 {
   "name": "Sage Dev Container",
-	"build": {
-		"dockerfile": "Dockerfile",
-		"args": {
-			"imageVersion": "jammy-20230624",
+  "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"
+  ]
 }
\ No newline at end of file

From d7fc5c82802fd3decaca272c758bb9de645a4c22 Mon Sep 17 00:00:00 2001
From: Thomas Schaffter <thomas.schaffter@gmail.com>
Date: Thu, 29 Aug 2024 16:50:37 +0000
Subject: [PATCH 05/10] split the dev container Dockerfile into logical parts

---
 tools/devcontainers/build-image.sh            |   7 -
 .../sage/.devcontainer/Dockerfile             | 147 ++++++++++--------
 .../sage/.devcontainer/README.md              |   4 +
 .../sage/.devcontainer/devcontainer.json      |   4 +-
 4 files changed, 84 insertions(+), 78 deletions(-)
 delete mode 100755 tools/devcontainers/build-image.sh

diff --git a/tools/devcontainers/build-image.sh b/tools/devcontainers/build-image.sh
deleted file mode 100755
index beafacef5a..0000000000
--- a/tools/devcontainers/build-image.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/usr/bin/env bash
-
-# This script must be run from the folder that includes it.
-
-devcontainer build \
-  --image-name ghcr.io/sage-bionetworks/sage-devcontainer:testing \
-  --workspace-folder sage
diff --git a/tools/devcontainers/sage/.devcontainer/Dockerfile b/tools/devcontainers/sage/.devcontainer/Dockerfile
index 107f9b6639..0c96525471 100644
--- a/tools/devcontainers/sage/.devcontainer/Dockerfile
+++ b/tools/devcontainers/sage/.devcontainer/Dockerfile
@@ -1,12 +1,11 @@
+# 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=${devcontainerVersion}
-
+# Arguments
 # https://github.com/nektos/act
 ARG actVersion="0.2.65"
 # https://github.com/sharkdp/hyperfine
@@ -31,12 +30,19 @@ ARG pnpmVersion="9.9.0"
 ARG sonarScannerVersion="5.0.1.3006"
 # https://github.com/hadolint/hadolint
 ARG hadolintVersion="2.12.0"
+# The version of this dev container image
+ARG devcontainerVersion=""
+# The username of the non-root user
+ARG user=vscode
+
+# Set environment variables
+ENV DEVCONTAINER_VERSION=${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`.
+# Install system packages
 # hadolint ignore=DL3008,DL3013
-RUN groupadd docker \
-  && apt-get update -qq -y && export DEBIAN_FRONTEND=noninteractive \
+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 \
@@ -52,13 +58,9 @@ RUN groupadd docker \
     xz-utils tk-dev libffi-dev liblzma-dev \
     # Required by Hadolint
     shellcheck \
-  # Add Node.js
+  # Add Node.js repository
   && curl -fsSL https://deb.nodesource.com/setup_${nodeVersionMajor}.x -o nodesource_setup.sh \
   && bash nodesource_setup.sh \
-  # Add Hadolint
-  && curl https://github.com/hadolint/hadolint/releases/download/v${hadolintVersion}/hadolint-Linux-x86_64 -o hadolint \
-  && mv hadolint /usr/local/bin/. \
-  && chmod +x /usr/local/bin/hadolint \
   # 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 \
@@ -70,64 +72,65 @@ 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 $(lsb_release -cs) main" | tee /etc/apt/sources.list.d/hashicorp.list \
-  # Install extra packages
+  # Install additional packages
   && apt-get update -qq -y \
-  && apt-get install --no-install-recommends -qq -y \
-    nodejs gh ngrok \
-    terraform \
-    vault \
+  && apt-get install --no-install-recommends -qq -y nodejs gh ngrok terraform vault \
+  # Enable corepack
+  && corepack enable \
   # Fix Vault CLI
   # See https://github.com/hashicorp/vault/issues/10924
   && setcap -r /usr/bin/vault \
-  # Enable corepack
-  && corepack enable \
-  # Install @devcontainers/cli
-  && npm install -g "@devcontainers/cli@${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_${hyperfineVersion}_amd64.deb" \
-    -o /tmp/hyperfine.deb \
-  && apt-get install --no-install-recommends -qq -y /tmp/hyperfine.deb \
-  && rm -fr /tmp/hyperfine.deb \
-  # Install AWS CLI
-  && curl https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip -o awscliv2.zip \
+  # Set up UTF-8 locale
+  && echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && locale-gen
+
+# Install Poetry
+RUN curl -sSL https://install.python-poetry.org | POETRY_HOME=/etc/poetry python3 - --version "${poetryVersion}" \
+  && ln -s /etc/poetry/bin/poetry /usr/local/bin/.
+
+# Install R
+RUN 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
+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${actVersion}/install.sh" | bash -
+
+# Install @devcontainers/cli
+RUN npm install -g "@devcontainers/cli@${devcontainerCliVersion}"
+
+# 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 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
 
-ARG user=vscode
+# 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
+
+# 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 \
@@ -143,9 +146,7 @@ RUN useradd -m $user \
     "  . ./dev-env.sh" \
     "  workspace-initialize-env" \
     "fi" \
-    "" | tee -a "/home/$user/.bashrc" \
-  # Install the default version of pnpm
-  && corepack install --global "pnpm@${pnpmVersion}"
+    "" | tee -a "/home/$user/.bashrc"
 
 # Install SonarScanner CLI
 ARG SONAR_SCANNER_HOME=/opt/sonar-scanner
@@ -159,23 +160,31 @@ 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}"
 
+# Cleanup
+RUN apt-get -y autoclean \
+  && apt-get -y autoremove \
+  && rm -rf /var/lib/apt/lists/* \
+  && pip install --no-cache-dir pipenv
+
+# Switch to non-root user
 USER $user
 
-# Install browsers used for e2e testing with Playwright
+# Install the global version of pnpm
+RUN corepack install --global "pnpm@${pnpmVersion}"
+
+# Install browsers for Playwright
 # Note: The version of Playwright should be the same as the one used by your project (package.json)
 RUN npx playwright@${playwrightVersion} install --with-deps \
     chromium \
     firefox \
-    webkit \
-  # Install pyenv as the non-root user
-  && curl https://raw.githubusercontent.com/pyenv/pyenv-installer/master/bin/pyenv-installer | bash -
+    webkit
+
+# Install pyenv
+RUN curl https://raw.githubusercontent.com/pyenv/pyenv-installer/master/bin/pyenv-installer | bash -
 
-# 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 pyenv install 3.9.2 3.10.14 3.11.8
 
 CMD ["bash"]
\ No newline at end of file
diff --git a/tools/devcontainers/sage/.devcontainer/README.md b/tools/devcontainers/sage/.devcontainer/README.md
index e0e0e4b767..50be24a3c7 100644
--- a/tools/devcontainers/sage/.devcontainer/README.md
+++ b/tools/devcontainers/sage/.devcontainer/README.md
@@ -1 +1,5 @@
+# Sage Dev Container
+
+Learn how to build and run dev containers with the devcontainer CLI:
+
 https://code.visualstudio.com/docs/remote/devcontainer-cli
\ No newline at end of file
diff --git a/tools/devcontainers/sage/.devcontainer/devcontainer.json b/tools/devcontainers/sage/.devcontainer/devcontainer.json
index 98e4d0ddd9..99c5cf5d0b 100644
--- a/tools/devcontainers/sage/.devcontainer/devcontainer.json
+++ b/tools/devcontainers/sage/.devcontainer/devcontainer.json
@@ -1,5 +1,5 @@
 {
-  "name": "Sage Dev Container",
+  "name": "Sage Dev Container (Test)",
   "build": {
     "dockerfile": "Dockerfile",
     "args": {
@@ -11,6 +11,6 @@
   "shutdownAction": "stopContainer",
   "runArgs": [
     "--name",
-    "sage_devcontainer"
+    "sage_devcontainer_testing"
   ]
 }
\ No newline at end of file

From 4dc475b91d16b15cdf643468b82c83723c65c4fa Mon Sep 17 00:00:00 2001
From: Thomas Schaffter <thomas.schaffter@gmail.com>
Date: Thu, 29 Aug 2024 18:36:00 +0000
Subject: [PATCH 06/10] improve image

---
 .../sage/.devcontainer/Dockerfile             | 51 +++++++------------
 .../sage/.devcontainer/devcontainer.json      |  2 +-
 2 files changed, 20 insertions(+), 33 deletions(-)

diff --git a/tools/devcontainers/sage/.devcontainer/Dockerfile b/tools/devcontainers/sage/.devcontainer/Dockerfile
index 0c96525471..56685e849b 100644
--- a/tools/devcontainers/sage/.devcontainer/Dockerfile
+++ b/tools/devcontainers/sage/.devcontainer/Dockerfile
@@ -5,7 +5,7 @@ FROM ubuntu:$imageVersion
 # Set safer bash scripts
 SHELL ["/bin/bash", "-euxo", "pipefail", "-c"]
 
-# Arguments
+# Image arguments
 # https://github.com/nektos/act
 ARG actVersion="0.2.65"
 # https://github.com/sharkdp/hyperfine
@@ -22,8 +22,6 @@ ARG trivyVersion="0.54.1"
 ARG renvVersion="1.0.0"
 # https://nodejs.org/en/about/previous-releases
 ARG nodeVersionMajor="20"
-# https://www.npmjs.com/package/playwright
-ARG playwrightVersion="1.40.1"
 # https://github.com/pnpm/pnpm/releases
 ARG pnpmVersion="9.9.0"
 # https://github.com/SonarSource/sonar-scanner-cli/releases
@@ -81,20 +79,23 @@ RUN apt-get update -qq -y && export DEBIAN_FRONTEND=noninteractive \
   # See https://github.com/hashicorp/vault/issues/10924
   && setcap -r /usr/bin/vault \
   # Set up UTF-8 locale
-  && echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && locale-gen
+  && 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 R
-RUN 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
 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 \
@@ -103,9 +104,6 @@ RUN curl -fsSL "https://github.com/aquasecurity/trivy/releases/download/v${trivy
 # Install act
 RUN curl "https://raw.githubusercontent.com/nektos/act/v${actVersion}/install.sh" | bash -
 
-# Install @devcontainers/cli
-RUN npm install -g "@devcontainers/cli@${devcontainerCliVersion}"
-
 # Install AWS CLI
 RUN curl https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip -o awscliv2.zip \
   && unzip awscliv2.zip \
@@ -116,6 +114,9 @@ RUN curl https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip -o awscliv2.zi
   && dpkg -i /tmp/session-manager-plugin.deb \
   && rm -fr /tmp/session-manager-plugin.deb
 
+# 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/. \
@@ -160,31 +161,17 @@ 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}"
 
-# Cleanup
-RUN apt-get -y autoclean \
-  && apt-get -y autoremove \
-  && rm -rf /var/lib/apt/lists/* \
-  && pip install --no-cache-dir pipenv
-
 # Switch to non-root user
 USER $user
 
 # Install the global version of pnpm
 RUN corepack install --global "pnpm@${pnpmVersion}"
 
-# Install browsers for Playwright
-# Note: The version of Playwright should be the same as the one used by your project (package.json)
-RUN npx playwright@${playwrightVersion} install --with-deps \
-    chromium \
-    firefox \
-    webkit
-
-# Install pyenv
-RUN curl https://raw.githubusercontent.com/pyenv/pyenv-installer/master/bin/pyenv-installer | bash -
-
 # Set up Python environments
 ENV PYENV_ROOT /home/${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 \
+  && curl https://raw.githubusercontent.com/pyenv/pyenv-installer/master/bin/pyenv-installer | bash - \
+  && pyenv install 3.9.2 3.10.14 3.11.8
 
 CMD ["bash"]
\ No newline at end of file
diff --git a/tools/devcontainers/sage/.devcontainer/devcontainer.json b/tools/devcontainers/sage/.devcontainer/devcontainer.json
index 99c5cf5d0b..99955be6b7 100644
--- a/tools/devcontainers/sage/.devcontainer/devcontainer.json
+++ b/tools/devcontainers/sage/.devcontainer/devcontainer.json
@@ -11,6 +11,6 @@
   "shutdownAction": "stopContainer",
   "runArgs": [
     "--name",
-    "sage_devcontainer_testing"
+    "sage_devcontainer_test"
   ]
 }
\ No newline at end of file

From 8551b13e5b258e8dab332eeedba2f9c6d7b599cc Mon Sep 17 00:00:00 2001
From: Thomas Schaffter <thomas.schaffter@gmail.com>
Date: Thu, 29 Aug 2024 20:15:30 +0000
Subject: [PATCH 07/10] move README

---
 .devcontainer/devcontainer.json               |  2 +-
 .../sage/.devcontainer/README.md              |  5 -----
 tools/devcontainers/sage/README.md            | 19 +++++++++++++++++++
 3 files changed, 20 insertions(+), 6 deletions(-)
 delete mode 100644 tools/devcontainers/sage/.devcontainer/README.md
 create mode 100644 tools/devcontainers/sage/README.md

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 1352fba0e2..0e97371af8 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,6 +1,6 @@
 {
   "name": "Sage Dev Container",
-  "image": "ghcr.io/sage-bionetworks/sage-devcontainer:3f79a5d",
+  "image": "ghcr.io/sage-bionetworks/sage-devcontainer:test",
   "containerEnv": {
     "NX_BASE": "${localEnv:NX_BASE}",
     "NX_BRANCH": "${localEnv:NX_BRANCH}",
diff --git a/tools/devcontainers/sage/.devcontainer/README.md b/tools/devcontainers/sage/.devcontainer/README.md
deleted file mode 100644
index 50be24a3c7..0000000000
--- a/tools/devcontainers/sage/.devcontainer/README.md
+++ /dev/null
@@ -1,5 +0,0 @@
-# Sage Dev Container
-
-Learn how to build and run dev containers with the devcontainer CLI:
-
-https://code.visualstudio.com/docs/remote/devcontainer-cli
\ No newline at end of file
diff --git a/tools/devcontainers/sage/README.md b/tools/devcontainers/sage/README.md
new file mode 100644
index 0000000000..6a934e4167
--- /dev/null
+++ b/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/
+```
\ No newline at end of file

From d8ad47e3d33cfceb411f1c265c8922ead2533045 Mon Sep 17 00:00:00 2001
From: Thomas Schaffter <thomas.schaffter@gmail.com>
Date: Thu, 29 Aug 2024 23:44:30 +0000
Subject: [PATCH 08/10] parametrize the versions of python installed

---
 tools/devcontainers/sage/.devcontainer/Dockerfile | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/tools/devcontainers/sage/.devcontainer/Dockerfile b/tools/devcontainers/sage/.devcontainer/Dockerfile
index 56685e849b..7fc7e3ed60 100644
--- a/tools/devcontainers/sage/.devcontainer/Dockerfile
+++ b/tools/devcontainers/sage/.devcontainer/Dockerfile
@@ -5,7 +5,7 @@ FROM ubuntu:$imageVersion
 # Set safer bash scripts
 SHELL ["/bin/bash", "-euxo", "pipefail", "-c"]
 
-# Image arguments
+# List of build arguments
 # https://github.com/nektos/act
 ARG actVersion="0.2.65"
 # https://github.com/sharkdp/hyperfine
@@ -22,8 +22,12 @@ ARG trivyVersion="0.54.1"
 ARG renvVersion="1.0.0"
 # 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="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
@@ -31,7 +35,7 @@ ARG hadolintVersion="2.12.0"
 # The version of this dev container image
 ARG devcontainerVersion=""
 # The username of the non-root user
-ARG user=vscode
+ARG user="vscode"
 
 # Set environment variables
 ENV DEVCONTAINER_VERSION=${devcontainerVersion} \
@@ -39,7 +43,7 @@ ENV DEVCONTAINER_VERSION=${devcontainerVersion} \
   LC_ALL=en_US.UTF-8
 
 # Install system packages
-# hadolint ignore=DL3008,DL3013
+# 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 \
@@ -170,8 +174,8 @@ RUN corepack install --global "pnpm@${pnpmVersion}"
 # Set up Python environments
 ENV PYENV_ROOT /home/${user}/.pyenv
 ENV PATH $PYENV_ROOT/shims:$PYENV_ROOT/bin:$PATH
-RUN pip install --no-cache-dir pipenv \
+RUN pip install --no-cache-dir pipenv==${pipenvVersion} \
   && curl https://raw.githubusercontent.com/pyenv/pyenv-installer/master/bin/pyenv-installer | bash - \
-  && pyenv install 3.9.2 3.10.14 3.11.8
+  && pyenv install ${pyenvPythonVersions}
 
 CMD ["bash"]
\ No newline at end of file

From eff31e8559352063162b51d897a27c9fc0603ba3 Mon Sep 17 00:00:00 2001
From: Thomas Schaffter <thomas.schaffter@gmail.com>
Date: Fri, 30 Aug 2024 00:02:39 +0000
Subject: [PATCH 09/10] update devcontainer CLI version

---
 .github/actions/setup-dev-container/action.yml    | 2 +-
 .github/workflows/build-devcontainer-image.yml    | 2 +-
 .github/workflows/schematic-api-ci.yml            | 2 +-
 tools/devcontainers/sage/.devcontainer/Dockerfile | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/actions/setup-dev-container/action.yml b/.github/actions/setup-dev-container/action.yml
index 610ad770ff..481d955516 100644
--- a/.github/actions/setup-dev-container/action.yml
+++ b/.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
diff --git a/.github/workflows/build-devcontainer-image.yml b/.github/workflows/build-devcontainer-image.yml
index bd703b3a3c..374925428d 100644
--- a/.github/workflows/build-devcontainer-image.yml
+++ b/.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}"
diff --git a/.github/workflows/schematic-api-ci.yml b/.github/workflows/schematic-api-ci.yml
index 2c5e756e73..2129cb116e 100644
--- a/.github/workflows/schematic-api-ci.yml
+++ b/.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: |
diff --git a/tools/devcontainers/sage/.devcontainer/Dockerfile b/tools/devcontainers/sage/.devcontainer/Dockerfile
index 7fc7e3ed60..2b46429dda 100644
--- a/tools/devcontainers/sage/.devcontainer/Dockerfile
+++ b/tools/devcontainers/sage/.devcontainer/Dockerfile
@@ -11,7 +11,7 @@ ARG actVersion="0.2.65"
 # https://github.com/sharkdp/hyperfine
 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="1.8.3"
 # https://docs.posit.co/resources/install-r/#specify-r-version

From aa9e9e6f26718b9ede6a51dd9ca156a923ab29eb Mon Sep 17 00:00:00 2001
From: Thomas Schaffter <thomas.schaffter@gmail.com>
Date: Fri, 30 Aug 2024 00:11:05 +0000
Subject: [PATCH 10/10] restore active dev container version

---
 .devcontainer/devcontainer.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 0e97371af8..1352fba0e2 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,6 +1,6 @@
 {
   "name": "Sage Dev Container",
-  "image": "ghcr.io/sage-bionetworks/sage-devcontainer:test",
+  "image": "ghcr.io/sage-bionetworks/sage-devcontainer:3f79a5d",
   "containerEnv": {
     "NX_BASE": "${localEnv:NX_BASE}",
     "NX_BRANCH": "${localEnv:NX_BRANCH}",