From de1c4d7d4a47a87f54ce898f3c9f2055b4571a3c Mon Sep 17 00:00:00 2001
From: Thomas Luechtefeld <tom@insilica.co>
Date: Wed, 26 Jun 2024 13:51:17 -0400
Subject: [PATCH] added devcontainer to brick-template

---
 .devcontainer/Dockerfile        | 55 +++++++++++++++++++++++++++++++++
 .devcontainer/devcontainer.json | 25 +++++++++++++++
 2 files changed, 80 insertions(+)
 create mode 100644 .devcontainer/Dockerfile
 create mode 100644 .devcontainer/devcontainer.json

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
new file mode 100644
index 0000000..e5414e5
--- /dev/null
+++ b/.devcontainer/Dockerfile
@@ -0,0 +1,55 @@
+FROM mcr.microsoft.com/devcontainers/python:3.9
+
+# Install necessary packages
+RUN apt-get update && apt-get install -y \
+    wget \
+    unzip \
+    xvfb \
+    libxi6 \
+    libgconf-2-4 \
+    libnss3-dev \
+    libxss1 \
+    libappindicator1 \
+    fonts-liberation \
+    libatk-bridge2.0-0 \
+    libgtk-3-0 \
+    libgbm1 \
+    libasound2 \
+    libdpkg-perl \
+    libatomic1 \
+    ca-certificates \
+    curl \
+    gnupg \
+    python3-venv \
+    awscli
+
+# Install pipx and biobricks
+RUN python3 -m pip install --user pipx \
+    && python3 -m pipx ensurepath
+
+# Create /mnt/biobricks directory and set permissions
+RUN mkdir -p /mnt/biobricks/biobricks-ai \
+    && chown -R vscode:vscode /mnt/biobricks
+
+# Add pipx binaries to the PATH for all users
+RUN echo 'export PATH="$PATH:$HOME/.local/bin"' >> /etc/bash.bashrc \
+    && echo 'export PATH="$PATH:$HOME/.local/bin"' >> /home/vscode/.bashrc
+
+# Switch to vscode user to perform user-specific installations
+USER vscode
+
+# Install Python dependencies
+COPY requirements.txt /tmp/requirements.txt
+RUN pip install -r /tmp/requirements.txt
+
+# Accept build argument for BIOBRICKS_TOKEN
+ARG BIOBRICKS_TOKEN
+ENV BIOBRICKS_TOKEN=${BIOBRICKS_TOKEN}
+
+# Install biobricks and configure it
+RUN /bin/bash -c 'source /etc/bash.bashrc && pipx install biobricks && biobricks version' \
+    && /bin/bash -c 'if [ -z "$BIOBRICKS_TOKEN" ] || [ ${#BIOBRICKS_TOKEN} -lt 5 ]; then echo "BIOBRICKS_TOKEN is not set or is too short (less than 5 characters)"; exit 1; fi' \
+    && /bin/bash -c 'source /etc/bash.bashrc && biobricks configure --bblib=/mnt/biobricks --token=${BIOBRICKS_TOKEN} --interactive=False'
+
+# Switch back to root user to complete setup
+USER root
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 0000000..370b64d
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,25 @@
+{
+    "name": "SMRT Development Container",
+    "build": {
+        "dockerfile": "Dockerfile",
+        "context": "..",
+        "args": {
+            "BIOBRICKS_TOKEN": "${localEnv:BIOBRICKS_TOKEN}"
+        }
+    },
+    "features": {
+        "ghcr.io/devcontainers/features/docker-in-docker:1": {}
+    },
+    "settings": {
+        "terminal.integrated.defaultProfile.linux": "bash",
+        "python.pythonPath": "/usr/local/bin/python"
+    },
+    "extensions": [
+        "ms-python.python",
+        "ms-toolsai.jupyter",
+        "ms-vsliveshare.vsliveshare",  // Live Share extension
+        "github.copilot",  // GitHub Copilot extension
+        "insilica.vscode-pycmd"
+    ],
+    "remoteUser": "vscode"
+}