Streamline documentation to focus on core functionality and conda
integration. Changes include:
- Clarify default design and conda environment usage
- Remove redundant workflow benefits section
- Simplify features list to focus on key capabilities
- Remove directory structure (available in repo)
- Add explicit push requirement in CLAUDE.md
- Update task completion requirements
This makes the documentation more focused and easier to understand while
emphasizing the project's integration with conda environments.
Added CLAUDE.md configuration section explaining the autonomous task
executor template and its usage with plan.md. Also documented the
task_log.md feature which captures execution details and insights.
π€ Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
Change git configuration to use Docker build args instead of .env file,
simplifying setup and improving security. This change:
- Removes git config from .env and startup.sh
- Adds GIT_USER_NAME and GIT_USER_EMAIL build args
- Updates documentation for new git config approach
- Improves task logging requirements in CLAUDE.md
The build arg approach provides better isolation and ensures git config is
properly set during image build rather than container runtime.
Remove temporary task-related files (plan.md, task_log.md) and update
.gitignore to prevent them from being tracked in the future. These files
are implementation-specific and should not be part of the repository as
they contain task execution details that are only relevant during the
development process.
Add required git user configuration to enable commits from within the container.
This change ensures proper attribution of git commits made inside the container by:
- Adding GIT_USER_NAME and GIT_USER_EMAIL to .env.example
- Configuring git user globally during Docker build
- Adding documentation for git configuration requirements
- Updating README with clearer setup instructions and requirements
The configuration is now required as part of the initial setup to prevent
issues with unattributed commits when using git inside the container.
Add comprehensive prerequisites section with detailed authentication steps.
Include comparison table showing differences from Anthropic's DevContainer.
Enhance documentation structure with better formatting and examples.
Add attribution section crediting dependencies and inspirations.
π€ Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
This script was not referenced anywhere in the codebase and used
an outdated approach for credential management. Current workflow
bakes credentials into Docker image from .env file in project root.
Update autonomous task executor template to gracefully handle cases
where Twilio is not configured. SMS notifications now only attempt
if ALL required environment variables are present:
- TWILIO_ACCOUNT_SID
- TWILIO_AUTH_TOKEN
- TWILIO_FROM_NUMBER
- TWILIO_TO_NUMBER
Task execution continues normally without SMS if any variable is missing.
Copy CLAUDE.md directly to final location instead of using /tmp
intermediate step. This ensures the COPY fails loudly if there's
an issue and simplifies the build process.
The MCP configuration is already handled by the Dockerfile using
claude mcp add-json command. The template file was unnecessary and
could cause confusion.
This template provides instructions for Claude when running in the Docker
container, including task execution workflow, coding standards, and
Twilio notification requirements.
Implemented SYSTEM_PACKAGES environment variable for flexible system library installation:
Key Features:
- Users specify packages in .env: SYSTEM_PACKAGES="libopenslide0 libgdal-dev"
- Packages installed during Docker build (secure, no runtime mounting)
- Automatic rebuild detection when packages change
- Documentation with common scientific computing packages
Technical Implementation:
- ARG SYSTEM_PACKAGES in Dockerfile with conditional apt-get install
- Build argument passed from claude-docker.sh script
- Clean package management with cache cleanup
Benefits:
- Secure: No system directory mounting required
- Flexible: Users choose exactly what they need
- Documented: Common packages listed in README
- Clean: Packages baked into image, not mounted at runtime
Tested successfully with OpenSlide: conda run -n prism python -c "import openslide"
Added CONDA_PKGS_DIRS environment variable setting to ensure conda
looks in the correct package cache directories inside the container.
This matches the pattern used for CONDA_ENVS_DIRS.
Enhanced conda support to handle custom environment and package directories:
Key Changes:
- Mount conda installation at original path (not /opt/miniconda3)
- Add CONDA_EXTRA_DIRS for mounting additional search paths
- Mount all conda-configured directories to preserve existing setup
- Update CLAUDE.md to use ${CONDA_EXE} environment variable
Technical Details:
- Preserves original conda paths so existing configuration works
- Handles multiple envs_dirs and pkgs_dirs automatically
- Provides feedback about which directories are mounted
- Falls back gracefully for missing directories
Example usage: CONDA_EXTRA_DIRS="/vol/path/.conda/envs /vol/path/conda_envs /vol/path/.conda/pkgs"
Result: All conda environments and packages accessible in container.
Major breakthrough solving the authentication chicken-and-egg problem:
Key Changes:
- Copy ~/.claude.json and ~/.claude/ during Docker build for baked-in auth
- Add -s user flag to claude mcp add-json for persistent MCP servers
- Simplify rebuild logic to prevent unnecessary rebuilds
- Update documentation with rebuild instructions
Technical Details:
- Authentication files placed before USER switch in Dockerfile
- MCP configuration now persists across all sessions
- Rebuild only occurs when image doesn't exist
- Clean separation of build vs runtime concerns
Result: Users authenticate once on host, then zero login prompts forever.
SMS notifications ready immediately on container start.
- Replace API Key/Secret auth with Account SID/Auth Token
- Configure MCP during Docker build instead of runtime
- Remove mcp-config.json and config directory
- Simplify startup script by removing MCP configuration logic
- Update documentation and test scripts for new auth method
The MCP server is now configured directly in the Dockerfile using
'claude mcp add-json' command, making the setup more reliable and
eliminating runtime configuration complexity.
- Add proper type and env sections to mcp-config.json
- Remove dynamic MCP add command, use pre-configured MCP
- Bake .env credentials into Docker image at build time
- Remove runtime .env volume mount - true one-time setup
- Auto-rebuild image when .env file changes
- Export Twilio env vars for MCP server subprocess
- Remove conflicting .mcp.json file
- Add authentication persistence to features section
- Update configuration section with claude-home directory
- Clarify what files go where in the setup
- Add persistent volume mount for Claude home directory (~/.claude)
- Create non-root user in Docker container for better security
- Mount host ~/.claude-docker/claude-home to container ~/.claude
- Update install script to create claude-home directory
- Check for existing credentials on startup
- Authentication tokens now persist across container restarts
- Container launches successfully after fixes
- Next priorities: auth persistence, firewall, command history
- Need to study Anthropic dev container implementation
- Change executable from claude-code to claude in startup.sh
- Fix .env parsing to handle comments using set -a/source
- Add explicit PATH for npm global binaries in Dockerfile
- Update scratchpad.md with fix documentation
- Update scratchpad with completed MVP status and Phase 2 roadmap
- Rewrite README with comprehensive setup instructions and feature overview
- Document next steps: firewall security and shell history persistence
- Dockerfile with Claude Code and Twilio MCP integration
- Wrapper script for easy invocation from anywhere
- Auto-setup of .claude directory in projects
- SMS notifications via Twilio when tasks complete
- Installation script for zshrc alias
- Full autonomous permissions with --dangerously-skip-permissions
- Context persistence via scratchpad.md
