CLI Reference
The scitex-container CLI provides unified container management for
Apptainer and Docker.
Global Options
scitex-container [OPTIONS] COMMAND [ARGS]...
Options:
-V, --version Show version and exit.
--help-recursive Show help for all commands recursively.
--json Emit machine-readable JSON output (where supported).
-h, --help Show this message and exit.
Apptainer Commands
All Apptainer commands are nested under the apptainer sub-group:
scitex-container apptainer COMMAND [ARGS]...
build
Build a SIF or sandbox from a definition (.def) file.
scitex-container apptainer build [OPTIONS] [NAME]
Options:
--sandbox— build a sandbox directory instead of SIF--force/-f— force rebuild even if up-to-date--output-dir/-o— output directory (default: parent of .def)--dry-run— preview without building
freeze
Extract pinned package versions (pip, dpkg, npm) from a built SIF.
scitex-container apptainer freeze [OPTIONS] SIF_PATH
Options:
--output-dir/-o— output directory for lock files
list
List all versioned SIF files with metadata.
scitex-container apptainer list [OPTIONS]
Options:
--dir/-d— containers directory--json— machine-readable JSON output
switch
Switch the active container version (updates current.sif symlink).
scitex-container apptainer switch [OPTIONS] VERSION
Options:
--dir/-d— containers directory--sudo— use sudo for symlink operations
rollback
Revert to the previous container version.
scitex-container apptainer rollback [OPTIONS]
Options:
--dir/-d— containers directory--sudo— use sudo for symlink operations--dry-run— preview without executing
deploy
Copy active SIF to a production target directory.
scitex-container apptainer deploy [OPTIONS]
Options:
--target/-t— deployment target directory (default: /opt/scitex/singularity)--dir/-d— source containers directory
clean
Remove old container versions, keeping the N most recent.
scitex-container apptainer clean [OPTIONS]
Options:
--keep/-k— number of recent versions to keep (default: 3)--dir/-d— containers directory--dry-run— preview without executing
verify
Verify container integrity: SHA256 hash, .def origin, lock file comparison.
scitex-container apptainer verify [OPTIONS] [SIF_PATH]
Options:
--def— path to .def file to verify against--lock-dir— directory containing lock files--json— output raw JSON
Sandbox Commands
scitex-container sandbox COMMAND [ARGS]...
create
Build a timestamped sandbox from a SIF image or .def file.
scitex-container sandbox create [OPTIONS]
Options:
--source/-s— source .sif or .def file (required)--dir/-d— containers directory--output/-o— explicit output directory--dry-run— preview without executing
maintain
Run a maintenance command inside a sandbox (writable + fakeroot).
scitex-container sandbox maintain [OPTIONS] COMMAND...
Options:
--sandbox-dir/-s— sandbox directory path (required)
list
List versioned sandbox directories.
scitex-container sandbox list [OPTIONS]
Options:
--dir/-d— containers directory--json— machine-readable JSON output
switch
Switch active sandbox to a specific version (timestamp).
scitex-container sandbox switch [OPTIONS] VERSION
Options:
--dir/-d— containers directory--sudo— use sudo for symlink operations
rollback
Revert to the previous sandbox version.
scitex-container sandbox rollback [OPTIONS]
Options:
--dir/-d— containers directory--sudo— use sudo for symlink operations--dry-run— preview without executing
clean
Remove old sandbox directories, keeping the N most recent.
scitex-container sandbox clean [OPTIONS]
Options:
--keep/-k— number of recent sandboxes to keep (default: 5)--dir/-d— containers directory--dry-run— preview without executing
update
Incrementally update ecosystem packages inside an existing sandbox.
scitex-container sandbox update [OPTIONS]
Options:
--sandbox-dir/-s— sandbox directory path (required)--proj-root/-r— project root containing repos (default: ~/proj)--pkg/-p— update only this package--deps— install dependencies too (slower)
configure-ps1
Configure PS1 prompt in a sandbox environment script.
scitex-container sandbox configure-ps1 [OPTIONS]
Options:
--sandbox-dir/-s— sandbox directory path--ps1— PS1 prompt string (default: W $ )
Docker Commands
scitex-container docker COMMAND [ARGS]...
rebuild
Rebuild Docker Compose services without cache.
scitex-container docker rebuild [OPTIONS]
Options:
--env/-e— environment (dev/prod, default: dev)--dry-run— preview without executing
restart
Restart Docker Compose services (down then up -d).
scitex-container docker restart [OPTIONS]
Options:
--env/-e— environment (dev/prod, default: dev)--dry-run— preview without executing
Host Commands
scitex-container host COMMAND [ARGS]...
install
Install host-side packages (TeX Live, ImageMagick) — requires sudo.
scitex-container host install [OPTIONS]
Options:
--texlive— install only TeX Live--imagemagick— install only ImageMagick--all— install all packages (default when no specific flag given)--dry-run— preview without executing
check
Check status of required host packages.
scitex-container host check [OPTIONS]
show-mounts
Show bind mount configuration for host packages.
scitex-container host show-mounts [OPTIONS]
Options:
--texlive-prefix— TeX Live installation prefix (default: /usr)--json— machine-readable JSON output
Status Dashboard
scitex-container show-status [OPTIONS]
scitex-container show-status --json
Displays a unified dashboard showing the status of Apptainer containers, Docker services, and host package installations.
Environment Snapshot
scitex-container save-env-snapshot [OPTIONS]
Capture a reproducibility snapshot of the current environment (container version + SIF hash + host packages + git commits + lock files). Output is a JSON-serializable dict.
Options:
--json— output raw JSON--dev-repo— git repo path to include (repeatable)--containers-dir— containers directory (auto-detected if not given)--dry-run— preview without executing
Skills
scitex-container skills COMMAND [ARGS]...
list
List available skill files bundled with the package.
scitex-container skills list [OPTIONS]
Options:
--json— machine-readable JSON output
get
Print the contents of a skill file by name (stem or path).
scitex-container skills get [OPTIONS] NAME
Options:
--json— machine-readable JSON output
install
Install skills to a target directory (default: ~/.scitex/dev/skills/scitex-container/).
scitex-container skills install [OPTIONS]
Options:
--dest— destination directory--no-link— copy files instead of symlinking--claude-symlink— also expose at ~/.claude/skills/scitex/--dry-run— preview without linking/copying
MCP Commands
scitex-container mcp COMMAND [ARGS]...
start
Start the MCP (Model Context Protocol) server.
scitex-container mcp start [OPTIONS]
Options:
--transport/-t— transport type (stdio/sse/http, default: stdio)--host/-h— host to bind (default: 0.0.0.0)--port/-p— port to bind (default: 8086)
doctor
Check FastMCP availability and tool health.
scitex-container mcp doctor [OPTIONS]
list-tools
List all registered MCP tools with signatures.
scitex-container mcp list-tools [OPTIONS]
Options:
-v/-vv— verbosity (signatures, descriptions)--json— machine-readable JSON output
install
Show MCP server installation instructions for Claude Code.
scitex-container mcp install [OPTIONS]
Options:
--claude-code— show Claude Code config snippet--json— output as JSON
Additional Commands
list-python-apis
List all public Python APIs (apptainer, docker, host modules) with signatures.
scitex-container list-python-apis [OPTIONS]
Options:
-v/-vv— verbosity (signatures, docstrings)--json— machine-readable JSON output