CLI Reference

SciTeX Linter provides a single scitex-linter command with subcommands.

Global Options

scitex-linter [-h] [-V] [--help-recursive] {check,format,python,rule,api,mcp} ...

-V, --version: Show version and exit.
--help-recursive: Show help for all commands and subcommands.

scitex-linter check

Check Python files for SciTeX pattern compliance.

scitex-linter check <path> [--json] [--no-color] [--severity LEVEL] [--category CAT]

path: Python file or directory to check. Directories are searched recursively.
--json: Output results as JSON.
--no-color: Disable colored output.
--severity {error,warning,info}: Minimum severity to report (default: info).
--category: Filter by category (comma-separated): structure, import, io, plot, stats, path, figure.

Exit codes:

0 — No issues (or only info-level)
1 — Warnings found
2 — Errors found

Examples:

# Check a single file
scitex-linter check script.py

# Check a directory, errors only
scitex-linter check ./src/ --severity error

# JSON output for CI
scitex-linter check . --json --no-color

scitex-linter format

Auto-fix SciTeX pattern issues in Python files.

scitex-linter format <path> [--check] [--diff]

path: Python file or directory to format.
--check: Dry run — exit 1 if changes would be made (no files modified).
--diff: Show a unified diff of changes.

Supported auto-fixes: fig.savefig() to stx.io.save(), np.save/load to stx.io, pd.read_csv to stx.io.load(), and missing INJECTED parameters.

Examples:

# Fix in place
scitex-linter format script.py

# Dry run
scitex-linter format script.py --check

# Show diff
scitex-linter format script.py --diff

scitex-linter python

Lint a Python script, then execute it.

scitex-linter python <script> [--strict] [-- script_args...]

script: Python script to lint and execute.
--strict: Abort execution if lint errors are found (exit code 2).
-- args...: Arguments passed to the script (after -- separator).

Examples:

# Lint and run
scitex-linter python experiment.py

# Strict mode
scitex-linter python experiment.py --strict

# Pass arguments to script
scitex-linter python experiment.py -- --epochs 100 --lr 0.001

scitex-linter rule

List all available lint rules.

scitex-linter rule [--json] [--category CAT] [--severity LEVEL]

--json: Output as JSON.
--category: Filter by category (comma-separated).
--severity {error,warning,info}: Filter by exact severity level.

scitex-linter api

List the public Python API.

scitex-linter api [--json]

--json: Output as JSON.

Displays a tree view of all public functions, classes, and variables across scitex_linter.checker, scitex_linter.fixer, scitex_linter.formatter, scitex_linter.rules, and scitex_linter.config.

scitex-linter mcp

MCP (Model Context Protocol) server commands.

scitex-linter mcp {start,list-tools}

scitex-linter mcp start [--transport {stdio,sse}]: Start the MCP server. Default transport is stdio.
scitex-linter mcp list-tools: List available MCP tools.

Requires the mcp extra: pip install scitex-linter[mcp]