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Command-line Interface (CLI)

Entry points for running the diagnostic pipeline from the command line.

Command-line wrapper for Harmonisation Diagnostics.

Usage examples

harmdiag run --data data.csv --covariates cov.csv --batch-col 3 harmdiag run --data data.csv --covariates cov.csv --outdir ./reports harmdiag gui

Usage

Run the main CLI from the package:

python -m DiagnoseHarmonisation.cli --help

This module exposes the high-level entrypoints used by the project-level harmdiag console script and includes helpers for parsing arguments and launching the cross-sectional workflow.

Common flags

  • --data, -d: Path to data file (subjects x features).
  • --covariates, -c: Path to covariates file (one row per subject).
  • --batch-col: 1-based index of covariates column containing batch labels (optional).
  • --outdir: Output directory for reports.
  • -v/--verbose: Verbose logging.