Standardize CLI output, logging, and progress indication across all scripts

[turbomam]

Background

The metpo codebase currently has inconsistent patterns for:

• Terminal output: Some scripts use click.echo(), others use rich.console.Console
• Logging: Mix of standard logging module and ad-hoc approaches
• Progress indication: Some use tqdm, others use rich progress bars or nothing
• Table display: Some use rich.table.Table, others print plain text

Current State

Existing metpo scripts (metpo/scripts/*.py, metpo/bactotraits/*.py, etc.):

• Output: click.echo()
• Progress: tqdm
• Logging: standard logging

Newly added madin scripts (metpo/scripts/madin/*.py):

• Output: rich.console.Console with markup
• Tables: rich.table.Table
• Logging: custom get_logger() wrapper

Proposal

Establish and document a consistent pattern for all CLI scripts:

1. Output: Choose one of:

   • click.echo() (simpler, no color)
   • rich.console.Console (richer formatting)

2. Logging: Standardize on:

   • Standard logging module with consistent format
   • Or rich's logging handler for colored logs

3. Progress: Choose one of:

   • tqdm (widely used)
   • rich.progress (integrates with rich console)

4. Tables: Choose one of:

   • Plain text / TSV output
   • rich.table.Table for terminal display

Tasks

• Document the chosen patterns in CLAUDE.md
• Create a shared utility module (e.g., metpo/cli_utils.py) with standard helpers
• Refactor existing scripts to use the standard patterns
• Update madin scripts to match

Related

• Added rich>=13.0.0 as a dependency to support madin scripts
• Scripts imported from biosample-enricher PR Release 2025-09-23 #200