21147361161

Committed 19 Jan 2026 06:04PM UTC coverage: 59.439% (+0.7%) from 58.726%

Build # 21147361161

Build Type

push

github

Committed by

iskandr

Commit Message

Add CLI input validation and fix documentation

- Add centralized CLI validation utilities in validation.py:
  - validate_cli_conditional_requirement() for conditionally required args
  - validate_cli_mutually_exclusive() for mutual exclusivity
  - validate_assemble_args(), validate_run_args(), validate_annotate_gex_args()

- Update CLI help strings with clear required/conditional sections:
  - assemble: Show --contigs-dir required for --leaders-from-contigs
  - annotate-gex: Show --gex-file as always required
  - match-til: Show --til-data as always required
  - Organize arguments into logical groups

- Add early validation in CLI commands to fail fast with helpful errors

- Add comprehensive tests for CLI validation (42 new tests)

- Fix all linting issues across test files:
  - Import sorting and unused imports
  - == True/False comparisons to truthiness checks

- Fix documentation inconsistencies with actual CLI:
  - docs/user-guide/cli.md: Major update to match actual options
  - docs/getting-started/quickstart.md: Remove non-existent --report flag

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

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