RepBox

RepBox is a Python-first CLI platform for transposable element discovery and annotation, evolved from the original PhD thesis-era workflow.

Current status

• Modernized CLI implementation is active under src/repbox/.
• Current commands: run, check, smoke, smoke-report, version.
• Adapter-based integration is in place for RepeatModeler/RepeatMasker paths.
• Current stable baseline is v2.0.0.

Quick start

From repository root:

python -m pip install -e .
python -m repbox version
python -m repbox check --legacy-config repbox_config.txt
python -m repbox smoke --input <genome.fa> --out <output_dir>
python -m repbox smoke-report --report <output_dir>/smoke_report.txt --json

Notes:

• check and smoke can return non-zero when legacy external tool paths are missing.
• smoke-report supports human-readable and --json machine-readable output.

CLI commands

• repbox version: print package version.
• repbox check --legacy-config <path>: validate configured external tools.
• repbox run --input <fa> --out <dir> [--threads N] [--engine ncbi]: run the current adapter-based pipeline path.
• repbox smoke --input <fa> --out <dir>: write smoke_report.txt with tool diagnostics.
• repbox smoke-report --report <path> [--json]: summarize or parse smoke reports.

Versioning and release model

• RepBox uses Semantic Versioning (MAJOR.MINOR.PATCH).
• v2.0.0 is the baseline milestone for the modernized CLI contract and release workflow.
• Ongoing work continues as small PR slices merged to master.

Development workflow

1. Create a focused branch (feat/*, fix/*, docs/*, test/*).
2. Make scoped changes and run local validation.
3. Update Changelog.md (Unreleased) for user-visible changes.
4. Open PR to master, merge when checks pass.

Documentation map

• Changelog: Changelog.md
• Release workflow: docs/process/releasing.md
• Release notes templates: docs/process/release_notes_templates.md
• GitHub project playbook: docs/process/github_project_playbook.md
• Legacy implementation spec: docs/legacy/IMPLEMENTATION_SPEC_V0.3.0.md
• Legacy thesis environment setup: docs/legacy/thesis_environment_setup.md

Research roadmap

v2.0.0 marks software baseline stabilization. Paper-oriented milestones can build on top:

• v2.1: reproducibility benchmarks and baseline comparisons.
• v2.2: broader biological validation datasets and analysis.
• v2.3: manuscript-aligned figures, tables, and methods narrative.
• v2.4: submission-ready reproducibility package.