Development#
CFTK is under active development. The current package version is 1.0.0 and the source repository is ChaorongC/CFTK.
Planned Release Work#
The repository TODO.md is the authoritative roadmap. Managed references,
cftk doctor, and the fail-fast beginner cftk run are implemented. The
current release work is the software-identity and tagged-artifact gate:
core schema-v4 and downstream schema-v2 manifests bind results and automatic resume to the exact CFTK payload identity; and
a
v<pyproject version>tag builds and validates a wheel, sdist, and SHA-256 checksum file before publishing GitHub release assets only.
The release workflow does not publish to PyPI or Conda/Bioconda. A clean, revision-bound identity is required for a new release gate; historical core schemas 1–3 remain readable and acceptable for their recorded validation. Conda/Bioconda packaging is the next distribution phase after the first immutable GitHub release.
The pinned managed default profile, local reference profiles, schema-v2 project initialization, doctor diagnostics, and manifest-backed beginner workflow are available now. Legacy configuration and alternative-tool compatibility remain available only through the expert commands.
Internal Validation#
The historical cohort audit and Sambamba-versus-Picard comparison are retained for maintainers and advanced users. They are technical diagnostics, not a required beginner step and not a claim that duplicate-marking tools are universally interchangeable.
Every terminal cftk run attempt now creates that evidence bundle under its
attempt directory. The source-checkout helper
scripts/validation/summarize_workflow_run.py remains as a compatibility
wrapper for historical run.json files and release records. Keep evidence
tables outside Git; the beginner stage contract in
Beginner Workflow remains the authoritative list of required
outputs, while the reporter checks and visualizes that contract.