Changelog

All notable changes to BioMetaHarmonizer are documented in this file. Format follows Keep a Changelog.

v1.1.0 — 2026-06-10

Added

biometaharmonizer build-dicts CLI subcommand — replaces direct invocation of scripts/build_dictionaries.py. Accepts the same flags (--base, --output, --taxdmp, --umls-key, --skip-ols, --skip-ncbi, --dry-run, --verbose-collisions).
biometaharmonizer build-ncbi-cache CLI subcommand — replaces direct invocation of scripts/build_ncbi_attribute_cache.py. Accepts --output-dir and --skip-fetch.
biometaharmonizer generate-report CLI subcommand — replaces direct invocation of scripts/generate_summary_report.py. Generates self-contained HTML (and optionally PDF) summary reports from a harmonized output file.

Changed

docs/installation.rst: added Post-install Setup section documenting the required build-ncbi-cache + build-dicts one-time setup step.
docs/quickstart.rst: added Before Your First Run section at the top.
docs/cli_reference.rst: reordered subcommands to reflect workflow order (setup → run → report); added full flag tables and examples for all three new subcommands; expanded exit code table.
docs/faq.rst: updated FAQ #13 and #14 to use biometaharmonizer subcommands instead of python scripts/; added FAQ #15 (build-ncbi-cache), FAQ #16 (generate-report); renumbered thread-safety entry to #17.

First stable release. All known bugs and robustness issues have been resolved before this milestone.