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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]​

[0.2.5] - 2026-03-16​

Added​

  • Documentation for PRD SMILES coverage by represent_as type (#127)
  • "Why This Table Exists" section in chem.md explaining unified table rationale (#127)

Changed​

  • __version__ now derived dynamically via importlib.metadata instead of hardcoded string (#129)

Fixed​

  • pmb --version displayed "0.2.3" in 0.2.4 release due to hardcoded __version__ (#128, #129)

[0.2.4] - 2026-03-16​

Added​

  • SMILES generation for PRD pipeline via ccd2rdmol on PRDCC blocks (#110, #122)
  • canonical_smiles and chem_comp_id columns on prd.brief_summary (#110, #122)
  • RDKit mol column, GiST index, and descriptor triggers for prd schema (#110, #122)
  • Unified chem.compounds table for cross-schema chemical searches (cc + prd) (#110, #122)
  • pmb compounds command to refresh chem.compounds table (#110, #122)
  • scripts/rdkit_functions_chem.sql with similarity/substructure search functions for chem schema (#110, #122)
  • Automatic compounds refresh after pmb update when cc/prd pipelines run (#110, #122)
  • pmb config --init to generate config from bundled template (#121)
  • Website documentation for chem schema and prd RDKit integration (#125)

Changed​

  • Extracted shared RDKit utilities to pipelines/rdkit_utils.py (from cc.py) (#110, #122)
  • pmb setup-rdkit now sets up both cc and prd schemas (#110, #122)
  • Docker test tasks use docker-compose (standalone) instead of docker compose (subcommand) (#122)
  • RdkitDescriptor uses NamedTuple for self-documenting descriptor definitions (#124)

Fixed​

  • Docker test container crashes on ARM Mac (mcs07/postgres-rdkit amd64-only image) by adding platform: linux/amd64 (#122)
  • Double file read in PRD pipeline when processing PRDCC blocks (#124)
  • refresh_compounds missing confirmation prompt when force=False (#124)

[0.2.3] - 2026-03-14​

Added​

  • pmb config command to display active configuration and resolved settings
    • Shows config file location, connection string (redacted), data directory, workers, pipelines, sync targets
    • pmb config --json for machine-readable output
    • pmb config --init to generate config from bundled template (~/.config/pmb/config.yml)
  • Config file auto-discovery: ./config.yml → ~/.config/pmb/config.yml
  • pmb schema command to inspect database schema definitions (no DB connection required)
    • pmb schema - list all schemas with table counts and entry PK
    • pmb schema <name> - list tables in a schema with column counts
    • pmb schema <name>.<table> - show columns with types, nullable, PK, and comments
    • pmb schema <name>.<table>.<column> - show single column detail
    • pmb schema --search <query> - search column names and comments across all schemas
    • pmb schema --json - JSON output for all modes (machine/AI-readable)
    • pmb schema <name> --json returns all tables and columns in one response
  • CLI Reference documentation page with all commands
  • Schema inspection guide in Getting Started docs
  • Query command added to Getting Started sidebar
  • RDKit integration section in cc schema documentation

[0.2.2] - 2026-03-08​

Added​

  • Interactive SQL query examples page with 75 examples across 10 categories (#95)
  • RDKit chemical search examples: substructure, similarity, SMARTS patterns (#97)
  • Fully config-driven sync: all targets defined in config.yml sync section (#102)
  • SyncTarget model with source/sources, dest, and options fields (#102)
  • Configurable rsync options per target (default: ["-av", "--size-only"]) (#102)
  • data-dir config field with priority resolution (config > env > CWD) (#100)
  • prdcc config field for explicit PRDCC file path in prd pipeline (#100)
  • PDBj dump file incompatibility warning in migration docs (#98)
  • Database size and entry count statistics (#93)
  • Missing data-nextgen-plus configuration documentation (#99)

Changed​

  • Sync command is now purely config-driven: no hardcoded URLs, destinations, or options (#102)
  • config.example.yml rewritten with full sync section and all available targets (#102)
  • Sync URLs updated from rsync.pdbj.org to data.pdbj.org (#100)
  • Sync targets cc, ccmodel, prd, prd-family now download only required files (#100)
  • SQL examples pipeline simplified to use sqlExamples.json as single source of truth (#96)

Fixed​

  • vrpt rsync include/exclude options had embedded quotes that broke filtering (#103)

Removed​

  • Hardcoded sync target definitions (SYNC_TARGETS, _PIPELINE_DEST_MAP, etc.) (#102)
  • sync-sources config field (replaced by sync section) (#102)
  • Legacy sync alias resolution (#102)
  • PDBj example fetching scripts (fetch_pdbj_examples.py, process_examples.py, generate_examples_json.py) (#96)

[0.2.1] - 2026-03-08​

Added​

  • pmb query command for executing SQL queries with multi-format output (table, CSV, JSON, Parquet)
  • Read-only connection mode for query command to prevent accidental destructive SQL
  • Polars dependency for DataFrame-based query result handling
  • Docker/Podman support for production deployment
  • Interactive Table Relations page with dynamic Mermaid ER diagrams
  • Schema tab picker with preset examples for quick exploration
  • SVG/PNG diagram download
  • Schema search page with cross-schema column search

Changed​

  • Migrated schema docs from .mdx to .md format
  • Extracted shared Schema interface and SCHEMA_PRIORITY to types module

Fixed​

  • Schema ordering bug (unknown schemas sorted incorrectly)
  • PNG download silent failures with proper error handling

[0.2.0] - 2026-03-07​

Initial release as an independent Python project. Rewritten from mine2updater (Node.js) by PDBj.

Added​

  • 7 data pipelines: pdbj, cc, ccmodel, prd, prd_family, vrpt, contacts
  • 2 schema-only definitions: emdb, ihm
  • Dual format support (CIF / mmJSON) for pdbj, cc, ccmodel, prd pipelines
  • Unified parsing via gemmi for both CIF and mmJSON
  • Multi-process parallel loading with ProcessPoolExecutor
  • Bulk load mode (COPY protocol) for initial data loading
  • Mtime-based skip optimization for incremental updates
  • RDKit PostgreSQL cartridge integration for chemical searches
  • SMILES generation from molecular structure via ccd2rdmol
  • SQLAlchemy Core schema definitions with Alembic migrations
  • CLI with 9 commands: sync, update, load, all, setup-rdkit, test, reset, stats, version
  • Pydantic-based configuration with YAML and environment variable support
  • Documentation website with auto-generated schema docs
  • Docker-based test environment (PostgreSQL + RDKit)
  • PyPI publishing support with trusted publishing
  • Environment version tests for Python and PostgreSQL
  • Alternative installation methods (pip, conda+pip)
  • config.example.yml with documented options
  • MIT license