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Changelog

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

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

[Unreleased]

2.0.0 - 2026-03-05

Added

  • Universal YAML template (data/template_example.yml).
  • Example CSV data file (data/data_example.csv) demonstrating the full column set.
  • Comprehensive test suite with coverage reporting via Codecov.
  • CI pipeline with Ruff linting, pytest + coverage, and Codecov upload (.github/workflows/ci.yml).
  • MkDocs documentation site with auto-generated API reference via mkdocstrings.
  • Tutorials rewritten to reflect the actual two-pass workflow (databus_example.py).
  • OpenSSF Best Practices badge tracking.

Changed

  • Major refactor of the validation/upload architecture (BU-334, BU-349): each validator now also handles insertion when a populated databus dict is supplied, eliminating the separate neotomaUploader module and reducing code duplication.
  • Refactored pull_params into smaller, testable helper functions in utils.py, removing the dependency on pandas.
  • Contact handling consolidated: all contact types (PI, collector, processor, analyst) now go through valid_contact, with chronology modeler assignment handled within valid_chronologies. This significantly reduces repeated code.
  • Data upload now tracks inserted IDs so that data uncertainties can be linked correctly.
  • Chronology handling improved to properly manage calendar years, default chronologies, and sample age linkage.
  • Geopolitical unit insertion updated to handle entities like Scotland under the UK.
  • Improved logging with logging_dict and per-file .valid.log output.
  • Adopted Ruff as the sole linter and formatter, replacing previous tooling.
  • Switched to uv for dependency management and script execution.

Fixed

  • Chron controls now handle calendar years properly.
  • U-Th series insertion works correctly when the number of geochron indices differs from sample indices.
  • Fixed dataset–publication and dataset–database linking during upload.
  • Fixed collector insertion for NODE community datasets.
  • Fixed variable validation to handle null values without comparing null against null.
  • Numerous typos across chroncontrols.py, sample.py, Chronology.py, and others.

1.0.0 - 2025-11-27

Added

  • Support for speleothem datasets (SISAL community): U-Th series, external speleothem data, speleothem reference inserts, and entity samples.
  • ExternalSpeleothem class and corresponding valid_external_speleothem validator.
  • UThSeries class with independent insertion of U-series analytical data.
  • Lead-210 (210Pb) community support with lead model classes and geochronology workflows.
  • Ostracode surface sample support.
  • Script for batch speleothem reference inserts after initial upload.
  • hash_file and check_file helpers for file integrity verification before upload.
  • safe_step wrapper for error-safe validation with automatic logging and rollback.
  • CITATION.cff for academic citation.
  • code_of_conduct.md.

Changed

  • Expanded contact name parsing to handle initials and periods in given names.
  • Improved handling of diverse data groups across communities.

Fixed

  • Geochronology data handling for SISAL-specific dating methods.
  • Entity cover insertion errors in the database layer.
  • Various fixes for community-specific edge cases (NODE, 210Pb, SISAL).

[] - 2023-11-15

Added

  • Initial release of DataBUS.
  • Core data classes: Site, CollectionUnit, AnalysisUnit, Sample, Dataset, Datum, Variable, Chronology, ChronControl, Geochron, GeochronControl, Contact, Geog, Hiatus, Response.
  • Validation framework with neotomaValidator module.
  • Helper utilities: template_to_dict, read_csv, pull_params, pull_required.
  • CLI argument parsing via parse_arguments.
  • Basic pollen dataset upload workflow.

[]: https://github.com/NeotomaDB/DataBUS/releases/tag/v0.0.1