Neotoma Paleoecology Database DataBUS

[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.