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v0.2.2

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@duceppemo duceppemo released this 18 Sep 12:20
· 38 commits to master since this release
v0.2.2
4b9caba

A patch release focused on real-data robustness and PyPI-readiness, prompted by running the pipeline against a real published dataset (Okrasińska et al. 2022, Environmental Microbiology — 53 real ITS2/UNITE soil-fungal samples, SRA BioProject PRJNA767765) end to end for the first time at production scale.

Fixed

  • Casava filename validation rejected sample identifiers containing dots (common in real SRA-derived names, e.g. K.BeL.1.1) — a valid file was rejected outright before the pipeline did anything else.
  • Sample-frequency parsing choked on QIIME2's comma thousands-separator formatting once a sample's frequency reached four digits (e.g. "110,406.0") — broke the PDF report on any real dataset with more than ~1000 reads/sample, which every prior test dataset was too small to trigger.

Both were found and fixed against the real failure case, not just in isolation — the run that hit each bug went on to complete successfully afterward.

Changed (PyPI packaging prep)

  • Fixed README links (logo, license) that were relative to the GitHub repo and would 404 on PyPI's project page.
  • Modernized license metadata to the SPDX form (license = "MIT" + license-files), replacing the table form setuptools was warning would stop being supported.
  • Added [project.urls] (Homepage/Repository/Documentation/Issues/Changelog) for PyPI's project-page sidebar.
  • Added CITATION.cff (enables GitHub's "Cite this repository").

Documentation

  • Documented Eukaryome as an additional, directly-fetchable ITS reference source alongside UNITE (qiime rescript get-eukaryome-data).
  • Documented why SILVA/GTDB/PR2 aren't usable for ITS classification (none cover the ITS region), including SILVA's pretrained classifier downloads for anyone using this pipeline on a non-ITS marker instead.
  • README quick start now leads with installing/activating QIIME2 itself instead of assuming it's already set up.
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