Changelog

Follow up on the latest improvements and updates.

RSS

improved

fixed

Client Library

Client library v0.19.0 released

The
onecodex
client library has a new release - v0.19.0. Details here.
Added
  • Adds Python 3.13 support
  • Adds numpy v2 support
Changed
  • Upgrades Altair to 5.5.0
  • Upgrades scikit-bio to 0.7.0. IMPORTANT: This changes the log base used in Shannon alpha diversity calculations from base 2 to
    e
    (natural log)
  • Upgrades urllib3 to >=2.5.0
  • Modernizes packaging and tooling by migrating to
    pyproject.toml
    ,
    uv
    , and
    ruff
  • Updates
    pytest
    to fail on warnings
  • Replaces Potion-Client resources with Pydantic v2 models
  • Changes
    metric=auto
    behavior based on the number of classification results with abundance estimates
Fixed
  • Fixes
    SampleCollection
    metadata fetching to only match canonical ranks
  • Fixes issue when plotting fields that look like JavaScript paths (e.g.
    field.name
    or
    field[name]
    )
  • Fixes various documentation issues
Removed
  • Removes
    Samples.init_multipart_upload()
    in favor of
    Samples.upload()
New
  • The latest version of the One Codex Database has been released. This includes increased viral genomes, for improved viral detection. The unique ID for the new database is
    7f6b028b9d964d87
    .
Improved
  • Metadata fields with leading or trailing whitespaces will now be stripped of those whitespaces upon metadata sheet uploads. This will prevent mismatches of metadata due to excess whitespaces
Fixed
  • Searching your samples by both sequencing state and by taxon previously produced an error. This has been fixed, so that you may now search for taxa in samples while filtered to a particular sequencing state.
Improved
  • We've sped up searches based on taxonomy.
Fixed
  • We fixed an issue preventing successful sequencing batch registration if more than two tracking numbers were available via the tracking number dropdown menu. Tracking numbers now show as separate items in the menu again.
New
  • We've added the ability to generate a .csv export for the Twist results from one or more samples. You'll find the export option from the samples page.
New
  • We've added a new dashboard where sequencing customers can track sequencing orders, including which tubes are in the order, and see shipment tracking details.
Improved
  • We've improved the efficiency of searching samples by taxon. You will now be able to find which samples have particular taxa much quicker!
Improved
  • Jupyter Notebooks service was upgraded to Python 3.13
New
  • We've now made it possible to use root functionality in Nextflow child tasks.
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