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RELEASE_NOTES.md

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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.

[0.11.7] - TBD

  • Unusable export_genome_features_protein_to_fasta function was removed
  • The genbanks_to_genomes method was added to allow users to upload multiple genome objects at once

[0.11.6] - 2022-01-29

Fixed performance issue with FastaGFF impacting metagenome uploads

[0.11.5] - 2021-3-16

Fixed issue with empty GFF download file PTV-1637

[0.11.4] - 2021-2-2

Fixed workspace and handle permission issue

[0.11.3] - 2020-11-24

Fixed/Changed

Rename CHANGELOG.md to RELEASE_NOTES.md

[0.11.2] - 2020-10-30

Fixed/Changed

Fixed false ontology_ref requirment

[0.11.1] - 2020-05-27

Fixed/Changed

  • behavior of the Genbank upload has been fixed to accurately load Ensembl data from users.
  • Duplicate ID's are now accpeted in genbank files with the string '.n' appended to duplicates. n = "the number of times this id has been seen previously"

[0.11.0] - 2020-02-18

Added

  • The update_taxon_assignments method was added to allow users to create, replace, or remove taxon assignments for a Genome object.

[0.10.4] - 2020-02-20

Changed

  • exporter function for Metagenome fasta + gff added.

[0.10.3] - 2020-02-20

Fixed

  • ws_obj_gff_to_genome and ws_obj_gff_to_metagenome bug on certain input types resolved

[0.10.2] - 2020-02-11

Fixed

  • keyError: "warnings" fix for Metagenome upload

[0.10.1] - 2020-02-10

Fixed

  • ws_obj_gff_to_metagenome was erroneously outputting non-metagenome filetypes when the "is_metagenome" parameter was not specified.
  • protein sequences were still sometimes saved for some metagenome objects within the parent gene of a cds. protein_translation no longer saved in metagenome.

[0.10.0] - 2020-02-05

Changed

  • Adding two new functions: ws_obj_gff_to_metagenome, ws_obj_gff_to_genome

[0.9.0] - 2019-10-24

Changed

  • Use the Relation Engine API for finding and populating taxonomy data
  • Use the NCBI taxonomy ID as the primary way to assign taxonomy data instead of sciname

[0.8.10] - 2018-11

Changed

  • Use WSLargeDataIO for saving and pulling genomes
  • Expand and refactor import of ontology ids

Fixed

  • Fix a few genome warnings

[0.8.9] - 2018-06-04

Fixed

  • Correct genbank download of old genomes with contig sets and long contig IDs
  • Make reference path though genome for assembly access to prevent permissions issues

[0.8.8] - 2018-05-30

Changed

  • Use searchapi2 in production & appdev

[0.8.7] - 2018-05-28

Fixed

  • Fix go term splitting for GFF uploads

Added

  • Add optional "upgrade" parameter to save_genome

[0.8.6] - 2018-05-15

Changed

  • Genome object refactor. Baseline for this log