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Commits on Apr 21, 2026

• Build funannotate2 Docker image (pixi + GitHub Actions) (#51)

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  nextgenusfs

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Commits on Apr 2, 2026

• Merge pull request #50 from nextgenusfs/review-taxonomy-mr

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  nextgenusfs

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• fix: update dbCAN database URLs to use new pro.unl.edu domain

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  Jon Palmer

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• fix: improve error handling and robustness in taxonomy and API requests

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  Jon Palmer

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• Merge pull request #48 from edgeemer/patch-1

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  nextgenusfs

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Commits on Apr 1, 2026

• Fix taxonomy check for kingdom in training script

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  edgeemer

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Commits on Mar 11, 2026

• Merge pull request #45 from nextgenusfs/clean-memory-log-output

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  nextgenusfs

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• Silence default predict memory log chatter

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  Jon Palmer

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Commits on Feb 13, 2026

• Fix CI: Install all dependencies from pyproject.toml on macOS

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  Jon Palmer

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• Revert "Fix: Make annorefine import optional for CI compatibility"

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  Jon Palmer

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• Fix: Make annorefine import optional for CI compatibility

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  Jon Palmer

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• Add annorefine integration for RNA-seq based gene prediction and UTR refinement

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  Jon Palmer

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Commits on Nov 25, 2025

• fix/train: busco results wrong genome

  nextgenusfs

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Commits on Nov 2, 2025

• Update CITATION.cff to version 2025.11.1 [skip ci]

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Commits on Nov 1, 2025

• add gene model length filtering prior to consensus #28

  

  Jon Palmer

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Commits on Oct 16, 2025

• bump version

  

  Jon Palmer

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• fix taxonomy selector; #30

  

  Jon Palmer

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Commits on Aug 6, 2025

• fix failing test due to change in function

  

  Jon Palmer

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Commits on Aug 5, 2025

• fix parsing annotations in annotate

  

  Jon Palmer

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Commits on Aug 4, 2025

• provide multiple ways of training genemark and using hints for prediction #24

  

  Jon Palmer

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• make memory aware abinitio default #22

  

  Jon Palmer

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• better parsing of annotation data #25

  

  Jon Palmer

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Commits on Jul 21, 2025

• bump version

  

  Jon Palmer

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• limit training models via CLI parameter #24

  

  Jon Palmer

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Commits on Jul 19, 2025

• min-contig for train #24; fix mem ab initio limit #22; --skip-predictors #22; bump version

  

  Jon Palmer

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Commits on Jul 17, 2025

• update memory requirements/predictions #22

  

  Jon Palmer

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Commits on Jul 16, 2025

• clean up logging in abinitio #23

  

  Jon Palmer

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Commits on Jul 14, 2025

• fix default predict after memory changes

  

  Jon Palmer

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• add ability to track memory usage for ab initio #22

  

  Jon Palmer

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Commits on Jul 7, 2025

• Fix release notes generation for first release (no previous tags)

  

  Jon Palmer

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• Merge branch 'main' of https://github.com/nextgenusfs/funannotate2

  

  Jon Palmer

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• Fix GitHub release checkout to handle tag properly

  

  Jon Palmer

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• Update CITATION.cff to version 25.7.1 [skip ci]

  github-actions[bot]

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• Fix GitHub Actions permissions for CITATION.cff updates in production release workflow

  

  Jon Palmer

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Commits on Jul 6, 2025

• Add --busco-lineage option to annotate, improve training model selection, fix CITATION.cff format

  

  Jon Palmer

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