funannotate2 v2025.11.1

Changes

• add gene model length filtering prior to consensus #28 (01cc254)
• fix taxonomy selector; #30 (b752659)
• fix failing test due to change in function (0f6651f)
• fix parsing annotations in annotate (563315f)
• provide multiple ways of training genemark and using hints for prediction #24 (d9578e8)
• make memory aware abinitio default #22 (f8ac1c8)
• better parsing of annotation data #25 (196bf62)
• limit training models via CLI parameter #24 (4d05412)
• update memory requirements/predictions #22 (4bfec78)
• clean up logging in abinitio #23 (f2d52f8)
• fix default predict after memory changes (ff71504)
• add ability to track memory usage for ab initio #22 (8652117)
• Fix release notes generation for first release (no previous tags) (9a30039)
• Merge branch 'main' of https://github.com/nextgenusfs/funannotate2 (c3f8b28)
• Fix GitHub release checkout to handle tag properly (2460fcc)
• Update CITATION.cff to version 25.7.1 [skip ci] (762c69f)
• Fix GitHub Actions permissions for CITATION.cff updates in production release workflow (e137bf2)

Full Changelog: 25.7.1...v2025.11.1

funannotate2 25.7.1

Changes

• Add --busco-lineage option to annotate, improve training model selection, fix CITATION.cff format (5c3b7ea)
• fix updated busco download links #16 (a225ae4)
• add override for --augustus-species and --busco-lineage to train; #13 (aa3d01f)
• fix typo in help menu (63f3aac)
• Merge branch 'main' of https://github.com/nextgenusfs/funannotate2 (0feba39)
• fix typo (2a7d441)
• bump so consistent with gfftk (4a983d9)
• fix login in citation update (c80a489)
• try conda for macos (1544a44)
• try to fix macos builds (d7acdda)
• update the actions again (afa1f44)
• update actions (d8bc909)
• fix --training-set for f2 train; #10 (2a47261)
• fix taxonomy issues #7 #8 (8b31146)
• dynamic odb for busco (1c97246)
• remove lint test (6d8332b)
• fix taxonomy, JGI changed format of superkingdom/domain;#8 (244ebad)
• update taxonomy selection functions #7 (7232365)
• make odb slug dynamic (5d67f2d)
• increase default min_cov=0.65 for align_mito (ba4158f)
• fix mito_align issue from #6 (8cc993a)
• clean up unused code in annotate; fix analyzeAssembly for masking #6 (a22045e)
• support .annotations.txt for annotate (03d86b9)
• add citation action updater (4d3fd5d)
• add proteins/transcripts to predict output; update docs (2486574)
• updates to convert to busco odb12 (c22b19a)
• update BUSCO to odb12; #5 (1c2ad1f)
• update a few more docs (a2a91e0)
• update docs again (3909736)
• add more linting and update docs (9cb68f7)
• update tutorial docs for list (c2f74be)
• update tutorial docs 2 (4da3aae)
• update tutorial docs (cba6562)
• fix gzip issue for fasta and update tutorial docs (6247f84)
• expand page width for sphinx (e9cceab)
• bump docs again to see if better (fbd34d6)
• format dropdown as code differnet way 2 (a516a9f)
• format dropdown as code differnet way (bce484d)
• format dropdown as code (4430e77)
• try dropdown docs again (bc8e8ab)
• update docs requirements (c895eeb)
• update docs again 2 (304c74c)
• update docs again (a9c1eb3)
• update some docs (29d084d)
• update README again (eda8d6c)
• update README (662a4f3)
• add -s,--show to f2 install to show installed databases (700778a)
• add robustness to download/install methods (9f69058)
• fix tests that were failing (98cd983)
• remove evm as its not working (82214fb)
• updates to several tools and documentation (0e96d20)
• add some name/product parsing (b38c103)
• update codecov and .gitignore (49bcaea)
• Fix code formatting with black (0e7452f)
• Fix linting issues in utilities.py (2608f1f)
• Fix test_consensus_coverage.py to handle different implementations (2e91ea0)
• Fix test_consensus_coverage.py to match actual implementation (8fed0da)
• update tests (e2370be)
• add tests from augment code agent (6ae3428)
• update parsing of predict params (32c51c1)
• typo in pyproject (83b6907)
• move to pyproject.toml (95f6041)
• explicitly use table=1 (214d687)
• ensure lowercase for source in external gffs (4c36ec8)
• more tweaking of weights (b005de4)
• slight tweak to calc weights (29f4fc0)
• add -e,--external option and adjust weightings (27d0b88)
• getting closer (6f9815f)
• add lots of docstrings (c7f0ed0)
• remove stupid linter (2c0eba3)
• more updates; add mitochondria screen (48400fd)
• few more fixes (6ff8f8c)
• moving forwards finally (38b778e)
• tax lookup skip verify warning (1c27555)
• try to fix cert/issue with jgi taxonomy lookup 3 (f445598)
• try to fix cert/issue with jgi taxonomy lookup 2 (bb7a833)
• try to fix cert/issue with jgi taxonomy lookup (241a2c0)
• trigger interlap black reformat 2 (ddc8cf8)
• trigger interlap black reformat (5f91cc7)
• few linting cleanups and fasta2chunks function (820e11d)
• updates for improved consensus calling (68f64cf)
• set consensus default to gfftk (bbd73eb)
• fix for evm typo (9904cb5)
• fix biowarning issue; add simplify contig mapping to predict (472bf09)
• Merge branch 'main' of https://github.com/nextgenusfs/funannotate2 (c7cdd8a)
• Update README.md (c51b808)
• Update README.md (6b2b088)
• change header default; might remove completely for tain #2 (e9331cc)
• change header default; might remove completely for tain #2 (99799d1)
• automatically rename training contigs #2 (54d4062)
• Merge branch 'main' of https://github.com/nextgenusfs/funannotate2 (5d1b78d)
• setup backend search (94f4230)
• add some installation details (7ddb1cb)
• update output file naming (2881396)
• whitespace cleanup pre-pre-commit (c359be4)
• add config for pre-commit (8faa326)
• fix evm bug (8d7aac1)
• evm use either v1 or v2 (f28480a)
• pin pyfastx>=2 to fix composition issues (c74f699)
• add tRNAscan; sort/rename combined models; output gff3/tbl/gbff to results (1d4a422)
• clean up evm; print annotation stats; print abintio stats (c305a66)
• black format (35af80c)
• add evm/gfftk consensus option to predict; add black formatting linter to actions (4fe4230)
• fix interlap import in train (178af9a)
• add interlap (cee26f1)
• update setup with requests (ca23026)
• fix a few typos and issues (04e2f92)
• update analyze assembly for softmasked (78c55bf)
• fix interlap import to be relative (2ba75b6)
• initial commit (3d2e78e)

Repository: https://github.com/nextgenusfs/funannotate2