diff --git a/CHANGELOG.md b/CHANGELOG.md index 8d1b1f1a..5881720f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,10 @@ release completed. ## [Unreleased] +## [0.8.1] — TBD — `v0.8.1` + +> DRAFT release prep (do not merge until the release is cut). The entries below are those of the merged pull requests; the definitive run (`--preset v0.8.1`, long `GENOME_TIMEOUT` for the nine rust genomes of the allow list) and its counts, and the date, are still to be filled in. v0.8.1 is a re-run of the definitive v0.8.0 run with: the #228 fallback after withheld hits (preset `v0.8.1`), the *S. pombe* silent-pair rule (#254; the #252 tie-break is reverted), report-only `resolution_flags`, the cross-family `cassette` indication with its shared-flank measurements, `two_idiomorphs` for Basidiomycota MAT and redPR, the rust allow list (#165) and the *Hyphopichia* MTLA1 record (#148; 11 of 389 sampled Serinales genomes drop a tier, tracked under #149). Not in v0.8.1: #255, the MATam family, the Ogataea candidate records. + ### Changed - *S. pombe* silent cassettes (#254; curator ruling 2026-11-05): a merged `mat1` call whose genes hold a P cluster and an M cluster 5-20 kb apart on one contig (the silent `mat2`-P / `mat3`-M pair, about 11 kb apart) is split into a `mat2` P call and a `mat3` M call, each with a `cassette` block (role `silent_pair`, the partner family and the distance). The #252 tie-break by core identity is reverted (it relabelled a lone P cassette `mat2`, probably wrong: the records are cassette-only so identity cannot tell mat1 from mat2); a lone cassette elsewhere stays `mat1`; a pair farther apart (35 kb in GCA_006386235.1) stays one call marked `arrangement_ambiguous`. It applies only where the species-scoped `mat2` and `mat3` families are in the genome's lineage (*S. pombe*), as part of `--cross-family-policy on` (`detect/silent_pair.py`). It changes *S. pombe* locus counts and labels. diff --git a/CITATION.cff b/CITATION.cff index 01ab808f..70b9e9d8 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -8,7 +8,7 @@ authors: affiliation: University of California-Riverside orcid: "https://orcid.org/0000-0002-7591-0020" title: "MATPredict: MAT locus identification in Fungi" -version: 0.8.0 +version: 0.8.1 doi: TBD date-released: 2026-10-31 url: "https://github.com/stajichlab/MATPredict" diff --git a/README.md b/README.md index 36d70025..1881c1cd 100644 --- a/README.md +++ b/README.md @@ -550,14 +550,14 @@ No paper describes MATPredict yet. Cite the software and the release you used. The citation metadata is in [CITATION.cff](CITATION.cff); GitHub shows it under "Cite this repository". -> Stajich JE. MATPredict: MAT locus identification in Fungi. Version 0.8.0. +> Stajich JE. MATPredict: MAT locus identification in Fungi. Version 0.8.1. > https://github.com/stajichlab/MATPredict ```bibtex @software{matpredict, author = {Stajich, Jason E.}, title = {MATPredict: MAT locus identification in Fungi}, - version = {0.8.0}, + version = {0.8.1}, url = {https://github.com/stajichlab/MATPredict}, year = {2026} } diff --git a/pyproject.toml b/pyproject.toml index 2e6049cd..571af152 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "MATPredict" -version = "0.8.0" +version = "0.8.1" description = "Fungal MAT locus annotator/classifier" authors = [{name = "Jason Stajich", email = "jason.stajich@ucr.edu"}] requires-python = ">=3.11" diff --git a/web/intro/about.md b/web/intro/about.md index 654db057..ceffafde 100644 --- a/web/intro/about.md +++ b/web/intro/about.md @@ -53,13 +53,13 @@ The command-line software is cited in the project README, under [Citation](https://github.com/stajichlab/MATPredict#citation). The citation metadata is in [CITATION.cff](https://github.com/stajichlab/MATPredict/blob/main/CITATION.cff), which GitHub shows under "Cite this repository". -> Stajich JE. MATPredict: MAT locus identification in Fungi. Version 0.8.0. https://github.com/stajichlab/MATPredict +> Stajich JE. MATPredict: MAT locus identification in Fungi. Version 0.8.1. https://github.com/stajichlab/MATPredict ```bibtex @software{matpredict, author = {Stajich, Jason E.}, title = {MATPredict: MAT locus identification in Fungi}, - version = {0.8.0}, + version = {0.8.1}, url = {https://github.com/stajichlab/MATPredict}, year = {2026} } diff --git a/web/spike/browser/run-detect.mjs b/web/spike/browser/run-detect.mjs index 8cf99702..f2e5b890 100644 --- a/web/spike/browser/run-detect.mjs +++ b/web/spike/browser/run-detect.mjs @@ -74,7 +74,7 @@ parser = argparse.ArgumentParser(prog="matpredict") subs = parser.add_subparsers(dest="cmd") detect_cli.register_subcommands(subs) args = parser.parse_args(["detect", "--genome", "/data/${basename(genome)}", "--phylum", "${phylum}", - "--preset", "v0.8", "--out-dir", "/out"]) + "--preset", "v0.8.1", "--out-dir", "/out"]) error = None try: rc = args.func(args) diff --git a/web/spike/page/app.mjs b/web/spike/page/app.mjs index f1bd33f4..8f85853c 100644 --- a/web/spike/page/app.mjs +++ b/web/spike/page/app.mjs @@ -107,7 +107,7 @@ from MATPredict.detect import cli as detect_cli parser = argparse.ArgumentParser(prog="matpredict") subs = parser.add_subparsers(dest="cmd") detect_cli.register_subcommands(subs) -args = parser.parse_args(["detect", "--genome", "/data/${genomeName}", "--phylum", "${phylum}", "--preset", "v0.8", "--out-dir", "/out"]) +args = parser.parse_args(["detect", "--genome", "/data/${genomeName}", "--phylum", "${phylum}", "--preset", "v0.8.1", "--out-dir", "/out"]) error = None rc = None try: