Release prep v0.8.1 (draft; do not merge until the release is cut)

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.
 

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"

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}
 }

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 = "[email protected]"}]
 requires-python = ">=3.11"

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}
 }

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)

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: