Release prep v0.9.0: version strings, draft changelog header, browser preset v0.9.1

CHANGELOG.md

@@ -6,6 +6,10 @@ release completed.
 
 ## [Unreleased]
 
+## [0.9.0] — TBD — `v0.9.0`
+
+> DRAFT release prep (do not tag until the definitive run is integrated). The entries below are those of the merged pull requests of the v0.9.0 cycle; the definitive run is `--preset v0.9.1 --withheld-detail-policy on` with the `tblastn` outlier policy (`MATPREDICT_TBLASTN_SEG=yes`, `MATPREDICT_TBLASTN_SEG_GENES=SLA2,APN2,MAT1-1-1`) and its counts are filled in once the tables are built. Rules that exist but are in no preset: `--weak-fragment-cap-policy`, `--weak-coverage-noise-policy`, `--strong-single-gene-policy`, `--confidence-cap-policy`.
+
 ### Added
 - `--preset v0.9.1` (curator's ruling 2026-11-07): v0.9 plus three rules that lower a tier or withhold an idiomorph label: `--weak-flank-cap-policy on` (#129: 23 loci in the v0.8.1 run go from `high` to `medium`), `--short-fragment-vote-policy undetermined` (#138: 107 loci become `undetermined`) and `--single-region-cap-policy on` (#167: 202 Basidiomycota loci go from `high` to `medium`). The weak-coverage rule (#149: 109 loci `medium` to `high`) is held out for the curator's review. It is the preset of the v0.9.0 full run.
 - `--preset v0.9` (curator's ruling 2026-11-07): v0.8.1 plus the three report-only rules of the v0.9.0 cycle: `--cross-family-policy keep_labelled` (#255: both calls kept where the kept call has no idiomorph label and the other has one; one genome in 23,579 v0.8.1 reports is affected), `--idiomorph-margin-policy separate` (#145: a single-candidate identity gap is reported as `idiomorph_identity_gap`; 74 of the loci in a 300-genome panel move the value), and `--scope-label-policy on` (#170: 10 `Basidiomycota:MAT` loci in the v0.8.1 run, on STE3, PAN6 and RPL39 alone outside the family's scope, are marked `family_unconfirmed`). No call, coordinate or tier changes. The rules that change a tier or an idiomorph label (`--weak-fragment-cap-policy`, `--weak-flank-cap-policy`, `--short-fragment-vote-policy`, `--single-region-cap-policy`, `--weak-coverage-noise-policy`) are in no preset until the curator approves their genome lists.

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: 0.8.1
+version: 0.9.0
 doi: TBD
 date-released: 2026-11-06
 url: "https://github.com/stajichlab/MATPredict"

README.md

@@ -552,14 +552,14 @@ 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 0.8.1.
+> Stajich JE. MATPredict: MAT locus identification in Fungi. Version 0.9.0.
 > https://github.com/stajichlab/MATPredict
 
 ```bibtex
 @software{matpredict,
   author  = {Stajich, Jason E.},
   title   = {MATPredict: MAT locus identification in Fungi},
-  version = {0.8.1},
+  version = {0.9.0},
   url     = {https://github.com/stajichlab/MATPredict},
   year    = {2026}
 }

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "MATPredict"
-version = "0.8.1"
+version = "0.9.0"
 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 0.8.1. https://github.com/stajichlab/MATPredict
+> Stajich JE. MATPredict: MAT locus identification in Fungi. Version 0.9.0. https://github.com/stajichlab/MATPredict
 
 ```bibtex
 @software{matpredict,
   author  = {Stajich, Jason E.},
   title   = {MATPredict: MAT locus identification in Fungi},
-  version = {0.8.1},
+  version = {0.9.0},
   url     = {https://github.com/stajichlab/MATPredict},
   year    = {2026}
 }

web/spike/browser/run-detect.mjs

@@ -15,7 +15,7 @@ const [genome, outDir, ...rest] = process.argv.slice(2);
 const phylum = rest[rest.indexOf("--phylum") + 1] ?? "Ascomycota";
 const ENGINE = process.env.ENGINE ?? "losat";  // tblastn engine: "losat" or "mmseqs"
 const home = "/Users/jstajich/projects/MATPredict";
-const WHEEL = process.env.WHEEL ?? join(home, "web/spike/dist/matpredict-0.8.1-py3-none-any.whl");
+const WHEEL = process.env.WHEEL ?? join(home, "web/spike/dist/matpredict-0.9.0-py3-none-any.whl");
 const DB_DIR = process.env.DB_DIR ?? join(home, "db");
 const WASM_DIR = process.env.WASM_DIR ?? join(process.env.HOME, "wasm-build");
 const LOC_DIR = process.env.LOCALIZER_DIR ?? join(home, "web/spike/localizer");
@@ -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", "v0.8.1", "--out-dir", "/out"])
+                          "--preset", "v0.9.1", "--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", "v0.8.1", "--out-dir", "/out"])
+args = parser.parse_args(["detect", "--genome", "/data/${genomeName}", "--phylum", "${phylum}", "--preset", "v0.9.1", "--out-dir", "/out"])
 error = None
 rc = None
 try: