From 8f83e29fac02f830f17c8be6dc2f6774b5b08907 Mon Sep 17 00:00:00 2001 From: Jason Stajich Date: Thu, 5 Nov 2026 09:13:04 -0800 Subject: [PATCH] Release prep v0.8.1 (draft; do not merge until the release is cut) Version strings, a draft 0.8.1 changelog header, and the browser tool preset v0.8.1. Co-Authored-By: Claude Sonnet 5.5 --- CHANGELOG.md | 4 ++++ CITATION.cff | 2 +- README.md | 4 ++-- pyproject.toml | 2 +- web/intro/about.md | 4 ++-- web/spike/browser/run-detect.mjs | 2 +- web/spike/page/app.mjs | 2 +- 7 files changed, 12 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0b315f70..5401dcb4 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 so far; the definitive run (`--preset v0.8.1`) and its counts, the curator's decisions on #254 (S. pombe labels), #148, #165, #169 and #255, and the date are still to be filled in. The release is a re-run of the definitive v0.8.0 run with the fixes of #228 and #227 (reverted by #270 if merged), the report-only `resolution_flags` and cross-family `cassette` indication, and the new rust allow list. + ### Added - Report-only `resolution_flags` on every detected locus (curator ruling 2026-11-04, #256): `contig_edge` (a core gene within 500 bp of a contig end) and `partial_core` (a core model covering under 50% of its reference at under 90% identity; a high-identity exon piece of an intact gene is not flagged), with the genes in `resolution_flag_genes`. They say a called locus may be a fragment; no call, score or confidence tier changes. New module `detect/resolution_flags.py`; `DetectionOutcome.contig_lengths`. 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: