From 508b645b56367f60d53dd2d2c4e027128f167a05 Mon Sep 17 00:00:00 2001
From: sfilges <stefan.filges@pm.me>
Date: Tue, 3 Mar 2026 14:15:54 +0100
Subject: [PATCH] Prepare for v1.0.0 release

---
 CHANGELOG.md          | 9 +++++++++
 README.md             | 2 +-
 docker/DOCKERFILE     | 2 +-
 docs/ROADMAP.md       | 2 ++
 pyproject.toml        | 2 +-
 src/plexus/version.py | 2 +-
 6 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e9b95a0..7714c56 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,15 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.0.0] - 2026-03-03
+
+First stable release. All v1.0 roadmap items complete — see `docs/ROADMAP.md` for the full list.
+Includes correctness fixes (BLAST annotation, coordinate handling, off-target filtering),
+compliance/audit infrastructure (provenance tracking, checksum verification, reproducible selectors),
+panel QC reporting, and CLI improvements (template generation, Docker wrapper, init wizard).
+
+No code changes from 1.0.0b4; this release promotes the beta to stable after final verification.
+
 ## [1.0.0b4] - 03-03-2026
 
 ### Changed
diff --git a/README.md b/README.md
index d81f623..068fd87 100644
--- a/README.md
+++ b/README.md
@@ -198,7 +198,7 @@ plexus docker \
 To run a specific tagged version or pass through extra `plexus run` flags:
 
 ```bash
-plexus docker --tag 1.0.0b2 \
+plexus docker --tag 1.0.0 \
   --fasta /data/hg38.fa \
   --input /data/junctions.csv \
   --output /data/results/ \
diff --git a/docker/DOCKERFILE b/docker/DOCKERFILE
index 9e8f2e8..9511e99 100644
--- a/docker/DOCKERFILE
+++ b/docker/DOCKERFILE
@@ -1,6 +1,6 @@
 ARG BLAST_VERSION=2.17.0
 ARG BCFTOOLS_VERSION=1.23
-ARG PLEXUS_VERSION=1.0.0b3
+ARG PLEXUS_VERSION=1.0.0
 
 # ── Stage 1: Python venv builder ─────────────────────────────────────────────
 FROM ghcr.io/astral-sh/uv:python3.13-bookworm-slim AS builder
diff --git a/docs/ROADMAP.md b/docs/ROADMAP.md
index ea01710..77df852 100644
--- a/docs/ROADMAP.md
+++ b/docs/ROADMAP.md
@@ -13,6 +13,8 @@ not necessarily by implementation order.
 
 ## v1.0 — Production Release
 
+> **Released: 2026-03-03** — All 21 items resolved (19 implemented, 1 cancelled, 1 was TEST-01).
+
 The v1.0 milestone covers correctness issues, science-blocking bugs, and architecture gaps that
 would compromise the reliability of a clinical-grade tool.
 
diff --git a/pyproject.toml b/pyproject.toml
index 4b8a7ea..eb5abeb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,7 @@ license = "GPL-2.0-or-later"
 requires-python = ">=3.10,<3.14"
 authors = [{ name = "Stefan Filges", email = "stefan.filges@pm.me" }]
 classifiers = [
-    "Development Status :: 4 - Beta",
+    "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
diff --git a/src/plexus/version.py b/src/plexus/version.py
index f96eeb6..5becc17 100644
--- a/src/plexus/version.py
+++ b/src/plexus/version.py
@@ -1 +1 @@
-__version__ = "1.0.0b4"
+__version__ = "1.0.0"