From f9c57c601d8ea77bdf2f8729a6d8862019335575 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Thu, 3 Aug 2023 21:20:40 +0200
Subject: [PATCH] Release v0.9.0

---
 CHANGELOG.md        | 16 +++++++++++++++-
 pyhmmer/__init__.py |  4 ++--
 2 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9219909..99788f8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,7 +6,21 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.8.2...HEAD
+[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.9.0...HEAD
+
+
+## [v0.9.0] - 2023-08-03
+[v0.9.0]: https://github.com/althonos/pyhmmer/compare/v0.8.2...v0.9.0
+
+### Added
+- `TopHits.mode` property showing from which pipeline mode (*search* or *scan*) the hits were obtained.
+
+### Changed
+- Updated the code for Cython `v3.0`.
+- Use fused types to mark the type of queries to `Pipeline` and `LongTargetsPipeline` search methods.
+
+### Fixed
+- `TopHits.merge` not properly handling inclusion and reporting for domains ([#46](https://github.com/althonos/pyhmmer/issues/46), [#47](https://github.com/althonos/pyhmmer/pull/47), by [@zdk123](https://github.com/zdk123)).
 
 
 ## [v0.8.2] - 2023-06-07
diff --git a/pyhmmer/__init__.py b/pyhmmer/__init__.py
index fa0d268..27b588d 100644
--- a/pyhmmer/__init__.py
+++ b/pyhmmer/__init__.py
@@ -14,7 +14,7 @@
     Larralde, Martin, and Georg Zeller.
     "PyHMMER: A Python Library Binding to HMMER for Efficient
     Sequence Analysis". Bioinformatics, 19 April 2023, btad214.
-    :doi:`10.1093/bioinformatics/btad214`.
+    :doi:`10.1093/bioinformatics/btad214`. :pmid:`37074928`.
 
 """
 
@@ -32,7 +32,7 @@
 
 __author__ = "Martin Larralde <martin.larralde@embl.de>"
 __license__ = "MIT"
-__version__ = "0.8.2"
+__version__ = "0.9.0"
 __all__ = [
     "errors",
     "easel",