From 05f950d07b744af6299fd15094bd158825d516c7 Mon Sep 17 00:00:00 2001
From: Tom Hunze <dev@thunze.de>
Date: Sun, 31 Aug 2025 11:49:52 +0200
Subject: [PATCH 1/3] python313Packages.pysam: 0.22.1-unstable-2024-10-30 ->
 0.23.3
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: László Kupcsik <dev@biobits.be>
---
 pkgs/development/python-modules/pysam/default.nix | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pkgs/development/python-modules/pysam/default.nix b/pkgs/development/python-modules/pysam/default.nix
index cdabdace5294..2282c6e12a54 100644
--- a/pkgs/development/python-modules/pysam/default.nix
+++ b/pkgs/development/python-modules/pysam/default.nix
@@ -15,9 +15,9 @@
   zlib,
 }:
 
-buildPythonPackage {
+buildPythonPackage rec {
   pname = "pysam";
-  version = "0.22.1-unstable-2024-10-30";
+  version = "0.23.3";
   pyproject = true;
 
   # Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is
@@ -26,8 +26,8 @@ buildPythonPackage {
   src = fetchFromGitHub {
     owner = "pysam-developers";
     repo = "pysam";
-    rev = "0eae5be21ac3ab3ac7aa770a3931e2977e37b909";
-    hash = "sha256-i8glYSpuCRNhNtK4i6eUrerz8daiMfY/YgDwgSuELbc=";
+    tag = "v${version}";
+    hash = "sha256-yOLnfuGQW+j0nHy4MRlwurZMpeRHTGmQ9eLmihcAGoQ=";
   };
 
   nativeBuildInputs = [

From 9eb0b6c71dc918f66518eb8b0d210d83ac21b494 Mon Sep 17 00:00:00 2001
From: Tom Hunze <dev@thunze.de>
Date: Sun, 31 Aug 2025 11:51:29 +0200
Subject: [PATCH 2/3] python313Packages.pysam: refactor

---
 pkgs/development/python-modules/pysam/default.nix | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/pysam/default.nix b/pkgs/development/python-modules/pysam/default.nix
index 2282c6e12a54..3553d9540381 100644
--- a/pkgs/development/python-modules/pysam/default.nix
+++ b/pkgs/development/python-modules/pysam/default.nix
@@ -30,12 +30,15 @@ buildPythonPackage rec {
     hash = "sha256-yOLnfuGQW+j0nHy4MRlwurZMpeRHTGmQ9eLmihcAGoQ=";
   };
 
-  nativeBuildInputs = [
+  build-system = [
     cython
-    samtools
     setuptools
   ];
 
+  nativeBuildInputs = [
+    samtools
+  ];
+
   buildInputs = [
     bzip2
     curl
@@ -73,11 +76,13 @@ buildPythonPackage rec {
     "pysam.libchtslib"
     "pysam.libcutils"
     "pysam.libcvcf"
+    "pysam.libcsamtools"
   ];
 
   meta = {
     description = "Python module for reading, manipulating and writing genome data sets";
     downloadPage = "https://github.com/pysam-developers/pysam";
+    changelog = "https://github.com/pysam-developers/pysam/releases/tag/${src.tag}";
     homepage = "https://pysam.readthedocs.io";
     maintainers = with lib.maintainers; [ unode ];
     license = lib.licenses.mit;

From 8500e52278abc5fdcd72078eec686a76813a01e2 Mon Sep 17 00:00:00 2001
From: Tom Hunze <dev@thunze.de>
Date: Mon, 1 Sep 2025 09:08:54 +0200
Subject: [PATCH 3/3] python313Packages.pysam: add nix-update-script
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: László Kupcsik <dev@biobits.be>
---
 pkgs/development/python-modules/pysam/default.nix | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pkgs/development/python-modules/pysam/default.nix b/pkgs/development/python-modules/pysam/default.nix
index 3553d9540381..da739b495b11 100644
--- a/pkgs/development/python-modules/pysam/default.nix
+++ b/pkgs/development/python-modules/pysam/default.nix
@@ -13,6 +13,7 @@
   setuptools,
   samtools,
   zlib,
+  nix-update-script,
 }:
 
 buildPythonPackage rec {
@@ -79,6 +80,8 @@ buildPythonPackage rec {
     "pysam.libcsamtools"
   ];
 
+  passthru.updateScript = nix-update-script { };
+
   meta = {
     description = "Python module for reading, manipulating and writing genome data sets";
     downloadPage = "https://github.com/pysam-developers/pysam";