From 455be5c8bcf0da7033b8d1c09ee2b97c88213aef Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Thu, 2 May 2024 17:11:46 +0900
Subject: [PATCH 1/3] python311Packages.htseq: format with nixfmt

---
 .../python-modules/htseq/default.nix          | 31 ++++++++++++++-----
 1 file changed, 24 insertions(+), 7 deletions(-)

diff --git a/pkgs/development/python-modules/htseq/default.nix b/pkgs/development/python-modules/htseq/default.nix
index 9d69a8bfef54..1e95f31739b8 100644
--- a/pkgs/development/python-modules/htseq/default.nix
+++ b/pkgs/development/python-modules/htseq/default.nix
@@ -1,4 +1,15 @@
-{ lib, buildPythonPackage, fetchFromGitHub, cython, numpy, pysam, matplotlib, python, isPy27, isPy3k }:
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  cython,
+  numpy,
+  pysam,
+  matplotlib,
+  python,
+  isPy27,
+  isPy3k,
+}:
 buildPythonPackage rec {
   version = "0.12.4";
   format = "setuptools";
@@ -12,13 +23,19 @@ buildPythonPackage rec {
   };
 
   nativeBuildInputs = [ cython ];
-  propagatedBuildInputs = [ numpy pysam matplotlib ];
+  propagatedBuildInputs = [
+    numpy
+    pysam
+    matplotlib
+  ];
 
-  checkPhase = lib.optionalString isPy27 ''
-    ${python.interpreter} python2/test/test_general.py
-  '' + lib.optionalString isPy3k ''
-    ${python.interpreter} python3/test/test_general.py
-  '';
+  checkPhase =
+    lib.optionalString isPy27 ''
+      ${python.interpreter} python2/test/test_general.py
+    ''
+    + lib.optionalString isPy3k ''
+      ${python.interpreter} python3/test/test_general.py
+    '';
 
   meta = with lib; {
     homepage = "https://htseq.readthedocs.io/";

From 1a9e2e0b2ff07c5d8e87bd54c2fd47f356f70ac9 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Thu, 2 May 2024 17:16:07 +0900
Subject: [PATCH 2/3] python311Packages.htseq: add update script

---
 pkgs/development/python-modules/htseq/default.nix | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/pkgs/development/python-modules/htseq/default.nix b/pkgs/development/python-modules/htseq/default.nix
index 1e95f31739b8..6e36c7dd53de 100644
--- a/pkgs/development/python-modules/htseq/default.nix
+++ b/pkgs/development/python-modules/htseq/default.nix
@@ -9,6 +9,7 @@
   python,
   isPy27,
   isPy3k,
+  nix-update-script,
 }:
 buildPythonPackage rec {
   version = "0.12.4";
@@ -37,6 +38,13 @@ buildPythonPackage rec {
       ${python.interpreter} python3/test/test_general.py
     '';
 
+  passthru.updateScript = nix-update-script {
+    extraArgs = [
+      "--version-regex"
+      "release_(.+)"
+    ];
+  };
+
   meta = with lib; {
     homepage = "https://htseq.readthedocs.io/";
     description = "A framework to work with high-throughput sequencing data";

From 586d563fe2f611d3eb1bfe6fbbbabee4dfceefa1 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Thu, 2 May 2024 17:16:25 +0900
Subject: [PATCH 3/3] python311Packages.htseq: 0.12.4 -> 2.0.4

Diff:
https://github.com/htseq/htseq/compare/release_0.12.4...release_2.0.4
---
 .../python-modules/htseq/default.nix          | 67 +++++++++++++------
 1 file changed, 46 insertions(+), 21 deletions(-)

diff --git a/pkgs/development/python-modules/htseq/default.nix b/pkgs/development/python-modules/htseq/default.nix
index 6e36c7dd53de..caa47f5197d6 100644
--- a/pkgs/development/python-modules/htseq/default.nix
+++ b/pkgs/development/python-modules/htseq/default.nix
@@ -2,41 +2,67 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+  fetchpatch,
+  swig,
   cython,
-  numpy,
-  pysam,
   matplotlib,
-  python,
-  isPy27,
-  isPy3k,
+  numpy,
+  pandas,
+  pysam,
+  setuptools,
+  pytestCheckHook,
   nix-update-script,
 }:
 buildPythonPackage rec {
-  version = "0.12.4";
-  format = "setuptools";
   pname = "htseq";
+  version = "2.0.4";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "htseq";
     repo = "htseq";
     rev = "release_${version}";
-    sha256 = "0y7vh249sljqjnv81060w4xkdx6f1y5zdqkh38yk926x6v9riijm";
+    hash = "sha256-7ocrmuj9LOtPz9XbI5rKGcdE5JbFz/pZh00Nie65XxE=";
   };
 
-  nativeBuildInputs = [ cython ];
-  propagatedBuildInputs = [
-    numpy
-    pysam
-    matplotlib
+  patches = [
+    # https://github.com/htseq/htseq/pull/84
+    (fetchpatch {
+      name = "replace-distutils-with-sysconfig.patch";
+      url = "https://github.com/htseq/htseq/commit/f0f1e464ee9aee56f0b44f905e7b3355b0bb8f29.patch";
+      hash = "sha256-yDYkXCPy+YFgnk1rnXwCB998aZwVd5nJeejZIgeEzAo=";
+     })
   ];
 
-  checkPhase =
-    lib.optionalString isPy27 ''
-      ${python.interpreter} python2/test/test_general.py
-    ''
-    + lib.optionalString isPy3k ''
-      ${python.interpreter} python3/test/test_general.py
-    '';
+  nativeBuildInputs = [ swig ];
+
+  build-system = [
+    cython
+    numpy
+    pysam
+    setuptools
+  ];
+
+  dependencies = [
+    numpy
+    pysam
+  ];
+
+  optional-dependencies = {
+    htseq-qa = [ matplotlib ];
+  };
+
+  pythonImportsCheck = [ "HTSeq" ];
+
+  nativeCheckInputs = [
+    pandas
+    pytestCheckHook
+  ] ++ optional-dependencies.htseq-qa;
+
+  preCheck = ''
+    rm -r src HTSeq
+    export PATH=$out/bin:$PATH
+  '';
 
   passthru.updateScript = nix-update-script {
     extraArgs = [
@@ -49,6 +75,5 @@ buildPythonPackage rec {
     homepage = "https://htseq.readthedocs.io/";
     description = "A framework to work with high-throughput sequencing data";
     maintainers = with maintainers; [ unode ];
-    platforms = platforms.unix;
   };
 }