From 26df8e7d72dc4741424d6cd0e2208cafff6f098f Mon Sep 17 00:00:00 2001
From: Pyrox <pyrox@pyrox.dev>
Date: Sun, 28 Jul 2024 19:12:40 -0400
Subject: [PATCH 1/2] python312Packages.bx-python: Drop nose dependency

---
 pkgs/development/python-modules/bx-python/default.nix | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/bx-python/default.nix b/pkgs/development/python-modules/bx-python/default.nix
index 2ea260df66f8..14b801945006 100644
--- a/pkgs/development/python-modules/bx-python/default.nix
+++ b/pkgs/development/python-modules/bx-python/default.nix
@@ -7,7 +7,7 @@
   cython,
   zlib,
   python-lzo,
-  nose,
+  pytestCheckHook,
 }:
 
 buildPythonPackage rec {
@@ -30,10 +30,13 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [
     numpy
+  nativeCheckInputs = [
     python-lzo
+    pytestCheckHook
   ];
 
-  nativeCheckInputs = [ nose ];
+  # https://github.com/bxlab/bx-python/issues/101
+  doCheck = false;
 
   postInstall = ''
     cp -r scripts/* $out/bin

From a007b9f78b9b9bdf172df5ce3ab7a5d9e1e20566 Mon Sep 17 00:00:00 2001
From: Pyrox <pyrox@pyrox.dev>
Date: Sun, 28 Jul 2024 19:12:50 -0400
Subject: [PATCH 2/2] python312Packages.bx-python: Modernize

---
 .../python-modules/bx-python/default.nix      | 33 ++++++++++++-------
 1 file changed, 21 insertions(+), 12 deletions(-)

diff --git a/pkgs/development/python-modules/bx-python/default.nix b/pkgs/development/python-modules/bx-python/default.nix
index 14b801945006..869440098f1d 100644
--- a/pkgs/development/python-modules/bx-python/default.nix
+++ b/pkgs/development/python-modules/bx-python/default.nix
@@ -2,34 +2,43 @@
   lib,
   fetchFromGitHub,
   buildPythonPackage,
-  pythonOlder,
   numpy,
   cython,
   zlib,
   python-lzo,
   pytestCheckHook,
+  setuptools,
+  oldest-supported-numpy,
 }:
 
 buildPythonPackage rec {
   pname = "bx-python";
-  version = "0.11.0";
-  format = "setuptools";
-
-  disabled = pythonOlder "3.8";
+  version = "0.12.0";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "bxlab";
     repo = "bx-python";
     rev = "refs/tags/v${version}";
-    hash = "sha256-evhxh/cCZFSK6EgMu7fC9/ZrPd2S1fZz89ItGYrHQck=";
+    hash = "sha256-ZpZjh7OXdUY7rd692h7VYHzC3qCrDKFme6r+wuG7GP4=";
   };
 
-  nativeBuildInputs = [ cython ];
+  postPatch = ''
+    # pytest-cython, which provides this option, isn't packaged
+    substituteInPlace pytest.ini \
+      --replace-fail "--doctest-cython" ""
+  '';
+
+  build-system = [
+    setuptools
+    cython
+    oldest-supported-numpy
+  ];
 
   buildInputs = [ zlib ];
 
-  propagatedBuildInputs = [
-    numpy
+  dependencies = [ numpy ];
+
   nativeCheckInputs = [
     python-lzo
     pytestCheckHook
@@ -48,12 +57,12 @@ buildPythonPackage rec {
     ln -s $out/bin scripts
   '';
 
-  meta = with lib; {
+  meta = {
     description = "Tools for manipulating biological data, particularly multiple sequence alignments";
     homepage = "https://github.com/bxlab/bx-python";
     changelog = "https://github.com/bxlab/bx-python/releases/tag/v${version}";
-    license = licenses.mit;
-    maintainers = with maintainers; [ jbedo ];
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ jbedo ];
     platforms = [ "x86_64-linux" ];
   };
 }