From 851d2f6b95cef3d6e3bb9a919b4143fdd457d700 Mon Sep 17 00:00:00 2001
From: Theodore Ni <3806110+tjni@users.noreply.github.com>
Date: Fri, 11 Aug 2023 14:45:45 -0700
Subject: [PATCH] macs2: 2.2.8 -> 2.2.9.1

---
 .../science/biology/macs2/default.nix         | 31 ++++++++++++-------
 1 file changed, 20 insertions(+), 11 deletions(-)

diff --git a/pkgs/applications/science/biology/macs2/default.nix b/pkgs/applications/science/biology/macs2/default.nix
index 934da2e8ab61..8884d41d9064 100644
--- a/pkgs/applications/science/biology/macs2/default.nix
+++ b/pkgs/applications/science/biology/macs2/default.nix
@@ -1,31 +1,40 @@
-{ lib, python3, fetchPypi }:
+{ lib, python3, fetchpatch, fetchPypi }:
 
 python3.pkgs.buildPythonPackage rec {
   pname = "macs2";
-  version = "2.2.8";
+  version = "2.2.9.1";
   format = "pyproject";
 
   src = fetchPypi {
     pname = lib.toUpper pname;
     inherit version;
-    hash = "sha256-KgpDasidj4yUoeQQaQA3dg5eN5Ka1xnFRpbnTvhKmOA=";
+    hash = "sha256-jVa8N/uCP8Y4fXgTjOloQFxUoKjNl3ZoJwX9CYMlLRY=";
   };
 
-  postPatch = ''
-    # prevent setup.py from installing numpy
-    substituteInPlace setup.py \
-      --replace "subprocess.call([sys.executable, \"-m\", 'pip', 'install', f'numpy{numpy_requires}'],cwd=cwd)" "0"
-  '';
+  patches = [
+    # https://github.com/macs3-project/MACS/pull/590
+    (fetchpatch {
+      name = "remove-pip-build-dependency.patch";
+      url = "https://github.com/macs3-project/MACS/commit/cf95a930daccf9f16e5b9a9224c5a2670cf67939.patch";
+      hash = "sha256-WB3Ubqk5fKtZt97QYo/sZDU/yya9MUo1NL4VsKXR+Yo=";
+    })
+  ];
 
   nativeBuildInputs = with python3.pkgs; [
     cython
+    numpy
     setuptools
+    wheel
   ];
 
-  propagatedBuildInputs = with python3.pkgs; [ numpy ];
+  propagatedBuildInputs = with python3.pkgs; [
+    numpy
+  ];
 
-  nativeCheckInputs = [
-    python3.pkgs.unittestCheckHook
+  __darwinAllowLocalNetworking = true;
+
+  nativeCheckInputs = with python3.pkgs; [
+    unittestCheckHook
   ];
 
   unittestFlagsArray = [