From ac3e621e7fc5501dd77dab6267de4a6a1a1b107e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= <nix@dotlambda.de>
Date: Sun, 28 Jan 2024 12:17:37 -0800
Subject: [PATCH] deeptools: fix build

---
 .../science/biology/deeptools/default.nix     | 36 ++++++++++++++-----
 pkgs/top-level/all-packages.nix               |  2 +-
 2 files changed, 29 insertions(+), 9 deletions(-)

diff --git a/pkgs/applications/science/biology/deeptools/default.nix b/pkgs/applications/science/biology/deeptools/default.nix
index a199e41d50aa..a7a1f77dfe90 100644
--- a/pkgs/applications/science/biology/deeptools/default.nix
+++ b/pkgs/applications/science/biology/deeptools/default.nix
@@ -1,19 +1,25 @@
-{ lib, python, fetchFromGitHub }:
-with python.pkgs;
-buildPythonApplication rec {
-  pname = "deepTools";
+{ lib
+, python3
+, fetchFromGitHub
+}:
+
+python3.pkgs.buildPythonApplication rec {
+  pname = "deeptools";
   version = "3.5.4";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "deeptools";
     repo = "deepTools";
     rev = version;
-    sha256 = "sha256-A8YdlMptmJyxWW0EYLjXFIWjIO/mttEC7VYdlCe9MaI=";
+    hash = "sha256-A8YdlMptmJyxWW0EYLjXFIWjIO/mttEC7VYdlCe9MaI=";
   };
 
-  format = "pyproject";
+  nativeBuildInputs = with python3.pkgs; [
+    setuptools
+  ];
 
-  propagatedBuildInputs = [
+  propagatedBuildInputs = with python3.pkgs; [
     numpy
     numpydoc
     scipy
@@ -26,7 +32,21 @@ buildPythonApplication rec {
     importlib-metadata
   ];
 
-  nativeCheckInputs = [ pytest ];
+  nativeCheckInputs = with python3.pkgs; [
+    pytestCheckHook
+  ];
+
+  preCheck = ''
+    export PATH="$out/bin:$PATH"
+  '';
+
+  disabledTestPaths = [
+    # tests trip on `len(sys.argv) == 1`
+    "deeptools/test/test_bigwigAverage.py"
+    "deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py"
+    "deeptools/test/test_heatmapper.py"
+    "deeptools/test/test_multiBamSummary.py"
+  ];
 
   meta = with lib; {
     homepage = "https://deeptools.readthedocs.io/en/develop";
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index ef7ee1bd9ebd..ac428acd9c94 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -38886,7 +38886,7 @@ with pkgs;
     python3 = python311;
   };
 
-  deeptools = callPackage ../applications/science/biology/deeptools { python = python3; };
+  deeptools = callPackage ../applications/science/biology/deeptools { };
 
   deep-translator = with python3Packages; toPythonApplication deep-translator;