From 0669232bbb9f73efcc8bbfcf3972bb75ed506f5c Mon Sep 17 00:00:00 2001
From: Nick Cao <nickcao@nichi.co>
Date: Tue, 11 Feb 2025 16:37:41 -0500
Subject: [PATCH] deeptools: 3.5.5 -> 3.5.6

Diff: https://github.com/deeptools/deepTools/compare/refs/tags/3.5.5...3.5.6
---
 pkgs/by-name/de/deeptools/package.nix | 35 ++++++++++++---------------
 1 file changed, 16 insertions(+), 19 deletions(-)

diff --git a/pkgs/by-name/de/deeptools/package.nix b/pkgs/by-name/de/deeptools/package.nix
index 97c76c7f05753..509242f7b5210 100644
--- a/pkgs/by-name/de/deeptools/package.nix
+++ b/pkgs/by-name/de/deeptools/package.nix
@@ -1,46 +1,43 @@
 {
   lib,
-  python3,
+  python3Packages,
   fetchFromGitHub,
+  addBinToPathHook,
 }:
 
-python3.pkgs.buildPythonApplication rec {
+python3Packages.buildPythonApplication rec {
   pname = "deeptools";
-  version = "3.5.5";
+  version = "3.5.6";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "deeptools";
     repo = "deepTools";
     tag = version;
-    hash = "sha256-2kSlL7Y5f/FjVtStnmz+GlTw2oymrtxOCaXlqgbQ7FU=";
+    hash = "sha256-dxXlOvOjF4KSc5YO+1A5hlp95sfeyPSbmp93tihm7Vo=";
   };
 
-  nativeBuildInputs = with python3.pkgs; [
+  build-system = with python3Packages; [
     setuptools
   ];
 
-  propagatedBuildInputs = with python3.pkgs; [
+  dependencies = with python3Packages; [
     numpy
-    numpydoc
     scipy
-    py2bit
-    pybigwig
-    pysam
     matplotlib
+    pysam
+    numpydoc
+    pybigwig
+    py2bit
     plotly
     deeptoolsintervals
-    importlib-metadata
   ];
 
-  nativeCheckInputs = with python3.pkgs; [
+  nativeCheckInputs = with python3Packages; [
     pytestCheckHook
+    addBinToPathHook
   ];
 
-  preCheck = ''
-    export PATH="$out/bin:$PATH"
-  '';
-
   disabledTestPaths = [
     # tests trip on `len(sys.argv) == 1`
     "deeptools/test/test_bigwigAverage.py"
@@ -49,7 +46,7 @@ python3.pkgs.buildPythonApplication rec {
     "deeptools/test/test_multiBamSummary.py"
   ];
 
-  meta = with lib; {
+  meta = {
     homepage = "https://deeptools.readthedocs.io/en/develop";
     description = "Tools for exploring deep DNA sequencing data";
     longDescription = ''
@@ -60,10 +57,10 @@ python3.pkgs.buildPythonApplication rec {
       publication-ready visualizations to identify enrichments and for functional
       annotations of the genome.
     '';
-    license = with licenses; [
+    license = with lib.licenses; [
       mit
       bsd3
     ];
-    maintainers = with maintainers; [ scalavision ];
+    maintainers = with lib.maintainers; [ scalavision ];
   };
 }