From 84c5341c9622c9fd1a846f317a9ef16fe308c68b Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Fri, 3 Mar 2023 16:17:54 +0100
Subject: [PATCH 1/3] python310Packages.pybigwig: add changelog to meta

---
 pkgs/development/python-modules/pybigwig/default.nix | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pkgs/development/python-modules/pybigwig/default.nix b/pkgs/development/python-modules/pybigwig/default.nix
index cb23c2a5732b..1a7a63ee5f48 100644
--- a/pkgs/development/python-modules/pybigwig/default.nix
+++ b/pkgs/development/python-modules/pybigwig/default.nix
@@ -20,13 +20,14 @@ buildPythonPackage rec {
   nativeCheckInputs = [ numpy pytest ];
 
   meta = with lib; {
-    homepage = "https://github.com/deeptools/pyBigWig";
     description = "File access to bigBed files, and read and write access to bigWig files";
     longDescription = ''
       A python extension, written in C, for quick access to bigBed files
       and access to and creation of bigWig files. This extension uses
       libBigWig for local and remote file access.
     '';
+    homepage = "https://github.com/deeptools/pyBigWig";
+    changelog = "https://github.com/deeptools/pyBigWig/releases/tag/${version}";
     license = licenses.mit;
     maintainers = with maintainers; [ scalavision ];
   };

From 151ff48bb4bf977311746c9a4e5f21b836c6e413 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Fri, 3 Mar 2023 16:19:10 +0100
Subject: [PATCH 2/3] python310Packages.pybigwWig: normalize pname

---
 pkgs/development/python-modules/pybigwig/default.nix | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/pybigwig/default.nix b/pkgs/development/python-modules/pybigwig/default.nix
index 1a7a63ee5f48..4e3f0d5af719 100644
--- a/pkgs/development/python-modules/pybigwig/default.nix
+++ b/pkgs/development/python-modules/pybigwig/default.nix
@@ -7,11 +7,12 @@
 }:
 
 buildPythonPackage rec {
-  pname = "pyBigWig";
+  pname = "pybigwig";
   version = "0.3.18";
 
   src = fetchPypi {
-    inherit pname version;
+    pname = "pyBigWig";
+    inherit version;
     sha256 = "4c2a8c571b4100ad7c4c318c142eb48558646be52aaab28215a70426f5be31bc";
   };
 

From da678d4e7404500ed3adf929e0eb52b8dc526e03 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Fri, 3 Mar 2023 16:44:20 +0100
Subject: [PATCH 3/3] python310Packages.pybigwig: 0.3.18 -> 0.3.20

Changelog: https://github.com/deeptools/pyBigWig/releases/tag/0.3.20
---
 .../python-modules/pybigwig/default.nix       | 46 +++++++++++++++----
 1 file changed, 36 insertions(+), 10 deletions(-)

diff --git a/pkgs/development/python-modules/pybigwig/default.nix b/pkgs/development/python-modules/pybigwig/default.nix
index 4e3f0d5af719..3101066ff251 100644
--- a/pkgs/development/python-modules/pybigwig/default.nix
+++ b/pkgs/development/python-modules/pybigwig/default.nix
@@ -1,29 +1,55 @@
 { lib
 , buildPythonPackage
-, fetchPypi
-, pytest
+, fetchFromGitHub
 , numpy
+, pytestCheckHook
+, pythonOlder
 , zlib
 }:
 
 buildPythonPackage rec {
   pname = "pybigwig";
-  version = "0.3.18";
+  version = "0.3.20";
+  format = "setuptools";
 
-  src = fetchPypi {
-    pname = "pyBigWig";
-    inherit version;
-    sha256 = "4c2a8c571b4100ad7c4c318c142eb48558646be52aaab28215a70426f5be31bc";
+  disabled = pythonOlder "3.7";
+
+  src = fetchFromGitHub {
+    owner = "deeptools";
+    repo = "pyBigWig";
+    rev = "refs/tags/${version}";
+    hash = "sha256-uYKxM0HOG4fus5geBFjbfbv6G1kDvMaAwhk0w/e1YII=";
   };
 
-  buildInputs = [ zlib ];
+  buildInputs = [
+    zlib
+  ];
 
-  nativeCheckInputs = [ numpy pytest ];
+  nativeCheckInputs = [
+    numpy
+    pytestCheckHook
+  ];
+
+  pythonImportsCheck = [
+    "pyBigWig"
+  ];
+
+  pytestFlagsArray = [
+    "pyBigWigTest/test*.py"
+  ];
+
+  disabledTests = [
+    # Test file is donwloaded from GitHub
+    "testAll"
+    "testBigBed"
+    "testFoo"
+    "testNumpyValues"
+  ];
 
   meta = with lib; {
     description = "File access to bigBed files, and read and write access to bigWig files";
     longDescription = ''
-      A python extension, written in C, for quick access to bigBed files
+      A Python extension, written in C, for quick access to bigBed files
       and access to and creation of bigWig files. This extension uses
       libBigWig for local and remote file access.
     '';