From 039ea42a9f5458d12927db8daac97686f7161025 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Fri, 11 Oct 2024 07:36:51 +0000
Subject: [PATCH] python312Packages.pyfaidx: 0.8.1.2 -> 0.8.1.3

---
 .../python-modules/pyfaidx/default.nix        | 46 +++++++++++--------
 1 file changed, 26 insertions(+), 20 deletions(-)

diff --git a/pkgs/development/python-modules/pyfaidx/default.nix b/pkgs/development/python-modules/pyfaidx/default.nix
index b3cb0f886bd71..eca3180a61768 100644
--- a/pkgs/development/python-modules/pyfaidx/default.nix
+++ b/pkgs/development/python-modules/pyfaidx/default.nix
@@ -1,26 +1,28 @@
 {
   lib,
   buildPythonPackage,
-  fetchPypi,
+  fetchFromGitHub,
   glibcLocales,
   importlib-metadata,
-  numpy,
+  packaging,
+  htslib,
+  fsspec,
   pytestCheckHook,
-  pythonOlder,
+  biopython,
   setuptools,
   setuptools-scm,
 }:
 
 buildPythonPackage rec {
   pname = "pyfaidx";
-  version = "0.8.1.2";
+  version = "0.8.1.3";
   pyproject = true;
 
-  disabled = pythonOlder "3.7";
-
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-2EUkcEVbHnePk5aUR9uOok3rRiTHxAdpUWRZy2+HvDM=";
+  src = fetchFromGitHub {
+    owner = "mdshw5";
+    repo = "pyfaidx";
+    rev = "refs/tags/v${version}";
+    hash = "sha256-PKcopIu/0ko4Jl2+G0ZivZXvMwACeIFFFlPt5dlDDfQ=";
   };
 
   build-system = [
@@ -28,27 +30,31 @@ buildPythonPackage rec {
     setuptools-scm
   ];
 
-  dependencies = [ importlib-metadata ];
+  dependencies = [
+    importlib-metadata
+    packaging
+  ];
 
   nativeCheckInputs = [
-    glibcLocales
-    numpy
     pytestCheckHook
-  ];
-
-  disabledTestPaths = [
-    # FileNotFoundError: [Errno 2] No such file or directory: 'data/genes.fasta.gz'
-    "tests/test_Fasta_bgzip.py"
+    biopython
+    htslib
+    fsspec
+    glibcLocales
   ];
 
   pythonImportsCheck = [ "pyfaidx" ];
 
-  meta = with lib; {
+  preCheck = ''
+    bgzip --keep tests/data/genes.fasta
+  '';
+
+  meta = {
     description = "Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index";
     homepage = "https://github.com/mdshw5/pyfaidx";
     changelog = "https://github.com/mdshw5/pyfaidx/releases/tag/v${version}";
-    license = licenses.bsd3;
-    maintainers = with maintainers; [ jbedo ];
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ jbedo ];
     mainProgram = "faidx";
   };
 }