From a30bd9c1992ddce61e9ecb4add359011fd30f669 Mon Sep 17 00:00:00 2001
From: Martin Weinelt <hexa@darmstadt.ccc.de>
Date: Sun, 29 Sep 2024 17:03:51 +0200
Subject: [PATCH] python3Packages.biopython: 1.83 -> 1.84

---
 .../biopython/close_parser_on_time.patch       | 18 ------------------
 .../python-modules/biopython/default.nix       | 18 +++++++-----------
 2 files changed, 7 insertions(+), 29 deletions(-)
 delete mode 100644 pkgs/development/python-modules/biopython/close_parser_on_time.patch

diff --git a/pkgs/development/python-modules/biopython/close_parser_on_time.patch b/pkgs/development/python-modules/biopython/close_parser_on_time.patch
deleted file mode 100644
index 05d22e22ed9e..000000000000
--- a/pkgs/development/python-modules/biopython/close_parser_on_time.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-diff --git a/Bio/SeqIO/SeqXmlIO.py b/Bio/SeqIO/SeqXmlIO.py
-index 8fe75ebb728..6758317d05f 100644
---- a/Bio/SeqIO/SeqXmlIO.py
-+++ b/Bio/SeqIO/SeqXmlIO.py
-@@ -498,11 +498,12 @@ def iterate(self, handle):
-             if not text:
-                 break
-             parser.feed(text)
-+        # Closing the parser ensures that all XML data fed into it are processed
-+        parser.close()
-         # We have reached the end of the XML file;
-         # send out the remaining records
-         yield from records
-         records.clear()
--        parser.close()
- 
- 
- class SeqXmlWriter(SequenceWriter):
diff --git a/pkgs/development/python-modules/biopython/default.nix b/pkgs/development/python-modules/biopython/default.nix
index 051f66845dec..900c3f019f28 100644
--- a/pkgs/development/python-modules/biopython/default.nix
+++ b/pkgs/development/python-modules/biopython/default.nix
@@ -1,7 +1,7 @@
 {
   lib,
   buildPythonPackage,
-  fetchPypi,
+  fetchFromGitHub,
   pythonOlder,
   setuptools,
   numpy,
@@ -9,22 +9,18 @@
 
 buildPythonPackage rec {
   pname = "biopython";
-  version = "1.83";
+  version = "1.84";
   pyproject = true;
 
   disabled = pythonOlder "3.9";
 
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-eOa/t43mMDQDev01/nfLbgqeW2Jwa+z3in2SKxbtg/c=";
+  src = fetchFromGitHub {
+    owner = "biopython";
+    repo = "biopython";
+    rev = "refs/tags/biopython-${lib.replaceChars [ "." ] [ "" ] version}";
+    hash = "sha256-zXUB/AkWc/cY9M02WheSvXjT/nwM+lGXfXgCcWfu0G4=";
   };
 
-  patches = [
-    # cherry-picked from https://github.com/biopython/biopython/commit/3f9bda7ef44f533dadbaa0de29ac21929bc0b2f1
-    # fixes SeqXMLIO parser to process all data. remove on next update
-    ./close_parser_on_time.patch
-  ];
-
   build-system = [ setuptools ];
 
   dependencies = [ numpy ];