python3Packages.biopython: revert update 1.83 -> 1.84 (#354437)

Author: mweinelt

pkgs/development/python-modules/biopython/close_parser_on_time.patch

@@ -0,0 +1,18 @@
+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):

pkgs/development/python-modules/biopython/default.nix

@@ -1,26 +1,30 @@
 {
   lib,
   buildPythonPackage,
-  fetchFromGitHub,
+  fetchPypi,
   pythonOlder,
   setuptools,
   numpy,
 }:
 
 buildPythonPackage rec {
   pname = "biopython";
-  version = "1.84";
+  version = "1.83";
   pyproject = true;
 
   disabled = pythonOlder "3.9";
 
-  src = fetchFromGitHub {
-    owner = "biopython";
-    repo = "biopython";
-    rev = "refs/tags/biopython-${lib.replaceStrings [ "." ] [ "" ] version}";
-    hash = "sha256-zXUB/AkWc/cY9M02WheSvXjT/nwM+lGXfXgCcWfu0G4=";
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-eOa/t43mMDQDev01/nfLbgqeW2Jwa+z3in2SKxbtg/c=";
   };
 
+  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 ];