Merge pull request #310411 from getchoo/pkgs/biopython/fix-test

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):

{ lib

, buildPythonPackage

, fetchPypi

, pythonOlder

, setuptools

, numpy

{

  lib,

  buildPythonPackage,

  fetchPypi,

  pythonOlder,

  setuptools,

  numpy,

}:

buildPythonPackage rec {

    hash = "sha256-eOa/t43mMDQDev01/nfLbgqeW2Jwa+z3in2SKxbtg/c=";

  };

  nativeBuildInputs = [

    setuptools

  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

  ];

  propagatedBuildInputs = [ numpy ];

  build-system = [ setuptools ];

  pythonImportsCheck = [

    "Bio"

  ];

  dependencies = [ numpy ];

  pythonImportsCheck = [ "Bio" ];

  checkPhase = ''

    runHook preCheck