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

python3Packages.biopython: patch SeqXMLIO parser, refactor

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

@@ -1,9 +1,10 @@
-{ lib
-, buildPythonPackage
-, fetchPypi
-, pythonOlder
-, setuptools
-, numpy
+{
+  lib,
+  buildPythonPackage,
+  fetchPypi,
+  pythonOlder,
+  setuptools,
+  numpy,
 }:
 
 buildPythonPackage rec {
@@ -18,15 +19,17 @@ 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