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..e4fbe51cbb5d 100644 --- a/pkgs/development/python-modules/biopython/default.nix +++ b/pkgs/development/python-modules/biopython/default.nix @@ -9,22 +9,16 @@ buildPythonPackage rec { pname = "biopython"; - version = "1.83"; + version = "1.85"; pyproject = true; disabled = pythonOlder "3.9"; src = fetchPypi { inherit pname version; - hash = "sha256-eOa/t43mMDQDev01/nfLbgqeW2Jwa+z3in2SKxbtg/c="; + hash = "sha256-Xa+rdAWd5OePSfa1aE7drm585G8Jz6BZwdEznoseoKY="; }; - 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 ];