From 220c6d0879f9bdf9c54901ec43809717119c7f2d Mon Sep 17 00:00:00 2001
From: Markus Kowalewski <markus.kowalewski@gmail.com>
Date: Fri, 8 Nov 2024 10:27:11 +0100
Subject: [PATCH 1/2] Revert "biopython: fix eval"

This reverts commit 74ae5abbf1bccee90e13997fa68a2664a6a48bcd.
---
 pkgs/development/python-modules/biopython/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/development/python-modules/biopython/default.nix b/pkgs/development/python-modules/biopython/default.nix
index 2a3d3d0b86e3..900c3f019f28 100644
--- a/pkgs/development/python-modules/biopython/default.nix
+++ b/pkgs/development/python-modules/biopython/default.nix
@@ -17,7 +17,7 @@ buildPythonPackage rec {
   src = fetchFromGitHub {
     owner = "biopython";
     repo = "biopython";
-    rev = "refs/tags/biopython-${lib.replaceStrings [ "." ] [ "" ] version}";
+    rev = "refs/tags/biopython-${lib.replaceChars [ "." ] [ "" ] version}";
     hash = "sha256-zXUB/AkWc/cY9M02WheSvXjT/nwM+lGXfXgCcWfu0G4=";
   };
 

From 95aa3d12c670528f16d01262cad53a2c199c8814 Mon Sep 17 00:00:00 2001
From: Markus Kowalewski <markus.kowalewski@gmail.com>
Date: Fri, 8 Nov 2024 10:27:23 +0100
Subject: [PATCH 2/2] Revert "python3Packages.biopython: 1.83 -> 1.84"

This reverts commit a30bd9c1992ddce61e9ecb4add359011fd30f669.
---
 .../biopython/close_parser_on_time.patch       | 18 ++++++++++++++++++
 .../python-modules/biopython/default.nix       | 18 +++++++++++-------
 2 files changed, 29 insertions(+), 7 deletions(-)
 create 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
new file mode 100644
index 000000000000..05d22e22ed9e
--- /dev/null
+++ b/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):
diff --git a/pkgs/development/python-modules/biopython/default.nix b/pkgs/development/python-modules/biopython/default.nix
index 900c3f019f28..051f66845dec 100644
--- a/pkgs/development/python-modules/biopython/default.nix
+++ b/pkgs/development/python-modules/biopython/default.nix
@@ -1,7 +1,7 @@
 {
   lib,
   buildPythonPackage,
-  fetchFromGitHub,
+  fetchPypi,
   pythonOlder,
   setuptools,
   numpy,
@@ -9,18 +9,22 @@
 
 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.replaceChars [ "." ] [ "" ] 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 ];