From e52b1e1085cab96c59504d8387e5952629bbc3cd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= <nix@dotlambda.de>
Date: Wed, 24 Sep 2025 01:03:45 -0700
Subject: [PATCH 1/2] python3Packages.affine-gaps: init at 0.2.3

---
 .../python-modules/affine-gaps/default.nix    | 49 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 51 insertions(+)
 create mode 100644 pkgs/development/python-modules/affine-gaps/default.nix

diff --git a/pkgs/development/python-modules/affine-gaps/default.nix b/pkgs/development/python-modules/affine-gaps/default.nix
new file mode 100644
index 000000000000..ac5bce042918
--- /dev/null
+++ b/pkgs/development/python-modules/affine-gaps/default.nix
@@ -0,0 +1,49 @@
+{
+  biopython,
+  buildPythonPackage,
+  colorama,
+  fetchFromGitHub,
+  hatchling,
+  lib,
+  numpy,
+  pytest-repeat,
+  pytestCheckHook,
+}:
+
+buildPythonPackage rec {
+  pname = "affine-gaps";
+  version = "0.2.3";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "gata-bio";
+    repo = "affine-gaps";
+    tag = "v${version}";
+    hash = "sha256-GP6Ahp1LQYnKp9V7jDEeFsntMC9Qav5kWm+5bSldtyM=";
+  };
+
+  build-system = [ hatchling ];
+
+  dependencies = [
+    colorama
+    numpy
+  ];
+
+  pythonImportsCheck = [ "affine_gaps" ];
+
+  nativeCheckInputs = [
+    biopython
+    pytest-repeat
+    pytestCheckHook
+  ];
+
+  enabledTestPaths = [ "test.py" ];
+
+  meta = {
+    changelog = "https://github.com/gata-bio/affine-gaps/releases/tag/${src.tag}";
+    homepage = "https://github.com/gata-bio/affine-gaps";
+    license = lib.licenses.asl20;
+    mainProgram = "affine-gaps";
+    maintainers = [ lib.maintainers.dotlambda ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 4f0135c1ca6d..5f28d4f932eb 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -122,6 +122,8 @@ self: super: with self; {
 
   affine = callPackage ../development/python-modules/affine { };
 
+  affine-gaps = callPackage ../development/python-modules/affine-gaps { };
+
   afsapi = callPackage ../development/python-modules/afsapi { };
 
   agate = callPackage ../development/python-modules/agate { };

From 1654317cb8b21222d5e2a02a6c12f03a493b6434 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= <nix@dotlambda.de>
Date: Wed, 24 Sep 2025 00:49:23 -0700
Subject: [PATCH 2/2] python3Packages.stringzilla: 3.12.6 -> 4.0.14

Diff: https://github.com/ashvardanian/stringzilla/compare/v3.12.6...v4.0.14

Changelog: https://github.com/ashvardanian/StringZilla/releases/tag/v4.0.0
---
 pkgs/development/python-modules/stringzilla/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/python-modules/stringzilla/default.nix b/pkgs/development/python-modules/stringzilla/default.nix
index f7195d63ae23..d85e0d16278f 100644
--- a/pkgs/development/python-modules/stringzilla/default.nix
+++ b/pkgs/development/python-modules/stringzilla/default.nix
@@ -11,14 +11,14 @@
 
 buildPythonPackage rec {
   pname = "stringzilla";
-  version = "3.12.6";
+  version = "4.0.14";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "ashvardanian";
     repo = "stringzilla";
     tag = "v${version}";
-    hash = "sha256-4Ze6yVNd2NX0E6vAJuiLZTIgicF7mSlGO8wKOF1jYds=";
+    hash = "sha256-kEo5lNCdC9676ZrBNIkav+9wT9qjzZHbauKuVnrXxK8=";
   };
 
   postPatch = lib.optionalString stdenv.hostPlatform.isDarwin ''
@@ -39,7 +39,7 @@ buildPythonPackage rec {
     pytestCheckHook
   ];
 
-  enabledTestPaths = [ "scripts/test.py" ];
+  enabledTestPaths = [ "scripts/test_stringzilla.py" ];
 
   meta = {
     changelog = "https://github.com/ashvardanian/StringZilla/releases/tag/${src.tag}";