From 0983642659d1258292362babde064530f9e71f4d Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Wed, 7 Jan 2026 13:46:41 +0000
Subject: [PATCH 01/19] tkgl: add alejo7797 to maintainers

---
 pkgs/by-name/tk/tkgl/package.nix | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/pkgs/by-name/tk/tkgl/package.nix b/pkgs/by-name/tk/tkgl/package.nix
index ba5497bf588e0..efdcb54d0c79e 100644
--- a/pkgs/by-name/tk/tkgl/package.nix
+++ b/pkgs/by-name/tk/tkgl/package.nix
@@ -46,6 +46,9 @@ tcl.mkTclDerivation {
     description = "OpenGL drawing surface for Tk 8 and 9";
     homepage = "https://github.com/3-manifolds/TkGL";
     license = lib.licenses.tcltk;
-    maintainers = with lib.maintainers; [ noiioiu ];
+    maintainers = with lib.maintainers; [
+      noiioiu
+      alejo7797
+    ];
   };
 }

From 889fa3550c869038f5125f694c1858081c57de70 Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Tue, 6 Jan 2026 09:03:58 -0500
Subject: [PATCH 02/19] tkgl: 1.2.1-unstable-2025-06-01 ->
 1.2.1-unstable-2026-01-07

---
 pkgs/by-name/tk/tkgl/package.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/by-name/tk/tkgl/package.nix b/pkgs/by-name/tk/tkgl/package.nix
index efdcb54d0c79e..915df735331bf 100644
--- a/pkgs/by-name/tk/tkgl/package.nix
+++ b/pkgs/by-name/tk/tkgl/package.nix
@@ -10,13 +10,13 @@
 
 tcl.mkTclDerivation {
   pname = "tkgl";
-  version = "1.2.1-unstable-2025-06-01";
+  version = "1.2.1-unstable-2026-01-07";
 
   src = fetchFromGitHub {
     owner = "3-manifolds";
     repo = "TkGL";
-    rev = "45bf16e6c28a070c70fc9a0eb8c47a0b6ff8a2e3";
-    hash = "sha256-AA5LZGhMTWmTZqI/wtycUYLsUe9BwO3voGMS7vGlCM0=";
+    rev = "e47636bc56f02ddca503f98abc65e31a0f0f0a7c";
+    hash = "sha256-Y5NIKWUjbtVn9qiVzc8TsKCm4M3KbNPiBjVTBWf7ALA=";
   };
 
   postPatch = lib.optionalString stdenv.hostPlatform.isDarwin ''

From 23f098949d8a8a82c0e4e9c9aeeecafca5e25091 Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Sun, 11 Jan 2026 10:51:10 +0000
Subject: [PATCH 03/19] python3Packages.tkinter-gl: add setuptools to
 build-system

---
 pkgs/development/python-modules/tkinter-gl/default.nix | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/python-modules/tkinter-gl/default.nix b/pkgs/development/python-modules/tkinter-gl/default.nix
index a39a6d940d4dc..a933980943801 100644
--- a/pkgs/development/python-modules/tkinter-gl/default.nix
+++ b/pkgs/development/python-modules/tkinter-gl/default.nix
@@ -1,11 +1,12 @@
 {
   lib,
+  fetchFromGitHub,
   python,
   buildPythonPackage,
-  fetchFromGitHub,
+  setuptools,
   setuptools-scm,
-  tkinter,
   tkgl,
+  tkinter,
 }:
 
 buildPythonPackage rec {
@@ -29,7 +30,10 @@ buildPythonPackage rec {
                      "pkg_dir = os.path.join(__path__[0], 'tk')"
   '';
 
-  build-system = [ setuptools-scm ];
+  build-system = [
+    setuptools
+    setuptools-scm
+  ];
 
   dependencies = [ tkinter ];
 

From 623dbeed8b8f7fb49778e00d80eded3bbd95eec1 Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Mon, 9 Feb 2026 17:05:41 -0500
Subject: [PATCH 04/19] python3Packages.tkinter-gl: add updateScript

---
 pkgs/development/python-modules/tkinter-gl/default.nix | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/pkgs/development/python-modules/tkinter-gl/default.nix b/pkgs/development/python-modules/tkinter-gl/default.nix
index a933980943801..14bc749258106 100644
--- a/pkgs/development/python-modules/tkinter-gl/default.nix
+++ b/pkgs/development/python-modules/tkinter-gl/default.nix
@@ -7,6 +7,7 @@
   setuptools-scm,
   tkgl,
   tkinter,
+  nix-update-script,
 }:
 
 buildPythonPackage rec {
@@ -48,6 +49,13 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "tkinter_gl" ];
 
+  passthru.updateScript = nix-update-script {
+    extraArgs = [
+      "--version-regex"
+      "v(.*)_as_released"
+    ];
+  };
+
   meta = {
     description = "Base class for GL rendering surfaces in tkinter";
     changelog = "https://github.com/3-manifolds/tkinter_gl/releases/tag/${src.tag}";

From 58ee9486422c65ba0ba51743cfce452f4c69d4ac Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Mon, 9 Feb 2026 17:06:11 -0500
Subject: [PATCH 05/19] python3Packages.tkinter-gl: 1.0 -> 1.1

---
 pkgs/development/python-modules/tkinter-gl/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/python-modules/tkinter-gl/default.nix b/pkgs/development/python-modules/tkinter-gl/default.nix
index 14bc749258106..8a4787f025fb6 100644
--- a/pkgs/development/python-modules/tkinter-gl/default.nix
+++ b/pkgs/development/python-modules/tkinter-gl/default.nix
@@ -12,14 +12,14 @@
 
 buildPythonPackage rec {
   pname = "tkinter-gl";
-  version = "1.0";
+  version = "1.1";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "3-manifolds";
     repo = "tkinter_gl";
     tag = "v${version}_as_released";
-    hash = "sha256-ObI8EEQ7mAOAuV6f+Ld4HH0xkFzqiAZqHDvzjwPA/wM";
+    hash = "sha256-PNxxjyVGoMw4J/SXWvVITuGMq/HypxUwDkSxeFy2Vag=";
   };
 
   postPatch = ''
@@ -27,7 +27,7 @@ buildPythonPackage rec {
     rm -r src/tkinter_gl/tk
     # Platform-specific directories are only necessary when using compiled TkGL
     substituteInPlace src/tkinter_gl/__init__.py \
-      --replace-fail "pkg_dir = os.path.join(__path__[0], 'tk', sys.platform,)" \
+      --replace-fail "pkg_dir = os.path.join(__path__[0], 'tk', target)" \
                      "pkg_dir = os.path.join(__path__[0], 'tk')"
   '';
 

From f2233d187d1fd9067bf061506bc4ea65a73afc4b Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Sun, 11 Jan 2026 11:26:35 +0000
Subject: [PATCH 06/19] python3Packages.cypari: rename static library
 derivation inputs

---
 .../python-modules/cypari/default.nix         | 31 +++++++++++++++----
 pkgs/top-level/python-packages.nix            | 18 +----------
 2 files changed, 26 insertions(+), 23 deletions(-)

diff --git a/pkgs/development/python-modules/cypari/default.nix b/pkgs/development/python-modules/cypari/default.nix
index 7bba34e3a9a8f..7b263b26720e2 100644
--- a/pkgs/development/python-modules/cypari/default.nix
+++ b/pkgs/development/python-modules/cypari/default.nix
@@ -1,14 +1,33 @@
 {
   lib,
+  fetchFromGitHub,
   python,
   buildPythonPackage,
-  fetchFromGitHub,
+  fetchurl,
   fetchpatch,
+
+  # build-time dependencies
   setuptools,
   cython,
-  gmp,
-  pari,
   perl,
+
+  # static libraries
+  pkgsStatic,
+  gmpStatic ? pkgsStatic.gmp,
+  pari,
+  pariStatic_2_15 ? pari.overrideAttrs (
+    finalAttrs: oldAttrs: {
+      version = "2.15.4";
+      src = fetchurl {
+        url = "https://pari.math.u-bordeaux.fr/pub/pari/OLD/${lib.versions.majorMinor finalAttrs.version}/pari-${finalAttrs.version}.tar.gz";
+        hash = "sha256-w1Rb/uDG37QLd/tLurr5mdguYAabn20ovLbPAEyMXA8=";
+      };
+      installTargets = [
+        "install"
+        "install-lib-sta"
+      ];
+    }
+  ),
 }:
 
 buildPythonPackage rec {
@@ -38,8 +57,8 @@ buildPythonPackage rec {
 
   preBuild = ''
     mkdir libcache
-    ln -s ${gmp} libcache/gmp
-    ln -s ${pari} libcache/pari
+    ln -s ${gmpStatic} libcache/gmp
+    ln -s ${pariStatic_2_15} libcache/pari
   '';
 
   build-system = [
@@ -62,11 +81,11 @@ buildPythonPackage rec {
   meta = {
     description = "Sage's PARI extension, modified to stand alone";
     homepage = "https://github.com/3-manifolds/CyPari";
+    changelog = "https://github.com/3-manifolds/CyPari/releases/tag/${src.tag}";
     license = lib.licenses.gpl2Plus;
     maintainers = with lib.maintainers; [
       noiioiu
       alejo7797
     ];
-    changelog = "https://github.com/3-manifolds/CyPari/releases/tag/${src.tag}";
   };
 }
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index fcf19791ac155..2551a0b785981 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -3476,23 +3476,7 @@ self: super: with self; {
 
   cynthion = callPackage ../development/python-modules/cynthion { };
 
-  cypari = callPackage ../development/python-modules/cypari {
-
-    inherit (pkgs.pkgsStatic) gmp;
-
-    pari = pkgs.pari.overrideAttrs rec {
-      version = "2.15.4";
-      src = pkgs.fetchurl {
-        url = "https://pari.math.u-bordeaux.fr/pub/pari/OLD/${lib.versions.majorMinor version}/pari-${version}.tar.gz";
-        hash = "sha256-w1Rb/uDG37QLd/tLurr5mdguYAabn20ovLbPAEyMXA8=";
-      };
-      installTargets = [
-        "install"
-        "install-lib-sta"
-      ];
-    };
-
-  };
+  cypari = callPackage ../development/python-modules/cypari { };
 
   cypari2 = callPackage ../development/python-modules/cypari2 { };
 

From 9284474b901c9ff3c9c28532a2ea94b69dda35a0 Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Mon, 9 Feb 2026 22:00:20 -0500
Subject: [PATCH 07/19] python3Packages.cypari: add updateScript

---
 pkgs/development/python-modules/cypari/default.nix | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/pkgs/development/python-modules/cypari/default.nix b/pkgs/development/python-modules/cypari/default.nix
index 7b263b26720e2..4343437554bc5 100644
--- a/pkgs/development/python-modules/cypari/default.nix
+++ b/pkgs/development/python-modules/cypari/default.nix
@@ -3,6 +3,7 @@
   fetchFromGitHub,
   python,
   buildPythonPackage,
+  nix-update-script,
   fetchurl,
   fetchpatch,
 
@@ -78,6 +79,13 @@ buildPythonPackage rec {
     runHook postCheck
   '';
 
+  passthru.updateScript = nix-update-script {
+    extraArgs = [
+      "--version-regex"
+      "(.*)_as_released"
+    ];
+  };
+
   meta = {
     description = "Sage's PARI extension, modified to stand alone";
     homepage = "https://github.com/3-manifolds/CyPari";

From 7b0caf2e0585044f7441816556924ce5a05d0ea3 Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Mon, 5 Jan 2026 17:12:40 -0600
Subject: [PATCH 08/19] python3Packages.cypari: 2.5.5 -> 2.5.6

---
 pkgs/development/python-modules/cypari/default.nix | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/pkgs/development/python-modules/cypari/default.nix b/pkgs/development/python-modules/cypari/default.nix
index 4343437554bc5..e71204f09963e 100644
--- a/pkgs/development/python-modules/cypari/default.nix
+++ b/pkgs/development/python-modules/cypari/default.nix
@@ -33,26 +33,21 @@
 
 buildPythonPackage rec {
   pname = "cypari";
-  version = "2.5.5";
+  version = "2.5.6";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "3-manifolds";
     repo = "CyPari";
     tag = "${version}_as_released";
-    hash = "sha256-RJ9O1KsDHmMkTCIFUrcSUkA5ijTsxmoI939QCsCib0Y=";
+    hash = "sha256-pzxnrWkoPW7fpxLbUQ+drIrdrjqaAiNnDfe9ky2IxaA=";
   };
 
   patches = [
-    (fetchpatch {
-      name = "support-aarch64-linux.patch";
-      url = "https://github.com/3-manifolds/CyPari/commit/6197171b52ee4f44a4954ddd0e2e36769b189dee.patch";
-      hash = "sha256-j2P7DEGD2B8q9Hh4G2mQng76fQdUpeAdFYoTD7Ui/Dk=";
-    })
     (fetchpatch {
       name = "fix-build-with-cython-3_1.patch";
-      url = "https://github.com/3-manifolds/CyPari/compare/622e112ffcf0383e2110954ff3ac3c42c006ebe1...50bcbd2b39177f5e4c5a3551a8a14f75ab05a5d6.patch";
-      hash = "sha256-6ayvtHMS3YtzzklHaaLzl9d4zHJhm0lVZQZFS9ykFY4=";
+      url = "https://github.com/3-manifolds/CyPari/compare/17bf39dc4508f2e46de75b95c65982c627652b60...d6cb914d2bdc74a51cc2a9136204ebf47b3e7369.diff";
+      hash = "sha256-c8sq80mYSMMvgFh7RXYwKcqwI7iVRQsm/8yaIL0+PHQ=";
     })
   ];
 

From 807436d41820f321dd9c3569edd53c2c516b1df0 Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Mon, 9 Feb 2026 17:11:08 -0500
Subject: [PATCH 09/19] python3Packages.plink: add updateScript

---
 pkgs/development/python-modules/plink/default.nix | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/pkgs/development/python-modules/plink/default.nix b/pkgs/development/python-modules/plink/default.nix
index 63e47bf2828e7..668cba46ffecc 100644
--- a/pkgs/development/python-modules/plink/default.nix
+++ b/pkgs/development/python-modules/plink/default.nix
@@ -5,6 +5,7 @@
   setuptools,
   sphinx,
   tkinter,
+  nix-update-script,
 }:
 
 buildPythonPackage rec {
@@ -28,6 +29,13 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "plink" ];
 
+  passthru.updateScript = nix-update-script {
+    extraArgs = [
+      "--version-regex"
+      "(.*)_as_released"
+    ];
+  };
+
   meta = {
     description = "Full featured Tk-based knot and link editor";
     mainProgram = "plink";

From 4b8eb301f12f0333b56e9500a0b6266bb67f4016 Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Mon, 5 Jan 2026 17:11:35 -0600
Subject: [PATCH 10/19] python3Packages.plink: 2.4.6 -> 2.4.9

---
 pkgs/development/python-modules/plink/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/plink/default.nix b/pkgs/development/python-modules/plink/default.nix
index 668cba46ffecc..d2073d710d381 100644
--- a/pkgs/development/python-modules/plink/default.nix
+++ b/pkgs/development/python-modules/plink/default.nix
@@ -10,14 +10,14 @@
 
 buildPythonPackage rec {
   pname = "plink";
-  version = "2.4.6";
+  version = "2.4.9";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "3-manifolds";
     repo = "plink";
     tag = "${version}_as_released";
-    hash = "sha256-+WUyQvQY9Fx47GikzJ4gcCpSIjvk5756FP0bDdF6Ack=";
+    hash = "sha256-+O371oWfvRvMfjXX6qZj91c7+4MBneZFNcfdrJQNCY8=";
   };
 
   build-system = [

From 4200a820c2420526d9414567702f1c575ec8700c Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Mon, 9 Feb 2026 17:13:44 -0500
Subject: [PATCH 11/19] python3Packages.snappy-manifolds: add updateScript

---
 .../python-modules/snappy-manifolds/default.nix           | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/pkgs/development/python-modules/snappy-manifolds/default.nix b/pkgs/development/python-modules/snappy-manifolds/default.nix
index 277924130b7f7..d9d1fe69baa4d 100644
--- a/pkgs/development/python-modules/snappy-manifolds/default.nix
+++ b/pkgs/development/python-modules/snappy-manifolds/default.nix
@@ -3,6 +3,7 @@
   buildPythonPackage,
   fetchFromGitHub,
   setuptools,
+  nix-update-script,
 }:
 
 buildPythonPackage rec {
@@ -21,6 +22,13 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "snappy_manifolds" ];
 
+  passthru.updateScript = nix-update-script {
+    extraArgs = [
+      "--version-regex"
+      "(.*)_as_released"
+    ];
+  };
+
   meta = {
     description = "Database of snappy manifolds";
     changelog = "https://github.com/3-manifolds/snappy_manifolds/releases/tag/${src.tag}";

From 97b62f92c8ba93e4c43b596b35a114ae5372ca58 Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Mon, 5 Jan 2026 17:13:20 -0600
Subject: [PATCH 12/19] python3Packages.snappy-manifolds: 1.2.1 -> 1.4

---
 pkgs/development/python-modules/snappy-manifolds/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/snappy-manifolds/default.nix b/pkgs/development/python-modules/snappy-manifolds/default.nix
index d9d1fe69baa4d..8136174762bc8 100644
--- a/pkgs/development/python-modules/snappy-manifolds/default.nix
+++ b/pkgs/development/python-modules/snappy-manifolds/default.nix
@@ -8,14 +8,14 @@
 
 buildPythonPackage rec {
   pname = "snappy-manifolds";
-  version = "1.2.1";
+  version = "1.4";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "3-manifolds";
     repo = "snappy_manifolds";
     tag = "${version}_as_released";
-    hash = "sha256-vxG3z6zWzG4S11fBxYGn4/c2f2sWOCIrzT+R27TR144=";
+    hash = "sha256-e+BoPvg0cuEqLq2f9ZPgqFMEYw7eeSEDkY42+l+kDCk=";
   };
 
   build-system = [ setuptools ];

From b2a36cb64d7b0b97c128eaa1ebaf88121f79e4eb Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Mon, 9 Feb 2026 17:18:27 -0500
Subject: [PATCH 13/19] python3Packages.spherogram: add checkPhase

---
 .../python-modules/spherogram/default.nix       | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/python-modules/spherogram/default.nix b/pkgs/development/python-modules/spherogram/default.nix
index e71af95407416..1589a8520e0fb 100644
--- a/pkgs/development/python-modules/spherogram/default.nix
+++ b/pkgs/development/python-modules/spherogram/default.nix
@@ -1,14 +1,19 @@
 {
   lib,
-  buildPythonPackage,
   fetchFromGitHub,
+  python,
+  buildPythonPackage,
+
+  # build-time dependencies
   setuptools,
   cython,
-  networkx,
+
+  # runtime dependencies
   decorator,
   knot-floer-homology,
-  snappy-manifolds,
+  networkx,
   snappy-15-knots,
+  snappy-manifolds,
 }:
 
 buildPythonPackage rec {
@@ -39,6 +44,12 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "spherogram" ];
 
+  checkPhase = ''
+    runHook preCheck
+    ${python.interpreter} -m spherogram.test
+    runHook postCheck
+  '';
+
   meta = {
     description = "Spherical diagrams for 3-manifold topology";
     homepage = "https://snappy.computop.org/spherogram.html";

From ee41532961ffc08a8d4b79607c354fa1a4340e40 Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Tue, 10 Feb 2026 14:56:28 -0500
Subject: [PATCH 14/19] python3Packages.spherogram: add sage tests

see
https://github.com/3-manifolds/Spherogram/blob/2.4_as_released/.github/workflows/test.yml#L36
---
 .../python-modules/spherogram/default.nix     | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/pkgs/development/python-modules/spherogram/default.nix b/pkgs/development/python-modules/spherogram/default.nix
index 1589a8520e0fb..7af4b90c6cef7 100644
--- a/pkgs/development/python-modules/spherogram/default.nix
+++ b/pkgs/development/python-modules/spherogram/default.nix
@@ -14,6 +14,11 @@
   networkx,
   snappy-15-knots,
   snappy-manifolds,
+
+  # tests
+  runCommand,
+  sage,
+  writableTmpDirAsHomeHook,
 }:
 
 buildPythonPackage rec {
@@ -50,6 +55,25 @@ buildPythonPackage rec {
     runHook postCheck
   '';
 
+  passthru.tests.sage =
+    let
+      sage' = sage.override {
+        extraPythonPackages = ps: [ ps.spherogram ];
+        requireSageTests = false;
+      };
+    in
+    runCommand "spherogram-sage-tests"
+      {
+        nativeBuildInputs = [
+          sage'
+          writableTmpDirAsHomeHook
+        ];
+      }
+      ''
+        sage -python -m spherogram.test
+        touch $out
+      '';
+
   meta = {
     description = "Spherical diagrams for 3-manifold topology";
     homepage = "https://snappy.computop.org/spherogram.html";

From 957535786a80e38ede03d08246381c02d7782840 Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Tue, 10 Feb 2026 15:56:59 -0500
Subject: [PATCH 15/19] python3Packages.spherogram: add updateScript

---
 pkgs/development/python-modules/spherogram/default.nix | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/pkgs/development/python-modules/spherogram/default.nix b/pkgs/development/python-modules/spherogram/default.nix
index 7af4b90c6cef7..0c927931e6f26 100644
--- a/pkgs/development/python-modules/spherogram/default.nix
+++ b/pkgs/development/python-modules/spherogram/default.nix
@@ -3,6 +3,7 @@
   fetchFromGitHub,
   python,
   buildPythonPackage,
+  nix-update-script,
 
   # build-time dependencies
   setuptools,
@@ -74,6 +75,13 @@ buildPythonPackage rec {
         touch $out
       '';
 
+  passthru.updateScript = nix-update-script {
+    extraArgs = [
+      "--version-regex"
+      "(.*)_as_released"
+    ];
+  };
+
   meta = {
     description = "Spherical diagrams for 3-manifold topology";
     homepage = "https://snappy.computop.org/spherogram.html";

From f242b99ce753400a94010b94024f2f600fa10452 Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Tue, 10 Feb 2026 15:58:44 -0500
Subject: [PATCH 16/19] python3Packages.spherogram: 2.3 -> 2.4.1

---
 pkgs/development/python-modules/spherogram/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/spherogram/default.nix b/pkgs/development/python-modules/spherogram/default.nix
index 0c927931e6f26..a750664ab817a 100644
--- a/pkgs/development/python-modules/spherogram/default.nix
+++ b/pkgs/development/python-modules/spherogram/default.nix
@@ -24,14 +24,14 @@
 
 buildPythonPackage rec {
   pname = "spherogram";
-  version = "2.3";
+  version = "2.4.1";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "3-manifolds";
     repo = "spherogram";
     tag = "${version}_as_released";
-    hash = "sha256-uqc+3xS4xulXR0tZlNuyC5Zz5OztR6c4PZWpsvU+4Pw=";
+    hash = "sha256-zQoNuy2rj02GAuRNDufMwA/wQ4U8ZeIADb8LpIvMFOY=";
   };
 
   build-system = [

From ae0854e9dc621194b733b280acdcef7bb6a2b747 Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Sat, 10 Jan 2026 14:16:46 -0500
Subject: [PATCH 17/19] python3Packages.snappy: add sage tests

see
https://github.com/3-manifolds/SnapPy/blob/3.3_as_released/.github/workflows/sage_test.yml
---
 .../python-modules/snappy/default.nix         | 44 ++++++++++++++++---
 1 file changed, 38 insertions(+), 6 deletions(-)

diff --git a/pkgs/development/python-modules/snappy/default.nix b/pkgs/development/python-modules/snappy/default.nix
index b9927c1aeb8b2..7c733a29279ba 100644
--- a/pkgs/development/python-modules/snappy/default.nix
+++ b/pkgs/development/python-modules/snappy/default.nix
@@ -1,16 +1,22 @@
 {
   lib,
   stdenv,
-  fetchpatch,
+  fetchFromGitHub,
   python,
   buildPythonPackage,
-  fetchFromGitHub,
+  fetchpatch,
+
+  # build-time dependencies
   setuptools,
-  cypari,
   cython,
+
+  # non-Python runtime dependencies
+  libGL,
+
+  # Python runtime dependencies
+  cypari,
   fxrays,
   ipython,
-  libGL,
   low-index,
   packaging,
   pickleshare,
@@ -20,9 +26,16 @@
   snappy-15-knots,
   snappy-manifolds,
   spherogram,
+  tkinter-gl,
+
+  # documentation
   sphinxHook,
   sphinx-rtd-theme,
-  tkinter-gl,
+
+  # tests
+  runCommand,
+  sage,
+  writableTmpDirAsHomeHook,
 }:
 
 buildPythonPackage rec {
@@ -58,7 +71,7 @@ buildPythonPackage rec {
   postPatch =
     lib.optionalString stdenv.hostPlatform.isLinux ''
       substituteInPlace setup.py \
-        --replace-fail "/usr/include/GL" "${libGL.dev}/include/GL"
+        --replace-fail "/usr/include/GL" "${lib.getDev libGL}/include/GL"
       substituteInPlace freedesktop/share/applications/snappy.desktop \
         --replace-fail "Exec=/usr/bin/env python3 -m snappy.app" "Exec=SnapPy"
     ''
@@ -117,6 +130,25 @@ buildPythonPackage rec {
     runHook postCheck
   '';
 
+  passthru.tests.sage =
+    let
+      sage' = sage.override {
+        extraPythonPackages = ps: [ ps.snappy ];
+        requireSageTests = false;
+      };
+    in
+    runCommand "snappy-sage-tests"
+      {
+        nativeBuildInputs = [
+          sage'
+          writableTmpDirAsHomeHook
+        ];
+      }
+      ''
+        sage -python -m snappy.test --skip-gui
+        touch $out
+      '';
+
   meta = {
     description = "Studying the topology and geometry of 3-manifolds, with a focus on hyperbolic structures";
     changelog = "https://snappy.computop.org/news.html";

From 180adfe6969ab198aa3a97a9a83d0d2af4662f4a Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Mon, 9 Feb 2026 17:24:59 -0500
Subject: [PATCH 18/19] python3Packages.snappy: add updateScript

---
 pkgs/development/python-modules/snappy/default.nix | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/pkgs/development/python-modules/snappy/default.nix b/pkgs/development/python-modules/snappy/default.nix
index 7c733a29279ba..4a83665023dbf 100644
--- a/pkgs/development/python-modules/snappy/default.nix
+++ b/pkgs/development/python-modules/snappy/default.nix
@@ -5,6 +5,7 @@
   python,
   buildPythonPackage,
   fetchpatch,
+  nix-update-script,
 
   # build-time dependencies
   setuptools,
@@ -149,6 +150,13 @@ buildPythonPackage rec {
         touch $out
       '';
 
+  passthru.updateScript = nix-update-script {
+    extraArgs = [
+      "--version-regex"
+      "(.*)_as_released"
+    ];
+  };
+
   meta = {
     description = "Studying the topology and geometry of 3-manifolds, with a focus on hyperbolic structures";
     changelog = "https://snappy.computop.org/news.html";

From b24794f9dc3d62d5d4a74a7da3b4a6d1319d1cce Mon Sep 17 00:00:00 2001
From: Alex Epelde <alex@epelde.net>
Date: Mon, 5 Jan 2026 17:13:34 -0600
Subject: [PATCH 19/19] python3Packages.snappy: 3.2 -> 3.3.2

---
 pkgs/development/python-modules/snappy/default.nix | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/pkgs/development/python-modules/snappy/default.nix b/pkgs/development/python-modules/snappy/default.nix
index 4a83665023dbf..886f52f385b0c 100644
--- a/pkgs/development/python-modules/snappy/default.nix
+++ b/pkgs/development/python-modules/snappy/default.nix
@@ -41,7 +41,7 @@
 
 buildPythonPackage rec {
   pname = "snappy";
-  version = "3.2";
+  version = "3.3.2";
   pyproject = true;
 
   outputs = [
@@ -53,7 +53,7 @@ buildPythonPackage rec {
     owner = "3-manifolds";
     repo = "SnapPy";
     tag = "${version}_as_released";
-    hash = "sha256-IwPxuyVDsL5yML+J06HTKlz52sYrPkohLJ0XDXDwTlo=";
+    hash = "sha256-Pl4Nl0LXNvdtQ/EFVQy0QdUA/Fqoz2QAFWW5nz0bv78=";
   };
 
   patches = [
@@ -62,11 +62,6 @@ buildPythonPackage rec {
       url = "https://github.com/3-manifolds/SnapPy/commit/c6aeeaaec7010a54e4ebdf2e8dad7b384c2ce8e5.patch";
       hash = "sha256-OV3Qr5wO5UHNzVFTPTujIpp5ptel6gvAlcMgrJ8C0KY=";
     })
-    (fetchpatch {
-      name = "fix-test-aarch64.patch";
-      url = "https://github.com/3-manifolds/SnapPy/commit/a8d57db39bc8f486746dc61027779168d0bc316a.patch";
-      hash = "sha256-RsuwaR+7UrVTKlPwQeHblTAN++La7b9BSMdFcJSiX5Q=";
-    })
   ];
 
   postPatch =