python3Packages.snappy: 3.2 -> 3.3.2, modernise

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 ''
@@ -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
+    ];
   };
 }

pkgs/development/python-modules/cypari/default.nix

@@ -1,45 +1,60 @@
 {
   lib,
+  fetchFromGitHub,
   python,
   buildPythonPackage,
-  fetchFromGitHub,
+  nix-update-script,
+  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 {
   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=";
     })
   ];
 
   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 = [
@@ -59,14 +74,21 @@ 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";
+    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}";
   };
 }

pkgs/development/python-modules/plink/default.nix

@@ -5,18 +5,19 @@
   setuptools,
   sphinx,
   tkinter,
+  nix-update-script,
 }:
 
 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 = [
@@ -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";

pkgs/development/python-modules/snappy-manifolds/default.nix

@@ -3,24 +3,32 @@
   buildPythonPackage,
   fetchFromGitHub,
   setuptools,
+  nix-update-script,
 }:
 
 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 ];
 
   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}";

pkgs/development/python-modules/snappy/default.nix

@@ -1,16 +1,23 @@
 {
   lib,
   stdenv,
-  fetchpatch,
+  fetchFromGitHub,
   python,
   buildPythonPackage,
-  fetchFromGitHub,
+  fetchpatch,
+  nix-update-script,
+
+  # build-time dependencies
   setuptools,
-  cypari,
   cython,
+
+  # non-Python runtime dependencies
+  libGL,
+
+  # Python runtime dependencies
+  cypari,
   fxrays,
   ipython,
-  libGL,
   low-index,
   packaging,
   pickleshare,
@@ -20,14 +27,21 @@
   snappy-15-knots,
   snappy-manifolds,
   spherogram,
+  tkinter-gl,
+
+  # documentation
   sphinxHook,
   sphinx-rtd-theme,
-  tkinter-gl,
+
+  # tests
+  runCommand,
+  sage,
+  writableTmpDirAsHomeHook,
 }:
 
 buildPythonPackage rec {
   pname = "snappy";
-  version = "3.2";
+  version = "3.3.2";
   pyproject = true;
 
   outputs = [
@@ -39,7 +53,7 @@ buildPythonPackage rec {
     owner = "3-manifolds";
     repo = "SnapPy";
     tag = "${version}_as_released";
-    hash = "sha256-IwPxuyVDsL5yML+J06HTKlz52sYrPkohLJ0XDXDwTlo=";
+    hash = "sha256-Pl4Nl0LXNvdtQ/EFVQy0QdUA/Fqoz2QAFWW5nz0bv78=";
   };
 
   patches = [
@@ -48,17 +62,12 @@ 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 =
     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 +126,32 @@ 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
+      '';
+
+  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";

pkgs/development/python-modules/spherogram/default.nix

@@ -1,26 +1,37 @@
 {
   lib,
-  buildPythonPackage,
   fetchFromGitHub,
+  python,
+  buildPythonPackage,
+  nix-update-script,
+
+  # build-time dependencies
   setuptools,
   cython,
-  networkx,
+
+  # runtime dependencies
   decorator,
   knot-floer-homology,
-  snappy-manifolds,
+  networkx,
   snappy-15-knots,
+  snappy-manifolds,
+
+  # tests
+  runCommand,
+  sage,
+  writableTmpDirAsHomeHook,
 }:
 
 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 = [
@@ -39,6 +50,38 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "spherogram" ];
 
+  checkPhase = ''
+    runHook preCheck
+    ${python.interpreter} -m spherogram.test
+    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
+      '';
+
+  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";