diff --git a/pkgs/development/python-modules/cypari/default.nix b/pkgs/development/python-modules/cypari/default.nix
new file mode 100644
index 000000000000..da8e988829ad
--- /dev/null
+++ b/pkgs/development/python-modules/cypari/default.nix
@@ -0,0 +1,80 @@
+{
+  lib,
+  python,
+  buildPythonPackage,
+  fetchFromGitHub,
+  fetchurl,
+  setuptools,
+  cython,
+  bash,
+  perl,
+  gnum4,
+  texliveBasic,
+}:
+
+let
+  pariVersion = "2.15.4";
+  gmpVersion = "6.3.0";
+
+  pariSrc = fetchurl {
+    url = "https://pari.math.u-bordeaux.fr/pub/pari/OLD/${lib.versions.majorMinor pariVersion}/pari-${pariVersion}.tar.gz";
+    hash = "sha256-w1Rb/uDG37QLd/tLurr5mdguYAabn20ovLbPAEyMXA8=";
+  };
+
+  gmpSrc = fetchurl {
+    url = "https://ftp.gnu.org/gnu/gmp/gmp-${gmpVersion}.tar.bz2";
+    hash = "sha256-rCghGnz7YJuuLiyNYFjWbI/pZDT3QM9v4uR7AA0cIMs=";
+  };
+in
+buildPythonPackage rec {
+  pname = "cypari";
+  version = "2.5.5";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "3-manifolds";
+    repo = "CyPari";
+    tag = "${version}_as_released";
+    hash = "sha256-RJ9O1KsDHmMkTCIFUrcSUkA5ijTsxmoI939QCsCib0Y=";
+  };
+
+  postPatch = ''
+    substituteInPlace ./setup.py \
+      --replace-fail "/bin/bash" "${lib.getExe bash}"
+    # final character is stripped from PARI error messages for some reason
+    substituteInPlace ./cypari/handle_error.pyx \
+      --replace-fail "not a function in function call" "not a function in function cal"
+    ln -s ${pariSrc} ${pariSrc.name}
+    ln -s ${gmpSrc} ${gmpSrc.name}
+  '';
+
+  build-system = [
+    setuptools
+    cython
+  ];
+
+  NIX_LDFLAGS = "-lc";
+
+  nativeBuildInputs = [
+    gnum4
+    perl
+    texliveBasic
+  ];
+
+  pythonImportsCheck = [ "cypari" ];
+
+  checkPhase = ''
+    runHook preCheck
+    rm -r cypari
+    ${python.interpreter} -m cypari.test
+    runHook postCheck
+  '';
+
+  meta = {
+    description = "Sage's PARI extension, modified to stand alone";
+    homepage = "https://github.com/3-manifolds/CyPari";
+    license = lib.licenses.gpl2Plus;
+    maintainers = with lib.maintainers; [ noiioiu ];
+    changelog = "https://github.com/3-manifolds/CyPari/releases/tag/${src.tag}";
+  };
+}
diff --git a/pkgs/development/python-modules/fxrays/default.nix b/pkgs/development/python-modules/fxrays/default.nix
new file mode 100644
index 000000000000..b7859e624117
--- /dev/null
+++ b/pkgs/development/python-modules/fxrays/default.nix
@@ -0,0 +1,42 @@
+{
+  lib,
+  python,
+  buildPythonPackage,
+  fetchFromGitHub,
+  setuptools,
+  cython,
+}:
+
+buildPythonPackage rec {
+  pname = "fxrays";
+  version = "1.3.6";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "3-manifolds";
+    repo = "FXrays";
+    tag = "${version}_as_released";
+    hash = "sha256-IwEY54zDXqMci7WRvhueDJidTsbMwv6eqQSGZzFOtnQ";
+  };
+
+  build-system = [
+    setuptools
+    cython
+  ];
+
+  pythonImportsCheck = [ "FXrays" ];
+
+  checkPhase = ''
+    runHook preCheck
+    ${python.interpreter} -m FXrays.test
+    runHook postCheck
+  '';
+
+  meta = {
+    description = "Computes extremal rays of polyhedral cones with filtering";
+    changelog = "https://github.com/3-manifolds/FXrays/releases/tag/${src.tag}";
+    homepage = "https://github.com/3-manifolds/FXrays";
+    license = lib.licenses.gpl2Plus;
+    maintainers = with lib.maintainers; [ noiioiu ];
+  };
+}
diff --git a/pkgs/development/python-modules/knot-floer-homology/default.nix b/pkgs/development/python-modules/knot-floer-homology/default.nix
new file mode 100644
index 000000000000..b483f3146bf3
--- /dev/null
+++ b/pkgs/development/python-modules/knot-floer-homology/default.nix
@@ -0,0 +1,42 @@
+{
+  lib,
+  python,
+  buildPythonPackage,
+  fetchFromGitHub,
+  setuptools,
+  cython,
+}:
+
+buildPythonPackage rec {
+  pname = "knot-floer-homology";
+  version = "1.2.2";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "3-manifolds";
+    repo = "knot_floer_homology";
+    tag = "${version}_as_released";
+    hash = "sha256-Gw9k9AaUVTBzE+ERUH8VgS//aVT03DdKozpL8xLG4No=";
+  };
+
+  build-system = [
+    setuptools
+    cython
+  ];
+
+  pythonImportsCheck = [ "knot_floer_homology" ];
+
+  checkPhase = ''
+    runHook preCheck
+    ${python.interpreter} -m knot_floer_homology.test
+    runHook postCheck
+  '';
+
+  meta = {
+    description = "Python wrapper for Zoltán Szabó's HFK Calculator";
+    changelog = "https://github.com/3-manifolds/knot_floer_homology/releases/tag/${src.tag}";
+    homepage = "https://github.com/3-manifolds/knot_floer_homology";
+    license = lib.licenses.gpl2Plus;
+    maintainers = with lib.maintainers; [ noiioiu ];
+  };
+}
diff --git a/pkgs/development/python-modules/low-index/default.nix b/pkgs/development/python-modules/low-index/default.nix
new file mode 100644
index 000000000000..7d21f3602b02
--- /dev/null
+++ b/pkgs/development/python-modules/low-index/default.nix
@@ -0,0 +1,38 @@
+{
+  lib,
+  python,
+  buildPythonPackage,
+  fetchFromGitHub,
+  setuptools,
+}:
+
+buildPythonPackage rec {
+  pname = "low-index";
+  version = "1.2.1";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "3-manifolds";
+    repo = "low_index";
+    tag = "v${version}_as_released";
+    hash = "sha256-T8hzC9ulikQ1pUdbXgjuKAX5oMJEycPvXWv74rCkQGY=";
+  };
+
+  build-system = [ setuptools ];
+
+  pythonImportsCheck = [ "low_index" ];
+
+  checkPhase = ''
+    runHook preCheck
+    ${python.interpreter} -m low_index.test
+    runHook postCheck
+  '';
+
+  meta = {
+    description = "Enumerates low index subgroups of a finitely presented group";
+    changelog = "https://github.com/3-manifolds/low_index/releases/tag/${src.tag}";
+    homepage = "https://github.com/3-manifolds/low_index";
+    license = lib.licenses.gpl2Plus;
+    maintainers = with lib.maintainers; [ noiioiu ];
+  };
+}
diff --git a/pkgs/development/python-modules/plink/default.nix b/pkgs/development/python-modules/plink/default.nix
new file mode 100644
index 000000000000..062d438058a4
--- /dev/null
+++ b/pkgs/development/python-modules/plink/default.nix
@@ -0,0 +1,39 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  setuptools,
+  sphinx,
+  tkinter,
+}:
+
+buildPythonPackage rec {
+  pname = "plink";
+  version = "2.4.6";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "3-manifolds";
+    repo = "plink";
+    tag = "${version}_as_released";
+    hash = "sha256-+WUyQvQY9Fx47GikzJ4gcCpSIjvk5756FP0bDdF6Ack=";
+  };
+
+  build-system = [
+    setuptools
+    sphinx
+  ];
+
+  dependencies = [ tkinter ];
+
+  pythonImportsCheck = [ "plink" ];
+
+  meta = {
+    description = "Full featured Tk-based knot and link editor";
+    mainProgram = "plink";
+    homepage = "https://3-manifolds.github.io/PLink";
+    changelog = "https://github.com/3-manifolds/PLink/releases/tag/${src.tag}";
+    license = lib.licenses.gpl2Plus;
+    maintainers = with lib.maintainers; [ noiioiu ];
+  };
+}
diff --git a/pkgs/development/python-modules/snappy-15-knots/default.nix b/pkgs/development/python-modules/snappy-15-knots/default.nix
new file mode 100644
index 000000000000..ec26a0bc8534
--- /dev/null
+++ b/pkgs/development/python-modules/snappy-15-knots/default.nix
@@ -0,0 +1,34 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  setuptools,
+  snappy-manifolds,
+}:
+
+buildPythonPackage rec {
+  pname = "snappy-15-knots";
+  version = "1.2.1";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "3-manifolds";
+    repo = "snappy_15_knots";
+    tag = "${version}_as_released";
+    hash = "sha256-fhJhHZFf4XuW/0V6LOuV4qoFWke3oFP0KArDpXLWh9g=";
+  };
+
+  build-system = [ setuptools ];
+
+  dependencies = [ snappy-manifolds ];
+
+  pythonImportsCheck = [ "snappy_15_knots" ];
+
+  meta = with lib; {
+    description = "Database of snappy manifolds";
+    homepage = "https://snappy.computop.org";
+    changelog = "https://github.com/3-manifolds/snappy_15_knots/releases/tag/${src.tag}";
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ noiioiu ];
+  };
+}
diff --git a/pkgs/development/python-modules/snappy-manifolds/default.nix b/pkgs/development/python-modules/snappy-manifolds/default.nix
new file mode 100644
index 000000000000..b5fb336f3b63
--- /dev/null
+++ b/pkgs/development/python-modules/snappy-manifolds/default.nix
@@ -0,0 +1,31 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  setuptools,
+}:
+
+buildPythonPackage rec {
+  pname = "snappy-manifolds";
+  version = "1.2.1";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "3-manifolds";
+    repo = "snappy_manifolds";
+    tag = "${version}_as_released";
+    hash = "sha256-vxG3z6zWzG4S11fBxYGn4/c2f2sWOCIrzT+R27TR144=";
+  };
+
+  build-system = [ setuptools ];
+
+  pythonImportsCheck = [ "snappy_manifolds" ];
+
+  meta = {
+    description = "Database of snappy manifolds";
+    changelog = "https://github.com/3-manifolds/snappy_manifolds/releases/tag/${src.tag}";
+    homepage = "https://snappy.computop.org";
+    license = lib.licenses.gpl2Plus;
+    maintainers = with lib.maintainers; [ noiioiu ];
+  };
+}
diff --git a/pkgs/development/python-modules/spherogram/default.nix b/pkgs/development/python-modules/spherogram/default.nix
new file mode 100644
index 000000000000..0e4a3da679d5
--- /dev/null
+++ b/pkgs/development/python-modules/spherogram/default.nix
@@ -0,0 +1,49 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  setuptools,
+  cython,
+  networkx,
+  decorator,
+  knot-floer-homology,
+  snappy-manifolds,
+  snappy-15-knots,
+}:
+
+buildPythonPackage rec {
+  pname = "spherogram";
+  version = "2.3";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "3-manifolds";
+    repo = "spherogram";
+    tag = "${version}_as_released";
+    hash = "sha256-uqc+3xS4xulXR0tZlNuyC5Zz5OztR6c4PZWpsvU+4Pw=";
+  };
+
+  build-system = [
+    setuptools
+    cython
+  ];
+
+  dependencies = [
+    networkx
+    decorator
+    snappy-manifolds
+    knot-floer-homology
+  ];
+
+  optional-dependencies.snappy-15-knots = [ snappy-15-knots ];
+
+  pythonImportsCheck = [ "spherogram" ];
+
+  meta = {
+    description = "Spherical diagrams for 3-manifold topology";
+    homepage = "https://snappy.computop.org/spherogram.html";
+    changelog = "https://github.com/3-manifolds/Spherogram/releases/tag/${src.tag}";
+    license = lib.licenses.gpl2Plus;
+    maintainers = with lib.maintainers; [ noiioiu ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index f8dd181768fa..1aa45ee6272e 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -3138,6 +3138,8 @@ self: super: with self; {
 
   cynthion = callPackage ../development/python-modules/cynthion { };
 
+  cypari = callPackage ../development/python-modules/cypari { };
+
   cypari2 = callPackage ../development/python-modules/cypari2 { };
 
   cypherpunkpay = callPackage ../development/python-modules/cypherpunkpay { };
@@ -5442,6 +5444,8 @@ self: super: with self; {
 
   fx2 = callPackage ../development/python-modules/fx2 { };
 
+  fxrays = callPackage ../development/python-modules/fxrays { };
+
   fyta-cli = callPackage ../development/python-modules/fyta-cli { };
 
   g2pkk = callPackage ../development/python-modules/g2pkk { };
@@ -7590,6 +7594,8 @@ self: super: with self; {
 
   knocki = callPackage ../development/python-modules/knocki { };
 
+  knot-floer-homology = callPackage ../development/python-modules/knot-floer-homology { };
+
   knx-frontend = callPackage ../development/python-modules/knx-frontend { };
 
   kombu = callPackage ../development/python-modules/kombu { };
@@ -8473,6 +8479,8 @@ self: super: with self; {
 
   lottie = callPackage ../development/python-modules/lottie { };
 
+  low-index = callPackage ../development/python-modules/low-index { };
+
   lox = callPackage ../development/python-modules/lox { };
 
   lpc-checksum = callPackage ../development/python-modules/lpc-checksum { };
@@ -11455,6 +11463,8 @@ self: super: with self; {
 
   plfit = toPythonModule (pkgs.plfit.override { inherit (self) python; });
 
+  plink = callPackage ../development/python-modules/plink { };
+
   plone-testing = callPackage ../development/python-modules/plone-testing { };
 
   ploomber-core = callPackage ../development/python-modules/ploomber-core { };
@@ -16317,6 +16327,10 @@ self: super: with self; {
 
   snapcast = callPackage ../development/python-modules/snapcast { };
 
+  snappy-15-knots = callPackage ../development/python-modules/snappy-15-knots { };
+
+  snappy-manifolds = callPackage ../development/python-modules/snappy-manifolds { };
+
   snapshottest = callPackage ../development/python-modules/snapshottest { };
 
   snaptime = callPackage ../development/python-modules/snaptime { };
@@ -16483,6 +16497,8 @@ self: super: with self; {
 
   spglib = callPackage ../development/python-modules/spglib { };
 
+  spherogram = callPackage ../development/python-modules/spherogram { };
+
   sphfile = callPackage ../development/python-modules/sphfile { };
 
   sphinx = callPackage ../development/python-modules/sphinx { };