From 3881e06a538c57c2a013caa356b6d9beb45380f2 Mon Sep 17 00:00:00 2001
From: Simon Hauser <simon.hauser@helsinki-systems.de>
Date: Mon, 30 Sep 2024 09:24:52 +0200
Subject: [PATCH] libsbml: 5.20.2 -> 5.20.4 and add python support (#344137)

Changelog: https://github.com/sbmlteam/libsbml/releases/tag/v5.20.4
---
 pkgs/by-name/li/libsbml/package.nix | 30 ++++++++++++++---------------
 pkgs/top-level/python-packages.nix  |  4 ++++
 2 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/pkgs/by-name/li/libsbml/package.nix b/pkgs/by-name/li/libsbml/package.nix
index 513e72f322bc..9fbb674f5d62 100644
--- a/pkgs/by-name/li/libsbml/package.nix
+++ b/pkgs/by-name/li/libsbml/package.nix
@@ -2,43 +2,35 @@
   lib,
   stdenv,
   fetchFromGitHub,
-  fetchpatch,
   cmake,
   pkg-config,
   bzip2,
   libxml2,
   swig,
+  python ? null,
+  withPython ? false,
 }:
 stdenv.mkDerivation (attrs: {
   pname = "libsbml";
-  version = "5.20.2";
+  version = "5.20.4";
 
   src = fetchFromGitHub {
     owner = "sbmlteam";
     repo = "libsbml";
     rev = "v${attrs.version}";
-    hash = "sha256-8JT2r0zuf61VewtZaOAccaOUmDlQPnllA0fXE9rT5X8=";
+    hash = "sha256-qWTN033YU4iWzt+mXQaP5W/6IF5nebF4PwNVkyL8wTg=";
   };
 
-  patches = [
-    # This should be in next release, remember to remove fetchpatch
-    (fetchpatch { # https://github.com/sbmlteam/libsbml/pull/358
-      name = "fix-xmlerror-conversion.patch";
-      url = "https://github.com/sbmlteam/libsbml/commit/de2f77ee6766fe933a1472200f5e08e7c5ba6f8c.patch";
-      hash = "sha256-uirG6XJ+w0hqBUEAGDnzhHoVtJVRdN1eqBYeneKMBao=";
-    })
-  ];
-
   nativeBuildInputs = [
     cmake
     pkg-config
     swig
-  ];
+  ] ++ lib.optional withPython python.pkgs.pythonImportsCheckHook;
 
   buildInputs = [
     bzip2.dev
     libxml2
-  ];
+  ] ++ lib.optional withPython python;
 
   # libSBML doesn't always make use of pkg-config
   cmakeFlags = [
@@ -46,13 +38,19 @@ stdenv.mkDerivation (attrs: {
     "-DLIBXML_LIBRARY=${lib.getLib libxml2}/lib/libxml2${stdenv.hostPlatform.extensions.sharedLibrary}"
     "-DPKG_CONFIG_EXECUTABLE=${lib.getBin pkg-config}/bin/pkg-config"
     "-DSWIG_EXECUTABLE=${lib.getBin swig}/bin/swig"
-  ];
+  ] ++ lib.optional withPython "-DWITH_PYTHON=ON";
+
+  postInstall = lib.optional withPython ''
+    mv $out/${python.sitePackages}/libsbml/libsbml.py $out/${python.sitePackages}/libsbml/__init__.py
+  '';
+
+  pythonImportsCheck = [ "libsbml" ];
 
   meta = with lib; {
     description = "Library for manipulating Systems Biology Markup Language (SBML)";
     homepage = "https://github.com/sbmlteam/libsbml";
     license = licenses.lgpl21Only;
-    maintainers = [maintainers.kupac];
+    maintainers = [ maintainers.kupac ];
     platforms = platforms.all;
   };
 })
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 6a22ba955f59..567c5866bc37 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -7132,6 +7132,10 @@ self: super: with self; {
 
   libsavitar = callPackage ../development/python-modules/libsavitar { };
 
+  libsbml = toPythonModule (pkgs.libsbml.override {
+    withPython = true;
+    inherit (self) python;
+  });
 
   libsixel = callPackage ../development/python-modules/libsixel {
     inherit (pkgs) libsixel;