openbabel: unstable-06-12-23 -> 3.1.1-unstable-2024-12-21

Diff: https://github.com/openbabel/openbabel/compare/32cf131444c1555c749b356dab44fb9fe275271f...889c350feb179b43aa43985799910149d4eaa2bc

pkgs/by-name/op/openbabel/package.nix

@@ -3,6 +3,7 @@
   lib,
   fetchFromGitHub,
   cmake,
+  ninja,
   perl,
   zlib,
   libxml2,
@@ -17,20 +18,24 @@
   coordgenlibs,
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "openbabel";
-  version = "unstable-06-12-23";
+  version = "3.1.1-unstable-2024-12-21";
 
   src = fetchFromGitHub {
     owner = "openbabel";
-    repo = pname;
-    rev = "32cf131444c1555c749b356dab44fb9fe275271f";
-    hash = "sha256-V0wrZVrojCZ9Knc5H6cPzPoYWVosRZ6Sn4PX+UFEfHY=";
+    repo = "openbabel";
+    rev = "889c350feb179b43aa43985799910149d4eaa2bc";
+    hash = "sha256-pJbvKBjpvXNjTZRxD2AqEarqmq+Pq08uvGvog/k/a7k=";
   };
 
-  postPatch = ''
-    sed '1i#include <ctime>' -i include/openbabel/obutil.h # gcc12
-  '';
+
+  nativeBuildInputs = [
+    cmake
+    ninja
+    swig
+    pkg-config
+  ];
 
   buildInputs = [
     perl
@@ -45,40 +50,17 @@ stdenv.mkDerivation rec {
     coordgenlibs
   ];
 
-  nativeBuildInputs = [
-    cmake
-    swig
-    pkg-config
+  cmakeFlags = [
+    (lib.cmakeBool "RUN_SWIG" true)
+    (lib.cmakeBool "PYTHON_BINDINGS" true)
+    (lib.cmakeFeature "PYTHON_INSTDIR" "${placeholder "out"}/${python3.sitePackages}")
   ];
 
-  preConfigure = ''
-    cmakeFlagsArray+=(
-      "-DRUN_SWIG=ON"
-      "-DPYTHON_BINDINGS=ON"
-      "-DPYTHON_INSTDIR=$out/${python3.sitePackages}"
-    )
-  '';
-
-  # Setuptools only accepts PEP 440 version strings. The "unstable" identifier
-  # can not be used. Instead we pretend to be the 3.2 beta release.
-  postFixup = ''
-    cat << EOF > $out/${python3.sitePackages}/setup.py
-    from setuptools import setup
-
-    setup(
-        name = 'pyopenbabel',
-        version = '3.2b1',
-        packages = ['openbabel'],
-        package_data = {'openbabel' : ['_openbabel.so']}
-    )
-    EOF
-  '';
-
-  meta = with lib; {
+  meta = {
     description = "Toolbox designed to speak the many languages of chemical data";
     homepage = "http://openbabel.org";
-    platforms = platforms.all;
-    license = licenses.gpl2Plus;
-    maintainers = with maintainers; [ danielbarter ];
+    platforms = lib.platforms.all;
+    license = lib.licenses.gpl2Plus;
+    maintainers = with lib.maintainers; [ danielbarter ];
   };
 }

pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix

@@ -20,7 +20,7 @@
 let
   pythonWP = python3.withPackages (
     p: with p; [
-      openbabel-bindings
+      openbabel
       numpy
     ]
   );

pkgs/development/python-modules/openbabel-bindings/default.nix

@@ -1,32 +0,0 @@
-{
-  lib,
-  openbabel,
-  python,
-  buildPythonPackage,
-}:
-
-buildPythonPackage {
-  format = "setuptools";
-  inherit (openbabel) pname version;
-
-  src = "${openbabel}/${python.sitePackages}";
-
-  buildInputs = [ openbabel ];
-
-  # these env variables are used by the bindings to find libraries
-  # they need to be included explicitly in your nix-shell for
-  # some functionality to work (inparticular, pybel).
-  # see https://openbabel.org/docs/dev/Installation/install.html
-  BABEL_LIBDIR = "${openbabel}/lib/openbabel/3.1.0";
-  LD_LIBRARY_PATH = "${openbabel}/lib";
-
-  doCheck = false;
-  pythonImportsCheck = [ "openbabel" ];
-
-  meta = with lib; {
-    homepage = "http://openbabel.org/wiki/Main_Page";
-    description = "Python bindings for openbabel";
-    license = licenses.gpl2Plus;
-    maintainers = with maintainers; [ danielbarter ];
-  };
-}

pkgs/top-level/python-aliases.nix

@@ -494,6 +494,7 @@ mapAliases ({
   openai-triton-cuda = triton-cuda; # added 2024-07-18
   openai-triton-no-cuda = triton-no-cuda; # added 2024-07-18
   openapi-schema-pydantic = throw "openapi-schema-pydantic has been removed, since it is no longer maintained"; # added 2023-10-30
+  openbabel-bindings = openbabel; # added 2025-09-17
   opencv3 = throw "opencv3 has been removed as it is obsolete"; # added 2023-10-12
   openllm = throw "openllm has moved to pkgs.openllm"; # added 2021-12-31
   openllm-client = throw "openllm-client has been removed, since it is abandoned due to a change in philosophy"; # added 2024-08-24

pkgs/top-level/python-packages.nix

@@ -10934,9 +10934,7 @@ self: super: with self; {
 
   openapi3 = callPackage ../development/python-modules/openapi3 { };
 
-  openbabel-bindings = callPackage ../development/python-modules/openbabel-bindings {
-    openbabel = pkgs.openbabel.override { python3 = python; };
-  };
+  openbabel = toPythonModule (pkgs.openbabel.override { python3 = python; });
 
   opencamlib = callPackage ../development/python-modules/opencamlib { };