Merge pull request #107845 from danielbarter/openbabel3

maintainers/maintainer-list.nix

@@ -2037,6 +2037,12 @@
     githubId = 23366017;
     name = "Dan Haraj";
   };
+  danielbarter = {
+    email = "danielbarter@gmail.com";
+    github = "danielbarter";
+    githubId = 8081722;
+    name = "Daniel Barter";
+  };
   danieldk = {
     email = "me@danieldk.eu";
     github = "danieldk";

pkgs/applications/science/chemistry/avogadro/default.nix

@@ -21,9 +21,9 @@ stdenv.mkDerivation rec {
     })
   ];
 
-  meta = {
+  meta = with lib; {
     description = "Molecule editor and visualizer";
-    maintainers = [ ];
+    maintainers = with maintainers; [ danielbarter ];
-    platforms = lib.platforms.mesaPlatforms;
+    platforms = platforms.mesaPlatforms;
   };
 }

pkgs/development/libraries/openbabel/2.nix

@@ -0,0 +1,31 @@
+{stdenv, lib, fetchurl, fetchpatch, cmake, zlib, libxml2, eigen, python, cairo, pcre, pkg-config }:
+
+stdenv.mkDerivation rec {
+  pname = "openbabel";
+  version = "2.4.1";
+
+  src = fetchurl {
+    url = "https://github.com/openbabel/openbabel/archive/openbabel-${stdenv.lib.replaceStrings ["."] ["-"] version}.tar.gz";
+    sha256 = "0xm7y859ivq2cp0q08mwshfxm0jq31xkyr4x8s0j6l7khf57yk2r";
+  };
+
+  patches = [
+    # ARM / AArch64 fixes.
+    (fetchpatch {
+      url = "https://github.com/openbabel/openbabel/commit/ee11c98a655296550710db1207b294f00e168216.patch";
+      sha256 = "0wjqjrkr4pfirzzicdvlyr591vppydk572ix28jd2sagnfnf566g";
+    })
+  ];
+
+  buildInputs = [ zlib libxml2 eigen python cairo pcre ];
+
+  nativeBuildInputs = [ cmake pkg-config ];
+
+  meta = with lib; {
+    description = "A toolbox designed to speak the many languages of chemical data";
+    homepage = "http://openbabel.org";
+    platforms = platforms.all;
+    maintainers = with maintainers; [ danielbarter ];
+    license = licenses.gpl2Plus;
+  };
+}

pkgs/development/libraries/openbabel/default.nix

@@ -1,34 +1,45 @@
-{stdenv, fetchurl, fetchpatch, cmake, zlib, libxml2, eigen, python, cairo, pcre, pkgconfig }:
+{stdenv, lib, fetchurl, cmake, zlib, libxml2, eigen, python, cairo, pcre, pkg-config, swig, rapidjson }:
 
 stdenv.mkDerivation rec {
   pname = "openbabel";
-  version = "2.4.1";
+  version = "3.1.1";
 
   src = fetchurl {
     url = "https://github.com/openbabel/openbabel/archive/openbabel-${stdenv.lib.replaceStrings ["."] ["-"] version}.tar.gz";
-    sha256 = "0xm7y859ivq2cp0q08mwshfxm0jq31xkyr4x8s0j6l7khf57yk2r";
+    sha256 = "c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02";
   };
 
-  patches = [
+
-    # ARM / AArch64 fixes.
+  buildInputs = [ zlib libxml2 eigen python cairo pcre swig rapidjson ];
-    (fetchpatch {
+
-      url = "https://github.com/openbabel/openbabel/commit/ee11c98a655296550710db1207b294f00e168216.patch";
+  nativeBuildInputs = [ cmake pkg-config ];
-      sha256 = "0wjqjrkr4pfirzzicdvlyr591vppydk572ix28jd2sagnfnf566g";
+
-    })
+  pythonMajorMinor = "${python.sourceVersion.major}.${python.sourceVersion.minor}";
+
+  cmakeFlags = [
+    "-DRUN_SWIG=ON"
+    "-DPYTHON_BINDINGS=ON"
   ];
 
-  # TODO : perl & python bindings;
-  # TODO : wxGTK: I have no time to compile
-  # TODO : separate lib and apps
-  buildInputs = [ zlib libxml2 eigen python cairo pcre ];
 
-  nativeBuildInputs = [ cmake pkgconfig ];
+  postFixup = ''
+    cat <<EOF > $out/lib/python$pythonMajorMinor/site-packages/setup.py
+    from distutils.core import setup
 
-  meta = {
+    setup(
+        name = 'pyopenbabel',
+        version = '${version}',
+        packages = ['openbabel'],
+        package_data = {'openbabel' : ['_openbabel.so']}
+    )
+    EOF
+    '';
+
+  meta = with lib; {
     description = "A toolbox designed to speak the many languages of chemical data";
     homepage = "http://openbabel.org";
-    platforms = stdenv.lib.platforms.all;
+    platforms = platforms.all;
-    maintainers = [ ];
+    license = licenses.gpl2Plus;
-    license = stdenv.lib.licenses.gpl2Plus;
+    maintainers = with maintainers; [ danielbarter ];
   };
 }

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

@@ -0,0 +1,27 @@
+{ stdenv, lib, openbabel, python, buildPythonPackage }:
+
+buildPythonPackage rec {
+  pname = "openbabel";
+  version = "3.1.1";
+
+  src = "${openbabel}/lib/python${python.sourceVersion.major}.${python.sourceVersion.minor}/site-packages";
+
+  nativeBuildInputs = [ openbabel ];
+
+  # these env variables are used by the bindings to find libraries
+  # they need to be included explicitly in your nix-shell for
+  # some functionality to work (inparticular, pybel).
+  # see https://openbabel.org/docs/dev/Installation/install.html
+  BABEL_LIBDIR = "${openbabel}/lib/openbabel/3.1.0";
+  LD_LIBRARY_PATH = "$LD_LIBRARY_PATH:${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/all-packages.nix

@@ -15799,7 +15799,11 @@ in
   };
   openal = openalSoft;
 
-  openbabel = callPackage ../development/libraries/openbabel { };
+  openbabel = openbabel3;
+
+  openbabel2 = callPackage ../development/libraries/openbabel/2.nix { };
+
+  openbabel3 = callPackages ../development/libraries/openbabel { };
 
   opencascade = callPackage ../development/libraries/opencascade {
     inherit (darwin.apple_sdk.frameworks) OpenCL Cocoa;
@@ -27369,6 +27373,7 @@ in
   ### SCIENCE/CHEMISTY
 
   avogadro = callPackage ../applications/science/chemistry/avogadro {
+    openbabel = openbabel2;
     eigen = eigen2;
   };
 

pkgs/top-level/python-packages.nix

@@ -4468,6 +4468,10 @@ in {
 
   openapi-spec-validator = callPackage ../development/python-modules/openapi-spec-validator { };
 
+  openbabel-bindings = callPackage ../development/python-modules/openbabel-bindings {
+      openbabel = (callPackage ../development/libraries/openbabel { python = self.python; });
+  };
+
   opencv3 = toPythonModule (pkgs.opencv3.override {
     enablePython = true;
     pythonPackages = self;