Merge pull request #288514 from sheepforce/avogadro2

avogadro2: 1.98.1 -> 1.99.0

pkgs/applications/editors/molsketch/default.nix

@@ -19,6 +19,10 @@ mkDerivation rec {
     hash = "sha256-Mpx4fHktxqBAkmdwqg2pXvEgvvGUQPbgqxKwXKjhJuQ=";
   };
 
+  patches = [
+    ./openbabel.patch
+  ];
+
   # uses C++17 APIs like std::transform_reduce
   postPatch = ''
     substituteInPlace molsketch/CMakeLists.txt \
@@ -34,7 +38,7 @@ mkDerivation rec {
   '';
 
   postFixup = ''
-    mv $out/lib/molsketch/* $out/lib
+    ln -s $out/lib/molsketch/* $out/lib/.
   '';
 
   nativeBuildInputs = [ cmake pkg-config qttools wrapQtAppsHook ];

pkgs/applications/editors/molsketch/openbabel.patch

@@ -0,0 +1,12 @@
+diff --git a/obabeliface/obabeliface.cpp b/obabeliface/obabeliface.cpp
+index 98a9020..a168803 100644
+--- a/obabeliface/obabeliface.cpp
++++ b/obabeliface/obabeliface.cpp
+@@ -196,6 +196,7 @@ namespace Molsketch
+ 
+   // TODO should be const, but OpenBabel iterator methods do not support const
+   bool hasCoordinates(OpenBabel::OBMol &molecule) {
++    using namespace OpenBabel;
+     FOR_ATOMS_OF_MOL(obatom, molecule) {
+       if (obatom->GetVector() != OpenBabel::VZero)
+         return true;

pkgs/applications/science/chemistry/avogadro2/default.nix

@@ -12,13 +12,13 @@ let
 
 in stdenv.mkDerivation rec {
   pname = "avogadro2";
-  version = "1.98.1";
+  version = "1.99.0";
 
   src = fetchFromGitHub {
     owner = "OpenChemistry";
     repo = "avogadroapp";
     rev = version;
-    hash = "sha256-N35WGYZbgfjKnorzGKCnbBvlrlt9Vr04YIG2R3k+b8A=";
+    hash = "sha256-m8kX4WzOmPE/BZQRePOoUAdMPdWb6pmcqtPvDdEIIao=";
   };
 
   postUnpack = ''
@@ -37,7 +37,7 @@ in stdenv.mkDerivation rec {
 
   propagatedBuildInputs = [ openbabel ];
 
-  qtWrapperArgs = [ "--prefix PATH : ${openbabel}/bin" ];
+  qtWrapperArgs = [ "--prefix PATH : ${lib.getBin openbabel}/bin" ];
 
   meta = with lib; {
     description = "Molecule editor and visualizer";

pkgs/development/libraries/openbabel/default.nix

@@ -1,21 +1,21 @@
-{ stdenv, lib, fetchFromGitHub, cmake, zlib, libxml2, eigen, python, cairo, pcre, pkg-config, swig, rapidjson }:
+{ stdenv, lib, fetchFromGitHub, cmake, perl, zlib, libxml2, eigen, python, cairo, pcre, pkg-config, swig, rapidjson }:
 
 stdenv.mkDerivation rec {
   pname = "openbabel";
-  version = "3.1.1";
+  version = "unstable-06-12-23";
 
   src = fetchFromGitHub {
     owner = "openbabel";
-    repo = "openbabel";
-    rev = "openbabel-${lib.replaceStrings ["."] ["-"] version}";
-    sha256 = "sha256-wQpgdfCyBAoh4pmj9j7wPTlMtraJ62w/EShxi/olVMY=";
+    repo = pname;
+    rev = "32cf131444c1555c749b356dab44fb9fe275271f";
+    hash = "sha256-V0wrZVrojCZ9Knc5H6cPzPoYWVosRZ6Sn4PX+UFEfHY=";
   };
 
   postPatch = ''
     sed '1i#include <ctime>' -i include/openbabel/obutil.h # gcc12
   '';
 
-  buildInputs = [ zlib libxml2 eigen python cairo pcre swig rapidjson ];
+  buildInputs = [ perl zlib libxml2 eigen python cairo pcre swig rapidjson ];
 
   nativeBuildInputs = [ cmake pkg-config ];
 
@@ -26,13 +26,15 @@ stdenv.mkDerivation rec {
     "-DPYTHON_BINDINGS=ON"
   ];
 
+  # 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 > $out/lib/python$pythonMajorMinor/site-packages/setup.py
     from distutils.core import setup
 
     setup(
         name = 'pyopenbabel',
-        version = '${version}',
+        version = '3.2b1',
         packages = ['openbabel'],
         package_data = {'openbabel' : ['_openbabel.so']}
     )

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

@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, cmake, zlib, eigen, libGL, doxygen, spglib
+{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, zlib, eigen, libGL, doxygen, spglib
 , mmtf-cpp, glew, python3, libarchive, libmsym, msgpack, qttools, wrapQtAppsHook
 }:
 
@@ -18,26 +18,43 @@ let
     rev = "1.0.1";
     sha256 = "sH/WuvLaYu6akOc3ssAKhnxD8KNoDxuafDSozHqJZC4=";
   };
+  fragmentsRepo = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "fragments";
+    rev = "8dc711a59d016604b3e9b6d59dec178b8e6ccd36";
+    hash = "sha256-Valc5zwlaZ//eDupFouCfWCeID7/4ObU1SDLFJ/mo/g=";
+  };
 
 in stdenv.mkDerivation rec {
   pname = "avogadrolibs";
-  version = "1.98.1";
+  version = "1.99.0";
 
   src = fetchFromGitHub {
     owner = "OpenChemistry";
     repo = pname;
     rev = version;
-    hash = "sha256-BuBMWW7N5Cu9tw5Vpwk+aoIaMWwHViRzLtIG7XDWjN4=";
+    hash = "sha256-3jUbzEd7tUeHlVFAO9KJ+LOQlkLzJQvwmHp8gOriZRI=";
   };
 
   postUnpack = ''
     cp -r ${moleculesRepo} molecules
     cp -r ${crystalsRepo} crystals
+    cp -r ${fragmentsRepo} fragments
   '';
 
+  patches = [
+    # Fix a Cmake error when searching the fragments directory.
+    # Can be removed upon next release
+    (fetchpatch {
+      url = "https://github.com/OpenChemistry/avogadrolibs/commit/6e2e84dbb088a40d69117c1836f4306792f57acd.patch";
+      hash = "sha256-0tY9kHh6e5IDZQ8cWPgTpwIBhfZQlgUEZbPHOmtOVUQ=";
+    })
+  ];
+
   nativeBuildInputs = [
     cmake
     wrapQtAppsHook
+    pythonWP
   ];
 
   buildInputs = [

pkgs/development/libraries/science/chemistry/avogadrolibs/fragments.patch

@@ -0,0 +1,13 @@
+diff --git a/avogadro/qtplugins/templatetool/CMakeLists.txt b/avogadro/qtplugins/templatetool/CMakeLists.txt
+index 3f68e6dd..822de4e5 100644
+--- a/avogadro/qtplugins/templatetool/CMakeLists.txt
++++ b/avogadro/qtplugins/templatetool/CMakeLists.txt
+@@ -24,7 +24,7 @@ avogadro_plugin(TemplateTool
+ )
+ 
+ # Install the fragments
+-set(_fragments "${AvogadroLibs_SOURCE_DIR}/../fragments")
++set(_fragments "${AvogadroLibs_SOURCE_DIR}/fragments")
+ 
+ # Look in parallel directory for the molecule fragment repository
+ if(NOT EXISTS "${_fragments}")

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

@@ -1,8 +1,7 @@
 { lib, openbabel, python, buildPythonPackage }:
 
 buildPythonPackage rec {
-  pname = "openbabel";
-  version = "3.1.1";
+  inherit (openbabel) pname version;
 
   src = "${openbabel}/lib/python${python.sourceVersion.major}.${python.sourceVersion.minor}/site-packages";