avogadrolibs: 1.98.1 -> 1.99.0

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}")