avogadrolibs: Upgrade 1.90.0 -> 1.92.0 and rework

Signed-off-by: Andreas Müller <schnitzeltony@gmail.com>

recipes-misc/recipes-chemistry/avogadro/avogadrolibs-native.bb

@@ -1,5 +1,7 @@
 require ${BPN}.inc
 
+FILESEXTRAPATHS_prepend := "${THISDIR}/${BPN}-native:"
+
 inherit native
 
 SRC_URI += " \

recipes-misc/recipes-chemistry/avogadro/avogadrolibs-native/0001-native-build-encodefile-only.patch

@@ -1,5 +1,5 @@
-From 1effb804467e23e617f4e1330422e7b4fae769da Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Andreas=20M=C3=BCller?= <schnitzeltony@googlemail.com>
+From d242b39515dbd268ecd4eaec63d3424497827488 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Andreas=20M=C3=BCller?= <schnitzeltony@mail.com>
 Date: Sun, 18 Dec 2016 23:02:14 +0100
 Subject: [PATCH] native: build encodefile only
 MIME-Version: 1.0
@@ -8,25 +8,26 @@ Content-Transfer-Encoding: 8bit
 
 Upstream-Status: Inappropriate [embedded specific]
 
-Signed-off-by: Andreas Müller <schnitzeltony@googlemail.com>
+Signed-off-by: Andreas Müller <schnitzeltony@gmail.com>
+
 ---
  CMakeLists.txt           | 3 +++
  utilities/CMakeLists.txt | 1 -
  2 files changed, 3 insertions(+), 1 deletion(-)
 
 diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 8a50914..60a94fc 100644
+index 52226cd..ff8863e 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -42,6 +42,7 @@ option(USE_MOLEQUEUE "Enable the MoleQueue dependent functionality" ON)
- option(USE_BOOST_PYTHON "Use Boost Python to wrap some of our API" OFF)
+@@ -54,6 +54,7 @@ option(USE_MOLEQUEUE "Enable the MoleQueue dependent functionality" ON)
+ option(USE_PYTHON "Use Python to wrap some of our API" OFF)
  
  add_subdirectory(utilities)
 +if(false)
  add_subdirectory(thirdparty)
  add_subdirectory(avogadro)
  
-@@ -89,3 +90,5 @@ install(FILES
+@@ -107,3 +108,5 @@ install(FILES
    DESTINATION "${INSTALL_LIBRARY_DIR}/cmake/avogadrolibs")
  install(EXPORT "AvogadroLibsTargets"
    DESTINATION "${INSTALL_LIBRARY_DIR}/cmake/avogadrolibs")
@@ -36,9 +37,7 @@ diff --git a/utilities/CMakeLists.txt b/utilities/CMakeLists.txt
 index e459934..6a76c75 100644
 --- a/utilities/CMakeLists.txt
 +++ b/utilities/CMakeLists.txt
-@@ -1,2 +1 @@
+@@ -1,3 +1,2 @@
 -add_subdirectory(bodr)
  add_subdirectory(encodefile)
--- 
-2.5.5
-
+ add_subdirectory(resdata)

recipes-misc/recipes-chemistry/avogadro/avogadrolibs.bb

@@ -7,23 +7,28 @@ DEPENDS = " \
    libeigen \
    molequeue \
    spglib \
+   libmsym \
+   libarchive \
 "
 
 inherit cmake_lib
 
-FILES_SOLIBSDEV = ""
+SRC_URI += "file://0001-Avoid-RPATH-if-not-configured.patch"
+
+EXTRA_OECMAKE += "-DENABLE_RPATH=OFF"
+
+# avogadrolibs has lots of include_directories(SYSTEM ${FOO_DIR})
+# have no better way to make gcc6 happy
+do_configure_append() {
+     sed -i 's:-isystem :-I :g' `find ${B} -name '*.ninja'`
+}
 
 FILES_${PN} += " \
-    ${libdir}/libAvogadro*.so \
     ${libdir}/avogadro2/scripts \
 "
 
 FILES_${PN}-staticdev += " \
     ${libdir}/avogadro2/staticplugins \
 "
-FILES_${PN}-dev += " \
-    ${libdir}/cmake \
-"
 
 CMAKE_ALIGN_SYSROOT[1] = "avogadrolibs, -S${prefix}, -S${STAGING_DIR_HOST}/${prefix}"
-

recipes-misc/recipes-chemistry/avogadro/avogadrolibs.inc

@@ -1,19 +1,12 @@
 SUMMARY = "Chemistry library"
 DESCRIPTION = "Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas"
 HOMEPAGE = "http://openchemistry.org/avogadro2"
-LICENSE = "BSD"
-LIC_FILES_CHKSUM = "file://COPYING;md5=2b10c3e46ff5e14f9e12acdd42cf9094"
+LICENSE = "BSD-3-Clause"
+LIC_FILES_CHKSUM = "file://LICENSE;md5=95b8695b33e17e83db253ab07da4455a"
 
 inherit cmake_qt5 pythonnative
 
-PV = "1.90.0"
-SRC_URI = "https://github.com/OpenChemistry/${BPN}/archive/${PV}.tar.gz"
-SRC_URI[md5sum] = "f2b7014f48da5b2a72d49c01dafaf225"
-SRC_URI[sha256sum] = "a562acae129901cb2c9878f5ca4cc8874a8a04260b93a700489dc85dc862c9b7"
-
-# avogadrolibs has lots of include_directories(SYSTEM ${FOO_DIR})
-# have no better way to make gcc6 happy
-do_configure_append() {
-     sed -i 's:-isystem ${STAGING_INCDIR} ::g' `find ${B} -name *.make`
-}
-
+PV = "1.92.0"
+SRC_URI = "git://github.com/OpenChemistry/avogadrolibs.git"
+SRCREV = "c22000b59a810529ce306089d1c78e0d1ebbd6c3"
+S = "${WORKDIR}/git"

recipes-misc/recipes-chemistry/avogadro/avogadrolibs/0001-Avoid-RPATH-if-not-configured.patch

@@ -0,0 +1,35 @@
+From 2f43dc82563eef7fe844315939231f3fcb4b7817 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Andreas=20M=C3=BCller?= <schnitzeltony@gmail.com>
+Date: Fri, 16 Nov 2018 13:42:48 +0100
+Subject: [PATCH] Avoid RPATH if not configured
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+Upstream-Status: Pending
+
+Signed-off-by: Andreas Müller <schnitzeltony@gmail.com>
+---
+ cmake/InstallLocation.cmake | 6 ++++--
+ 1 file changed, 4 insertions(+), 2 deletions(-)
+
+diff --git a/cmake/InstallLocation.cmake b/cmake/InstallLocation.cmake
+index ca9e375..6061201 100644
+--- a/cmake/InstallLocation.cmake
++++ b/cmake/InstallLocation.cmake
+@@ -39,8 +39,10 @@ endif()
+ 
+ # Set up RPATH for the project too.
+ option(ENABLE_RPATH "Enable rpath support on Linux and Mac" ON)
+-if(NOT CMAKE_INSTALL_RPATH)
+-  set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${INSTALL_LIBRARY_DIR}")
++if(ENABLE_RPATH)
++  if(NOT CMAKE_INSTALL_RPATH)
++    set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${INSTALL_LIBRARY_DIR}")
++  endif()
+ endif()
+ if(APPLE AND NOT CMAKE_INSTALL_NAME_DIR)
+   set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${INSTALL_LIBRARY_DIR}")
+-- 
+2.14.4
+