openbabel: upgrade 2.4.1 -> 3.0.0

This should build without python2

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

recipes-misc/recipes-chemistry/openbabel/files/0001-Workaround-xdr-linker-error.patch

@@ -0,0 +1,30 @@
+From fce5f3a38a62dd4927adaa8372b73eedeeffbe46 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Andreas=20M=C3=BCller?= <schnitzeltony@gmail.com>
+Date: Tue, 3 Dec 2019 19:25:03 +0100
+Subject: [PATCH] Workaround xdr linker error
+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>
+---
+ CMakeLists.txt | 1 -
+ 1 file changed, 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 33bf2da29..178231b62 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -224,7 +224,6 @@ check_include_file(conio.h      HAVE_CONIO_H)
+ check_include_file(sys/time.h   HAVE_SYS_TIME_H)
+ check_include_file(time.h       HAVE_TIME_H)
+ check_include_file(strings.h    HAVE_STRINGS_H)
+-check_include_file(rpc/xdr.h    HAVE_RPC_XDR_H)
+ check_include_file(regex.h      HAVE_REGEX_H)
+ check_include_file_cxx(sstream  HAVE_SSTREAM)
+ 
+-- 
+2.21.0
+

recipes-misc/recipes-chemistry/openbabel/files/0001-take-care-for-ARM-s-unsigned-char.patch

@@ -1,58 +0,0 @@
-From 52851a453a1da3452d55e44f13323389b3a689c2 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Andreas=20M=C3=BCller?= <schnitzeltony@googlemail.com>
-Date: Fri, 16 Dec 2016 18:39:34 +0100
-Subject: [PATCH] take care for ARM's unsigned char
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-Stolen from [1]
-
-[1] http://pkgs.fedoraproject.org/cgit/rpms/openbabel.git/tree/openbabel-narrowing-conversion.patch
-
-Upstream-Status: Pending
-
-Signed-off-by: Andreas Müller <schnitzeltony@googlemail.com>
----
- src/formats/pngformat.cpp    | 2 +-
- src/formats/yasaraformat.cpp | 4 ++--
- 2 files changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/src/formats/pngformat.cpp b/src/formats/pngformat.cpp
-index 49bff17..375d42c 100644
---- a/src/formats/pngformat.cpp
-+++ b/src/formats/pngformat.cpp
-@@ -218,7 +218,7 @@ bool PNGFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
-     _count=0;
-     _hasInputPngFile=true;
-   }
--  const char pngheader[] = {-119,80,78,71,13,10,26,10,0};
-+  const signed char pngheader[] = {-119,80,78,71,13,10,26,10,0};
-   char readbytes[9];
-   ifs.read(readbytes, 8);
- 
-diff --git a/src/formats/yasaraformat.cpp b/src/formats/yasaraformat.cpp
-index cfc0a53..5a4d413 100644
---- a/src/formats/yasaraformat.cpp
-+++ b/src/formats/yasaraformat.cpp
-@@ -472,7 +472,7 @@ bool YOBFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
- 
-   //  bool hetatom;
-   char buffer[32],/*resname[4],*/atomname[5];
--  char double1[8]={0,0,0,0,0,0,-16,0x3f};
-+  const signed char double1[8]={0,0,0,0,0,0,-16,0x3f};
-   //   char *str;
-   int i,j,/*m,q,*/pos;
-   int /*resno,chainNum,link,linktype,*/atoms,element,links/*,chain*/;
-@@ -500,7 +500,7 @@ bool YOBFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
-   mem_set(buffer,0,8);
-   for (i=0;i<4;i++)
-   { for (j=0;j<4;j++)
--    { if (i==j) ofs.write(double1,8);
-+    { if (i==j) ofs.write(reinterpret_cast<const char*>(double1),8);
-       else ofs.write(buffer,8); } }
-   storeint32le(buffer,MOB_INFOEND);
-   storeint32le(&buffer[4],MOB_INFOENDSIZE);
--- 
-2.5.5
-

recipes-misc/recipes-chemistry/openbabel/openbabel_git.bb

@@ -9,15 +9,17 @@ DEPENDS = " \
     cairo \
     libxml2 \
     zlib \
+    libtirpc \
 "
 
 SRC_URI = " \
-    ${SOURCEFORGE_MIRROR}/project/${BPN}/${BPN}/${PV}/${BPN}-${PV}.tar.gz \
+    git://github.com/openbabel/openbabel.git \
+    file://0001-Workaround-xdr-linker-error.patch \
     file://openbabel-gui.desktop \
-    file://0001-take-care-for-ARM-s-unsigned-char.patch \
 "
-SRC_URI[md5sum] = "d9defcd7830b0592fece4fe54a137b99"
+SRCREV = "49f9cfb32bd0bc6ea440639d338123eb27accbe2"
-SRC_URI[sha256sum] = "204136582cdfe51d792000b20202de8950218d617fd9c6e18cee36706a376dfc"
+S = "${WORKDIR}/git"
+PV = "3.0.0"
 
 do_install_append() {
     install -d ${D}${datadir}/applications
@@ -27,4 +29,4 @@ do_install_append() {
     convert.im7 ${S}/src/GUI/babel.xpm -transparent white ${D}${datadir}/pixmaps/babel.png
 }
 
-FILES_${PN} += "${libdir}/cmake"
+FILES_${PN}-dev += "${libdir}/cmake"