openbabel: do not download dependencies during build

Explicitly depend against maeparser, coordgenlibs and rapidjson, so that
the build does not download the current version from github (!).

Also fix the coordgenlibs detection logic -- this is also submitted
upstream.

Fixes PR pkg/55755

4 files changed, 43 insertions, 41 deletions

diff --git a/biology/openbabel/Makefile b/biology/openbabel/Makefile
index d9971e4913b..b6209230676 100644
--- a/biology/openbabel/Makefile
+++ b/biology/openbabel/Makefile
@@ -1,9 +1,9 @@
-# $NetBSD: Makefile,v 1.42 2020/08/17 20:17:17 leot Exp $
+# $NetBSD: Makefile,v 1.43 2020/11/04 19:54:12 bsiegert Exp $
 #
 
 GITHUB_PROJECT=	openbabel
 DISTNAME=	openbabel-${RELVERSION:S/-/./g}
-PKGREVISION=	1
+PKGREVISION=	2
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=openbabel/}
 GITHUB_TAG=	${PKGBASE}-${RELVERSION}
@@ -31,10 +31,13 @@ CMAKE_ARGS+=	-DLLVM_CONFIG=${LLVM_CONFIG_PATH:Q}
 post-extract:
 	${MKDIR} ${WRKDIR}/build
 
+.include "../../biology/coordgenlibs/buildlink3.mk"
+.include "../../biology/maeparser/buildlink3.mk"
 .include "../../devel/boost-headers/buildlink3.mk"
 .include "../../devel/boost-libs/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../graphics/cairo/buildlink3.mk"
 .include "../../math/eigen3/buildlink3.mk"
 .include "../../textproc/libxml2/buildlink3.mk"
+.include "../../textproc/rapidjson/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/openbabel/PLIST b/biology/openbabel/PLIST
index 6c3d9ca17a2..187cf1a8d2a 100644
--- a/biology/openbabel/PLIST
+++ b/biology/openbabel/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.7 2020/11/01 23:06:39 mef Exp $
+@comment $NetBSD: PLIST,v 1.8 2020/11/04 19:54:12 bsiegert Exp $
 bin/obabel
 bin/obconformer
 bin/obdistgen
@@ -20,34 +20,7 @@ bin/obsym
 bin/obtautomer
 bin/obthermo
 bin/roundtrip
-include/coordgen/CoordgenConfig.hpp
-include/coordgen/CoordgenFragmentBuilder.h
-include/coordgen/CoordgenFragmenter.h
-include/coordgen/CoordgenMacrocycleBuilder.h
-include/coordgen/CoordgenMinimizer.h
-include/coordgen/sketcherMinimizer.h
-include/coordgen/sketcherMinimizerAtom.h
-include/coordgen/sketcherMinimizerBendInteraction.h
-include/coordgen/sketcherMinimizerBond.h
-include/coordgen/sketcherMinimizerClashInteraction.h
-include/coordgen/sketcherMinimizerEZConstrainInteraction.h
-include/coordgen/sketcherMinimizerFragment.h
-include/coordgen/sketcherMinimizerInteraction.h
-include/coordgen/sketcherMinimizerMarchingSquares.h
-include/coordgen/sketcherMinimizerMaths.h
-include/coordgen/sketcherMinimizerMolecule.h
-include/coordgen/sketcherMinimizerResidue.h
-include/coordgen/sketcherMinimizerResidueInteraction.h
-include/coordgen/sketcherMinimizerRing.h
-include/coordgen/sketcherMinimizerStretchInteraction.h
 include/inchi/inchi_api.h
-include/maeparser/Buffer.hpp
-include/maeparser/MaeBlock.hpp
-include/maeparser/MaeConstants.hpp
-include/maeparser/MaeParser.hpp
-include/maeparser/MaeParserConfig.hpp
-include/maeparser/Reader.hpp
-include/maeparser/Writer.hpp
 include/openbabel3/LBFGS.h
 include/openbabel3/LBFGS/LineSearchBacktracking.h
 include/openbabel3/LBFGS/LineSearchBracketing.h
@@ -138,23 +111,13 @@ include/openbabel3/openbabel/text.h
 include/openbabel3/openbabel/tokenst.h
 include/openbabel3/openbabel/typer.h
 include/openbabel3/openbabel/xml.h
-lib/cmake/coordgen-config-release.cmake
-lib/cmake/coordgen-config.cmake
-lib/cmake/maeparser-config-release.cmake
-lib/cmake/maeparser-config.cmake
 lib/cmake/openbabel3/OpenBabel3Config.cmake
 lib/cmake/openbabel3/OpenBabel3ConfigVersion.cmake
 lib/cmake/openbabel3/OpenBabel3_EXPORTS-release.cmake
 lib/cmake/openbabel3/OpenBabel3_EXPORTS.cmake
-lib/libcoordgen.so
-lib/libcoordgen.so.1
-lib/libcoordgen.so.1.4.2
 lib/libinchi.so
 lib/libinchi.so.0
 lib/libinchi.so.0.4.1
-lib/libmaeparser.so
-lib/libmaeparser.so.1
-lib/libmaeparser.so.1.2.3
 lib/libopenbabel.so
 lib/libopenbabel.so.7
 lib/libopenbabel.so.7.0.0
diff --git a/biology/openbabel/distinfo b/biology/openbabel/distinfo
index c5ba9cd5dff..b1d76383700 100644
--- a/biology/openbabel/distinfo
+++ b/biology/openbabel/distinfo
@@ -1,6 +1,7 @@
-$NetBSD: distinfo,v 1.11 2020/06/29 12:10:34 ryoon Exp $
+$NetBSD: distinfo,v 1.12 2020/11/04 19:54:12 bsiegert Exp $
 
 SHA1 (openbabel-3.1.1.tar.gz) = 22d5eea2492d4ea55fd29f9dcea34fd972af2a27
 RMD160 (openbabel-3.1.1.tar.gz) = 74c74c3129d47ecf70f37d17c1caa42693f6be28
 SHA512 (openbabel-3.1.1.tar.gz) = d46807e8f4e2f0f691e69943e5c5eda9c271271cfca6f66b6df136bbf384502fd3b65a4adf134a4e9e1f2452e1316c9515aa92292b73205b9eb4d7e4d7a85f18
 Size (openbabel-3.1.1.tar.gz) = 36688499 bytes
+SHA1 (patch-cmake_modules_Findcoordgen.cmake) = 5906ee8b00a60640a0a9cfd0481f674bea419ad1
diff --git a/biology/openbabel/patches/patch-cmake_modules_Findcoordgen.cmake b/biology/openbabel/patches/patch-cmake_modules_Findcoordgen.cmake
new file mode 100644
index 00000000000..c7303ef296d
--- /dev/null
+++ b/biology/openbabel/patches/patch-cmake_modules_Findcoordgen.cmake
@@ -0,0 +1,35 @@
+$NetBSD: patch-cmake_modules_Findcoordgen.cmake,v 1.1 2020/11/04 19:54:12 bsiegert Exp $
+
+coordgenlibs does not install the template file, and it is not needed.
+
+--- cmake/modules/Findcoordgen.cmake.orig	2020-05-08 15:38:02.000000000 +0000
++++ cmake/modules/Findcoordgen.cmake
+@@ -6,7 +6,6 @@
+ #
+ # coordgen_INCLUDE_DIRS   - CoordGen's includes directory
+ # coordgen_LIBRARIES      - CoordGen's shared libraries
+-# coordgen_TEMPLATE_FILE  - CoordGen templates file
+ #
+ #
+ 
+@@ -28,19 +27,9 @@ find_library(coordgen_LIBRARIES
+ )
+ message(STATUS "coordgen libraries set as '${coordgen_LIBRARIES}'")
+ 
+-# Just in case, add parent directory above libraries to templates search hints
+-get_filename_component(libs_parent_dir ${coordgen_LIBRARIES} PATH)
+-find_file(coordgen_TEMPLATE_FILE
+-    NAMES templates.mae
+-    HINTS ${coordgen_DIR} ${libs_parent_dir}
+-    PATH_SUFFIXES "share" "share/coordgen"
+-    DOC "templates file for coordgen"
+-)
+-message(STATUS "coordgen templates file set as '${coordgen_TEMPLATE_FILE}'")
+-
+ find_package_handle_standard_args(coordgen FOUND_VAR coordgen_FOUND
+                                   REQUIRED_VARS coordgen_INCLUDE_DIRS
+-                                  coordgen_LIBRARIES coordgen_TEMPLATE_FILE)
++                                  coordgen_LIBRARIES)
+ 
+ 
+