[pkgsrc/trunk]: pkgsrc/biology/openbabel openbabel: do not download dependenc...

[bsiegert <bsiegert%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/93adb98630a1
branches:  trunk
changeset: 441485:93adb98630a1
user:      bsiegert <bsiegert%pkgsrc.org@localhost>
date:      Wed Nov 04 19:54:12 2020 +0000

description:
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

diffstat:

 biology/openbabel/Makefile                                       |   7 +-
 biology/openbabel/PLIST                                          |  39 +---------
 biology/openbabel/distinfo                                       |   3 +-
 biology/openbabel/patches/patch-cmake_modules_Findcoordgen.cmake |  35 ++++++++
 4 files changed, 43 insertions(+), 41 deletions(-)

diffs (148 lines):

diff -r 1b3d5bd01a48 -r 93adb98630a1 biology/openbabel/Makefile
--- a/biology/openbabel/Makefile        Wed Nov 04 19:25:01 2020 +0000
+++ b/biology/openbabel/Makefile        Wed Nov 04 19:54:12 2020 +0000
@@ -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 @@
 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 -r 1b3d5bd01a48 -r 93adb98630a1 biology/openbabel/PLIST
--- a/biology/openbabel/PLIST   Wed Nov 04 19:25:01 2020 +0000
+++ b/biology/openbabel/PLIST   Wed Nov 04 19:54:12 2020 +0000
@@ -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/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/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 -r 1b3d5bd01a48 -r 93adb98630a1 biology/openbabel/distinfo
--- a/biology/openbabel/distinfo        Wed Nov 04 19:25:01 2020 +0000
+++ b/biology/openbabel/distinfo        Wed Nov 04 19:54:12 2020 +0000
@@ -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 -r 1b3d5bd01a48 -r 93adb98630a1 biology/openbabel/patches/patch-cmake_modules_Findcoordgen.cmake
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/openbabel/patches/patch-cmake_modules_Findcoordgen.cmake  Wed Nov 04 19:54:12 2020 +0000
@@ -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)
+ 
+ 
+