CVS commit: pkgsrc/biology/openbabel

["Benny Siegert" <bsiegert%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bsiegert
Date:           Wed Nov  4 19:54:12 UTC 2020

Modified Files:
        pkgsrc/biology/openbabel: Makefile PLIST distinfo
Added Files:
        pkgsrc/biology/openbabel/patches:
            patch-cmake_modules_Findcoordgen.cmake

Log Message:
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


To generate a diff of this commit:
cvs rdiff -u -r1.42 -r1.43 pkgsrc/biology/openbabel/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/biology/openbabel/PLIST
cvs rdiff -u -r1.11 -r1.12 pkgsrc/biology/openbabel/distinfo
cvs rdiff -u -r0 -r1.1 \
    pkgsrc/biology/openbabel/patches/patch-cmake_modules_Findcoordgen.cmake

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/openbabel/Makefile
diff -u pkgsrc/biology/openbabel/Makefile:1.42 pkgsrc/biology/openbabel/Makefile:1.43
--- pkgsrc/biology/openbabel/Makefile:1.42      Mon Aug 17 20:17:17 2020
+++ pkgsrc/biology/openbabel/Makefile   Wed Nov  4 19:54:12 2020
@@ -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
 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"

Index: pkgsrc/biology/openbabel/PLIST
diff -u pkgsrc/biology/openbabel/PLIST:1.7 pkgsrc/biology/openbabel/PLIST:1.8
--- pkgsrc/biology/openbabel/PLIST:1.7  Sun Nov  1 23:06:39 2020
+++ pkgsrc/biology/openbabel/PLIST      Wed Nov  4 19:54:12 2020
@@ -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

Index: pkgsrc/biology/openbabel/distinfo
diff -u pkgsrc/biology/openbabel/distinfo:1.11 pkgsrc/biology/openbabel/distinfo:1.12
--- pkgsrc/biology/openbabel/distinfo:1.11      Mon Jun 29 12:10:34 2020
+++ pkgsrc/biology/openbabel/distinfo   Wed Nov  4 19:54:12 2020
@@ -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

Added files:

Index: pkgsrc/biology/openbabel/patches/patch-cmake_modules_Findcoordgen.cmake
diff -u /dev/null pkgsrc/biology/openbabel/patches/patch-cmake_modules_Findcoordgen.cmake:1.1
--- /dev/null   Wed Nov  4 19:54:13 2020
+++ pkgsrc/biology/openbabel/patches/patch-cmake_modules_Findcoordgen.cmake     Wed Nov  4 19:54:12 2020
@@ -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)
+ 
+ 
+