[pkgsrc/trunk]: pkgsrc/biology/openbabel openbabel: Update to 3.1.1

To: source-changes-hg%NetBSD.org@localhost
Subject: [pkgsrc/trunk]: pkgsrc/biology/openbabel openbabel: Update to 3.1.1
From: ryoon <ryoon%pkgsrc.org@localhost>
Date: Mon, 29 Jun 2020 13:01:23 +0000
details:   https://anonhg.NetBSD.org/pkgsrc/rev/808e137590b2
branches:  trunk
changeset: 434956:808e137590b2
user:      ryoon <ryoon%pkgsrc.org@localhost>
date:      Mon Jun 29 12:10:34 2020 +0000

description:
openbabel: Update to 3.1.1

* Depends on boost. If you have boost, cmake detects boost and it causes
  build failure.

Changelog:
3.1.1
This version primarily reflects fixes for packaging on Linux and FreeBSD
relative to 3.1.0. No features or significant bug fixes were involved.

3.1.0
This version represents additional API and is backwards-compatible with the 3.0 release.

Significant features and fixes

    Fixed tautomer code (by timvdm #2171)
    New functionality: Support for periodic boundary conditions. See additional option -p for MMCIF format, and write option 'g' for CIF. (by bbucior, #1853)
    New functionality: Add distance geometry method (by n-yoshikawa, #1875, by timvdm #2158)
    Fixed crashes with new 3D coordinate generation (by timvdm #2149 and ghutchis #2150)


New features and improvements

    New file format: Wiswesser Line Notation reader from Roger Sayle (by baoilleach, #2084)
    New option: Add the --neutralize operation to convert charged atoms to neutral (by baoilleach, #2109)
    Update GAS CONSTANT to 2018 CODATA recommended value (by e-kwsm, #2045)
    Support #0 in SMARTS so that asterisks can be matched (by baoilleach, #2079)
    Bring back support for lowercase elements and D/T in GetAtomicNum(). (by baoilleach, #2100)
    Change docstrings of add/delete hydrogens to better reflect their functionality (by baoilleach, #2110)
    Support kekulization of aromatic sulfoxides (by baoilleach, #2121)
    Enable casting to StereoBase in the Python bindings (by baoilleach, #2124)
    OBBuilder: Add error message for ring/rigid fragments with all zero coords. (by timvdm, #2149)
    R script updates (by khoran, #2145)
    Be more strict when parsing charges in SMILES (by baoilleach, #2132)
    Improve tools/obconformer.cpp (by e-kwsm, #2154)


Bug fixes

    Fix CMake error with R and C# bindings (by ghutchis, #2051)
    Rename MAESTRO extensions from uppercase to lowercase (by baoilleach, #2053)
    Fix file format docstrings that were causing problems with Sphinx or GUI (by baoilleach, #2054)
    Fix BUILD_SHARED=OFF (by dkoes, #2056)
    Fix import of openbabel (by e-kwsm, #2058)
    Update for Open Babel 3 (by e-kwsm, #2060)
    Fix maeparser compile error with some Boost configs (by fredrikw, #2076)
    Find or build maeparser & coordgen libraries (by ricrogz, #2064)
    Fix issue #2095, caused by incorrect application of protonated SMARTS (by au1985, #2102)
    Fix issue #1794, UFF atom typing for deuterium (by ghutchis, #2114)
    Fix segfault on SMI to InChI conversion when using "-d" (by timvdm, #2115)
    Correct the path to the openbabel-python.cpp (by baoilleach, #2119)
    Remove fragments with zero coordinates - fixes #2144. (by ghutchis, #2150)
    Fix issue #2125 - Zero occupancy in cif file treated as 1.0. (by orex, #2136)
    Fix #2071 - obrms parser segmentation fault (by e-kwsm, #2073)
    Fix #2098 - OBDistanceGeometry is unavailable to users (by n-yoshikawa, #2105)
    Set MAEPARSER_BUILD_SHARED_LIBS (fix #2089) (by e-kwsm, #2155)
    Fix the import of Tkinter in Python 3+ (by mrakitin, #2157)
    Fix for segault (with regression test) (by dkoes, #2162)
    Follow-up with missing spelling fixes from #2163 (by mrakitin, #2166)
    Prefer std::fabs resolves build problem on mac-current (by ghutchis, #2168)
    Fix distance geometry stereo issues (by timvdm, #2158)
    Merge of "Improve OBConversion::WriteString() and WriteFile() initialization" (adalke) #1923 (by baoilleach, #2176)
    Fix output format in the cifformat writer (by afonari, #2170)


Development/Build/Install improvements

    Avoid using namespace in headers (by e-kwsm, #2055)
    Remove babel doc (by e-kwsm, #2057)
    Do not hard-code Open Babel major version for include directory (by e-kwsm, #2059)
    Patched to build on NetBSD (by voidpin, #2093)
    Update download link (by njzjz, #2094)
    Fix GitHub ISSUE_TEMPLATE (by RMeli, #2082)
    Define OpenBabel3_LIBRARY (by dkoes, #2086)
    Initial GitHub action - misspell-fixer (by ghutchis, #2163)
    Automated GitHub builds (by ghutchis, #2165)

diffstat:

 biology/openbabel/Makefile                                   |   11 +-
 biology/openbabel/PLIST                                      |  414 ++++++----
 biology/openbabel/distinfo                                   |   15 +-
 biology/openbabel/options.mk                                 |    6 +-
 biology/openbabel/patches/patch-doc_CMakeLists.txt           |   13 -
 biology/openbabel/patches/patch-openbabel-3.pc.cmake         |   13 -
 biology/openbabel/patches/patch-src_conformersearch.cpp      |   12 -
 biology/openbabel/patches/patch-src_formats_confabreport.cpp |   17 -
 biology/openbabel/patches/patch-test_addhtest.cpp            |   17 -
 9 files changed, 244 insertions(+), 274 deletions(-)

diffs (truncated from 627 to 300 lines):

diff -r 5d3aa89077cd -r 808e137590b2 biology/openbabel/Makefile
--- a/biology/openbabel/Makefile        Mon Jun 29 12:07:00 2020 +0000
+++ b/biology/openbabel/Makefile        Mon Jun 29 12:10:34 2020 +0000
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.40 2020/06/02 08:22:32 adam Exp $
+# $NetBSD: Makefile,v 1.41 2020/06/29 12:10:34 ryoon Exp $
 #
 
 GITHUB_PROJECT=        openbabel
 DISTNAME=      openbabel-${RELVERSION:S/-/./g}
-PKGREVISION=   5
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=openbabel/}
 GITHUB_TAG=    ${PKGBASE}-${RELVERSION}
@@ -13,7 +12,7 @@
 COMMENT=       Chemistry file translation program
 LICENSE=       gnu-gpl-v2
 
-RELVERSION=    3-0-0
+RELVERSION=    3-1-1
 
 USE_LANGUAGES= c gnu++11
 USE_TOOLS+=    pkg-config
@@ -31,8 +30,10 @@
 post-extract:
        ${MKDIR} ${WRKDIR}/build
 
-.include "../../graphics/cairo/buildlink3.mk"
+.include "../../devel/boost-headers/buildlink3.mk"
+.include "../../devel/boost-libs/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
-.include "../../math/eigen2/buildlink3.mk"
+.include "../../graphics/cairo/buildlink3.mk"
+.include "../../math/eigen3/buildlink3.mk"
 .include "../../textproc/libxml2/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff -r 5d3aa89077cd -r 808e137590b2 biology/openbabel/PLIST
--- a/biology/openbabel/PLIST   Mon Jun 29 12:07:00 2020 +0000
+++ b/biology/openbabel/PLIST   Mon Jun 29 12:10:34 2020 +0000
@@ -1,6 +1,8 @@
-@comment $NetBSD: PLIST,v 1.4 2019/11/20 17:02:12 kamil Exp $
+@comment $NetBSD: PLIST,v 1.5 2020/06/29 12:10:34 ryoon Exp $
 bin/obabel
 bin/obconformer
+bin/obdistgen
+${PLIST.wx-gui}bin/obgui
 bin/obenergy
 bin/obfit
 bin/obfitall
@@ -10,6 +12,7 @@
 bin/obmm
 bin/obprobe
 bin/obprop
+bin/obrms
 bin/obrotamer
 bin/obrotate
 bin/obspectrophore
@@ -17,7 +20,39 @@
 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
+include/openbabel3/LBFGS/LineSearchNocedalWright.h
+include/openbabel3/LBFGS/Param.h
 include/openbabel3/openbabel/alias.h
 include/openbabel3/openbabel/atom.h
 include/openbabel3/openbabel/babelconfig.h
@@ -103,143 +138,154 @@
 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.1.4.0
 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.6
-lib/libopenbabel.so.6.0.0
-lib/openbabel/${PKGVERSION}/APIInterface.so
-lib/openbabel/${PKGVERSION}/CSRformat.so
-lib/openbabel/${PKGVERSION}/MCDLformat.so
-lib/openbabel/${PKGVERSION}/MNAformat.so
-lib/openbabel/${PKGVERSION}/PQSformat.so
-lib/openbabel/${PKGVERSION}/abinitformat.so
-lib/openbabel/${PKGVERSION}/acesformat.so
-lib/openbabel/${PKGVERSION}/acrformat.so
-lib/openbabel/${PKGVERSION}/adfformat.so
-lib/openbabel/${PKGVERSION}/alchemyformat.so
-lib/openbabel/${PKGVERSION}/amberformat.so
-lib/openbabel/${PKGVERSION}/aoforceformat.so
-lib/openbabel/${PKGVERSION}/asciiformat.so
-lib/openbabel/${PKGVERSION}/balstformat.so
-lib/openbabel/${PKGVERSION}/bgfformat.so
-lib/openbabel/${PKGVERSION}/boxformat.so
-lib/openbabel/${PKGVERSION}/cacaoformat.so
-lib/openbabel/${PKGVERSION}/cacheformat.so
-lib/openbabel/${PKGVERSION}/carformat.so
-lib/openbabel/${PKGVERSION}/castepformat.so
-lib/openbabel/${PKGVERSION}/cccformat.so
-lib/openbabel/${PKGVERSION}/cdxmlformat.so
-lib/openbabel/${PKGVERSION}/chem3dformat.so
-lib/openbabel/${PKGVERSION}/chemdoodlejsonformat.so
-lib/openbabel/${PKGVERSION}/chemdrawcdx.so
-lib/openbabel/${PKGVERSION}/chemdrawct.so
-lib/openbabel/${PKGVERSION}/chemkinformat.so
-lib/openbabel/${PKGVERSION}/chemtoolformat.so
-lib/openbabel/${PKGVERSION}/cifformat.so
-lib/openbabel/${PKGVERSION}/cmlformat.so
-lib/openbabel/${PKGVERSION}/cmlreactformat.so
-lib/openbabel/${PKGVERSION}/cofformat.so
-lib/openbabel/${PKGVERSION}/confabreport.so
-lib/openbabel/${PKGVERSION}/copyformat.so
-lib/openbabel/${PKGVERSION}/crkformat.so
-lib/openbabel/${PKGVERSION}/crystal09format.so
-lib/openbabel/${PKGVERSION}/cssrformat.so
-lib/openbabel/${PKGVERSION}/daltonformat.so
-lib/openbabel/${PKGVERSION}/dlpolyformat.so
-lib/openbabel/${PKGVERSION}/dmolformat.so
-lib/openbabel/${PKGVERSION}/exyzformat.so
-lib/openbabel/${PKGVERSION}/fastaformat.so
-lib/openbabel/${PKGVERSION}/fastsearchformat.so
-lib/openbabel/${PKGVERSION}/fchkformat.so
-lib/openbabel/${PKGVERSION}/featformat.so
-lib/openbabel/${PKGVERSION}/fhformat.so
-lib/openbabel/${PKGVERSION}/fhiaimsformat.so
-lib/openbabel/${PKGVERSION}/fingerprintformat.so
-lib/openbabel/${PKGVERSION}/fpsformat.so
-lib/openbabel/${PKGVERSION}/freefracformat.so
-lib/openbabel/${PKGVERSION}/gamessformat.so
-lib/openbabel/${PKGVERSION}/gamessukformat.so
-lib/openbabel/${PKGVERSION}/gausscubeformat.so
-lib/openbabel/${PKGVERSION}/gaussformat.so
-lib/openbabel/${PKGVERSION}/gausszmatformat.so
-lib/openbabel/${PKGVERSION}/ghemicalformat.so
-lib/openbabel/${PKGVERSION}/groformat.so
-lib/openbabel/${PKGVERSION}/gromos96format.so
-lib/openbabel/${PKGVERSION}/gulpformat.so
-lib/openbabel/${PKGVERSION}/hinformat.so
-lib/openbabel/${PKGVERSION}/inchiformat.so
-lib/openbabel/${PKGVERSION}/jaguarformat.so
-lib/openbabel/${PKGVERSION}/lmpdatformat.so
-lib/openbabel/${PKGVERSION}/lpmdformat.so
-lib/openbabel/${PKGVERSION}/mdffformat.so
-lib/openbabel/${PKGVERSION}/mdlformat.so
-lib/openbabel/${PKGVERSION}/mmcifformat.so
-lib/openbabel/${PKGVERSION}/mmodformat.so
-lib/openbabel/${PKGVERSION}/mol2format.so
-lib/openbabel/${PKGVERSION}/moldenformat.so
-lib/openbabel/${PKGVERSION}/molproformat.so
-lib/openbabel/${PKGVERSION}/molreport.so
-lib/openbabel/${PKGVERSION}/mopacformat.so
-lib/openbabel/${PKGVERSION}/mpdformat.so
-lib/openbabel/${PKGVERSION}/mpqcformat.so
-lib/openbabel/${PKGVERSION}/msiformat.so
-lib/openbabel/${PKGVERSION}/msmsformat.so
-lib/openbabel/${PKGVERSION}/nulformat.so
-lib/openbabel/${PKGVERSION}/nwchemformat.so
-lib/openbabel/${PKGVERSION}/opendxformat.so
-lib/openbabel/${PKGVERSION}/orcaformat.so
-lib/openbabel/${PKGVERSION}/outformat.so
-lib/openbabel/${PKGVERSION}/painterformat.so
-lib/openbabel/${PKGVERSION}/pcmodelformat.so
-lib/openbabel/${PKGVERSION}/pdbformat.so
-lib/openbabel/${PKGVERSION}/pdbqtformat.so
-lib/openbabel/${PKGVERSION}/plugin_charges.so
-lib/openbabel/${PKGVERSION}/plugin_descriptors.so
-lib/openbabel/${PKGVERSION}/plugin_fingerprints.so
-lib/openbabel/${PKGVERSION}/plugin_forcefields.so
-lib/openbabel/${PKGVERSION}/plugin_ops.so
-lib/openbabel/${PKGVERSION}/png2format.so
-lib/openbabel/${PKGVERSION}/pngformat.so
-lib/openbabel/${PKGVERSION}/pointcloudformat.so
-lib/openbabel/${PKGVERSION}/posformat.so
-lib/openbabel/${PKGVERSION}/povrayformat.so
-lib/openbabel/${PKGVERSION}/pqrformat.so
-lib/openbabel/${PKGVERSION}/pubchem.so
-lib/openbabel/${PKGVERSION}/pubchemjsonformat.so
-lib/openbabel/${PKGVERSION}/pwscfformat.so
-lib/openbabel/${PKGVERSION}/qchemformat.so
-lib/openbabel/${PKGVERSION}/reportformat.so
-lib/openbabel/${PKGVERSION}/rinchiformat.so
-lib/openbabel/${PKGVERSION}/rsmiformat.so
-lib/openbabel/${PKGVERSION}/rxnformat.so
-lib/openbabel/${PKGVERSION}/shelxformat.so
-lib/openbabel/${PKGVERSION}/siestaformat.so
-lib/openbabel/${PKGVERSION}/smilesformat.so
-lib/openbabel/${PKGVERSION}/smileyformat.so
-lib/openbabel/${PKGVERSION}/stlformat.so
-lib/openbabel/${PKGVERSION}/svgformat.so
-lib/openbabel/${PKGVERSION}/textformat.so
-lib/openbabel/${PKGVERSION}/thermoformat.so
-lib/openbabel/${PKGVERSION}/tinkerformat.so
-lib/openbabel/${PKGVERSION}/titleformat.so
-lib/openbabel/${PKGVERSION}/turbomoleformat.so
-lib/openbabel/${PKGVERSION}/unichemformat.so
-lib/openbabel/${PKGVERSION}/vaspformat.so
-lib/openbabel/${PKGVERSION}/viewmolformat.so
-lib/openbabel/${PKGVERSION}/xedformat.so
-lib/openbabel/${PKGVERSION}/xmlformat.so
-lib/openbabel/${PKGVERSION}/xsfformat.so
-lib/openbabel/${PKGVERSION}/xyzformat.so
-lib/openbabel/${PKGVERSION}/yasaraformat.so
-lib/openbabel/${PKGVERSION}/zindoformat.so
+lib/libopenbabel.so.7
+lib/libopenbabel.so.7.0.0
+lib/openbabel/3.1.0/APIInterface.so
+lib/openbabel/3.1.0/CSRformat.so
+lib/openbabel/3.1.0/MCDLformat.so
+lib/openbabel/3.1.0/MNAformat.so
+lib/openbabel/3.1.0/PQSformat.so
+lib/openbabel/3.1.0/abinitformat.so
+lib/openbabel/3.1.0/acesformat.so
+lib/openbabel/3.1.0/acrformat.so
+lib/openbabel/3.1.0/adfformat.so
+lib/openbabel/3.1.0/alchemyformat.so
+lib/openbabel/3.1.0/amberformat.so
+lib/openbabel/3.1.0/aoforceformat.so
+lib/openbabel/3.1.0/asciiformat.so
+lib/openbabel/3.1.0/balstformat.so
+lib/openbabel/3.1.0/bgfformat.so
+lib/openbabel/3.1.0/boxformat.so
+lib/openbabel/3.1.0/cacaoformat.so
+lib/openbabel/3.1.0/cacheformat.so
+lib/openbabel/3.1.0/carformat.so
+lib/openbabel/3.1.0/castepformat.so
+lib/openbabel/3.1.0/cccformat.so
+lib/openbabel/3.1.0/cdxmlformat.so
+lib/openbabel/3.1.0/chem3dformat.so
+lib/openbabel/3.1.0/chemdoodlejsonformat.so
+lib/openbabel/3.1.0/chemdrawcdx.so
+lib/openbabel/3.1.0/chemdrawct.so
+lib/openbabel/3.1.0/chemkinformat.so
+lib/openbabel/3.1.0/chemtoolformat.so
+lib/openbabel/3.1.0/cifformat.so
+lib/openbabel/3.1.0/cmlformat.so
+lib/openbabel/3.1.0/cmlreactformat.so
+lib/openbabel/3.1.0/cofformat.so
+lib/openbabel/3.1.0/confabreport.so
+lib/openbabel/3.1.0/copyformat.so
+lib/openbabel/3.1.0/crkformat.so
+lib/openbabel/3.1.0/crystal09format.so
+lib/openbabel/3.1.0/cssrformat.so
+lib/openbabel/3.1.0/daltonformat.so
+lib/openbabel/3.1.0/dlpolyformat.so
+lib/openbabel/3.1.0/dmolformat.so
+lib/openbabel/3.1.0/exyzformat.so
+lib/openbabel/3.1.0/fastaformat.so
+lib/openbabel/3.1.0/fastsearchformat.so
+lib/openbabel/3.1.0/fchkformat.so
+lib/openbabel/3.1.0/featformat.so
+lib/openbabel/3.1.0/fhformat.so
+lib/openbabel/3.1.0/fhiaimsformat.so
+lib/openbabel/3.1.0/fingerprintformat.so
+lib/openbabel/3.1.0/fpsformat.so
+lib/openbabel/3.1.0/freefracformat.so
+lib/openbabel/3.1.0/gamessformat.so
+lib/openbabel/3.1.0/gamessukformat.so
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