academic/avogadrolibs: Added (Libraries for Avogadro 2)
Signed-off-by: Dave Woodfall <dave@slackbuilds.org> Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Giancarlo Dessì
Willy Sudiarto Raharjo
parent
0ddfde4be4
commit
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Avogadro Libraries is a subproject of Avogadro 2 as implementation of
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Avogadro 1.x mantained by OpenChemistry. It provides 3D rendering,
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visualization, analysis and data processing useful in computational
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chemistry, molecular modeling, bioinformatics, materials science, and
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related areas.
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Avogadro Libraries is a dependency required by the graphic interface
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user Avogadro Application (avogadroapp).
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This slackbuild requires as needed some dependencies (autodetected)
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that improve Avogadro Libraries. You can enable or disable them by
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passing variables to the script
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(e.g. VAR=yes|no ./avogadrolibs.SlackBuild):
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LIBMSYM=yes|no (default: yes, libmsym required)
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SPGLIB=yes|no (default: yes, spglib required)
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MMTF=yes|no (default: yes, mmtf-cpp required)
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HDF5=yes|no (default: no, hdf5 required)
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The extension Avogadro Generators (disabled by default) installs
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Python input generators that can be run by the Avogadro 2 application
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(avogadroapp) to generate input for various codes (Dalton, Q-Chem,
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Orca, NWChem, ecc.): these scripts will be installed in a location
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where the Avogadro 2 application can find them if the Plugin
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Downloader is executed from the graphic interface user.
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To enable the extension the dependency pybind11 is required and you
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have to pass the variable PYTHON=yes to the slackbuild script:
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PYTHON=yes ./avogadrolibs.SlackBuild
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#!/bin/bash
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# Slackware build script for avogadrolibs
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# Copyright 2020-2022 Giancarlo Dessì, Cagliari, IT
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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cd $(dirname $0) ; CWD=$(pwd)
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PRGNAM=avogadrolibs
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VERSION=${VERSION:-1.95.1}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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PKGTYPE=${PKGTYPE:-tgz}
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MVERSION=${MVERSION:-1.0.0}
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CVERSION=${CVERSION:-1.0.1}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
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echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
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exit 0
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fi
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#These are features which are disabled by default
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USEHDF5="" ; [ "${HDF5:-no}" = "yes" ] && USEHDF5="-DUSE_HDF5=ON"
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USEPYTHON="" ; [ "${PYTHON:-no}" = "yes" ] && USEPYTHON="-DUSE_PYTHON=ON"
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#These are features which are enabled by default
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USELIBMSYM="" ; [ "${LIBMSYM:-yes}" = "no" ] && USELIBMSYM="-DUSE_LIBMSYM=OFF"
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USESPGLIB="-DSPGLIB_INCLUDE_DIR=/usr/include/spglib" ; [ "${SPGLIB:-yes}" = "no" ] && \
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USESPGLIB="-DUSE_SPGLIB=OFF"
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USEMMTF="" ; [ "${MMTF:-yes}" = "no" ] && USEMMTF="-DUSE_MMTF=OFF"
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i586" ]; then
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SLKCFLAGS="-O2 -march=i586 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM-$VERSION molecules crystals avogadrogenerators
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tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
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# Following archives must be unpacked in /tmp since the build process
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# searches them as parallel directories and tries to connect to github
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# if not found
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tar xvf $CWD/molecules-$MVERSION.tar.gz
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tar xvf $CWD/crystals-$CVERSION.tar.gz
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mv molecules-$MVERSION molecules
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mv crystals-$CVERSION crystals
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if [ "${PYTHON}" = "yes" ]; then
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tar xvf $CWD/avogadrogenerators.tar.gz
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fi
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# Now we can change directory to $PRGNAM-$VERSION
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cd $PRGNAM-$VERSION
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# fix issues that generate cmake warnings
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patch -p1 < $CWD/fix_cmake-find-package.diff
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mkdir -p build
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cd build
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cmake \
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-DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \
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-DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \
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-DCMAKE_INSTALL_PREFIX=/usr \
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-DCMAKE_BUILD_TYPE=Release \
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-DCMAKE_POLICY_DEFAULT_CMP0072=NEW \
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-DENABLE_TESTING=OFF \
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-DENABLE_TRANSLATIONS=ON \
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$USEHDF5 \
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$USEPYTHON \
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$USELIBMSYM \
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$USESPGLIB \
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$USEMMTF \
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..
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make
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make install DESTDIR=$PKG
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cd ..
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rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a *.md LICENSE $PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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# Remove doc files installed by make install in /usr/share/doc/AvogadroLibs that are redundant
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rm -rf $PKG/usr/share/doc
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE
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@ -0,0 +1,16 @@
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PRGNAM="avogadrolibs"
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VERSION="1.95.1"
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HOMEPAGE="https://github.com/OpenChemistry/avogadrolibs"
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DOWNLOAD="https://github.com/OpenChemistry/avogadrolibs/archive/1.95.1/avogadrolibs-1.95.1.tar.gz \
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https://github.com/OpenChemistry/molecules/archive/1.0.0/molecules-1.0.0.tar.gz \
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https://github.com/OpenChemistry/crystals/archive/1.0.1/crystals-1.0.1.tar.gz \
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https://github.com/giandex/misc/raw/main/avogadrogenerators.tar.gz"
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MD5SUM="8e86fd39799bcc614f8982b3408f30b5 \
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bad118f80a942fe0f082b2a9075ae3b9 \
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b05b526928b89fd27a5784b24c419613 \
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4d8fe7ddb99069d777bead7d261abac9"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="molequeue mmtf-cpp libmsym spglib"
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MAINTAINER="Giancarlo Dessì"
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EMAIL="slack@giand.it"
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@ -0,0 +1,42 @@
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--- avogadrolibs-1.95.1/cmake/FindSpglib.cmake 2022-17-04 15:40:00.000000000 +0200
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+++ avogadrolibs-1.95.1-fixed/cmake/FindSpglib.cmake 2022-17-04 15:40:01.000000000 +0200
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@@ -12,7 +12,7 @@
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set(SPGLIB_INCLUDE_DIRS "${SPGLIB_INCLUDE_DIR}")
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include(FindPackageHandleStandardArgs)
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-find_package_handle_standard_args(SPGLIB DEFAULT_MSG SPGLIB_INCLUDE_DIR
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+find_package_handle_standard_args(Spglib DEFAULT_MSG SPGLIB_INCLUDE_DIR
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SPGLIB_LIBRARY)
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mark_as_advanced(SPGLIB_INCLUDE_DIR SPGLIB_LIBRARY)
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--- avogadrolibs-1.95.1/cmake/FindLibArchive.cmake 2022-17-04 15:50:00.000000000 +0200
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+++ avogadrolibs-1.95.1-fixed/cmake/FindLibArchive.cmake 2022-17-04 15:50:01.000000000 +0200
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@@ -14,7 +14,7 @@
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set(LIBARCHIVE_LIBRARIES "${LIBARCHIVE_LIBRARY}")
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include(FindPackageHandleStandardArgs)
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-find_package_handle_standard_args(LIBARCHIVE DEFAULT_MSG LIBARCHIVE_INCLUDE_DIR
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+find_package_handle_standard_args(LibArchive DEFAULT_MSG LIBARCHIVE_INCLUDE_DIR
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LIBARCHIVE_LIBRARY)
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mark_as_advanced(LIBARCHIVE_INCLUDE_DIR LIBARCHIVE_LIBRARY)
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--- avogadrolibs-1.95.1/python/CMakeLists.txt 2022-17-04 16:00:00.000000000 +0200
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+++ avogadrolibs-1.95.1-fixed/python/CMakeLists.txt 2022-17-04 16:00:01.000000000 +0200
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@@ -1,7 +1,7 @@
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find_package(PythonInterp 3 REQUIRED)
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find_package(PythonLibs 3 REQUIRED)
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set(PYBIND11_PYTHON_VERSION "3" CACHE STRING "")
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-set(PYBIND11_CPP_STANDARD "-std=c++11" CACHE STRING "")
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+set(CMAKE_CXX_STANDARD 14 CACHE STRING "")
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find_package(pybind11 REQUIRED)
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find_package(Eigen3 REQUIRED)
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--- avogadrolibs-1.95.1/avogadro/qtplugins/quantuminput/CMakeLists.txt 2022-18-04 19:00:00.000000000 +0200
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+++ avogadrolibs-1.95.1-fixed/avogadro/qtplugins/quantuminput/CMakeLists.txt 2022-18-04 19:00:01.000000000 +0200
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@@ -41,3 +41,5 @@
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else()
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+ if(USE_PYTHON)
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- message("Avogadro Generators not found at ${_prefix}!")
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+ message("Avogadro Generators not found at ${_prefix}!")
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+ endif()
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endif()
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@ -0,0 +1,19 @@
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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avogadrolibs: avogadrolibs (Libraries for Avogadro 2)
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avogadrolibs:
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avogadrolibs: Avogadro libraries provide 3D rendering, visualization, analysis and
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avogadrolibs: data processing useful in computational chemistry, molecular
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avogadrolibs: modeling, bioinformatics, materials science, and related areas.
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avogadrolibs: Avogadro 2 is being developed as part of the Open Chemistry project
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avogadrolibs: at Kitware, along with companion tools and libraries to support.
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avogadrolibs:
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avogadrolibs: Homepage: https://github.com/OpenChemistry/avogadrolibs
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avogadrolibs:
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avogadrolibs:
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