diff options
| -rw-r--r-- | academic/avogadrolibs/README | 28 | ||||
| -rw-r--r-- | academic/avogadrolibs/avogadrolibs.SlackBuild | 142 | ||||
| -rw-r--r-- | academic/avogadrolibs/avogadrolibs.info | 16 | ||||
| -rw-r--r-- | academic/avogadrolibs/fix_cmake-find-package.diff | 42 | ||||
| -rw-r--r-- | academic/avogadrolibs/slack-desc | 19 |
5 files changed, 247 insertions, 0 deletions
diff --git a/academic/avogadrolibs/README b/academic/avogadrolibs/README new file mode 100644 index 0000000000..4877412d76 --- /dev/null +++ b/academic/avogadrolibs/README @@ -0,0 +1,28 @@ +Avogadro Libraries is a subproject of Avogadro 2 as implementation of +Avogadro 1.x mantained by OpenChemistry. It provides 3D rendering, +visualization, analysis and data processing useful in computational +chemistry, molecular modeling, bioinformatics, materials science, and +related areas. +Avogadro Libraries is a dependency required by the graphic interface +user Avogadro Application (avogadroapp). + +This slackbuild requires as needed some dependencies (autodetected) +that improve Avogadro Libraries. You can enable or disable them by +passing variables to the script +(e.g. VAR=yes|no ./avogadrolibs.SlackBuild): + +LIBMSYM=yes|no (default: yes, libmsym required) +SPGLIB=yes|no (default: yes, spglib required) +MMTF=yes|no (default: yes, mmtf-cpp required) +HDF5=yes|no (default: no, hdf5 required) + +The extension Avogadro Generators (disabled by default) installs +Python input generators that can be run by the Avogadro 2 application +(avogadroapp) to generate input for various codes (Dalton, Q-Chem, +Orca, NWChem, ecc.): these scripts will be installed in a location +where the Avogadro 2 application can find them if the Plugin +Downloader is executed from the graphic interface user. +To enable the extension the dependency pybind11 is required and you +have to pass the variable PYTHON=yes to the slackbuild script: + +PYTHON=yes ./avogadrolibs.SlackBuild diff --git a/academic/avogadrolibs/avogadrolibs.SlackBuild b/academic/avogadrolibs/avogadrolibs.SlackBuild new file mode 100644 index 0000000000..fc45449bca --- /dev/null +++ b/academic/avogadrolibs/avogadrolibs.SlackBuild @@ -0,0 +1,142 @@ +#!/bin/bash + +# Slackware build script for avogadrolibs + +# Copyright 2020-2022 Giancarlo Dessì, Cagliari, IT +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=avogadrolibs +VERSION=${VERSION:-1.95.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} +MVERSION=${MVERSION:-1.0.0} +CVERSION=${CVERSION:-1.0.1} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +#These are features which are disabled by default +USEHDF5="" ; [ "${HDF5:-no}" = "yes" ] && USEHDF5="-DUSE_HDF5=ON" +USEPYTHON="" ; [ "${PYTHON:-no}" = "yes" ] && USEPYTHON="-DUSE_PYTHON=ON" + +#These are features which are enabled by default +USELIBMSYM="" ; [ "${LIBMSYM:-yes}" = "no" ] && USELIBMSYM="-DUSE_LIBMSYM=OFF" +USESPGLIB="-DSPGLIB_INCLUDE_DIR=/usr/include/spglib" ; [ "${SPGLIB:-yes}" = "no" ] && \ + USESPGLIB="-DUSE_SPGLIB=OFF" +USEMMTF="" ; [ "${MMTF:-yes}" = "no" ] && USEMMTF="-DUSE_MMTF=OFF" + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION molecules crystals avogadrogenerators +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +# Following archives must be unpacked in /tmp since the build process +# searches them as parallel directories and tries to connect to github +# if not found +tar xvf $CWD/molecules-$MVERSION.tar.gz +tar xvf $CWD/crystals-$CVERSION.tar.gz +mv molecules-$MVERSION molecules +mv crystals-$CVERSION crystals +if [ "${PYTHON}" = "yes" ]; then + tar xvf $CWD/avogadrogenerators.tar.gz +fi + +# Now we can change directory to $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# fix issues that generate cmake warnings +patch -p1 < $CWD/fix_cmake-find-package.diff + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_POLICY_DEFAULT_CMP0072=NEW \ + -DENABLE_TESTING=OFF \ + -DENABLE_TRANSLATIONS=ON \ + $USEHDF5 \ + $USEPYTHON \ + $USELIBMSYM \ + $USESPGLIB \ + $USEMMTF \ + .. + make + make install DESTDIR=$PKG +cd .. + +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a *.md LICENSE $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +# Remove doc files installed by make install in /usr/share/doc/AvogadroLibs that are redundant +rm -rf $PKG/usr/share/doc + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/avogadrolibs/avogadrolibs.info b/academic/avogadrolibs/avogadrolibs.info new file mode 100644 index 0000000000..98b38a281f --- /dev/null +++ b/academic/avogadrolibs/avogadrolibs.info @@ -0,0 +1,16 @@ +PRGNAM="avogadrolibs" +VERSION="1.95.1" +HOMEPAGE="https://github.com/OpenChemistry/avogadrolibs" +DOWNLOAD="https://github.com/OpenChemistry/avogadrolibs/archive/1.95.1/avogadrolibs-1.95.1.tar.gz \ + https://github.com/OpenChemistry/molecules/archive/1.0.0/molecules-1.0.0.tar.gz \ + https://github.com/OpenChemistry/crystals/archive/1.0.1/crystals-1.0.1.tar.gz \ + https://github.com/giandex/misc/raw/main/avogadrogenerators.tar.gz" +MD5SUM="8e86fd39799bcc614f8982b3408f30b5 \ + bad118f80a942fe0f082b2a9075ae3b9 \ + b05b526928b89fd27a5784b24c419613 \ + 4d8fe7ddb99069d777bead7d261abac9" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="molequeue mmtf-cpp libmsym spglib" +MAINTAINER="Giancarlo Dessì" +EMAIL="slack@giand.it" diff --git a/academic/avogadrolibs/fix_cmake-find-package.diff b/academic/avogadrolibs/fix_cmake-find-package.diff new file mode 100644 index 0000000000..542919c2cc --- /dev/null +++ b/academic/avogadrolibs/fix_cmake-find-package.diff @@ -0,0 +1,42 @@ +--- avogadrolibs-1.95.1/cmake/FindSpglib.cmake 2022-17-04 15:40:00.000000000 +0200 ++++ avogadrolibs-1.95.1-fixed/cmake/FindSpglib.cmake 2022-17-04 15:40:01.000000000 +0200 +@@ -12,7 +12,7 @@ + set(SPGLIB_INCLUDE_DIRS "${SPGLIB_INCLUDE_DIR}") + + include(FindPackageHandleStandardArgs) +-find_package_handle_standard_args(SPGLIB DEFAULT_MSG SPGLIB_INCLUDE_DIR ++find_package_handle_standard_args(Spglib DEFAULT_MSG SPGLIB_INCLUDE_DIR + SPGLIB_LIBRARY) + + mark_as_advanced(SPGLIB_INCLUDE_DIR SPGLIB_LIBRARY) +--- avogadrolibs-1.95.1/cmake/FindLibArchive.cmake 2022-17-04 15:50:00.000000000 +0200 ++++ avogadrolibs-1.95.1-fixed/cmake/FindLibArchive.cmake 2022-17-04 15:50:01.000000000 +0200 +@@ -14,7 +14,7 @@ + set(LIBARCHIVE_LIBRARIES "${LIBARCHIVE_LIBRARY}") + + include(FindPackageHandleStandardArgs) +-find_package_handle_standard_args(LIBARCHIVE DEFAULT_MSG LIBARCHIVE_INCLUDE_DIR ++find_package_handle_standard_args(LibArchive DEFAULT_MSG LIBARCHIVE_INCLUDE_DIR + LIBARCHIVE_LIBRARY) + + mark_as_advanced(LIBARCHIVE_INCLUDE_DIR LIBARCHIVE_LIBRARY) +--- avogadrolibs-1.95.1/python/CMakeLists.txt 2022-17-04 16:00:00.000000000 +0200 ++++ avogadrolibs-1.95.1-fixed/python/CMakeLists.txt 2022-17-04 16:00:01.000000000 +0200 +@@ -1,7 +1,7 @@ + find_package(PythonInterp 3 REQUIRED) + find_package(PythonLibs 3 REQUIRED) + set(PYBIND11_PYTHON_VERSION "3" CACHE STRING "") +-set(PYBIND11_CPP_STANDARD "-std=c++11" CACHE STRING "") ++set(CMAKE_CXX_STANDARD 14 CACHE STRING "") + find_package(pybind11 REQUIRED) + + find_package(Eigen3 REQUIRED) +--- avogadrolibs-1.95.1/avogadro/qtplugins/quantuminput/CMakeLists.txt 2022-18-04 19:00:00.000000000 +0200 ++++ avogadrolibs-1.95.1-fixed/avogadro/qtplugins/quantuminput/CMakeLists.txt 2022-18-04 19:00:01.000000000 +0200 +@@ -41,3 +41,5 @@ + else() ++ if(USE_PYTHON) +- message("Avogadro Generators not found at ${_prefix}!") ++ message("Avogadro Generators not found at ${_prefix}!") ++ endif() + endif() diff --git a/academic/avogadrolibs/slack-desc b/academic/avogadrolibs/slack-desc new file mode 100644 index 0000000000..a04b7ca223 --- /dev/null +++ b/academic/avogadrolibs/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +avogadrolibs: avogadrolibs (Libraries for Avogadro 2) +avogadrolibs: +avogadrolibs: Avogadro libraries provide 3D rendering, visualization, analysis and +avogadrolibs: data processing useful in computational chemistry, molecular +avogadrolibs: modeling, bioinformatics, materials science, and related areas. +avogadrolibs: Avogadro 2 is being developed as part of the Open Chemistry project +avogadrolibs: at Kitware, along with companion tools and libraries to support. +avogadrolibs: +avogadrolibs: Homepage: https://github.com/OpenChemistry/avogadrolibs +avogadrolibs: +avogadrolibs: |