From 358548170ebead50e745f33b441ae25380fb603c Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Mon, 10 Mar 2025 14:47:13 +0100
Subject: [PATCH] pymol-open-source: update to 3.1.0

Version 2.5.0 was installed three years ago, Time to
move a bit forward.
---
 pymol-open-source-3.1.0-0.build.sh | 143 +++++++++++++++++++++++++++++
 1 file changed, 143 insertions(+)
 create mode 100755 pymol-open-source-3.1.0-0.build.sh

diff --git a/pymol-open-source-3.1.0-0.build.sh b/pymol-open-source-3.1.0-0.build.sh
new file mode 100755
index 0000000..adfdb3e
--- /dev/null
+++ b/pymol-open-source-3.1.0-0.build.sh
@@ -0,0 +1,143 @@
+#! /bin/bash
+
+# COOKIE=$(mcookie|cut -c-8); grep -v V_GREP_ME $0 > /dev/shm/runme-$COOKIE.sh ; sleep 0.3; exec bash /dev/shm/runme-$COOKIE.sh
+# TESTING=1
+
+PKG=pymol-open-source
+VERSION=3.1.0
+BUILD=0
+
+PREFIX=/pkg/$PKG-$VERSION-$BUILD
+if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$PKG-$VERSION-$BUILD ; fi
+
+PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
+
+set -eu
+umask 022
+
+BUILD_TMPDIR=/scratch/local2/$PKG-$VERSION-$BUILD.$USER.build.tmp
+
+test -d $BUILD_TMPDIR && ( chmod -R u+rwx $BUILD_TMPDIR || true ; rm -rf $BUILD_TMPDIR )
+export TMPDIR=$BUILD_TMPDIR
+export HOME=$BUILD_TMPDIR/home
+
+exec </dev/null
+
+mkdir -p $PREFIX
+cat >$PREFIX/profile <<-EOF
+	# pymol is build with current system python-3.12.8-0, if it is phased out, source it ...
+	PYFP='3.12.8.*Jan  6 2025, 13:15:47'
+	python -VV | grep -q "\$PYFP" || . /pkg/python-3.12.8-0/profile
+
+	PATH=$PREFIX/bin:\$PATH
+	export LD_LIBRARY_PATH=$PREFIX/lib\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH}
+	PKG_CONFIG_PATH=$PREFIX/lib/pkgconfig\${PKG_CONFIG_PATH:+:\$PKG_CONFIG_PATH}
+	export PKG_CONFIG_PATH
+	if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} ; fi
+EOF
+. $PREFIX/profile
+
+NPROC=$(( $(nproc) * 4 / 5 + 1 ))
+export MAKEFLAGS="-j $NPROC"
+
+BUILDDIR=$PREFIX/build
+
+mkdir -p $BUILDDIR
+cd $BUILDDIR
+
+if /bin/true ; then
+
+(
+
+  # orig: https://github.com/msgpack/msgpack-c/archive/refs/tags/cpp-6.1.1.tar.gz
+  BEEHIVE=https://beehive.molgen.mpg.de/a0398798d8b9733bd5cd87a6d2f0b05f/msgpack-c-cpp-6.1.1.tar.gz
+  test -e msgpack-c-cpp-6.1.1.tar.gz || wget -nv $BEEHIVE
+  test -d msgpack-c-cpp-6.1.1 || tar -xf msgpack-c-cpp-6.1.1.tar.gz
+  cd msgpack-c-cpp-6.1.1
+
+  mkdir -p build
+  cd build
+
+  cmake \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX=$PREFIX \
+    -DCMAKE_VERBOSE_MAKEFILE=ON \
+    ..
+
+  make -j $NPROC
+  make install
+)
+
+(
+
+  # orig: https://github.com/rcsb/mmtf-cpp/archive/refs/tags/v1.1.0.tar.gz
+  BEEHIVE=https://beehive.molgen.mpg.de/ec961ff406a1636b4c5a25de7d9bd47b/mmtf-cpp-1.1.0.tar.gz
+
+  test -e mmtf-cpp-1.1.0.tar.gz || wget -nv $BEEHIVE
+  test -d mmtf-cpp-1.1.0 || tar -xf mmtf-cpp-1.1.0.tar.gz
+  cd mmtf-cpp-1.1.0
+
+  mkdir -p build
+  cd build
+
+  cmake \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX=$PREFIX \
+    -DCMAKE_VERBOSE_MAKEFILE=ON \
+    -DCMAKE_PREFIX_PATH=$PREFIX \
+    ..
+
+  make -j $NPROC
+  make install
+)
+
+(
+
+  # orig: https://github.com/g-truc/glm/archive/refs/tags/1.0.1.tar.gz
+  BEEHIVE=https://beehive.molgen.mpg.de/f824ac50e16310a95279032f82cbd341/glm-1.0.1.tar.gz
+  test -e glm-1.0.1.tar.gz || wget -nv $BEEHIVE
+  test -d glm-1.0.1 || tar -xf glm-1.0.1.tar.gz
+  cd glm-1.0.1
+
+  mkdir -p build
+  cd build
+
+  cmake \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX=$PREFIX \
+    -DCMAKE_VERBOSE_MAKEFILE=ON \
+    -DCMAKE_PREFIX_PATH=$PREFIX \
+    -DGLM_TEST_ENABLE=OFF \
+    ..
+
+  make -j $NPROC
+  mkdir -p $PREFIX/include
+  cp -ax ../glm $PREFIX/include
+)
+
+fi
+
+(
+  # orig: https://github.com/schrodinger/pymol-open-source/archive/refs/tags/v3.1.0.tar.gz
+  BEEHIVE=https://beehive.molgen.mpg.de/459f483231e1d521824b0e74df5ba640/pymol-open-source-3.1.0.tar.gz
+  test -e pymol-open-source-3.1.0.tar.gz || wget -nv $BEEHIVE
+  test -d pymol-open-source-3.1.0 || tar -xf pymol-open-source-3.1.0.tar.gz
+  cd pymol-open-source-3.1.0
+
+  # patch setup.py, great, everthing else but a hack is a waste of time ...
+  # needed -lcurl -lhdf5_hl -lhdf5_cpp -lhdf5, hdf 5 is static, curl was forgotten ?
+  # old:   extra_link_args = ext_link_args,
+  # new:   extra_link_args = ['-lcurl', '-lhdf5_hl', '-lhdf5_cpp', '-lhdf5'] + ext_link_args,
+  sed -i -e '/\s\s*extra_link_args/ s/= /= \["-lcurl", "-lhdf5_hl", "-lhdf5_cpp", "-lhdf5"\] + /' setup.py
+
+  export PREFIX_PATH=$PREFIX
+  export CXXFLAGS='-I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2'
+
+  python setup.py build --use-msgpackc c++11
+  python setup.py install --prefix=$PREFIX
+
+  # autsch ...
+  sed -i -e  "s|/pkg/python-3.12.8-0/lib|$PREFIX/lib|"  $PREFIX/bin/pymol
+
+)
+