fixed python file headers

4 files changed, 144 insertions, 3 deletions

diff --git a/.SRCINFO b/.SRCINFO
index a0ac8e29275c..659b726fb25c 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -8,8 +8,10 @@ pkgbase = eman2
 	options = !strip
 	source = http://ncmi.bcm.edu/ncmi/software/counter_222/software_133/manage_addProduct/NCMI/attendee_factory/eman2.12.linux64.tar.gz
 	source = eman2.sh
+	source = eman2-installer
 	md5sums = 2e21b310c957fc3b21f8c6b551b60fdb
 	md5sums = SKIP
+	md5sums = SKIP
 
 pkgname = eman2
 
diff --git a/PKGBUILD b/PKGBUILD
index e51fdfd1823b..50f466882ad2 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -13,12 +13,22 @@ url="http://blake.bcm.edu/emanwiki/EMAN2"
 license=('GPL')
 depends=()
 source=("http://ncmi.bcm.edu/ncmi/software/counter_222/software_133/manage_addProduct/NCMI/attendee_factory/eman$pkgver.linux64.tar.gz" 
-'eman2.sh')
-md5sums=('2e21b310c957fc3b21f8c6b551b60fdb' 'SKIP')
+'eman2.sh' 'eman2-installer')
+md5sums=('2e21b310c957fc3b21f8c6b551b60fdb' 'SKIP' 'SKIP')
 options=(!strip)
 
+prepare () {
+	cd "$srcdir/EMAN2"
+	rm eman2-installer
+	cp ../eman2-installer .
+}
 build() {
 	cd "$srcdir/EMAN2"
+#	sed -e 's,export EMAN2DIR=`pwd`,export EMAN2DIR=/opt/eman2,' $srcdir/EMAN2/eman2-installer > 
+#$srcdir/EMAN2/eman2-installer.tmp
+#	mv $srcdir/EMAN2/eman2-installer.tmp $srcdir/EMAN2/eman2-installer
+#	chmod +x eman2-installer	
+#	EMAN2DIR=pwd
 	./eman2-installer
 }
 
diff --git a/eman2-installer b/eman2-installer
new file mode 100755
index 000000000000..8254f7181222
--- /dev/null
+++ b/eman2-installer
@@ -0,0 +1,129 @@
+#!/bin/bash
+
+# Purpose: Assist to install eman2 binary release.
+# Usage: eman2-installer
+# Date: 9/1/2004, by Liwei Peng
+# Date: 10/25/2007, modified by Grant Tang for EMAN2
+# Date: 1/28/2009, modified by Grant Tang for EMAN2 Pythn2.6
+# Date: 2/12/2009, change back to Python 2.5.4, Grant Tang
+# Date: 9/1/2009, --disable_cache, Grant Tang
+# Date: 6/30/2013, Significant updates by Ian Rees for new build system.
+# Date: 8/01/2013, changed disable_cache to disable_gui
+
+usage()
+{
+	echo "usage: `basename $0` [--disable_gui]"
+	echo "       --disable_gui: no GUI"
+	exit 0
+}
+
+setup_shell() {
+	# Setup bashrc or cshrc
+	MYSHELL=`basename ${SHELL}`
+	RCFILE=""
+	if test ${MYSHELL} = "tcsh" || test ${MYSHELL} = "csh"; then
+		RCFILE=".cshrc"
+		setup_csh ${EMAN2DIR}/eman2${RCFILE}
+	elif test ${MYSHELL} = "bash" || test ${MYSHELL} = "sh"; then
+		RCFILE=".bashrc"
+		setup_bash ${EMAN2DIR}/eman2$RCFILE
+	elif test ${MYSHELL} = "zsh"; then
+		RCFILE=".zshrc"
+		setup_bash ${EMAN2DIR}/eman2$RCFILE
+	else
+		echo "Unkown shell. You will need set up your enviroment variables manually."
+	fi
+	if test "X${RCFILE}" != "X"; then
+    	echo "Please add the following line to the end of your ${HOME}/${RCFILE} :"
+    	echo "source ${EMAN2DIR}/eman2${RCFILE}"
+	fi
+}
+
+setup_csh() {
+	OUT=$1
+	echo "setenv EMAN2DIR ${EMAN2DIR}" > ${OUT}
+	echo 'setenv PATH ${EMAN2DIR}/bin:${EMAN2DIR}/extlib/bin:${PATH}' >> ${OUT}
+	echo 'if ($?PYTHONPATH == 0) then' >> ${OUT}
+	echo '    setenv PYTHONPATH ${EMAN2DIR}/lib:${EMAN2DIR}/bin' >> ${OUT}
+	echo 'else' >> ${OUT}
+	echo '    setenv PYTHONPATH ${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}' >> ${OUT}
+	echo 'endif' >> ${OUT}
+	echo 'alias sparx sx.py' >> ${OUT}
+	echo "setenv LC_CTYPE=en_US.utf8"
+	echo "setenv LC_ALL=en_US.utf8"
+}
+
+setup_bash()
+{
+	OUT=$1
+	echo "export EMAN2DIR=${EMAN2DIR}" > ${OUT}
+	echo 'export PATH=${EMAN2DIR}/bin:${EMAN2DIR}/extlib/bin:$PATH' >> ${OUT}
+	echo 'export PYTHONPATH=${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}' >> ${OUT}
+	echo 'export LC_CTYPE=en_US.utf8'
+	echo 'export LC_ALL=en_US.utf8'
+	echo 'alias sparx=sx.py' >> ${OUT}
+}
+
+setup_python()
+{
+	EMAN2PYTHON=$1
+    # Update python interpreter
+	find ${EMAN2DIR}/extlib/bin -name "ipython" \
+		-exec sed -i "s%^\#\!.*python.*$%\#\!/opt/eman2/extlib/bin/python%" {} \;
+	find ${EMAN2DIR}/test ${EMAN2DIR}/bin ${EMAN2DIR}/lib ${EMAN2DIR}/examples -name "*.py" \
+		-exec sed -i "s%^\#\!.*python.*$%\#\!/opt/eman2/extlib/bin/python%" {} \;
+	find ${EMAN2DIR}/test ${EMAN2DIR}/bin ${EMAN2DIR}/lib ${EMAN2DIR}/examples -name "*.py" \
+		-exec chmod a+x {} \;
+    # ... and for SPARX
+	# sed -i "s%^\#\!.*python.*$%\#\!${EMAN2PYTHON}%" ${EMAN2DIR}/bin/sparx
+}
+
+disable_cache()
+{
+	cd ${EMAN2DIR}/lib
+	echo "start substituting..."
+	mv global_def.py global_def.py.bak
+	sed -e 's/CACHE_DISABLE = False/CACHE_DISABLE = True/'  global_def.py.bak > global_def.py
+	rm -f  global_def.py.bak
+	cd ${EMAN2DIR}/bin
+	mv sx_real.py sx_real.py.bak
+	sed  -e 's/GUIUSE = True/GUIUSE = False/' sx_real.py.bak > sx_real.py
+	rm -f  sx_real.py.bak
+	cd ${EMAN2DIR}
+}
+
+main()
+{
+	# Use the run directory as the EMAN2DIR.
+	export EMAN2DIR=`pwd`
+	export EMAN2PYTHON=${EMAN2DIR}/extlib/bin/python
+	
+	# Setup the Python interpreter
+	if [ -f $EMAN2PYTHON ]
+		then
+			setup_python $EMAN2PYTHON
+		fi
+
+	# Setup bashrc or cshrc
+	setup_shell
+
+	# This is for Fedora Linux's SELinux limitation on shared libraries
+	cd ${EMAN2DIR}/lib
+	if [ -x /usr/bin/chcon ]; then
+		chcon -t texrel_shlib_t *.so 2>/dev/null >/dev/null
+	fi
+	cd ${EMAN2DIR}
+
+	# # This is for Pawel's cluster working
+	local value1=$1	
+	if [[ "${value1}" = "--disable_gui" ]]; then
+		disable_cache
+	fi
+
+	#for mpi_eman compilation
+	# cd ${EMAN2DIR}/mpi_eman
+    # sed -i 's,/usr/include/python2.6,${EMAN2DIR}/Python/include/python2.7,g' Makefile.*
+}
+
+main $1
+exit 0
diff --git a/eman2.sh b/eman2.sh
index 3ad2f0523e19..a2b8e8eda9ff 100644
--- a/eman2.sh
+++ b/eman2.sh
@@ -1,4 +1,4 @@
-source /opt/eman2/eman2.bashrc
+#source /opt/eman2/eman2.bashrc
 export EMAN2DIR=/opt/eman2
 export PATH=$PATH:${EMAN2DIR}/bin:${EMAN2DIR}/extlib/bin
 export PYTHONPATH=${PYTHONPATH}:${EMAN2DIR}/lib:${EMAN2DIR}/bin