Merge branch 'rf/copyrights' into 'master'

Rf/copyrights

See merge request !3

CHANGELOG.md

 # FSL base project changelog
 
 
+## 2101.0 (Monday 4th January 2020)
+
+ - Moved the copyright insertion machinery (script and templates) from
+   `config/common/` into `share/fsl/`.
+ - Unify `fsl.sh` and `fsl-devel.sh` so the latter simply invokes the former.
+ - Fix an issue with argument pass-through in the `fslpython[w]` wrapper
+   scripts.
+ - Removed the `etc/fslconf/fslmachtype.sh` script, as neither it, nor the
+   `FSLMACHTYPE` environment variable, are used by anything.
+
+
 ## 2012.0 (Wednesday 2nd December 2020)
 
  - Added `creeateFSLWrapper` and `removeFSLWrapper`, utility commands, which

README.md

@@ -4,9 +4,9 @@ This project contains the "base" of an FSL installation. It includes:
 
  - Configuration scripts for setting up an environment to use FSL
  - Makefile infrastructure used to compile and install FSL projects
- - Various other small configuration and auxillary files
+ - Various other small configuration, data, and auxillary files
 
-Prior to FSL 6.0.X, the contents of this project were provided by the
+Prior to FSL 6.1.X, the contents of this project were provided by the
 [etc](https://git.fmrib.ox.ac.uk/fsl/etc) and
 [config](https://git.fmrib.ox.ac.uk/fsl/config) projects.
 

bin/fslpython

@@ -5,4 +5,4 @@ if [ "$FSLDIR" = "" ] ; then
   exit 1
 fi
 
-exec ${FSLDIR}/bin/python $*
+exec ${FSLDIR}/bin/python "$@"

bin/fslpythonw

@@ -6,7 +6,7 @@ if [ "$FSLDIR" = "" ] ; then
 fi
 
 if [ -e ${FSLDIR}/bin/pythonw ]; then
-  exec ${FSLDIR}/bin/pythonw $*
+  exec ${FSLDIR}/bin/pythonw "$@"
 else
-  exec ${FSLDIR}/bin/pythonw $*
+  exec ${FSLDIR}/bin/python "$@"
 fi

config/common/rules.mk

@@ -14,7 +14,7 @@ clean:
       ${XFILES} ${FXFILES} ${SOFILES} ${AFILES} ${TESTXFILES}
 
 insertcopyright:
-	${FSLCONFDIR}/common/insertcopyright * */*
+	${FSLDIR}/share/fsl/sbin/insertcopyright * */*
 
 depend:
 	${RM} -f depend.mk

etc/fslconf/fsl-devel.sh

-# FSL configuration file 
+# FSL configuration file for developers
 #  - to be sourced by the user, typically in .bashrc or equivalent
-#  - note that the user should set 
-
+#
 # Written by Mark Jenkinson
 #  FMRIB Analysis Group, University of Oxford
 
 # SHBASECOPYRIGHT
 
-
-#### Set up standard FSL user environment variables ####
-
-# The following variable selects the default output image type
-# Legal values are:  ANALYZE  NIFTI  NIFTI_PAIR  ANALYZE_GZ  NIFTI_GZ  NIFTI_PAIR_GZ
-# This would typically be overwritten in ${HOME}/.fslconf/fsl.sh if the user wished
-#  to write files with a different format
-FSLOUTPUTTYPE=NIFTI_GZ
-export FSLOUTPUTTYPE
-
-# Comment out the definition of FSLMULTIFILEQUIT to enable 
-#  FSL programs to soldier on after detecting multiple image
-#  files with the same basename ( e.g. epi.hdr and epi.nii )
-FSLMULTIFILEQUIT=TRUE ; export FSLMULTIFILEQUIT
-
-
-# The following variables specify paths for programs and can be changed
-#  or replaced by different programs ( e.g. FSLDISPLAY=open   for MacOSX)
-
-FSLTCLSH=$FSLDIR/bin/fsltclsh
-FSLWISH=$FSLDIR/bin/fslwish
-
-export FSLTCLSH FSLWISH 
-
-# The following variables are used for running code in parallel across
-#  several machines ( i.e. for FDT )
-
-FSLLOCKDIR=
-FSLMACHINELIST=
-FSLREMOTECALL=
-
-export FSLLOCKDIR FSLMACHINELIST FSLREMOTECALL
-
-# The following variables are used to configure CUDA capable queues - if you
-# are using Grid Engine then this queue will be used to enqueue tasks that
-# support execution on NVIDIA CUDA hardware.
-FSLGECUDAQ=cuda.q
-
-export FSLGECUDAQ
-
-# Set up development variables (not for the faint-hearted)
-
 FSLCONFDIR=$FSLDIR/config
-FSLMACHTYPE=`$FSLDIR/etc/fslconf/fslmachtype.sh`
-
-export FSLCONFDIR FSLMACHTYPE
-
-
-###################################################
-### Add other global environment variables here ###
-###      or change the definitions above        ###
-###################################################
-
-
-# USER VARIABLES HERE
-
-
-###################################################
-####    DO NOT ADD ANYTHING BELOW THIS LINE    ####
-###################################################
-
-if [ -f /usr/local/etc/fslconf/fsl.sh ] ; then
-  . /usr/local/etc/fslconf/fsl.sh ;
-fi
-
-
-if [ -f /etc/fslconf/fsl.sh ] ; then
-  . /etc/fslconf/fsl.sh ;
-fi
 
+export FSLCONFDIR
 
-if [ -f "${HOME}/.fslconf/fsl.sh" ] ; then
-  . "${HOME}/.fslconf/fsl.sh" ;
-fi
+source $FSLDIR/etc/fslconf/fsl.sh

etc/fslconf/fsl.csh

-# FSL configuration file 
+# FSL configuration file
 #  - to be sourced by the user, typically in .bashrc or equivalent
-#  - note that the user should set 
+#  - note that the user should set
 
 # Written by Mark Jenkinson
 #  FMRIB Analysis Group, University of Oxford
@@ -16,7 +16,7 @@
 #  to write files with a different format
 setenv FSLOUTPUTTYPE NIFTI_GZ
 
-# Comment out the definition of FSLMULTIFILEQUIT to enable 
+# Comment out the definition of FSLMULTIFILEQUIT to enable
 #  FSL programs to soldier on after detecting multiple image
 #  files with the same basename ( e.g. epi.hdr and epi.nii )
 setenv FSLMULTIFILEQUIT TRUE
@@ -31,9 +31,9 @@ setenv FSLWISH $FSLDIR/bin/fslwish
 # The following variables are used for running code in parallel across
 #  several machines ( i.e. for FDT )
 
-setenv FSLLOCKDIR 
-setenv FSLMACHINELIST 
-setenv FSLREMOTECALL 
+setenv FSLLOCKDIR
+setenv FSLMACHINELIST
+setenv FSLREMOTECALL
 
 # The following variables are used to configure CUDA capable queues - if you
 # are using Grid Engine then this queue will be used to enqueue tasks that
@@ -43,8 +43,6 @@ setenv FSLGECUDAQ cuda.q
 # Set up development variables (not for the faint-hearted)
 # Uncomment the following if you wish to compile FSL source code
 #setenv FSLCONFDIR $FSLDIR/config
-#setenv FSLMACHTYPE `$FSLDIR/etc/fslconf/fslmachtype.sh`
-
 
 ###################################################
 ### Add other global environment variables here ###

etc/fslconf/fsl.sh

-# FSL configuration file 
+# FSL configuration file
 #  - to be sourced by the user, typically in .bashrc or equivalent
-#  - note that the user should set 
-
+#
 # Written by Mark Jenkinson
 #  FMRIB Analysis Group, University of Oxford
 
@@ -17,7 +16,7 @@
 FSLOUTPUTTYPE=NIFTI_GZ
 export FSLOUTPUTTYPE
 
-# Comment out the definition of FSLMULTIFILEQUIT to enable 
+# Comment out the definition of FSLMULTIFILEQUIT to enable
 #  FSL programs to soldier on after detecting multiple image
 #  files with the same basename ( e.g. epi.hdr and epi.nii )
 FSLMULTIFILEQUIT=TRUE ; export FSLMULTIFILEQUIT
@@ -29,7 +28,7 @@ FSLMULTIFILEQUIT=TRUE ; export FSLMULTIFILEQUIT
 FSLTCLSH=$FSLDIR/bin/fsltclsh
 FSLWISH=$FSLDIR/bin/fslwish
 
-export FSLTCLSH FSLWISH 
+export FSLTCLSH FSLWISH
 
 # The following variables are used for running code in parallel across
 #  several machines ( i.e. for FDT )
@@ -47,13 +46,6 @@ FSLGECUDAQ=cuda.q
 
 export FSLGECUDAQ
 
-# Set up development variables (not for the faint-hearted)
-# Uncomment the following if you wish to compile FSL source code
-#FSLCONFDIR=$FSLDIR/config
-#FSLMACHTYPE=`$FSLDIR/etc/fslconf/fslmachtype.sh`
-
-#export FSLCONFDIR FSLMACHTYPE
-
 
 ###################################################
 ### Add other global environment variables here ###

etc/fslconf/fslmachtype.sh

-#!/bin/sh
-# FSL Host type identifier
-#  - Used by several scripts to identify the host type for build environment
-
-# Written by Duncan Mortimer
-#  FMRIB Analysis Group, University of Oxford
-
-# SHCOPYRIGHT
-
-
-#### Identify machine ####
-machtype=""
-
-system_type=`uname -s`
-case ${system_type} in
-    SunOS)
-        AWK=nawk
-        ;;
-    *)
-        AWK=awk
-        ;;
-esac
-
-gcc_version=`gcc -dumpversion 2> /dev/null`
-if [ $? -eq 0 ]; then
-    # GCC is installed
-    gcc_version=`echo $gcc_version | $AWK -F . '{ printf "%s.%s", $1,$2 }'`
-    gcc_host=`gcc -dumpmachine`
-
-    gcc_cpu_type=`echo $gcc_host | $AWK -F - '{ printf "%s", $1; }'`
-    gcc_os_vendor=`echo $gcc_host | $AWK -F - '{ printf "%s", $2; }'`
-    gcc_os_name=`echo $gcc_host | $AWK -F - '{ printf "%s", $3; }'`
-
-    case ${system_type} in
-        Darwin)
-            # We are going to build a universal (ppc32, ppc64, x86_32, x86_64)
-            #    combined binary, so we only need 1 host type
-            os_release=`uname -r | $AWK -F . '{ printf "%s", $1 }'`
-	    if [ $os_release -ge 12 ]; then
-		# Using LLVM/clang from now on
-		llvm_vstr=`cc -v 2>&1`
-		# Find the LLVM version and reduce to major.minor version number
-		llvm_v=`echo ${llvm_vstr} | awk '{ print $4 }' | cut -d . -f 1,2`
-		# Find the LLVM major version number
-		llvm_maj=`echo ${llvm_v} | cut -d . -f 1`
-		if [ ${llvm_maj} -ge 7 ]; then
-		    os_v=`echo ${llvm_vstr} | awk '{ print $7 }' | awk -F. '{ print $1 }' | sed 's/x86_64-//'`
-		else
-		    os_v=`echo ${llvm_vstr} | awk '{ print $11 }' | awk -F. '{ print $1 }' | sed 's/x86_64-//'`
-                fi
-		machtype=${os_v}-llvm${llvm_v}
-            elif [ $os_release -ge 8 ]; then
-                # This is 10.4 so Universal builds possible
-                gcc_host="${gcc_os_vendor}-${gcc_os_name}"
-                # Note, for BSDish platforms, gcc_os_name includes a version
-		machtype=${gcc_host}-gcc${gcc_version}
-            else
-	        # Prior to Tiger and gcc4, things were a mess...
-		gcc_host="${gcc_cpu_type}-${gcc_os_vendor}"
-		machtype=${gcc_host}-gcc${gcc_version}
-                # Note, gcc_os_vendor in this case is actually gcc_os_name above
-	    fi
-	    ;;
-        Linux)
-	    if [ "${gcc_cpu_type}" = "x86_64" -o "${gcc_cpu_type}" = "x86-64" ]; then
-		gcc_host="${gcc_os_name}_64"
-	    elif [ `echo ${gcc_cpu_type} | grep i.86` ]; then
-		gcc_host="${gcc_os_name}_32"
-	    else
-		gcc_host="${gcc_cpu_type}-${gcc_os_vendor}-${gcc_os_name}"
-            fi
-	    machtype=${gcc_host}-gcc${gcc_version}
-	    ;;
-	*)
-	    gcc_host="${gcc_cpu_type}-${gcc_os_vendor}-${gcc_os_name}"
-	    machtype=${gcc_host}-gcc${gcc_version}
-	    ;;
-    esac
-    
-fi
-echo ${machtype}
-exit 0
-

etc/fslversion

-6.0.5
+6.1.X
\ No newline at end of file

config/common/insertcopyright → share/fsl/sbin/insertcopyright

@@ -24,12 +24,12 @@ for fname in $@ ; do
     if [ $num1 != "0" ]; then
 	sed -n $com1 $fname > $fname.copytmp
     fi
-    cat ${FSLCONFDIR}/common/copyrights/ccopyright.c >> $fname.copytmp
+    cat ${FSLDIR}/share/fsl/copyrights/ccopyright.c >> $fname.copytmp
     sed -n $com2 $fname >> $fname.copytmp
     cp -f $fname.copytmp $fname
     rm -f $fname.copytmp
   fi
-  
+
   # Insert TCLCOPYRIGHT message
   num=`grep -n TCLCOPYRIGHT $fname | head -1 | cut -d':' -f1 `; export num
   if [ "X${num}X" != XX ] ; then
@@ -39,7 +39,7 @@ for fname in $@ ; do
     com2="${num2},\$p"; export com2
     rm -f $fname.copytmp
     sed -n $com1 $fname > $fname.copytmp
-    cat ${FSLCONFDIR}/common/copyrights/tclcopyright.tcl >> $fname.copytmp
+    cat ${FSLDIR}/share/fsl/copyrights/tclcopyright.tcl >> $fname.copytmp
     sed -n $com2 $fname >> $fname.copytmp
     cp -f $fname.copytmp $fname
     rm -f $fname.copytmp
@@ -54,14 +54,14 @@ for fname in $@ ; do
     com2="${num2},\$p"; export com2
     rm -f $fname.copytmp
     sed -n $com1 $fname > $fname.copytmp
-    cat ${FSLCONFDIR}/common/copyrights/shcopyright.sh >> $fname.copytmp
+    cat ${FSLDIR}/share/fsl/copyrights/shcopyright.sh >> $fname.copytmp
     echo "export LC_ALL=C" >> $fname.copytmp
     sed -n $com2 $fname >> $fname.copytmp
     cp -f $fname.copytmp $fname
     rm -f $fname.copytmp
   fi
 
-  # Insert SHBASECOPYRIGHT message                                                                                                                                                              
+  # Insert SHBASECOPYRIGHT message
   num=`grep -n SHBASECOPYRIGHT $fname | head -1 | cut -d':' -f1 `; export num
   if [ "X${num}X" != XX ] ; then
     num1=`echo "$num 1 - p" | dc`; export num1
@@ -70,11 +70,11 @@ for fname in $@ ; do
     com2="${num2},\$p"; export com2
     rm -f $fname.copytmp
     sed -n $com1 $fname > $fname.copytmp
-    cat ${FSLCONFDIR}/common/copyrights/shcopyright.sh >> $fname.copytmp
+    cat ${FSLDIR}/share/fsl/copyrights/shcopyright.sh >> $fname.copytmp
     sed -n $com2 $fname >> $fname.copytmp
     cp -f $fname.copytmp $fname
     rm -f $fname.copytmp
   fi
 
  fi
-done  
+done