Merge branch 'mnt/devel-base-environment' into 'master'

Mnt/devel base environment

Closes #1 and #2

See merge request !6

CHANGELOG.md

 # FSL base project changelog
 
+## 2101.3 (Thursday 14th January 2021)
 
-## 2101.0 (Monday 4th January 2020)
+ - The `$FSLDIR/etc/fslconf/fsl.sh` script now automatically adds
+   `$FSLDIR/share/fsl/bin/` to the `$PATH`, for official
+   (`fslinstaller`-installed) FSL installations.
+ - The `$FSLDIR/etc/fslconf/fsl-devel.sh` script now activates the `$FSLDIR`
+   conda environment, for official (`fslinstaller`-installed) FSL
+   installations.
+ - The `$FSLDIR/etc/fslconf/fsl-devel.sh` script now assigns default values
+   to `$FSLDEVDIR` and `$FSLCONFDIR`, if they are not set by the user.
+
+
+## 2101.2 (Friday 8th January 2021)
+
+ - Removed the legacy `bin/fsl_sub` script - `fsl-sub` is now available on
+   conda, so can be listed as a dependency of the `fsl/base` project.
+
+
+## 2101.1 (Tuesday 5th January 2021)
+
+ - Move contents of `config/common/` into `config/` - there is no need for
+   a separate directory level now that we aren't maintaining separate
+   configurations for different architectures/compilers.
+ - The default C++ compilation standard is now `-std=c++11` (previously
+   it was `-std=c++98`/`-ansi`).
+ - Allow projects to set custom C preprocessor flags, via `USRCPPFLAGS`.
+
+
+## 2101.0 (Monday 4th January 2021)
 
  - Moved the copyright insertion machinery (script and templates) from
    `config/common/` into `share/fsl/`.

etc/fslconf/fsl-devel.sh

 # FSL configuration file for developers
-#  - to be sourced by the user, typically in .bashrc or equivalent
 #
-# Written by Mark Jenkinson
-#  FMRIB Analysis Group, University of Oxford
+# This file must be sourced in order to compile
+# Makefile-based FSL projects.
+#
+# $FSLDIR must be set before this script is called.
+#
+# Standard environment configuration for developing FSL is:
+#   export FSLDIR=/usr/local/fsl
+#   source $FSLDIR/etc/fslconf/fsl-devel.sh
+#
 
 # SHBASECOPYRIGHT
 
-FSLCONFDIR=$FSLDIR/config
 
-export FSLCONFDIR
+# If this is an official (fslinstaller-installed)
+# FSL installation, we activate the $FSLDIR conda
+# environment so that we have access to its compiler
+# toolchain (if one is installed).
+if [ -f "$FSLDIR/share/fsl/base_environment" ]; then
+  baseenv=$(cat "$FSLDIR/share/fsl/base_environment")
+  source $baseenv/bin/activate $FSLDIR
+fi
+
+# FSLCONFDIR contains the FSL Makefile machinery
+# for compiling and installing FSL Makefile-based
+# projects.
+if [ ! -d "$FSLCONFDIR" ]; then
+  export FSLCONFDIR=$FSLDIR/config
+fi
+
+# FSLDEVDIR is an optional installation destination
+# for development, so that locally built projects
+# can be installed separately from FSLDIR.
+if [ ! -d "$FSLDEVDIR" ]; then
+  export FSLDEVDIR=$FSLDIR
+fi
 
 source $FSLDIR/etc/fslconf/fsl.sh

etc/fslconf/fsl.sh

 # FSL configuration file
 #  - to be sourced by the user, typically in .bashrc or equivalent
 #
+# $FSLDIR must be set before this script is called.
+#
+# Standard environment configuration for using FSL is:
+#   export FSLDIR=/usr/local/fsl
+#   source $FSLDIR/etc/fslconf/fsl.sh
+#
+# See fsl-devel.sh if you are a developer.
+#
 # Written by Mark Jenkinson
 #  FMRIB Analysis Group, University of Oxford
 
@@ -9,42 +17,64 @@
 
 #### Set up standard FSL user environment variables ####
 
+# If this is an official (fslinstaller-installed)
+# FSL installation, wrappers to FSL executables
+# will have been created in $FSLDIR/share/fsl/bin/
+# We add this to the $PATH, rather than adding
+# $FSLDIR/bin/ to the path, to avoid clobbering
+# the user's environment with other executalbes
+# that have been installed into $FSLDIR/bin/ (e.g.
+# python).
+#
+# The fslinstaller creates a file called
+# base_environment when it installs official
+# FSL installations.
+#
+# If this is a manually managed installation, it
+# is the user's responsibility to add $FSLDIR/bin
+# to the $PATH
+if [ -f "$FSLDIR/share/fsl/base_environment" ]; then
+  export PATH=$FSLDIR/share/fsl/bin:$PATH
+fi
+
 # The following variable selects the default output image type
-# Legal values are:  ANALYZE  NIFTI  NIFTI_PAIR  ANALYZE_GZ  NIFTI_GZ  NIFTI_PAIR_GZ
+# Legal values are:
+#   NIFTI
+#   NIFTI2
+#   NIFTI_PAIR
+#   NIFTI2_PAIR
+#   NIFTI_GZ
+#   NIFTI2_GZ
+#   NIFTI_PAIR_GZ
+#   NIFTI2_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
+# to write files with a different format
+export FSLOUTPUTTYPE=NIFTI_GZ
 
 # 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
+# FSL programs to soldier on after detecting multiple image
+# files with the same basename ( e.g. epi.hdr and epi.nii )
+export FSLMULTIFILEQUIT=TRUE
 
 
 # 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
+# or replaced by different programs
 
-export FSLTCLSH FSLWISH
+export FSLTCLSH=$FSLDIR/bin/fsltclsh
+export FSLWISH=$FSLDIR/bin/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
+export FSLLOCKDIR=
+export FSLMACHINELIST=
+export 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
+export FSLGECUDAQ=cuda.q
 
 
 ###################################################