bin: Do not set environment variables set by guix shell.

The Guix python package accepts GUIX_PYTHONPATH instead of
PYTHONPATH. `guix shell' sets GI_TYPELIB_PATH, GIO_EXTRA_MODULES,
GUIX_GTK3_PATH, GUIX_PYTHONPATH, PATH, R_LIB_SITE and XDG_DATA_DIRS
when necessary. There is no need to set these environment variables
explicitly.

* bin/genenetwork2: Do not set GI_TYPELIB_PATH, GIO_EXTRA_MODULES,
GUIX_GTK3_PATH, PATH, PYTHONPATH, R_LIBS_SITE and XDG_DATA_DIRS.
* README.md [Development]: Remove paragraph on injecting python
modules locally.

1 files changed, 0 insertions, 34 deletions

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 93ab02f8..934a10d8 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -91,14 +91,7 @@ fi
 export GN2_SETTINGS=$settings     # Python
 echo GN2_SETTINGS=$settings
 
-export PATH=$GN2_PROFILE/bin:$PATH
-export PYTHONPATH="$GN2_PROFILE/lib/python3.8/site-packages" # never inject another PYTHONPATH!!
-export R_LIBS_SITE=$GN2_PROFILE/site-library
 export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript
-export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0"
-export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0"
-export XDG_DATA_DIRS="$GN2_PROFILE/share"
-export GIO_EXTRA_MODULES="$GN2_PROFILE/lib/gio/modules"
 export LC_ALL=C # FIXME
 export GUIX_GENENETWORK_FILES="$GN2_PROFILE/share/genenetwork2"
 export PLINK_COMMAND="$GN2_PROFILE/bin/plink2"
@@ -106,25 +99,6 @@ export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma"
 if [ -z $GEMMA_WRAPPER_COMMAND ]; then
     export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper"
 fi
-while IFS=":" read -ra PPATH; do
-    for PPART in "${PPATH[@]}"; do
-        if [ ! -d $PPART ] ; then echo "$PPART in PYTHONPATH not valid $PYTHONPATH" ; exit 1 ; fi
-    done
-done <<< "$PYTHONPATH"
-if [ ! -d $R_LIBS_SITE ] ; then echo "R_LIBS_SITE not valid "$R_LIBS_SITE ; exit 1 ; fi
-if [ -z $PYTHONPATH ] ; then
-    echo "ERROR PYTHONPATH has not been set - use GN2_PROFILE!"
-    exit 1
-fi
-if [ ! -d $R_LIBS_SITE ] ; then
-    echo "ERROR R_LIBS_SITE has not been set correctly (we only allow one path) - use GN2_PROFILE!"
-    echo "Paste into your shell the output of (for example)"
-    echo "guix package -p \$GN2_PROFILE --search-paths"
-    exit 1
-fi
-
-# We may change this one:
-export PYTHONPATH=$PYTHON_GN_PATH:$GN2_BASE_DIR/wqflask:$GN3_PYTHONPATH:$PYTHONPATH
 
 # Our UNIX TMPDIR defaults to /tmp - change this on a shared server
 if [ -z $TMPDIR ]; then
@@ -140,7 +114,6 @@ set|grep TMPDIR
 if [ "$1" = '-c' ] ; then
     cd $GN2_BASE_DIR/wqflask
     cmd=${2#wqflask/}
-    echo PYTHONPATH=$PYTHONPATH
     shift ; shift
     echo RUNNING COMMAND $cmd $*
     python $cmd $*
@@ -151,7 +124,6 @@ fi
 if [ "$1" = "-cli" ] ; then
     cd $GN2_BASE_DIR/wqflask
     cmd=$2
-    echo PYTHONPATH=$PYTHONPATH
     shift ; shift
     echo RUNNING COMMAND $cmd $*
     $cmd $*
@@ -160,14 +132,12 @@ fi
 if [ "$1" = '-gunicorn' ] ; then
     cd $GN2_BASE_DIR/wqflask
     cmd=$2
-    echo PYTHONPATH=$PYTHONPATH
     echo RUNNING gunicorn $cmd
     gunicorn $cmd
     exit $?
 fi
 if [ "$1" = '-gunicorn-dev' ] ; then
     cd $GN2_BASE_DIR/wqflask
-    echo PYTHONPATH=$PYTHONPATH
     if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
     cmd="--bind 0.0.0.0:$SERVER_PORT --workers=1 --timeout 180 --reload wsgi"
     echo RUNNING gunicorn $cmd
@@ -176,7 +146,6 @@ if [ "$1" = '-gunicorn-dev' ] ; then
 fi
 if [ "$1" = '-gunicorn-prod' ] ; then
     cd $GN2_BASE_DIR/wqflask
-    echo PYTHONPATH=$PYTHONPATH
     if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
     PID=$TMPDIR/gunicorn.$USER.pid
     cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID --workers 20 --keep-alive 6000 --max-requests 100 --max-requests-jitter 30 --timeout 1200 wsgi"
@@ -190,9 +159,6 @@ echo -n "dir $TMPDIR
 dbfilename gn2.rdb
 " | redis-server - &
 
-# Overrides for packages that are not yet public (currently r-auwerx)
-# export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib
-
 # Start the flask server running GN2
 cd $GN2_BASE_DIR/wqflask
 echo "Starting with $settings"