Add run.def for HydroLakes and Environment file

Tools/HydroDATA_shapefile/Environment_GEOM

+#!/bin/bash
+#
+#########################################
+#
+# Script to build and maintain en environment to run
+# the python code in this directory. We verify that
+# all needed packages are available.
+# This is based on the anaconda python system : https://www.anaconda.com/distribution/
+#
+# Usage : source Environment
+#
+#########################################
+#
+# Functions
+#
+function hasanaconda (){
+    ipsl="ipsl camelot climserv ciclad"
+    idris="idris jean-zay"
+    case $(hostname -d) in
+	climserv*|private.ipsl.fr|ipsl.polytechnique.fr)
+	    echo "IPSL"
+	    eval  "$1='ipsl'"
+	    ;;
+	idris*|jean-zay*)
+	    echo "IDRIS"
+	    eval "$1='idris'"
+	    ;;
+	*)
+	    echo "unknown machine : $(hostname -d)"
+	    eval "$1='unknown'"
+    esac
+}
+
+function checkenv (){
+    rm -f checkenv.py
+    cat <<EOF > checkenv.py
+from osgeo import ogr
+import netCDF4
+import configparser
+import numba
+import pyproj
+print ("OK")
+EOF
+    python checkenv.py > /dev/null
+    if [ $? -gt 0 ] ; then
+	echo "Environment not OK. Some packages must be missing."
+	echo "This was tested with the checkenv.py code."
+    else
+	rm -f checkenv.py
+    fi
+}
+#
+# Main
+#
+loc=''
+hasanaconda loc
+
+if [ loc != "unknown" ] ; then
+    #
+    # Make sure the right version of Python
+    #
+    case $loc in
+	"ipsl")
+	    #module unload python
+	    #module load python/3.6-anaconda50
+	    #
+	    # Test if the MPI environment is installed.
+	    #
+	    if [ ! -e ${HOME}/.conda/envs/GEOM ] ; then
+		#
+		# Create the MPI environment as it does not exist.
+		#
+		conda create -y -n GEOM -c conda-forge python=3.7.* cython GDAL pyproj rasterio configparser netcdf4 numba shapely pip
+		source activate GEOM
+                pip install argparse
+	    else
+		source activate GEOM
+	    fi
+	    ;;
+	"idris")
+	    module load python/3.7.3
+	    if [[ -L ${HOME}/.conda && -d ${HOME}/.conda ]] ; then
+		if [ ! -e ${WORK}/.conda/envs/GEOM ] ; then
+		    conda create -y -n GEOM -c conda-forge python=3.7.* cython GDAL pyproj rasterio configparser netcdf4 numba shapely pip
+		    conda activate GEOM
+                    pip install argparse
+		else
+		    conda activate GEOM
+                fi
+	    else
+		echo "Make sure \$HOME/.conda is a link to your \$WORK/.conda"
+	    fi
+	    ;;
+	*)
+	    echo "Environment for $loc is not foreseen yet"
+	    exit
+	    ;;
+	esac
+fi
+#
+# Verify we can load all the needed modules.
+#
+	
+checkenv

Tools/HydroDATA_shapefile/run.def.HydroLakes

+[OverAll]
+#
+EarthRadius = 6370000.
+#
+# If Debug = True, there will not have overlap calculation (everything = 1)
+# Quicker because it s the heavier step, allow to check if everything works
+#
+Debug = False
+
+# [DEF] input_type : geogrid, hydro
+#
+input_type = hydro
+dinput = /bdd/ORCHIDEE_Forcing/Routing/Hydro4ORCH/MERIT_Global.nc 
+
+# output file direction
+doutput = ./MERIT_frac_lakes.nc
+
+# Shapefile direction
+shpdir = /homedata/aschrapffer/TODEMTOOLS/HydroLAKES_polys_v10_shp/HydroLAKES_polys_v10.shp
+
+# Name of the output variable
+varnamefrac = lake_frac
+varnameid = lake_id