Change working dir to pwd so output folder ends up in the right place
@@ -92,7 +92,8 @@ echo "Building surface model using config file $input/basic_surface.json"
python -c "from isofit.utils import surface_model; surface_model('$input/basic_surface.json')"
# Run isofit
-isofit_cmd="""python $apply_oe_exe $rdn_path $loc_ort_path $obs_ort_path output ang --presolve=1 --empirical_line=1 \
+working_dir=$(pwd)
+isofit_cmd="""python $apply_oe_exe $rdn_path $loc_ort_path $obs_ort_path $working_dir ang --presolve=1 --empirical_line=1 \
--emulator_base=$EMULATOR_DIR --n_cores 8 --wavelength_path $input/wavelengths.txt \
--surface_path $input/basic_surface.mat"""
echo "Executing command: $isofit_cmd"
