Fixes and changes since august 13

.gitignore

@@ -5,7 +5,9 @@
 *log
 *job.in
 *last.out
- /reference_comparison/AtlasExplorer/AtlasExplorer_reference_comparison_C-ESM-EP_*
-/reference_comparison/AtlasExplorer/AtlasExplorer_reference_comparison_C-ESM-EP.e921695
-/reference_comparison/AtlasExplorer/copy_html_error_page.sh.e921696
-slurm-*.out
+/*/*/*_comparison_C-ESM-EP_*
+/*/*/copy_html_error_page.sh.e*
+slurm-*.out
+/test_comparison
+/*/launched_jobs
+/*/mailjob

README.md

@@ -8,4 +8,6 @@ The result is a front html page with links to the html pages of the atlases of t
 Atlas Explorer is an easy and flexible way to produce an html page showing climatologies and difference maps (with a reference) on a set of datasets (simulations, models, different periods…).
 The main goal of the Atlas Explorer is to provide the user with a set of predefined features to assess a variable (plotting parameters, default observational reference) while keeping a lot of control on the diagnostics from only one parameter file.
 
-The C-ESM-EP works on Ciclad and Curie at IPSL, and at CNRM.
+The C-ESM-EP works on Spirit, Jean-Zay and Irene at IPSL, and at CNRM.
+
+Its documentation lies on its [GitHub repository Wiki](https://github.com/jservonnat/C-ESM-EP/wiki)

custom_plot_params.py

@@ -2,12 +2,14 @@
 # Created : S.Sénési - nov 2015
 # Adapter : J.Servonnat - april 2016
 
+from climaf.utils import ranges_to_string
+
 dict_plot_params = {
     'evap': {
-        'default': {'color': 'precip3_16lev', 'units': '', 'scale':86400},
+        'default': {'color': 'precip3_16lev', 'units': '', 'scale': 86400},
         'full_field': {'colors': '0 0.1 0.5 1 2 3 4 5 6 7 8 9 10'},
-        'bias': {'min':-1,'max':1,'delta':0.01, 'color': 'BlueWhiteOrangeRed'},
-        'model_model': {'min':-0.7,'max':0.7,'delta':0.05, 'color': 'BlueWhiteOrangeRed'},
+        'bias': {'min': -1, 'max': 1, 'delta': 0.01, 'color': 'BlueWhiteOrangeRed'},
+        'model_model': {'min': -0.7, 'max': 0.7, 'delta': 0.05, 'color': 'BlueWhiteOrangeRed'},
 
     },
     'pr': {
@@ -57,9 +59,16 @@
     # 'mrro': {'full_field': dict(colors='0 0.1 0.25 0.5 0.75 1 2 5')},
     # 'mrros': {'full_field': dict(colors='0 0.1 0.25 0.5 0.75 1 2 5')},
 
-
-
-
+    # Next two entries in order to fix a typo in CLiMAF V3.0, for the 'full_field' entries
+    'ta700': {
+        'default': {'units': 'degC', 'color': 'BlueWhiteOrangeRed', 'offset': -273.15},
+        'full_field': {'colors': ranges_to_string(ranges=[[-40, 0, 10], [0, 25, 5]])},
+        'bias': {'min': -5, 'max': 5, 'delta': 1, 'offset': 0},
+        'model_model': {'min': -10, 'max': 10, 'delta': 1, 'offset': 0}},
+    'ta500': {
+        'default': {'units': 'degC', 'color': 'BlueWhiteOrangeRed', 'offset': -273.15},
+        'full_field': {'colors': ranges_to_string(ranges=[[-40, 0, 10], [0, 25, 5]])},
+        'bias': {'min': -5, 'max': 5, 'delta': 1, 'offset': 0},
+        'model_model': {'min': -10, 'max': 10, 'delta': 1, 'offset': 0}}
 
 }
-

install_lite.sh

@@ -22,15 +22,27 @@
 cesmep_dir=$(cd $(dirname $0) ; pwd)  # Dir of current code
 [ -h $cesmep_dir/share ] && echo "Cannot work from a lite install" && exit 1
 
-target=${1?} 
-comparison=${2?}
+target=${1?"Provide target directory as first argument"} 
+comparison=${2?"Provide comparison name as second argument"}
 with_libIGCM=${3:-no}  # If arg #3 is set, also link scripts used by libIGCM
 
 target=$(cd $target ; pwd)
 [ ! -d $target ] && \
     echo "$0 : Must provide an existing directory as first argument" && exit 1
 target=$target/cesmep_lite
 if [ -d $target ] ; then
+    echo -e "\033[1;32mThere's already a C-ESM-EP lite install at $target."
+    echo -n -e " Do you want to supersede it (y/N) ? : \033[m"
+    read reponse
+    case ${reponse} in
+	oui|OUI|o|y|yes|YES)
+	    echo "OK"
+	    ;;
+	non|NON|n|no|NO|*)
+	    echo "No C-ESM-EP install !"
+	    exit 9
+	    ;;
+    esac
     chmod -R 777 $target
     rm -fR $target
 fi
@@ -52,20 +64,19 @@ fi
     (cd $target; tar -xf - )
 
 # Link a few files at C-ESM-EP root level 
-links="share job_C-ESM-EP.sh job_PMP_C-ESM-EP.sh locations.py"
+links="share job_C-ESM-EP.sh job_PMP_C-ESM-EP.sh locations.py custom_obs_dict.py"
 [ $with_libIGCM != no ] && links+=" libIGCM_clean.sh libIGCM_post.sh"
 for file in $links; do
      ln -sf $cesmep_dir/$file $target
 done
 
-# Copy some pyhton files (cannot link because of side effect in PYTHONPATH)
+# Copy some python files (cannot link because of side effect in PYTHONPATH)
 copies="run_C-ESM-EP.py main_C-ESM-EP.py"
 for file in $copies; do
      cp -f $cesmep_dir/$file $target
 done
 
-
-# Copy only files that will or could be changed
+# Copy also files that will or could be changed
 cp -f $cesmep_dir/settings.py $target
 
 # Set root directory in setenv_C-ESM-EP.sh