Merge pull request #162 from rigoudyg/V1.2.13

Finalize new version.

Author: rigoudyg

bin/climaf

@@ -17,22 +17,22 @@ fi
 
 if [ "$*" ] ; then 
     if [ -f "$1" ] ; then 
-	(echo 'from climaf.api import *'; cat $*) | python 
+	(echo 'from climaf.api import *'; cat $*) | python2 
     else
-	echo -e 'from climaf.api import *\n'$*  | python 2> climaf.stderr
+	echo -e 'from climaf.api import *\n'$*  | python2 2> climaf.stderr
 	rep=$?
 	[ $rep -ne 0 ] && cat climaf.stderr >&2
 	rm climaf.stderr
 	exit $rep
     fi
 else
     # Interactive session (or read stdin)
-    if [ ! -d /cnrm ] ; then
+    if [ ! -d /cnrm ] && [ "$EMACS" != t ]; then
 	# Can use ipython
 	ipython -i -c 'from climaf.api import *'
     else
 	# ipython at CNRM for now implies Python3, which is notcompatible with CliMAF
-	python -i -c 'from climaf.api import *'
+	python2 -i -c 'from climaf.api import *'
     fi
 fi
 

bin/climaf-notebook

@@ -0,0 +1,53 @@
+#!/bin/bash
+myport=$( grep $USER  /ciclad-home/jservon/Evaluation/CliMAF/climaf_installs/climaf_V1.2.13/bin/cmip6.notebook.txt | awk '{print $2 }' )
+
+SHORT_HOST="$(hostname -s)"
+echo
+case $SHORT_HOST in
+    ciclad-ng|ciclad2|loholt*|camelot)
+    echo -e  "\033[1;31mplease do not run this on login node $SHORT_HOST use:\033[m"
+    echo -e  "First, submit an interactive session then load module and run notebook:" 
+    echo -e  "\033[1;31mYou could cut and past the 3 command line under:\033[m"
+    echo -e  "qsub -IVX -l mem=9g,vmem=9g,walltime=06:00:00"
+    echo -e  "module load climaf"
+    echo -e  "climaf-notebook"
+    exit 1 ;;
+    ciclad*) SSH_TUNNEL="ssh -L ${myport}:${SHORT_HOST}:${myport} ${USER}@ciclad2.ipsl.jussieu.fr" ;;
+    merlin*) SSH_TUNNEL="ssh -L ${myport}:${SHORT_HOST}:${myport} ${USER}@loholt2.ipsl.polytechnique.fr" ;;
+esac
+if netstat -at | grep -w $myport > /dev/null
+then 
+   echo "You already have a climaf-notebook running" 
+   echo "only one per user could be running" 
+   lsof|grep "$myport (LISTEN)" 
+   exit 1
+fi
+echo
+echo -e "\033[1;31m FIRST STEP: Open your port \033[m"
+echo "     - open a terminal on your computer (!! not on Ciclad, Loholt, Cerbere, Idefix... on your local machine)"
+echo "     - and connect to the Mesocenter with this blue command: "
+echo -e "\033[1;34m $SSH_TUNNEL \033[m"
+echo
+echo -e "\033[1;31m And keep this terminal open until the end of your jupyter session. \033[m"
+echo 
+#echo -e "\033[1;31mCOMMAND 2 IN THE URL PRODUCED BY NOTEBOOK, YOU HAVE TO REPLACE \033[m$SHORT_HOST\033[1;31m BY \033[mlocalhost"
+#echo -e "\033[1;31m          BEFORE PASTING IN YOUR LOCAL LAPTOP OR WORKSTATION BROWSER (firefox,chrome ...)\033[m"  
+if [ ! "analyse_env_2.7"="$CONDA_DEFAULT_ENV" ]
+then
+  source activate analyse_env_2.7
+fi
+echo
+echo -e "\033[1;31m SECOND STEP: \033[m"
+echo "    - in the url below (returned by Jupyter), replace --> $SHORT_HOST with --> localhost"
+echo "    - and paste in a browser on your computer (Chrome, Firefox...)"
+echo "    # Example: this is what Jupyter should typically return:"
+echo "    http://ciclad17:7144/?token=fa3b97e0ecf84afa9954da15056e9c6aef8bf6353e64ba81&token=fa3b97e0ecf84afa9954da15056e9c6aef8bf6353e64ba81"
+echo "    # And this is what you should copy and paste in your local browser:"
+echo "    http://localhost:7144/?token=fa3b97e0ecf84afa9954da15056e9c6aef8bf6353e64ba81&token=fa3b97e0ecf84afa9954da15056e9c6aef8bf6353e64ba81"
+echo
+echo -e "\033[1;31m Have fun! \033[m"
+echo
+echo -e "\033[1;31m (wait until Jupyter returns the url... it might take some seconds...) \033[m"
+
+jupyter notebook --no-browser --port=${myport} --ip=$SHORT_HOST 
+# dommage ca marche pas 2>&1 |sed -e 's/$SHORT_HOST/localhost/'

bin/cmip6.notebook.txt

@@ -124,3 +124,11 @@ jllod 7223
 ledel 7224
 jypmce 7225
 gevin 7226
+mlalande 7227
+mbeaudor 7228
+jharle 7229
+loruba 7230
+jbeaumet 7231
+cjlmd 7232
+cjunquas 7233
+fpalliser 7234

climaf/__init__.py

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
 Climaf is documented at ReadTheDocs : http://climaf.readthedocs.org/
@@ -11,11 +11,11 @@
 
 # Created : S.Sénési - 2014
 
-__all__ = ["site_settings", "cache", "classes", "clogging", "dataloc", "driver", "netcdfbasics",
+__all__ = ["cache", "classes", "dataloc", "driver", "netcdfbasics",
            "operators", "period", "standard_operators", "cmacro", "html", "functions", "plot",
            "projects", "derived_variables"]
 
-version = "1.2.12"
+version = "1.2.13"
 
 
 def tim(string=None):
@@ -52,52 +52,89 @@ def tim(string=None):
 
     tim("atexit")
     #
-    import clogging
-    import site_settings
+    import env.clogging as clogging
+    import env.site_settings as site_settings
     import cache
     import standard_operators
     import cmacro
     import operators
     import subprocess
     import commands
-    
+
+
     def my_which(soft):
-        p = subprocess.Popen(["which",soft], stdout=subprocess.PIPE)
-        return str.replace(p.stdout.readlines()[0],'\n','')
+        p = subprocess.Popen(["which", soft], stdout=subprocess.PIPE)
+        return str.replace(p.stdout.readlines()[0], '\n', '')
+
+
     def bash_command_to_str(cmd):
-        return str.replace(subprocess.Popen(str.split(cmd,' '), stdout=subprocess.PIPE).stdout.readlines()[0],'\n','')
+        return str.replace(subprocess.Popen(str.split(cmd, ' '), stdout=subprocess.PIPE).stdout.readlines()[0], '\n',
+                           '')
+
 
     tim("imports")
     print("CliMAF version = " + version, file=sys.stderr)
     print("CliMAF install => " + "/".join(__file__.split("/")[:-2]))
-    print("python => "+my_which('python'))
-    print("---")
-    print("Required softwares to run CliMAF => you are using the following versions/installations:")
-    try:
-       print("ncl "+commands.getoutput(my_which('ncl')+' -V')+" => "+my_which('ncl'))
-    except:
-       print("Warning: ncl not found -> can't use CliMAF plotting scripts")
-    try:
-       tmp = str.split(commands.getstatusoutput(my_which('cdo')+' -V')[1],' ')
-       print("cdo "+tmp[tmp.index('version')+1]+" => "+my_which('cdo'))
-    except:
-       print("Error: cdo not found -> CDO is mandatory to run CliMAF")
-       my_which('cdo')
-    try:
-       tmp = str.split(commands.getstatusoutput(my_which('ncks')+' --version')[1], ' ')
-       print("nco (ncks) "+tmp[tmp.index('version')+1]+" => "+my_which('ncks'))
-    except:
-       print("Warning: nco not found -> can't use nco from CliMAF")
-    try:
-       if site_settings.atTGCC or site_settings.atIPSL or site_settings.onCiclad:
-          print("ncdump "+commands.getstatusoutput('/prodigfs/ipslfs/dods/jservon/miniconda/envs/cesmep_env/bin/ncdump')[-1].split('\n')[-1].split()[3]+" => "+my_which('ncdump'))
-       else:
-          binary_info = commands.getstatusoutput(my_which("ncdump") + " --version")[-1].split("\n")[-1]
-          binary_info = binary_info.split("version")[-1].split("of")[0].strip()
-          print("ncdump "+binary_info+" => "+my_which('ncdump'))
-    except:
-       print("Warning: ncdump not found -> can't use ncdump from CliMAF")
-    print("---")
+    if os.environ.get('CLIMAF_CHECK_DEPENDENCIES', "yes") == "yes" :
+        print("python => " + my_which('python'))
+        print("---")
+        print("Required softwares to run CliMAF => you are using the following versions/installations:")
+        try:
+            print("ncl " + commands.getoutput(my_which('ncl') + ' -V') + " => " + my_which('ncl'))
+        except:
+            print("Warning: ncl not found -> can't use CliMAF plotting scripts")
+        try:
+            tmp = str.split(commands.getstatusoutput(my_which('cdo') + ' -V')[1], ' ')
+            print("cdo " + tmp[tmp.index('version') + 1] + " => " + my_which('cdo'))
+        except:
+            print("Error: cdo not found -> CDO is mandatory to run CliMAF")
+        try:
+            tmp = str.split(commands.getstatusoutput(my_which('ncks') + ' --version')[1], ' ')
+            print("nco (ncks) " + tmp[tmp.index('version') + 1] + " => " + my_which('ncks'))
+        except:
+            print("Warning: nco not found -> can't use nco from CliMAF")
+        try:
+            if site_settings.atTGCC or site_settings.atIPSL or site_settings.onCiclad:
+                ncdump_ret = commands.getstatusoutput('/prodigfs/ipslfs/dods/jservon/miniconda/envs/cesmep_env/bin/ncdump')
+                print("ncdump " + ncdump_ret[-1].split('\n')[-1].split()[3] + " => " + my_which('ncdump'))
+            else:
+                binary_info = commands.getstatusoutput(my_which("ncdump") + " --version")[-1].split("\n")[-1]
+                binary_info = binary_info.split("version")[-1].split("of")[0].strip()
+                print("ncdump " + binary_info + " => " + my_which('ncdump'))
+        except:
+            print("Warning: ncdump not found -> can't use ncdump from CliMAF")
+        # Check that tools for stamping are available or enforce stamping to None
+        print("Check stamping requirements")
+        do_stamping = True
+        try:
+            print("nco (ncatted) found -> " + my_which("ncatted"))
+        except:
+            print("nco (ncatted) not available, can not stamp netcdf files")
+            do_stamping = False
+        try:
+            print("convert found -> " + my_which("convert"))
+        except:
+            print("convert not available, can not stamp png files")
+            do_stamping = False
+        try:
+            print("pdftk found -> " + my_which("pdftk"))
+        except:
+            print("pdftk not available, can not stamp pdf files")
+            do_stamping = False
+        try:
+            print("exiv2 found -> " + my_which("exiv2"))
+        except:
+            print("exiv2 not available, can not stamp eps files")
+            do_stamping = False
+        if not do_stamping and cache.stamping is True:
+            print("At least one stamping requirement is not fulfilled, turn it to None.")
+            cache.stamping = None
+        print("---")
+    #
+    # Check that the variable TMPDIR, if defined, points to an existing directory
+    if "TMPDIR" in os.environ and not os.path.isdir(os.environ["TMPDIR"]):
+        # raise OSError("TMPDIR points to a non existing directory! Change the value of the variable to go on.")
+        os.makedirs(os.environ["TMPDIR"])
 
     logdir = os.path.expanduser(os.getenv("CLIMAF_LOG_DIR", "."))
     #

climaf/anynetcdf.py

@@ -1,7 +1,7 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from climaf.clogging import clogger
+from env.clogging import clogger
 
 try:
     from Scientific.IO.NetCDF import NetCDFFile as ncf

climaf/api.py

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
 CliMAF module ``api`` defines functions for basic CliMAF use : a kind of Application Program Interface for scripting in
@@ -87,8 +87,8 @@
 from dataloc import dataloc
 from operators import cscript, scripts as cscripts, operators, fixed_fields, derive
 from cache import craz, csync, cdump, cdrop, clist, cls, crm, cdu, cwc, cprotect
-from clogging import clogger, clog, clog_file, logdir
-from site_settings import atCNRM, onCiclad, atTGCC, atIDRIS, atIPSL, onSpip
+from env.clogging import clogger, clog, clog_file, logdir
+from env.site_settings import atCNRM, onCiclad, atTGCC, atIDRIS, atIPSL, onSpip
 from plot.plot_params import plot_params, hovm_params
 from plot.varlongname import varlongname
 from derived_variables import *