Merge branch 'issue42_rebranding'

doc/README.txt

@@ -1,4 +1,4 @@
-WGNE/WGCM metrics panel package - alpha v0.1
+PCMDI metrics panel package - alpha v0.1
 
 mean_climate_metrics_driver.py
 ------------------------------

install_metrics.bash

@@ -3,7 +3,7 @@
 ## SYSTEM SPECIFIC OPTIONS, EDIT THESE TO MATCH YOUR SYSTEM
 
 ## Directory where to install UVCDAT and the METRICS Packages
-install_prefix="WGNE"
+install_prefix="PCMDI_METRICS"
 
 ## Temporary build directory
 build_directory="${install_prefix}/tmp"
@@ -346,9 +346,9 @@ main() {
     cdat_repo_http=http://github.com/UV-CDAT/uvcdat.git
     cdat_repo_https=https://github.com/UV-CDAT/uvcdat.git
     cdat_version="master"
-    metrics_repo=git://github.com/PCMDI/wgne-wgcm_metrics.git
-    metrics_repo_http=http://github.com/PCMDI/wgne-wgcm_metrics.git
-    metrics_repo_https=https://github.com/PCMDI/wgne-wgcm_metrics.git
+    metrics_repo=git://github.com/PCMDI/pcmdi_metrics.git
+    metrics_repo_http=http://github.com/PCMDI/pcmdi_metrics.git
+    metrics_repo_https=https://github.com/PCMDI/pcmdi_metrics.git
     metrics_checkout="master"
     install_prefix=$(_full_path ${install_prefix})
     if [ $? != 0 ]; then
@@ -367,19 +367,19 @@ main() {
     cdat_home=${install_prefix}
     echo "Installing into: "${install_prefix}
     echo "Temporary build directory: "${build_directory}
-    ## clone wgne repo
+    ## clone pcmdi_metrics repo
     git clone ${metrics_repo} ${metrics_build_directory}
     if [ ! -e ${metrics_build_directory}/.git/config ]; then
       echo " WARN: Could not clone metrics repo via git protocol (port 9418)! Trying https protocol"
-        git clone ${metrics_repo_https} ${metrics_build_directory}
+      git clone ${metrics_repo_https} ${metrics_build_directory}
+      if [ ! -e ${metrics_build_directory}/.git/config ]; then
+        echo " WARN: Could not clone metrics repo via https (port 22)! Trying http protocol (port 80)"
+        git clone ${metrics_repo_http} ${metrics_build_directory}
         if [ ! -e ${metrics_build_directory}/.git/config ]; then
-          echo " WARN: Could not clone metrics repoi via https (port 22)! Trying http protocol (port 80)"
-          git clone ${metrics_repo_http} ${metrics_build_directory}
-          if [ ! -e ${metrics_build_directory}/.git/config ]; then
-              echo " ERROR: Could not clone metrics repo via git/https/http! Check you are connected to the internet or your firewall settings"
-              exit 1
-          fi
+            echo " ERROR: Could not clone metrics repo via git/https/http! Check you are connected to the internet or your firewall settings"
+            exit 1
         fi
+      fi
     fi
 
     cd ${metrics_build_directory} >& /dev/null
@@ -415,13 +415,13 @@ main() {
     echo "*******************************"
     echo "Please test as follow:"
     echo "source ${cdat_home}/bin/setup_runtime.sh"
-    echo "wgne_metrics_driver.py -p ${install_prefix}/test/wgne/basic_test_parameters_file.py"
-    echo "compare: ${install_prefix}/test/wgne/tos_2.5x2.5_esmf_linear_metrics.json.good with wgne_install_test_results/metrics_results/installationTest/tos_2.5x2.5_esmf_linear_metrics.json"
+    echo "pcmdi_metrics_driver.py -p ${install_prefix}/test/pcmdi/basic_test_parameters_file.py"
+    echo "compare: diff ${install_prefix}/test/pcmdi/tos_2.5x2.5_esmf_linear_metrics.json.good pcmdi_install_test_results/metrics_results/installationTest/tos_2.5x2.5_esmf_linear_metrics.json"
     echo "*******************************"
-    echo "Create your customized input_parameters.py (inspire yourself from examples in ${install_prefix}/doc/wgne_input_parameters_sample.py"
+    echo "Create your customized input_parameters.py (inspire yourself from examples in ${install_prefix}/doc/pcmdi_input_parameters_sample.py"
     echo "Once you have a parameter file run:"
     echo "source ${install_prefix}/bin/setup_runtime.sh"
-    echo "wgne_metrics_driver.py -p /path/to/your/edited/parameter_file.py"
+    echo "pcmdi_metrics_driver.py -p /path/to/your/edited/parameter_file.py"
     echo "*******************************"
     echo "Once everything is ok, you can safely remove the temporary directory: ${build_directory}"
     echo "*******************************"

setup.py

@@ -1,7 +1,7 @@
 from distutils.core import setup, Extension
 import os,sys
 import numpy
-Version="0.1.0"
+Version="0.2.0"
 import subprocess
 p = subprocess.Popen(("git","log","-n1","--pretty=short"),stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
 try:
@@ -13,26 +13,26 @@
 print >>f, "__git_sha1__ = '%s'" % commit
 f.close()
 
-setup (name = "metrics",
+setup (name = "pcmdi_metrics",
        version=Version,
        author='PCMDI',
        description = "model metrics tools",
-       url = "http://github.com/PCMDI/wgne-wgcm_metrics",
-       packages = ['metrics','metrics.io','metrics.wgne'],
-       package_dir = {'metrics': 'src/python',
-                      'metrics.io': 'src/python/io',
-                      'metrics.wgne': 'src/python/wgne'},
-       scripts = ["src/python/wgne/scripts/wgne_metrics_driver.py",
-                  "src/python/wgne/scripts/build_obs_meta_dictionary.py"],
-       data_files = [('share/wgne',('doc/obs_info_dictionary.json',)),
-                     ('doc',('doc/wgne_input_parameters_sample.py',)),
-                     ('test/wgne',('test/wgne/basic_test_parameters_file.py','test/wgne/tos_GFDL-ESM2G_Omon_historical_r1i1p1_198501-200512-clim.nc','test/wgne/sftlf_GFDL-ESM2G_fx_historical_r0i0p0_198501-200512-clim.nc','test/wgne/tos_2.5x2.5_esmf_linear_metrics.json.good')),
-                     ('test/wgne/obs/ocn/mo/tos/UKMETOFFICE-HadISST-v1-1/ac',('test/wgne/tos_pcmdi-metrics_Omon_UKMETOFFICE-HadISST-v1-1_198002-200501-clim.nc',)),
-                     ('test/wgne/obs/fx/mo/sftlf/UKMETOFFICE-HadISST-v1-1/ac',('test/wgne/sftlf_pcmdi-metrics_fx_UKMETOFFICE-HadISST-v1-1_198002-200501-clim.nc',)),
+       url = "http://github.com/PCMDI/pcmdi_metrics",
+       packages = ['pcmdi_metrics','pcmdi_metrics.io','pcmdi_metrics.pcmdi'],
+       package_dir = {'pcmdi_metrics': 'src/python',
+                      'pcmdi_metrics.io': 'src/python/io',
+                      'pcmdi_metrics.pcmdi': 'src/python/pcmdi'},
+       scripts = ["src/python/pcmdi/scripts/pcmdi_metrics_driver.py",
+                  "src/python/pcmdi/scripts/build_obs_meta_dictionary.py"],
+       data_files = [('share/pcmdi',('doc/obs_info_dictionary.json',)),
+                     ('doc',('doc/pcmdi_input_parameters_sample.py',)),
+                     ('test/pcmdi',('test/pcmdi/basic_test_parameters_file.py','test/pcmdi/tos_GFDL-ESM2G_Omon_historical_r1i1p1_198501-200512-clim.nc','test/pcmdi/sftlf_GFDL-ESM2G_fx_historical_r0i0p0_198501-200512-clim.nc','test/pcmdi/tos_2.5x2.5_esmf_linear_metrics.json.good')),
+                     ('test/pcmdi/obs/ocn/mo/tos/UKMETOFFICE-HadISST-v1-1/ac',('test/pcmdi/tos_pcmdi-metrics_Omon_UKMETOFFICE-HadISST-v1-1_198002-200501-clim.nc',)),
+                     ('test/pcmdi/obs/fx/mo/sftlf/UKMETOFFICE-HadISST-v1-1/ac',('test/pcmdi/sftlf_pcmdi-metrics_fx_UKMETOFFICE-HadISST-v1-1_198002-200501-clim.nc',)),
                      ]
        #include_dirs = [numpy.lib.utils.get_include()],
        #       ext_modules = [
-       #    Extension('metrics.exts',
+       #    Extension('pcmdi_metrics.exts',
        #              ['src/C/add.c',],
        #              library_dirs = [],
        #              libraries = [],

src/python/__init__.py

@@ -1,5 +1,5 @@
 #  put here the impor calls to expose whatever we want to the user
 import io
-import wgne
+import pcmdi
 from version import __version__ , __git_sha1__
 

src/python/io/__init__.py

@@ -1,2 +1,2 @@
-#init for metrics.io
+#init for pcmdi_metrics.io
 import base

src/python/io/base.py

@@ -3,7 +3,7 @@
 import MV2
 import genutil
 import os
-import metrics
+import pcmdi_metrics
 import cdat_info
 
 value = 0
@@ -64,7 +64,7 @@ def write(self,data, type="json", mode="w", *args, **kargs):
             raise RuntimeError, "Could not create output directory: %s" % (os.path.split(fnm)[0])
         if type.lower() == "json":
             f=open(fnm,mode)
-            data["metrics_git_sha1"] = metrics.__git_sha1__
+            data["metrics_git_sha1"] = pcmdi_metrics.__git_sha1__
             data["uvcdat_version"] = cdat_info.get_version()
             json.dump(data,f,*args,**kargs)            
         elif type.lower() in ["asc","ascii","txt"]:
@@ -74,7 +74,7 @@ def write(self,data, type="json", mode="w", *args, **kargs):
         elif type.lower() == "nc":
             f=cdms2.open(fnm,mode)
             f.write(data,*args,**kargs)
-            f.metrics_git_sha1 = metrics.__git_sha1__
+            f.metrics_git_sha1 = pcmdi_metrics.__git_sha1__
             f.uvcdat_version = cdat_info.get_version()
         else:
             raise RuntimeError,"Unknown type: %s" % type

src/python/io/getOurModelData.py

@@ -1,5 +1,5 @@
 import cdms2
-import string  
+import os
 
 ##############################################################################
 # PJG 20130522
@@ -23,9 +23,9 @@ def getOurModelData(exp,var):
 
  filename_tmp = 'cmip5.NorESM1-M.historical.r1i1p1.mo.atm.Amon.VARNAME.ver-1.1980-1999.AC.nc'
 
- filename_new = string.replace(filename_tmp,'VARNAME',var)
+ filename_new = filename_tmp.replace('VARNAME',var)
 
- f = cdms.open(pathin + var + '/' + filename_new)
+ f = cdms.open(os.path.join(pathin, var, filename_new))
  d = f(var + '_ac')
  f.close()
 

src/python/io/transform_our_model_to_metrics_grid_and_structure.py

@@ -1,6 +1,4 @@
 import cdms2
-import string, os
-import ESMP
 
 ###################################### 
 value = 0 

src/python/wgne/io.py → src/python/pcmdi/io.py

@@ -1,9 +1,9 @@
-import metrics
-class OBS(metrics.io.base.Base):
+import pcmdi_metrics
+class OBS(pcmdi_metrics.io.base.Base):
     def __init__(self,root,var,obs_dic,reference="default"):
 
         template = "%(realm)/mo/%(variable)/%(reference)/ac/%(variable)_pcmdi-metrics_%(obs_table)_%(reference)_%(period)-clim.%(ext)" 
-        metrics.io.base.Base.__init__(self,root,template)
+        pcmdi_metrics.io.base.Base.__init__(self,root,template)
         obs_name = obs_dic[var][reference]
         ref = obs_dic[var][obs_name]
         period = ref["period"]

src/python/wgne/mean_climate_metrics_calculations.py → src/python/pcmdi/mean_climate_metrics_calculations.py

@@ -2,7 +2,7 @@
 import cdms2 as cdms
 from genutil import statistics
 import cdutil
-import metrics
+import pcmdi_metrics
 
 
 
@@ -35,21 +35,21 @@ def compute_metrics(var,dm_glb,do_glb):
 
     ### ANNUAL CYCLE SPACE-TIME RMS AND CORRELATION
     print '---- shapes ', dm.shape,' ', do.shape
-    rms_xyt = metrics.wgne.rms_xyt.compute(dm,do)
-    cor_xyt = metrics.wgne.cor_xyt.compute(dm,do)
+    rms_xyt = pcmdi_metrics.pcmdi.rms_xyt.compute(dm,do)
+    cor_xyt = pcmdi_metrics.pcmdi.cor_xyt.compute(dm,do)
 
     ### CALCUALTE ANNUAL MEANS OF DATA
-    do_am, dm_am =  metrics.wgne.annual_mean.compute(dm,do)
+    do_am, dm_am =  pcmdi_metrics.pcmdi.annual_mean.compute(dm,do)
 
   ### ANNUAL MEAN BIAS
-    bias_xy = metrics.wgne.bias.compute(dm_am,do_am)
+    bias_xy = pcmdi_metrics.pcmdi.bias.compute(dm_am,do_am)
     print var,'  ', 'annual mean bias is ' , bias_xy
 
    ### MEAN ABSOLOUTE ERROR 
-    mae_xy = metrics.wgne.meanabs_xy.compute(dm_am,do_am)
+    mae_xy = pcmdi_metrics.pcmdi.meanabs_xy.compute(dm_am,do_am)
 
     ### ANNUAL MEAN RMS
-    rms_xy = metrics.wgne.rms_xy.compute(dm_am,do_am)
+    rms_xy = pcmdi_metrics.pcmdi.rms_xy.compute(dm_am,do_am)
 
     conv = 1.
     if var == 'pr': conv = 1.e5
@@ -68,14 +68,14 @@ def compute_metrics(var,dm_glb,do_glb):
 
     for sea in ['djf','mam','jja','son']:
 
-     dm_sea = metrics.wgne.seasonal_mean.compute(dm,sea)  
-     do_sea = metrics.wgne.seasonal_mean.compute(do,sea)
+     dm_sea = pcmdi_metrics.pcmdi.seasonal_mean.compute(dm,sea)  
+     do_sea = pcmdi_metrics.pcmdi.seasonal_mean.compute(do,sea)
 
    ### SEASONAL RMS AND CORRELATION
-     rms_sea = metrics.wgne.rms_xy.compute(dm_sea,do_sea)
-     cor_sea = metrics.wgne.cor_xy.compute(dm_sea,do_sea) 
-     mae_sea = metrics.wgne.meanabs_xy.compute(dm_sea,do_sea)
-     bias_sea = metrics.wgne.bias.compute(dm_sea,do_sea)
+     rms_sea = pcmdi_metrics.pcmdi.rms_xy.compute(dm_sea,do_sea)
+     cor_sea = pcmdi_metrics.pcmdi.cor_xy.compute(dm_sea,do_sea) 
+     mae_sea = pcmdi_metrics.pcmdi.meanabs_xy.compute(dm_sea,do_sea)
+     bias_sea = pcmdi_metrics.pcmdi.bias.compute(dm_sea,do_sea)
 
      metrics_dictionary['bias_xy_' + sea + '_' + dom] = format(bias_sea*conv,sig_digits)
      metrics_dictionary['rms_xy_' + sea + '_' + dom] = format(rms_sea*conv,sig_digits) 

src/python/wgne/scripts/build_obs_meta_dictionary.py → src/python/pcmdi/scripts/build_obs_meta_dictionary.py

@@ -1,6 +1,6 @@
 #!python
-import cdms2 as cdms
-import json, os, sys, string
+import cdms2
+import json, os, sys
 if len(sys.argv)>1:
     data_path = sys.argv[1]
 else:
@@ -39,22 +39,22 @@
 
 
 for l in lst:
-  subp = string.split(l,'obs')[1]
+  subp = l.split('obs')[1]
 # print subp
 
-  var = string.split(subp,'/')[3]
+  var = subp.split('/')[3]
 
   if var not in obs_dic.keys(): obs_dic[var] = {}
 
-  product = string.split(subp,'/')[4]
+  product = subp.split('/')[4]
 
   if product not in obs_dic[var].keys(): obs_dic[var][product] = {}
 
-  partial_filename = string.split(subp,'pcmdi-metrics')[1]
+  partial_filename = subp.split('pcmdi-metrics')[1]
 
-  realm = string.split(partial_filename,'_')[1]
-  period = string.split(partial_filename,'_')[3]
-  period = string.split(period,'-clim.nc')[0]
+  realm = partial_filename.split('_')[1]
+  period = partial_filename.split('_')[3]
+  period = period.split('-clim.nc')[0]
 
   obs_dic[var][product]['CMIP_CMOR_TABLE'] = realm
   obs_dic[var][product]['period'] = period 
@@ -67,7 +67,7 @@
 
   print var,' ', product,'  ', realm,' ', period
 
-  f = cdms.open(l[:-1])
+  f = cdms2.open(l[:-1])
   d = f(var)
   shape = d.shape
   f.close()