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Subject svn commit: r1517753 [1/33] - in /incubator/climate/branches/rcmet-2.1.1: ./ src/ src/main/ src/main/python/ src/main/python/bin/ src/main/python/docs/ src/main/python/docs/_static/ src/main/python/docs/_templates/ src/main/python/rcmes/ src/main/pytho...
Date Tue, 27 Aug 2013 05:35:49 GMT
Author: pramirez
Date: Tue Aug 27 05:35:42 2013
New Revision: 1517753

Version presented at 2nd WCRP CORDEX Science and Training Workshop in South Asia.

    incubator/climate/branches/rcmet-2.1.1/LICENSE.txt   (with props)
    incubator/climate/branches/rcmet-2.1.1/readme_v2.1a   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/bin/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/Bottle Web Service Documentation.docx   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/Makefile   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/RCMET_documentation.docx   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/index.rst   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/make.bat   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/rcmes.cli.rst   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/rcmes.rst   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/rcmes.toolkit.rst   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/rcmes.utils.rst   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/README   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/cli/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/cli/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/cli/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/cli/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/resources/cordexIndia.cfg   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/resources/cordexSubRegions.txt   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/resources/narccap.cfg   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/resources/watersheds/CAwsdCU_wgt_ep36_d01   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/resources/watersheds/CAwsdCU_wgt_ep36_d02   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/resources/watersheds/CAwsdDWR_wgt_ep36_d01   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/resources/watersheds/CAwsdDWR_wgt_ep36_d02   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/resources/watersheds/shasta_d02.txt   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/services/README.txt   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/services/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/services/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/services/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/services/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/services/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/services/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/services/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/services/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/services/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/services/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/storage/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/storage/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/storage/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/storage/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/temp.metrics   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/toolkit/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/toolkit/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/toolkit/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/toolkit/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/utils/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/utils/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/utils/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/rcmes/utils/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/missingSubRegionParam.cfg   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/validSubRegionConfigFile.cfg   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/files/validSubRegions.cfg   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/python/tests/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/resources/PyLintREADME.txt   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/resources/pyLintRcFile.txt   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/resources/rcmet_use_case.txt   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/css/app.css   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/css/bootstrap-responsive.min.css   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/css/bootstrap.min.css   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/css/font-awesome.min.css   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/css/jasny-bootstrap-responsive.min.css   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/css/jasny-bootstrap.min.css   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/font/FontAwesome.otf   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/font/fontawesome-webfont.eot   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/font/fontawesome-webfont.svg   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/font/fontawesome-webfont.ttf   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/font/fontawesome-webfont.woff   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/img/glyphicons-halflings-white.png   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/img/glyphicons-halflings.png   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/index-async.html   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/index.html   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/js/app.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/js/bootstrap.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/js/bootstrap.min.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/js/controllers.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/js/directives.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/js/filters.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/js/jasny-bootstrap.min.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/js/jquery-1.9.1.min.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/js/leaflet.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/js/services.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/lib/angular/angular-cookies.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/lib/angular/angular-cookies.min.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/lib/angular/angular-loader.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/lib/angular/angular-loader.min.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/lib/angular/angular-resource.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/lib/angular/angular-resource.min.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/lib/angular/angular-sanitize.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/lib/angular/angular-sanitize.min.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/lib/angular/angular.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/lib/angular/angular.min.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/lib/angular/version.txt   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/partials/modelSelect.html   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/partials/partial1.html   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/partials/partial2.html   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/partials/selectObservation.html   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/app/partials/selectRcmed.html   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/config/testacular-e2e.conf.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/config/testacular.conf.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/scripts/e2e-test.bat   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/scripts/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/scripts/test.bat   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/scripts/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/scripts/testacular-e2e.conf.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/scripts/testacular.conf.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/scripts/watchr.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/scripts/web-server.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/test/e2e/runner.html   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/test/e2e/scenarios.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/test/lib/angular/angular-mocks.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/test/lib/angular/angular-scenario.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/test/lib/angular/version.txt   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/test/unit/controllersSpec.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/test/unit/directivesSpec.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/test/unit/filtersSpec.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/ui/test/unit/servicesSpec.js   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/build/Vagrantfile   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/README.rdoc   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/attributes/default.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/definitions/apache_conf.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/definitions/apache_module.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/definitions/apache_site.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/definitions/web_app.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/files/default/   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/metadata.json   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/metadata.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/default.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/god_monitor.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_alias.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_auth_basic.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_auth_digest.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_auth_openid.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_authn_file.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_authnz_ldap.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_authz_default.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_authz_groupfile.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_authz_host.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_authz_user.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_autoindex.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_cgi.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_dav.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_dav_svn.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_deflate.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_dir.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_env.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_expires.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_fcgid.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_headers.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_ldap.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_log_config.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_mime.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_negotiation.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_php5.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_proxy.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_proxy_ajp.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_proxy_balancer.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_proxy_connect.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_proxy_http.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_python.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_rewrite.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_setenvif.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_ssl.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_status.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/recipes/mod_wsgi.rb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/templates/default/a2dismod.erb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/templates/default/a2dissite.erb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/templates/default/a2enmod.erb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/templates/default/a2ensite.erb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/templates/default/apache2.conf.erb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/templates/default/apache2.god.erb   (with props)
    incubator/climate/branches/rcmet-2.1.1/src/main/vm/src/cookbooks/apache2/templates/default/charset.erb   (with props)
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Added: incubator/climate/branches/rcmet-2.1.1/LICENSE.txt
--- incubator/climate/branches/rcmet-2.1.1/LICENSE.txt (added)
+++ incubator/climate/branches/rcmet-2.1.1/LICENSE.txt Tue Aug 27 05:35:42 2013
@@ -0,0 +1,202 @@
+                                 Apache License
+                           Version 2.0, January 2004
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Propchange: incubator/climate/branches/rcmet-2.1.1/LICENSE.txt
    svn:executable = *

Added: incubator/climate/branches/rcmet-2.1.1/readme_v2.1a
--- incubator/climate/branches/rcmet-2.1.1/readme_v2.1a (added)
+++ incubator/climate/branches/rcmet-2.1.1/readme_v2.1a Tue Aug 27 05:35:42 2013
@@ -0,0 +1,111 @@
+Updates to /nas/share3-wf/jinwonki/rcmet/rcmet2.1/src/main/python/rcmes/storage/ by Cam has been implemented.
+Updated to version 2.1 with the feature to read reference data from users' own data files.
+This code has been tested with daily precipitation data (both model and reference) for the NARCCAP domain
+NOTE: * This version still have problem in regridding daily data into monthly - most likely due to the memory management problem.
+          Will be fixed in the next modification for generalized handling of both reference and model datasets.
+-----------    Summary of code modification    ----------------
+Log for the creation of rcmet2.1 from rcmet version latest on 5/28/2013
+(001) Modification: Implement an option to read reference data from users' local disk.
+  * Add entries into the configuration file (e.g.,resources/cordexAF.cfg):
+        obsSource, obsInputFile, obsFileName, obsLonVar, obsLatVar, obsTimeVar, obsDltaTime
+  * Modify 'rcmet.runUsingConfig' to read extra config parameters 'obsSource' (source indicator), 'obsInputfile'
+        (user-provided reference data file name), 'obsVarName' (the name of obs variable in the obs data file), 
+        'obsFileName' (data file identifier), 'obsTimeVar' (name of the time variable in the obs data file),
+        'obsLonVar' and 'obsLatVar' (the names indicating longitude and latititude variables in the obs data file), and
+        'obsDltaTime' (time step increment of the observed data). All these fields are read in from meta data if the reference
+        data are read from RCMED.
+        - create additional parameters & lists to be passed into do_data_prep.prep_data: obsSource,obsList,obsTimestep
+        - create obsDatasetList according to the specified reference data source
+        - pass 'obsSource' into misc.userDefinedStartEndTimes(obsSource,obsDatasetList,models)
+        - pass additional arguments into do_data_prep.prep_data \
+            (jobProperties,obsSource,obsDatasetList,obsList,obsVarName,obsLonName,obsLatName,obsTimeName,obsTimestep,gridBox,models)
+          note: arguments "obsSource, obsList, obsVarName, obsLonName, obsLatName, obsTimeName, obsTimestep" may be passed via "jobProperties"
+  * Modify ''
+        - add 'import toolkit.process'
+        - modify 'userDefinedStartEndTimes' so that the observational inputs from RCMED and user's own files can be handled separately.
+  * Modify 'do_data_prep'
+        - Additional arguments from the calling routine (see the modification to 'rcmet.runUsingConfig' above)
+        - 'obsSource' is used throughout 'do_data_prep' to indicate the source of reference data. Follow this index to identify
+          the features specific to the source of reference data (RCMED or users' own file(s))
+        - All user-provided ref data must be netCDF files. This is hardwired before the loop in which the ref data files are read & regridded.
+        - User-provided data files are read in using the same routine that is used to read model data files.
+        - Extraction of the reference data for the user-specified is done in the same way as for the model data.
+        - BUG! In the current code, 'mdlList' is updated to store model ensemble (ENS-MDL). This is WRONG. Update 'mdlName' instead of 'mdlList'
+  * Modify 'metrics.metrics_plots'
+        - If 'maskLonMin' or 'maskLonMax' exceeds 180, subtract 360 to be consistent with defauls longitude order (from -180 to 180)
+(002) Combined handling of the reference and model data in metrics calculations
+  * Modify 'rcmet.runUsingConfig' to combine the reference and model data
+        - Cosmetic: 'obsList' in the line to receive the names of the reference datasets in the 'do_data_prep.prep_data' string has been replaced with
+                    'obsName' for a better consistency with 'mdlName' in the same string that are used to store the names of the model datasets
+        - import numpy and
+        - Pack the data in the order: All reference data sets + Ref ensemble (if any) + all model datasets + model ensemble (if any)
+        - New vars introduced for handling the combined variable:
+          ^ numDatasets = numOBS + numMDL is the tot no. of datasets of the combined ref and mdl data including the ref and mdl ens, if exist.
+          ^ dataName = obsName + mdlName contains the names of all reference and model datasets
+          ^ allData = obsData[for 0:numOBS] + mdlData[for numOBS:numDatasets]
+        -  Modify the line to call 'metrics.metrics_plots' to pass the combined variable and related parameters:
+          ^ OLD: metrics.metrics_plots(modelVarName,numOBS,numMDL,nT,ngrdY,ngrdX,Times,lons,lats,obsData,mdlData,obsList,mdlName,workdir,subRegions,fileOutputOption)
+            NEW: metrics.metrics_plots(modelVarName,numOBS,numMDL,nT,ngrdY,ngrdX,Times,lons,lats,allData,dataName,workdir,subRegions,fileOutputOption)
+  * Modify
+        - Note that the changes to handle multiple data evaluation makes all metrics to be either 3-d or 4-d (monthly) fields. Modify
+               'elif metricDat.ndim == 2' with 'elif metricDat.ndim == 3' and 'elif metricDat.ndim == 4'
+        - import additional libraries
+          ^ import matplotlib
+          ^ import matplotlib.dates
+          ^ import matplotlib.pyplot as plt
+          ^ from matplotlib.font_manager import FontProperties
+          ^ from utils.Taylor import TaylorDiagram
+        - Modify the argument list for 'calling metrics_plots' to be consistent with the changes in 'rcmet.runUsingConfig'
+        - Modify the line to call 'files.writeNCfile' --> 'files.writeNCfile1'.
+        - Modify the (mp.004) Select the model/obs data for evaluation.
+          Also use modified 'misc.select_data_combined' in the place of 'misc.select_data'
+        - Modify the calculation of obs and model time series & climatology to accommodate the evaluation of multiple model datasets (mp.005)
+        - Modify calc_pat_cor in such as way that the correlation can be calculated for both 1d vs 1d, 2d vs 2d and 3d vs 3d cases
+        - Modify calc_spatial_pat_cor to ensure that std dev and corrln are calculated over the same set of unmasked (i.e., good) data
+          (a) first find masks for both variables
+          (b) re-define the input data in such a way that the data at the location of the masked values in either var are masked.
+        - Make sure to use masked array whenever calculations are performed over the domain
+        - 2-d contour plotting
+          todo: the current multi-frame plot routine (drawCntrMap) must be replaced with a matlab-based routine (remove Ngl dependence)
+        - x-y plot routine has been updated
+          can select axis options between 'log' and 'linear'
+        - Procedure to calculate & plot portrait diagrams for the anaual cycle of multiple obs and/or multiple models in multiple subregions.
+  * Bug fix:
+        - calc_clim_mo in
+            replace 'mm = months[t]' with 'mm = months[t] - 1' (otherwise mm=12 is out of bound)
+        - calc_spatial_anom_cor
+            replace the string 'd1 = ((oD - mo)*(oD - mo)).sum()' --> 'd2 = ((oD - mo)*(oD - mo)).sum()'
+  * Modify storage/
+        - Create 'files.writeNCfile1' in'storage/' with the argument list consistent with the combined datasets handling.
+        - Create 'files.loadDataIntoNetCDF1' for handling the unified datasets.
+  * Modify misc.select_metrics
+        - Add an option to draw a Taylor diagram
+  * Modify utils/
+        - Add a new routine 'reshapeMonthlyData' introduced by Alex Goodman
++  7/11/2013:                                                                                         +
++  This version modifies the release version rcmet2.1 with features specific for the cordex-sa study  +
++  Need to implement the changes in the hydro version                                                 +
+  * Add options to enter any combinations of data for evaluation
+      - modify in the data selection block [e.g., refID = int(misc.select_data_combined(numDatasets, Times, dataList, 'ref'))]
+      - modify misc.select_data_combined
+  * New inpterpolation scheme "scipy.interpolate.griddata" replaces old "process.do_regrid".
+      - Inputs (x and y coordinates, data values) can be either regular grid on irregular grid.
+        Must specify masked values as "np.nan" to properly handle missing data.

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Added: incubator/climate/branches/rcmet-2.1.1/src/main/python/bin/
--- incubator/climate/branches/rcmet-2.1.1/src/main/python/bin/ (added)
+++ incubator/climate/branches/rcmet-2.1.1/src/main/python/bin/ Tue Aug 27 05:35:42 2013
@@ -0,0 +1,305 @@
+# Python Standard Lib Imports
+import argparse
+import ConfigParser
+import datetime
+import glob
+import os
+import sys
+import numpy as np
+import as ma
+# RCMES Imports
+import storage.rcmed as db
+from toolkit import do_data_prep, process, metrics
+from utils import misc
+from classes import JobProperties, Model, GridBox
+from cli import rcmet_ui as ui
+parser = argparse.ArgumentParser(description='Regional Climate Model Evaluation Toolkit.  Use -h for help and options')
+parser.add_argument('-c', '--config', dest='CONFIG', help='Path to an evaluation configuration file')
+args = parser.parse_args()
+def checkConfigSettings(config):
+    """ This function will check the SETTINGS block of the user supplied config file.
+    This will only check if the working and cache dirs are writable from this program.
+    Additional configuration parameters can be checked here later on.
+    Input::
+        config - ConfigParser configuration object
+    Output::
+        none - An exception will be raised if something goes wrong
+    """
+    settings = config.items('SETTINGS')
+    for key_val in settings:
+        # Check the user provided directories are valid
+        if key_val[0] == 'workDir' or key_val[0] == 'cacheDir':
+            _ =  misc.isDirGood(os.path.abspath(key_val[1]))
+        else:
+            pass    
+def setSettings(settings, config):
+    """
+    This function is used to set the values within the 'SETTINGS' dictionary when a user provides an external
+    configuration file.
+    Input::
+        settings - Python Dictionary object that will collect the key : value pairs
+        config - A configparse object that contains the external config values
+    Output::
+        None - The settings dictionary will be updated in place.
+    """
+    pass
+def generateModels(modelConfig):
+    """
+    This function will return a list of Model objects that can easily be used for 
+    metric computation and other processing tasks.
+    Input::  
+        modelConfig - list of ('key', 'value') tuples.  Below is a list of valid keys
+            filenamepattern - string i.e. '/nas/run/model/output/MOD*precip*.nc'
+            latvariable - string i.e. 'latitude'
+            lonvariable - string i.e. 'longitude'
+            timevariable - string i.e. 't'
+            timestep - string 'monthly' | 'daily' | 'annual'
+            varname - string i.e. 'pr'
+    Output::
+        modelList - List of Model objects
+    """
+    # Setup the config Data Dictionary to make parsing easier later
+    configData = {}
+    for entry in modelConfig:
+        configData[entry[0]] = entry[1]
+    modelFileList = None
+    for keyValTuple in modelConfig:
+        if keyValTuple[0] == 'filenamePattern':
+            modelFileList = glob.glob(keyValTuple[1])
+            modelFileList.sort()
+    # Remove the filenamePattern from the dict since it is no longer used
+    configData.pop('filenamePattern')
+    models = []
+    for modelFile in modelFileList:
+        # use getModelTimes(modelFile,timeVarName) to generate the modelTimeStep and time list
+        _ , configData['timeStep'] = process.getModelTimes(modelFile, configData['timeVariable'])
+        configData['filename'] = modelFile
+        model = Model(**configData)
+        models.append(model)
+    return models
+def generateSettings(config):
+    """
+    Helper function to decouple the argument parsing from the Settings object creation
+    Input::  
+        config - list of ('key', 'value') tuples.
+            workdir - string i.e. '/nas/run/rcmet/work/'
+            cachedir - string i.e. '/tmp/rcmet/cache/'
+    Output::
+        JobProperties - JobProperties Object
+    """
+    # Setup the config Data Dictionary to make parsing easier later
+    configData = {}
+    for entry in config:
+        configData[entry[0]] = entry[1]
+    return JobProperties(**configData)
+def makeDatasetsDictionary(rcmedConfig):
+    """
+    Helper function to decouple the argument parsing from the RCMEDDataset object creation
+    Input::  
+        rcmedConfig - list of ('key', 'value') tuples.
+            obsDatasetId=3,10
+            obsParamId=36,32
+            obsTimeStep=monthly,monthly
+    Output::
+        datasetDict - Dictionary with dataset metadata
+    # Setup the config Data Dictionary to make parsing easier later
+    """
+    delimiter = ','
+    configData = {}
+    for entry in rcmedConfig:
+        if delimiter in entry[1]:
+            # print 'delim found - %s' % entry[1]
+            valueList = entry[1].split(delimiter)
+            configData[entry[0]] = valueList
+        else:
+            configData[entry[0]] = entry[1:]
+    return configData
+def tempGetYears():
+    startYear = int(raw_input('Enter start year YYYY \n'))
+    endYear = int(raw_input('Enter end year YYYY \n'))
+    # CGOODALE - Updating the Static endTime to be 31-DEC
+    startTime = datetime.datetime(startYear, 1, 1, 0, 0)
+    endTime = datetime.datetime(endYear, 12, 31, 0, 0)
+    return (startTime, endTime)
+def runUsingConfig(argsConfig):
+    """
+    This function is called when a user provides a configuration file to specify an evaluation job.
+    Input::
+        argsConfig - Path to a ConfigParser compliant file
+    Output::
+        Plots that visualize the evaluation job. These will be output to SETTINGS.workDir from the config file
+    """
+    print 'Running using config file: %s' % argsConfig
+    # Parse the Config file
+    userConfig = ConfigParser.SafeConfigParser()
+    userConfig.optionxform = str # This is so the case is preserved on the items in the config file
+    try:
+        checkConfigSettings(userConfig)
+    except:
+        raise
+    jobProperties = generateSettings(userConfig.items('SETTINGS'))
+    workdir = jobProperties.workDir
+    try:
+        gridBox = GridBox(jobProperties.latMin, jobProperties.lonMin, jobProperties.latMax,
+                          jobProperties.lonMax, jobProperties.gridLonStep, jobProperties.gridLatStep)
+    except:
+        gridBox = None
+    models = generateModels(userConfig.items('MODEL'))
+    # 5/28/2013, JK: The RCMED block has been modified to accommodate ref data input from users' local disk
+    datasetDict = makeDatasetsDictionary(userConfig.items('RCMED'))
+    # Go get the parameter listing from the database
+    try:
+        params = db.getParams()
+    except:
+        raise
+    obsDatasetList = []
+    obsList = []
+    obsVarName = datasetDict['obsVarName'][0]
+    obsTimeName = datasetDict['obsTimeVar'][0]
+    obsLonName = datasetDict['obsLonVar'][0]
+    obsLatName = datasetDict['obsLatVar'][0]
+    obsTimestep = []
+    obsSource = int(datasetDict['obsSource'][0])
+    #print 'Obs datasetDict'
+    #print datasetDict
+    if obsSource < 0:                             # no obs data to be processed
+        obsVarName = []
+        obsTimeName = []
+        obsLonName = []
+        obsLatName = []
+    elif obsSource == 0:                          # input from RCMED
+        for param_id in datasetDict['obsParamId']:
+            for param in params:
+                if param['parameter_id'] == int(param_id):
+                    obsDatasetList.append(param)
+                else:
+                    pass
+    elif obsSource == 1:                        # input from local disk
+        for param in datasetDict['obsInputFile']:
+            obsDatasetList.append(param)
+        for param in datasetDict['obsFileName']:
+            obsList.append(param)
+        for param in datasetDict['obsDltaTime']:
+            obsTimestep.append(param)
+    #print obsSource,obsDatasetList,obsList,obsTimeName,obsTimestep
+    #TODO: Unhardcode this when we decided where this belongs in the Config File
+    jobProperties.maskOption = True
+    # User must provide startTime and endTime if not defined
+    if jobProperties.startDate == None or jobProperties.endDate == None:
+        jobProperties.startDate,jobProperties.endDate = misc.userDefinedStartEndTimes(obsSource,obsList,obsTimeName,obsDatasetList,models)
+    numOBS,numMDL,nT,ngrdY,ngrdX,Times,lons,lats,obsData,mdlData,obsName,mdlName = do_data_prep.prep_data   \
+          (jobProperties,obsSource,obsDatasetList,obsList,obsVarName,obsLonName,obsLatName,obsTimeName,obsTimestep,gridBox,models)
+    # 6/3/2013: Combine the regridded reference and model datasets. The packing order is: 
+    #               First pack all ref (obs) data with the ref enseble in the end (if exists).
+    #               Then pack all model data with the model ensemble in the end (if exists)
+    #           Release 'obsData' and 'mdlData' after their values are transferred to 'allData'
+    print 'Input and regridding of both obs and model data are completed. Combine the obs and model data'
+    numDatasets = numOBS + numMDL
+    allData = ma.zeros((numDatasets, nT, ngrdY, ngrdX))
+    if (numOBS>0) & (numMDL>0):
+        dataName = obsName + mdlName
+        allData[0:numOBS, :, :, :] = obsData[0:numOBS, :, :, :]
+        allData[numOBS:numDatasets, :, :, :] = mdlData[0:numMDL, :, :, :]
+        obsData = 0.
+        mdlData = 0.
+    elif numOBS==0:
+        dataName = mdlName
+        allData = mdlData
+        mdlData = 0.
+    else:
+        dataName = obsName
+        allData = obsData
+        obsData = 0
+    print ''
+    print 'dataName: ',dataName,' shape of all data= ',allData.shape
+    ##################################################################################
+    # calculate metrics and make plots using the regridded reference and model data. #
+    ##################################################################################
+    print 'Data preparation is completed; now move to metrics calculations'
+    try:
+        subRegionConfig = misc.configToDict(userConfig.items('SUB_REGION'))
+        subRegions = misc.parseSubRegions(subRegionConfig)
+        # REORDER SUBREGION OBJECTS until we standardize on Python 2.7
+        # TODO Remove once Python 2.7 support is finalized
+        if subRegions:
+            subRegions.sort(key=lambda
+    except ConfigParser.NoSectionError:
+        counts = {'observations': numOBS,
+                  'models'      : numMDL,
+                  'times'       : nT}
+        subRegions = misc.getSubRegionsInteractively(counts, workdir)
+        if len(subRegions) == 0:
+            print 'Processing without SubRegion support'
+    # TODO: New function Call
+    timeRegridOption = jobProperties.temporalGrid
+    fileOutputOption = jobProperties.writeOutFile
+    modelVarName = models[0].varName
+    metrics.metrics_plots(modelVarName, numOBS, numMDL, nT, ngrdY, ngrdX, Times, lons, lats, allData, dataName, workdir, subRegions, \
+                          timeRegridOption, fileOutputOption)
+if __name__ == "__main__":
+    if args.CONFIG:
+        runUsingConfig(args.CONFIG)
+    else:
+        print 'Interactive mode has been enabled'
+        ui.rcmetUI()
+    #rcmet_cordexAF()

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Added: incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/Makefile
--- incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/Makefile (added)
+++ incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/Makefile Tue Aug 27 05:35:42 2013
@@ -0,0 +1,153 @@
+# Makefile for Sphinx documentation
+# You can set these variables from the command line.
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+# the i18n builder cannot share the environment and doctrees with the others
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	-rm -rf $(BUILDDIR)/*
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/rcmes.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/rcmes.qhc"
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/rcmes"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/rcmes"
+	@echo "# devhelp"
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."

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Added: incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/
--- incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/ (added)
+++ incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/ Tue Aug 27 05:35:42 2013
@@ -0,0 +1,242 @@
+# -*- coding: utf-8 -*-
+# rcmes documentation build configuration file, created by
+# sphinx-quickstart on Tue Aug 14 14:18:41 2012.
+# This file is execfile()d with the current directory set to its containing dir.
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+import sys, os
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+sys.path.insert(0, os.path.abspath('../'))
+# -- General configuration -----------------------------------------------------
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo', 'sphinx.ext.coverage']
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+# The suffix of source filenames.
+source_suffix = '.rst'
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+# The master toctree document.
+master_doc = 'index'
+# General information about the project.
+project = u'rcmes'
+copyright = u'2012, Duane Waliser, Chris Mattmann, Jinwon Kim, Andrew Hart, Cameron Goodale, Paul Ramirez, Paul Zimdars, Kim Whitehall, Jesslyn Whittell, Peter Lean'
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+# The short X.Y version.
+version = '1.2'
+# The full version, including alpha/beta/rc tags.
+release = '1.2.0'
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build']
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+# -- Options for HTML output ---------------------------------------------------
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'default'
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+# If false, no module index is generated.
+#html_domain_indices = True
+# If false, no index is generated.
+#html_use_index = True
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'rcmesdoc'
+# -- Options for LaTeX output --------------------------------------------------
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+  ('index', 'rcmes.tex', u'rcmes Documentation',
+   u'Duane Waliser, Chris Mattmann, Jinwon Kim, Andrew Hart, Cameron Goodale, Paul Ramirez, Paul Zimdars, Kim Whitehall, Jesslyn Whittell, Peter Lean', 'manual'),
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+# If false, no module index is generated.
+#latex_domain_indices = True
+# -- Options for manual page output --------------------------------------------
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'rcmes', u'rcmes Documentation',
+     [u'Duane Waliser, Chris Mattmann, Jinwon Kim, Andrew Hart, Cameron Goodale, Paul Ramirez, Paul Zimdars, Kim Whitehall, Jesslyn Whittell, Peter Lean'], 1)
+# If true, show URL addresses after external links.
+#man_show_urls = False
+# -- Options for Texinfo output ------------------------------------------------
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+  ('index', 'rcmes', u'rcmes Documentation',
+   u'Duane Waliser, Chris Mattmann, Jinwon Kim, Andrew Hart, Cameron Goodale, Paul Ramirez, Paul Zimdars, Kim Whitehall, Jesslyn Whittell, Peter Lean', 'rcmes', 'One line description of project.',
+   'Miscellaneous'),
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'

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Added: incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/index.rst
--- incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/index.rst (added)
+++ incubator/climate/branches/rcmet-2.1.1/src/main/python/docs/index.rst Tue Aug 27 05:35:42 2013
@@ -0,0 +1,22 @@
+.. rcmes documentation master file, created by
+   sphinx-quickstart on Tue Aug 14 14:18:41 2012.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+Welcome to rcmes's documentation!
+.. toctree::
+   :maxdepth: 2
+Indices and tables
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

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