Merge pull request #685 from PCMDI/doc_test2_pjg

starting to work on mean climate

docs/Supporting-data.html

@@ -84,7 +84,7 @@
 
  <p class="caption"><span class="caption-text">Contents:</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="Technical-overview.html">Technical Overview</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Technical-overview.html">Usage Overview</a></li>
 <li class="toctree-l1"><a class="reference internal" href="install.html">Install using Anaconda</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Retrieving data for demos and use of the PMP</a></li>
 <li class="toctree-l1"><a class="reference internal" href="metrics-overview.html">Documentation and Demos</a></li>

docs/Technical-overview.html

@@ -7,7 +7,7 @@
 
  <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
- <title>Technical Overview &mdash; PCMDI Metrics 1.2.1 documentation</title>
+ <title>Usage Overview &mdash; PCMDI Metrics 1.2.1 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 
  <link rel="index" title="Index" href="genindex.html" />
  <link rel="search" title="Search" href="search.html" />
- <link rel="next" title="Retrieving data for demos and use of the PMP" href="Supporting-data.html" />
+ <link rel="next" title="Install using Anaconda" href="install.html" />
  <link rel="prev" title="PCMDI Metrics Package (PMP)" href="index.html" /> 
 </head>
 
@@ -84,7 +84,7 @@
 
  <p class="caption"><span class="caption-text">Contents:</span></p>
 <ul class="current">
-<li class="toctree-l1 current"><a class="current reference internal" href="#">Technical Overview</a><ul>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Usage Overview</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#summary">Summary</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#software-framework-and-dependancies">Software framework and dependancies</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#input-output-format">Input/Output format</a></li>
@@ -93,6 +93,7 @@
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="install.html">Install using Anaconda</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Supporting-data.html">Retrieving data for demos and use of the PMP</a></li>
 <li class="toctree-l1"><a class="reference internal" href="metrics-overview.html">Documentation and Demos</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pmpparser.html">Miscellaneous</a></li>
@@ -142,7 +143,7 @@
 
  <li><a href="index.html" class="icon icon-home"></a> &raquo;</li>
 
- <li>Technical Overview</li>
+ <li>Usage Overview</li>
 
 
  <li class="wy-breadcrumbs-aside">
@@ -161,8 +162,8 @@
  <div role="main" class="document" itemscope="itemscope" itemtype="http:https://schema.org/Article">
  <div itemprop="articleBody">
 
- <div class="section" id="technical-overview">
-<h1>Technical Overview<a class="headerlink" href="#technical-overview" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="usage-overview">
+<h1>Usage Overview<a class="headerlink" href="#usage-overview" title="Permalink to this headline">¶</a></h1>
 <div class="section" id="summary">
 <h2>Summary<a class="headerlink" href="#summary" title="Permalink to this headline">¶</a></h2>
 <p>The PMP provides a diverse suite of analysis utilities each of which produce summary statistics that gauge the consistency between climate model simulations and available observations. The primary application of the PMP is to evaluate simulations from the <a class="reference external" href="https://www.wcrp-climate.org/wgcm-cmip">Coupled Model Intercomparison Project (CMIP)</a>. It can also be used to provide objective performance summaries during the model development process as well as selected research purposes. The notes below provide a brief summary of some of the key aspects of the PMP design.</p>
@@ -177,17 +178,17 @@ <h3>Input/Output format<a class="headerlink" href="#input-output-format" title="
 </div>
 <div class="section" id="basic-operation">
 <h3>Basic Operation<a class="headerlink" href="#basic-operation" title="Permalink to this headline">¶</a></h3>
-<p>The summary statistics available with the PMP can be run independently or as a collective (the later to be available via the next PMP version). Here is a glimpse of how the mean climate statistics are executed from the unix command prompt ($):</p>
+<p>The summary statistics available with the PMP can be run independently or as a collective (the later to be available via the next PMP version). Here is a glimpse of how the mean climate statistics are executed from the unix command prompt:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ mean_climate_driver.py -p e3sm_parameterfile.py
 </pre></div>
 </div>
-<p>Because there are often multiple parameters to set before executing a PMP code, routine operation often involves setting these options in an “input parameter” python file such as the filename immediately following the “-p” flag above. The PMP input parameter files are similiar to a “namelist” text file used in other climate analysis packages but having the input parameters set in a python file enables us to leverage the power of python. For example, the contents of an input parameter file might look something like this ($):</p>
+<p>Because there are often multiple parameters to set before executing a PMP code, routine operation often involves setting these options in an “input parameter” python file such as the filename immediately following the “-p” flag above. The PMP input parameter files are similiar to a “namelist” text file used in other climate analysis packages but having the input parameters set in a python file enables us to leverage the power of python. For example, the contents of an input parameter file might look something like this:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ more input_parameters.py
 $ test_data_set = [&#39;ACCESS-1-0&#39;,&#39;CESM2&#39;]
 $ period = &#39;1981-2005&#39;
 </pre></div>
 </div>
-<p>which includes both a string variable (period) and a python list (test_data_set). Other python objects can be included in input parameter files, notably python dictionaries. Additional functionality is shown in another example command ($):</p>
+<p>which includes both a string variable (period) and a python list (test_data_set). Other python objects can be included in input parameter files, notably python dictionaries. Additional functionality is shown in another example command:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ mean_climate_driver.py -p e3sm_parameterfile.py --variable pr
 </pre></div>
 </div>
@@ -205,7 +206,7 @@ <h3>Basic Operation<a class="headerlink" href="#basic-operation" title="Permalin
 
  <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
- <a href="Supporting-data.html" class="btn btn-neutral float-right" title="Retrieving data for demos and use of the PMP" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="install.html" class="btn btn-neutral float-right" title="Install using Anaconda" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
  <a href="index.html" class="btn btn-neutral float-left" title="PCMDI Metrics Package (PMP)" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>

docs/_sources/Technical-overview.rst.txt

@@ -1,4 +1,4 @@
-Technical Overview
+Usage Overview
 ***********
 
 Summary
@@ -23,19 +23,19 @@ The PMP statistics are output in `JSON format <https://www.json.org/json-en.html
 Basic Operation
 ---------------
 
-The summary statistics available with the PMP can be run independently or as a collective (the later to be available via the next PMP version). Here is a glimpse of how the mean climate statistics are executed from the unix command prompt ($): ::
+The summary statistics available with the PMP can be run independently or as a collective (the later to be available via the next PMP version). Here is a glimpse of how the mean climate statistics are executed from the unix command prompt: ::
 
-$ mean_climate_driver.py -p e3sm_parameterfile.py 
+ $ mean_climate_driver.py -p e3sm_parameterfile.py 
 
-Because there are often multiple parameters to set before executing a PMP code, routine operation often involves setting these options in an "input parameter" python file such as the filename immediately following the "-p" flag above. The PMP input parameter files are similiar to a "namelist" text file used in other climate analysis packages but having the input parameters set in a python file enables us to leverage the power of python. For example, the contents of an input parameter file might look something like this ($): ::
+Because there are often multiple parameters to set before executing a PMP code, routine operation often involves setting these options in an "input parameter" python file such as the filename immediately following the "-p" flag above. The PMP input parameter files are similiar to a "namelist" text file used in other climate analysis packages but having the input parameters set in a python file enables us to leverage the power of python. For example, the contents of an input parameter file might look something like this: ::
 
-$ more input_parameters.py
-$ test_data_set = ['ACCESS-1-0','CESM2']
-$ period = '1981-2005'
+ $ more input_parameters.py
+ $ test_data_set = ['ACCESS-1-0','CESM2']
+ $ period = '1981-2005'
 
-which includes both a string variable (period) and a python list (test_data_set). Other python objects can be included in input parameter files, notably python dictionaries. Additional functionality is shown in another example command ($): ::
+which includes both a string variable (period) and a python list (test_data_set). Other python objects can be included in input parameter files, notably python dictionaries. Additional functionality is shown in another example command: ::
 
-$ mean_climate_driver.py -p e3sm_parameterfile.py --variable pr 
+ $ mean_climate_driver.py -p e3sm_parameterfile.py --variable pr 
 
 Here, the "---variable" option is used to specify "pr" (precipitation) with other options included in the file after the "-p" flag. 
 

docs/_sources/index.rst.txt

@@ -31,7 +31,7 @@ GETTING STARTED
 ===============
 Installation requirements and instructions are available on the :ref:`install` page
 
-An overview for using the package and template scripts are detailed on the :ref:`metrics-overview` page
+An overview of the summary statistics available via the package are summarized with interactive Jupyter notebooks in the :ref:`metrics-overview` page
 
 Some installation support for CMIP participating modeling groups is available: [email protected]
 

docs/_sources/mean-climate.rst.txt

@@ -18,11 +18,43 @@ The mean climate summary statistics are some of the most routine analysis availa
 Observational climatologies
 ###########################
 
-A database of `observational climatologies <https://github.com/PCMDI/PCMDIobs-cmor-tables/blob/master/catalogue/pcmdiobs2_clims_byVar_catalogue_v20201210.json>`_ is available to users of the PMP. To obtain this, please contact the PMP user group ([email protected]) and you will promptly provided with the database. A subset of this database is available via the demo data made available for the PMP tutorials via a `jupyter notebook demo <https://github.com/PCMDI/pcmdi_metrics/blob/master/doc/jupyter/Demo/Demo_0_download_data.ipynb>`_ or via the version of python included as part of the PMP environment. 
+A database of `observational climatologies <https://github.com/PCMDI/PCMDIobs-cmor-tables/blob/master/catalogue/pcmdiobs2_clims_byVar_catalogue_v20201210.json>`_ is available to users of the PMP. To obtain this, please contact the PMP user group ([email protected]) and you will be promptly provided with the database. A subset of this database is available via the demo data made available for the PMP tutorials via a `jupyter notebook demo <https://github.com/PCMDI/pcmdi_metrics/blob/master/doc/jupyter/Demo/Demo_0_download_data.ipynb>`_. Once you have downloaded this demo data you can interactively run the mean climate and other demos. 
+
+The `mean climate notebook <https://github.com/PCMDI/pcmdi_metrics/blob/master/doc/jupyter/Demo/Demo_1_mean_climate.ipynb>`_ provides a series of examples that demonstrate the options available. 
+
+Preparation of model climatologies
+##################################
+
+Sample model climatologies are available as part of the PMP demo database noted above and are used for the mean climate notebook. However, if a user wants to create and use their own model climatologies the a simple example is provide in the mean climate notebook itself or the `PMP github repository <https://github.com/PCMDI/pcmdi_metrics/tree/master/sample_setups/pcmdi_parameter_files/mean_climate/make_clims>`_. 
+
+
+Construction of an input paramater file
+#######################################
+
+The PMP mean climate metrics can be controlled via an input parameter file, the command line, or both. With the command line only it is executed via: ::
+
+
+ mean_climate_driver.py -p basic_param.py
+
+or as a combination of an input parameter file and the command line, e.g.: ::
+
+ mean_climate_driver.py -p basic_param.py --vars rlut pr 
+
+where the list of variables to run the analysis on includes the variables 'rlut' (outgoing TOA longwave radiation) and 'pr' (precipitation). 
+
+Because there are a minimum of 5(?) parameters to be set with the mean climate statistics. 
+
+SOME DISCUSSION HERE ON THE MINIMUM SET OF INPUT PARAMETERS.
+
 
-
 
+In addition to the minimum set of parameters noted above, the following summarizes additional options than can be controlled for the mean climate:
 
 
+* Select regridding option
+* Define a different set of regions
+* Provide or estimate a land-sea mask
+* Define regional masking (e.g., land-only or ocean-only)
+* Select to output (or not) interpolate climatologies including masking
 
 

docs/_sources/metrics-overview.rst.txt

@@ -1,4 +1,4 @@
-.. _using-the-package:
+.. _metrics-overview:
 
 *****************
 Documentation and Demos

docs/clivar-enso-metrics.html

@@ -84,7 +84,8 @@
 
  <p class="caption"><span class="caption-text">Contents:</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="Technical-overview.html">Technical Overview</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Technical-overview.html">Usage Overview</a></li>
+<li class="toctree-l1"><a class="reference internal" href="install.html">Install using Anaconda</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Supporting-data.html">Retrieving data for demos and use of the PMP</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="metrics-overview.html">Documentation and Demos</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="metrics-overview.html#overview">Overview</a><ul class="current">

docs/extrop-mov.html

@@ -84,7 +84,7 @@
 
  <p class="caption"><span class="caption-text">Contents:</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="Technical-overview.html">Technical Overview</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Technical-overview.html">Usage Overview</a></li>
 <li class="toctree-l1"><a class="reference internal" href="install.html">Install using Anaconda</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Supporting-data.html">Retrieving data for demos and use of the PMP</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="metrics-overview.html">Documentation and Demos</a><ul class="current">

docs/genindex.html

@@ -82,7 +82,7 @@
 
  <p class="caption"><span class="caption-text">Contents:</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="Technical-overview.html">Technical Overview</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Technical-overview.html">Usage Overview</a></li>
 <li class="toctree-l1"><a class="reference internal" href="install.html">Install using Anaconda</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Supporting-data.html">Retrieving data for demos and use of the PMP</a></li>
 <li class="toctree-l1"><a class="reference internal" href="metrics-overview.html">Documentation and Demos</a></li>