minor doc updates

PCMDI · lee1043 · Nov 4, 2020 · Nov 4, 2020 · Nov 4, 2020 · Nov 4, 2020
commit adc9a413b5ebd9e0bbfb08e9819eb156e72f68c3
diff --git a/docs/Supporting-data.html b/docs/Supporting-data.html
@@ -36,8 +36,7 @@
 
  <link rel="index" title="Index" href="genindex.html" />
  <link rel="search" title="Search" href="search.html" />
- <link rel="next" title="Documentation and Demos" href="metrics-overview.html" />
- <link rel="prev" title="Install using Anaconda" href="install-using-anaconda.html" /> 
+ <link rel="next" title="Documentation and Demos" href="metrics-overview.html" /> 
 </head>
 
 <body class="wy-body-for-nav">
@@ -85,13 +84,12 @@
  <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="install-using-anaconda.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><ul>
 <li class="toctree-l2"><a class="reference internal" href="#overview">Overview</a></li>
 </ul>
 </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">PMPParser</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pmpparser.html">Miscellaneous</a></li>
 </ul>
 
 
@@ -161,7 +159,24 @@
 <span id="using-the-package"></span><h1>Retrieving data for demos and use of the PMP<a class="headerlink" href="#retrieving-data-for-demos-and-use-of-the-pmp" title="Permalink to this headline">¶</a></h1>
 <div class="section" id="overview">
 <h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<p>A combination of static examples/doc and notebooks</p>
+<p>Sample model and observational data are provided via a <a class="reference external" href="https://github.com/acordonez/pcmdi_metrics/blob/645_notebooks/doc/jupyter/Demo/Demo_0_download_data.ipynb">jupyter notebook demo</a>.</p>
+<p>For users that are unfamiliar with Jupyter notebooks, a little python code for retrieving the demo data is repeated below.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">requests</span>
+<span class="n">r</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;https://pcmdiweb.llnl.gov/pss/pmpdata/cmec_tutorial_files.txt&quot;</span><span class="p">)</span>
+<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;data_files.txt&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">content</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>To retrieve these sample files locally, one first sets the location where they want the demo data to be stored locally.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">demo_data_directory</span> <span class="o">=</span> <span class="s1">&#39;MyDemoPath&#39;</span>
+</pre></div>
+</div>
+<p>The last line sets the demo_output directories. After that, data is downloaded as follows:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">cdat_info</span>
+<span class="n">cdat_info</span><span class="o">.</span><span class="n">download_sample_data_files</span><span class="p">(</span><span class="s2">&quot;data_files.txt&quot;</span><span class="p">,</span> <span class="n">demo_data_directory</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>First, make sure you are in a functioning PMP environemnt (see <a class="reference internal" href="install.html#install"><span class="std std-ref">Install using Anaconda</span></a>).</p>
 </div>
 </div>
 
@@ -176,8 +191,6 @@ <h2>Overview<a class="headerlink" href="#overview" title="Permalink to this head
  <a href="metrics-overview.html" class="btn btn-neutral float-right" title="Documentation and Demos" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
- <a href="install-using-anaconda.html" class="btn btn-neutral float-left" title="Install using Anaconda" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
-
  </div>
 
 

diff --git a/docs/Technical-overview.html b/docs/Technical-overview.html
@@ -96,7 +96,7 @@
 <li class="toctree-l1"><a class="reference internal" href="install-using-anaconda.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">PMPParser</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pmpparser.html">Miscellaneous</a></li>
 </ul>
 
 

diff --git a/docs/_sources/Supporting-data.rst.txt b/docs/_sources/Supporting-data.rst.txt
@@ -7,6 +7,26 @@ Retrieving data for demos and use of the PMP
 Overview
 ========
 
-A combination of static examples/doc and notebooks
+Sample model and observational data are provided via a `jupyter notebook demo <https://github.com/acordonez/pcmdi_metrics/blob/645_notebooks/doc/jupyter/Demo/Demo_0_download_data.ipynb>`_.
 
+For users that are unfamiliar with Jupyter notebooks, a little python code for retrieving the demo data is repeated below. :: 
+
+ import requests
+ r = requests.get("https://pcmdiweb.llnl.gov/pss/pmpdata/cmec_tutorial_files.txt")
+ with open("data_files.txt","wb") as f:
+ f.write(r.content)
+
+
+To retrieve these sample files locally, one first sets the location where they want the demo data to be stored locally. ::
+
+ demo_data_directory = 'MyDemoPath' 
+
+
+The last line sets the demo_output directories. After that, data is downloaded as follows: ::
+
+ import cdat_info
+ cdat_info.download_sample_data_files("data_files.txt", demo_data_directory)
+
+
+First, make sure you are in a functioning PMP environemnt (see :ref:`install`). 
 
diff --git a/docs/_sources/install.rst.txt b/docs/_sources/install.rst.txt
@@ -1,15 +1,39 @@
 .. _install:
 
-*******
-Installation
-*******
+**********************
+Install using Anaconda
+**********************
 
-The supported method for installing the PMP within a local environment is via `Anaconda <https://conda.io/en/latest/>`.
-The source code is also available to developers via the PMP Github repository. 
+We offer an installation for anaconda users under linux-64 or osx-64.
+Support for Windows is not available yet.
 
-Anaconda installation (recommended)
-===================================
+https://anaconda.org/PCMDI/pcmdi_metrics/files
 
-* :ref:`install-anaconda` - Installation instructions for Anaconda users
+All Platforms System Requirements
+=================================
+ * Install the `Anaconda for Python 3.7 <https://www.anaconda.com/products/individual#Downloads>`_ package (we recommend installing this for each user)
+ * Make sure anaconda is in your PATH (assuming anaconda is installed in ${HOME}/anaconda
+ * ``export PATH=${HOME}/anaconda/bin:${PATH}`` # for [ba]sh
+ * ``setenv PATH ${HOME}/anaconda/bin:${PATH}`` # for [t]csh
 
-A primary advantage of the Anaconda install path is that it is user-centric. This allows users on super computing systems with limited permissions to fully configure their local PMP install
+Make sure you have no environment variables set from an old UV-CDAT installation in your PATH/PYTHONPATH,LD_LIBRARY_PATH etc
+
+Bypassing firewalls
+===================
+If your institution has tight ssl certificate/security issues try:
+ * ``conda config --set ssl_verify False``
+ * ``binstar config --set ssl_verify False``
+
+Installing the PCMDI Metrics Package (PMP)
+==========================================
+Using the conda package manager, you can install the PCMDI Metrics package from the PCMDI conda channel, and from an environment containing [CDAT](https://cdat.llnl.gov/).
+ * ``source activate [YOUR_CDAT_ENABLED_CONDA_ENVIRONMENT]`` (See `CDAT Install <https://github.com/CDAT/cdat/wiki/install>`_)
+ * ``conda install pcmdi_metrics -c cdat-forge``
+
+Getting the latest nightly of PMP and CDAT
+==========================================
+ * ``conda create -n [YOUR_ENV_NAME_HERE] -c cdat/label/nightly -c pcmdi/label/nightly -c conda-forge -c cdat pcmdi_metrics``
+ * ``source activate [YOUR_ENV_NAME_HERE]``
+
+
+To learn more about conda environments see: http:https://conda.pydata.org/docs/using/envs.html
diff --git a/docs/_sources/mean-climate.rst.txt b/docs/_sources/mean-climate.rst.txt
@@ -7,6 +7,22 @@ Mean Climate
 Overview
 ========
 
-A combination of static examples/doc and notebooks
+The mean climate summary statistics are the most routine analysis available from the PMP. At the same time, because of the number of options available they do require some preparation in advance of the analysis, including:
 
+* Placement of observational climatologies
 
+* Preparation of model climatologies 
+
+* Construction of an input parameter file 
+
+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 for the example below.
+
+
+
+
+
+
+
diff --git a/docs/_sources/pmpparser.rst.txt b/docs/_sources/pmpparser.rst.txt
@@ -1,5 +1,5 @@
 *********
-PMPParser
+Miscellaneous 
 *********
 
 Installing PMPParser

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -83,10 +83,9 @@
  <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="install-using-anaconda.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">PMPParser</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pmpparser.html">Miscellaneous</a></li>
 </ul>
 
 

diff --git a/docs/index.html b/docs/index.html
@@ -84,10 +84,9 @@
  <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="install-using-anaconda.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">PMPParser</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pmpparser.html">Miscellaneous</a></li>
 </ul>
 
 
@@ -163,15 +162,14 @@ <h1>PCMDI Metrics Package (PMP)<a class="headerlink" href="#pcmdi-metrics-packag
 <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="install-using-anaconda.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">PMPParser</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pmpparser.html">Miscellaneous</a></li>
 </ul>
 </div>
 <div class="section" id="getting-started">
 <h2>GETTING STARTED<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h2>
-<p>Installation requirements and instructions are available on the <a class="reference internal" href="install.html#install"><span class="std std-ref">Installation</span></a> page</p>
+<p>Installation requirements and instructions are available on the <a class="reference internal" href="install.html#install"><span class="std std-ref">Install using Anaconda</span></a> page</p>
 <p>An overview for using the package and template scripts are detailed on the <span class="xref std std-ref">metrics-overview</span> page</p>
 <p>Some installation support for CMIP participating modeling groups is available: <a class="reference external" href="mailto:pcmdi-metrics&#37;&#52;&#48;llnl&#46;gov">pcmdi-metrics<span>&#64;</span>llnl<span>&#46;</span>gov</a></p>
 </div>