Merge branch 'develop' into issue_156_scorecard

build.xml

@@ -319,7 +319,7 @@
         </copy>
         <delete file="${build}/MANIFEST.MF"/>
         <manifest file="${build}/MANIFEST.MF">
-            <attribute name="Specification-Version" value="6.0.0-beta2-dev"/>
+            <attribute name="Specification-Version" value="6.0.0-beta3-dev"/>
         </manifest>
 
         <jar jarfile="${dist}/lib/metviewer.jar" basedir="${build}" manifest="${build}/MANIFEST.MF">

docker/Dockerfile

@@ -5,10 +5,10 @@ MAINTAINER Tatiana Burek <tatiana@ucar.edu>
 #
 # This Dockerfile checks out METviewer from GitHub and builds the specified branch or tag.
 #
-ENV METVIEWER_GIT_NAME main_v5.1
-ENV METCALCPY_GIT_NAME main_v2.1
-ENV METPLOTPY_GIT_NAME main_v2.1
-ENV METDATAIO_GIT_NAME main_v2.1
+ENV METVIEWER_GIT_NAME v6.0.0-beta2
+ENV METCALCPY_GIT_NAME v3.0.0-beta2
+ENV METPLOTPY_GIT_NAME v3.0.0-beta2
+ENV METDATAIO_GIT_NAME v3.0.0-beta2
 
 #
 # Constants

docs/Contributors_Guide/index.rst

@@ -1,7 +1,6 @@
-
-===================
+###################
 Contributor's Guide
-===================
+###################
 
 .. toctree::
    :titlesonly:

docs/Contributors_Guide/testing.rst

@@ -1,8 +1,9 @@
+**************
 Testing Module
-==============
+**************
 
-Testing example - install and run on dakota
--------------------------------------------
+Testing Example - Install and Run on dakota
+===========================================
 
 **Testing directory and branch information**
 
@@ -45,8 +46,8 @@ stored in the
 `git store <https://git-scm.com/book/en/v2/Git-Tools-Credential-Storage>`_ .
 Also, **auto_test.sh** should be modified to send emails with testing results.
 
-Testing - capture
------------------
+Testing - Capture
+=================
 
 The testing module is used to execute the regression testing of a specified
 version of METviewer. The capture tool is invoked by using the mv_test.sh
@@ -173,13 +174,13 @@ directory structure might look like this, for example...
                  ...
 
 
-Testing - verify
-----------------
+Testing - Verify
+================
 
 The mv_compare.sh script accepts a branch and a tag that it uses to identify a test subdirectory and a second "expected" branch and tag that it uses to identify a comparison test directory. If tags are omitted the HEAD is used. The compare script looks for corresponding image files in the corresponding plots directories and does a binary comparison of the corresponding files. Differences will be reported as errors.
 
-auto test
----------
+Auto Test
+=========
 
 The auto_test.sh script defines the branch, optionally a tag, directories, and database credentials for a version under test and a comparison version. It performs the following steps.
 
@@ -286,8 +287,8 @@ to pass, produced and expected files should be byte identical.
 NOTE: R scripts create visually similar results but bitwise different
 image files on different platforms.
 
-Testing submodules
-------------------
+Testing Submodules
+==================
 
 **LoadDataTest** recreates and refills the mv_test database with MET output
 data and compares the number of rows in each table with the expected number.

docs/Users_Guide/barplots.rst

@@ -1,8 +1,9 @@
+*********
 Bar Plots
-=========
+*********
 
 Description
------------
+===========
 
 A bar plot shows comparisons among discrete categories. One axis of the
 chart shows the specific categories being compared, while the other
@@ -22,7 +23,7 @@ Bar plots often represent counts or frequencies, however, bar plots can
 represent means, medians, standard deviations, or any other statistic.
 
 How-To
--------
+======
 
 Selection of options to produce the plot proceeds approximately
 counter-clockwise around the METviewer window. The steps to create a series
@@ -92,7 +93,7 @@ plot are:
 There are many other options for plots, but these are the basics.
 
 Example
---------
+=======
 
 The image below shows an example of the plot and set-up options for a
 series plot in METviewer. This example uses the database

docs/Users_Guide/batch.rst

@@ -1,5 +1,6 @@
+*********************
 Batch Plotting Module
-=====================
+*********************
 
 The batch plotting system is used to generate a number of plots of data in
 the METviewer database. The usage statement:
@@ -170,7 +171,8 @@ conceptually, a list of **<date_range>** structures.
 |               **<listDiffSeries2>:** Turns on a difference curve should be plotted for the y2 series; calculated as the pairwise difference between the members of the first series minus the second - example:list(c("series1","series2"), c("series3","series4")).
 |
 
-**Template Formatting**
+Template Formatting
+===================
 
 Template values have the syntax
 {var_name[?param1=val1[&amp;param2=val2[...]]]}. For example,
@@ -439,10 +441,11 @@ starting at 1 for each fcst_var.
 |
 
 MODE Statistics
----------------
+===============
 
 Single Object Statistics
-~~~~~~~~~~~~~~~~~~~~~~~~
+------------------------
+
 MODE statistics are broken up into two categories: single and pair
 statistics. Single statistics are suffixed with a three letter code which
 indicates the group of objects over which the statistic should be calculated
@@ -597,7 +600,7 @@ RATIO\_ with AREARAT\_ and OBJ with OBJA.
     - OBJFBIAS
 
 Pair Object Statistics
-~~~~~~~~~~~~~~~~~~~~~~
+----------------------
 
 MODE object pair statistics are specified using the following format:
 STATNAME_CC where STATNAME is one of the Object Pair Statistics in the

docs/Users_Guide/boxplot.rst

@@ -1,8 +1,9 @@
+*********
 Box Plots
-=========
+*********
 
 Description
------------
+===========
 
 Box plots, or box and whisker plots, are a way to summarize a distribution
 of values using Tukey's 5-number summary
@@ -27,7 +28,7 @@ threshold. Here, each forecast and observation is binary, but the
 verification statistic is continuous. 
 
 How-To
----------
+======
 
 Selection of options to produce the plot proceeds approximately
 counter-clockwise around the METviewer window. The steps to create a
@@ -105,7 +106,7 @@ There are many other options for plots, but these are the basics.
 
 
 Example
---------
+=======
 
 The example below shows a boxplot of the RMSE for 2m temperature over
 the CONUS. Many of the standard METviewer plotting options are available

docs/Users_Guide/common.rst

@@ -1,5 +1,6 @@
+*********************
 Common XML Structures
-=====================
+*********************
 
 The database loading module and batch plotting module both use XML input files. Some XML structures can be used in either input file. These common structures are documented below.
 

docs/Users_Guide/contourplot.rst

@@ -1,8 +1,9 @@
+*************
 Contour Plots
-=============
+*************
 
 Description
------------
+===========
 
 Contour plots are a very general plot type somewhat similar to a scatter
 plot. The axes are specified by the user, and any will do so long as the
@@ -13,7 +14,7 @@ examine the difference in statistics between two NWP models as a contour
 plot, as is shown in the example below. 
 
 How-To
--------
+======
 
 Selection of options to produce the plot proceeds approximately
 counter-clockwise around the METviewer window. The steps to create a contour
@@ -76,7 +77,7 @@ plot are:
 There are many other options for plots, but these are the basics.
 
 Example
---------
+=======
 
 The example is a contour plot of temperature mean error (bias) for one
 model at different pressure levels over a range of initialization times.

docs/Users_Guide/database_loading.rst

@@ -1,5 +1,6 @@
+***********************
 Database Loading Module
-=======================
+***********************
 
 The database loading module is used to insert, update, and delete MET output
 data in the database. The tool is invoked using the mv_load.sh script. The
@@ -134,7 +135,7 @@ change it to
 
 
 Example
--------
+=======
 
 Here is a simple example:
 
@@ -203,7 +204,8 @@ specified by the <date_offset> named folder_dates.
         ...
 
 Troubleshooting
----------------
+===============
+
 .. _test:
 
 .. list-table:: 

docs/Users_Guide/database_scrubbing.rst

@@ -1,5 +1,6 @@
+*************************
 Database Scrubbing Module
-=========================
+*************************
 
 The database scrubbing utility is used to to delete data from METviewer
 databases that meets some user-specified selection criteria. The usage
@@ -58,7 +59,7 @@ performed (**FALSE**).
 |
 
 Examples
---------
+========
 
 **Example 1: Prune by describing the data (<fields>)**
 

docs/Users_Guide/eclvplots.rst

@@ -1,8 +1,9 @@
+******************************
 Economic Cost/Loss Value Plots
-==============================
+******************************
 
 Description
------------
+===========
 
 The Economic Cost Loss Value statistic is sometimes also called the
 Relative value score (:ref:`Richardson, 2000<Richardson>`;
@@ -23,11 +24,12 @@ The ECLV score can range from -:math:`\infty` to 1.
 Like ROC diagrams, it gives information that can be used in decision making.
 
 Line Type
----------
+=========
+
 ECLV requires the ECLV line type generated by either Point-Stat or Grid-Stat.
 
 How-To
-------
+======
 
 Selection of options to produce the ECLV plot proceeds approximately
 counter-clockwise around the METviewer window.
@@ -81,7 +83,7 @@ counter-clockwise around the METviewer window.
 
 
 Example
---------
+=======
 
 The figure below shows an ECLV plot. In this example, three different
 forecasting systems are used to predict precipitation at two different

docs/Users_Guide/etb_plot.rst

@@ -1,8 +1,9 @@
+********************************
 Equivalence Testing Bounds Plots
-================================
+********************************
 
 Description
------------
+===========
 
 A statistical hypothesis is an assertion about the distribution function for one or more random variables.
 Generally, two hypotheses are considered, a null hypothesis denoted by H0, and an alternative denoted by
@@ -32,7 +33,7 @@ In this case, H0 is accepted if the CI bounds fall completely between the tolera
 and H0 is rejected otherwise.
 
 How-To
--------
+======
 
 Selection of options to produce the plot proceeds approximately
 counter-clockwise around the METviewer window. The steps to create a
@@ -104,7 +105,7 @@ There are many other options for plots, but these are the basics.
 
 
 Example
---------
+=======
 
 The image below shows an example of the plot and set-up options for a
 series plot in METviewer. This example uses the database

docs/Users_Guide/index.rst

@@ -1,6 +1,6 @@
-============
+############
 User's Guide
-============
+############
 
 **Foreword: A note to METviewer users**
 

docs/Users_Guide/installation.rst

@@ -1,17 +1,18 @@
 .. _install:
 
+****************************
 METviewer Installation Guide
-============================
+****************************
 
 Introduction
-------------
+============
 
 This chapter describes how to install METviewer. METviewer has been
 developed and tested on Linux operating systems. Support for additional
 platforms and compilers may be added in future releases. 
 
 Installing METviewer
---------------------
+====================
 
 METviewer relies on the following tools. These must be installed and tested
 prior to installing METviewer:
@@ -117,8 +118,8 @@ clone   `METdataio repository <https://github.com/dtcenter/METdataio>`_
 
      git clone https://github.com/dtcenter/METdataio.git
 
-Configure and build METviewer
-_____________________________
+Configure and Build METviewer
+-----------------------------
 
 #. Configure the batch and loading tools:
 
@@ -225,7 +226,8 @@ _____________________________
         ln -s /d3/projects/METViewer/src_dev/apps/verif/metviewer/sql/mv_mysql.sql mv_mysql.sql
 
 Making a Database Accessible in the METviewer Web Application
--------------------------------------------------------------
+=============================================================
+
 To make a new database accessible in the METviewer Web Application click
 on "Reload list of databases" button in the upper right corner of the
 main JSP page. The list of available databases should be updated and a