"""
StatAnalysis: IODAv2
====================

model_applications/data_assimilation/StatAnalysis_fcstGFS_HofX_obsIODAv2_PyEmbed.conf

"""
##############################################################################
# .. contents::
#   :depth: 1
#   :local:
#   :backlinks: none

##############################################################################
# Scientific Objective
# --------------------
#
# This use case demonstrates the Stat-Analysis tool and ingestion of HofX NetCDF files 
# that have been output from the Joint Effort for Data assimilation Integration (JEDI)
# data assimilation system. JEDI uses IODA version 2 formatted files, which are NetCDF files
# with certain requirements of variables and naming conventions. These files
# hold observations to be assimilated into forecasts, in this case taken from the JEDI software 
# test data, which contained a small number of Global observation-forecast pairs
# derived from the hofx application.
#
# UFO is a component of HofX, which maps the background forecast to observation space
# to form O minus B pairs. The HofX application of JEDI takes the input IODAv2 files and
# adds an additional variable which is the forecast value as interpolated to the 
# observation location. These HofX files are used as input to form Matched Pair (MPR) 
# formatted lists via Python embedding. In this case, Stat-Analysis then performs an aggregate_stat
# job and outputs statistics in an ascii file.
#
# This use case adopts the IODAv2 formatted NetCDF files, which replace the previous variable
# formatting scheme to make use of NetCDF groups.

##############################################################################
# Version Added
# -------------
#
# METplus version 5.0

##############################################################################
# Datasets
# --------
#
# **Forecast:** [UPDATE]
#
# **Observation:** [UPDATE]
#
# **Climatology:** [UPDATE]
#
# **Location:** All of the input data required for this use case can be 
# found in a sample data tarball. Each use case category will have 
# one or more sample data tarballs. It is only necessary to download 
# the tarball with the use case’s dataset and not the entire collection 
# of sample data. Click here to access the METplus releases page and download sample data 
# for the appropriate release: https://github.com/dtcenter/METplus/releases
# This tarball should be unpacked into the directory that you will 
# set the value of INPUT_BASE. See :ref:`running-metplus` section for more information.
#
# **Data source:** JEDI HofX output files in IODAv2 format

##############################################################################
# METplus Components
# ------------------
#
# This use case utilizes the METplus StatAnalysis wrapper to search for
# files that are valid for the given case and generate a command to run
# the MET tool stat_analysis.

##############################################################################
# METplus Workflow
# ----------------
#
# **Beginning time (INIT_BEG):** 2018041500
#
# **End time (INIT_END):** 2018041500
#
# **Increment between beginning and end times (INIT_INCREMENT):** 12H
#
# **Sequence of forecast leads to process (LEAD_SEQ):** 0
#
# StatAnalysis is the only tool called in this example. It processes the following
# run times:
#
# | **Valid:** 2018-04-15_00Z  
# | **Forecast lead:** 0 hour

##############################################################################
# METplus Configuration
# ---------------------
#
# METplus first loads all of the configuration files found in parm/metplus_config,
# then it loads any configuration files passed to METplus via the command line,
# i.e. parm/use_cases/model_applications/data_assimilation/StatAnalysis_fcstGFS_HofX_obsIODAv2_PyEmbed.conf
#
# .. highlight:: bash
# .. literalinclude:: ../../../../parm/use_cases/model_applications/data_assimilation/StatAnalysis_fcstGFS_HofX_obsIODAv2_PyEmbed.conf

##############################################################################
# MET Configuration
# -----------------
#
# METplus sets environment variables based on user settings in the METplus configuration file. 
# See :ref:`How METplus controls MET config file settings<metplus-control-met>` for more details. 
#
# **YOU SHOULD NOT SET ANY OF THESE ENVIRONMENT VARIABLES YOURSELF! THEY WILL BE OVERWRITTEN BY METPLUS WHEN IT CALLS THE MET TOOLS!**
#
# If there is a setting in the MET configuration file that is currently not supported by METplus you'd like to control, please refer to:
# :ref:`Overriding Unsupported MET config file settings<met-config-overrides>`
#
# .. dropdown:: STATAnalysisConfig_wrapped
#
#   .. highlight:: bash
#   .. literalinclude:: ../../../../parm/met_config/STATAnalysisConfig_wrapped

##############################################################################
# Python Embedding
# ----------------
#
# This use case uses a Python embedding script to read input data.
#
# .. dropdown:: parm/use_cases/model_applications/data_assimilation/StatAnalysis_fcstGFS_HofX_obsIODAv2_PyEmbed/read_iodav2_mpr.py
#
#   .. highlight:: python
#   .. literalinclude:: ../../../../parm/use_cases/model_applications/data_assimilation/StatAnalysis_fcstGFS_HofX_obsIODAv2_PyEmbed/read_iodav2_mpr.py

##############################################################################
# User Scripting
# --------------
#
# This use case does not use additional scripts.

###############################################################################
# Running METplus
# ---------------
#
# Pass the use case configuration file to the run_metplus.py script along 
# with any user-specific system configuration files if desired::
#
#   run_metplus.py /path/to/StatAnalysis_fcstGFS_HofX_obsIODAv2_PyEmbed.conf /path/to/user_system.conf
#
# See :ref:`running-metplus` for more information.

##############################################################################
# Expected Output
# ---------------
#
# A successful run will output the following both to the screen and to the logfile::
#
#   INFO: METplus has successfully finished running.
#
# Refer to the value set for **OUTPUT_BASE** to find where the output data was generated.
# Output for this use case will be found in {OUTPUT_BASE}/StatAnalysis_IODAv2
# and will contain the following file::
#
# * dump.out

##############################################################################
# Keywords
# --------
#
# .. note::
#
#   * StatAnalysisToolUseCase 
#   * PythonEmbeddingFileUseCase 
#   * DataAssimilationUseCase
#   * IODA2NCToolUseCase
#
#   Navigate to the :ref:`quick-search` page to discover other similar use cases.
#
#
#

# sphinx_gallery_thumbnail_path = '_static/data_assimilation-StatAnalysis_fcstGFS_HofX_obsIODAv2_PyEmbed.png'