1. Structure of SLOOP code 
##########################



Overview
==========

.. image:: images/sloop_code.png


Details of directories
=======================

* **Bin**

  This directory contain python binaries that refer to *SLOOP TASKS* (see :ref:`tasklist`)

  Each binary match with a function inside **models.croco.cli**

* **doc**

  This is the Sphinx source code for this documentation

* **templates**

  It contains various templates of config and ini files :

 * Ini files for the configuration on Datarmor

   * Environment for compilation
   * Environment for PBS

 * A full example of a config file for CROCO (**croco_med.cfg**) that allow to custom the differents sloop tasks

* **env**

  This contains **yml** files to install directly conda environment dedicated to sloop

* **install**

  A python routine named *conda_install.py* is provided to install everything automatically

* **sloop**

  The core of the library containing all python routines. It will be described in the next part.

Detail of **sloop** library
===========================

This directory contain the following files: 

.. list-table:: Sloop source routines 
   :header-rows: 1

   * - Name of the file
     - Description
   * - **cf.py**
     - file relative to CF conventions (https://cfconventions.org/) and functions to get names from dataset 
   * - **env.py**
     - Functions relative to environment (load sections from config, guess HPC env) 
   * - **filters.py**
     - Functions that allow to erode mask and coast on a Dataset 
   * - **grid.py**
     - Functions to select an geographical area from a dataset
   * - **interp.py**
     - Functions that perform time interpolation (manage persistency) and spatial interpolation (based on xesmf) 
   * - **io.py**
     - Functions relative to reading and writing of netcdf files or config files
   * - **job.py**
     - Functions that manage the commands to submit jobs on HPC
   * - **log.py**
     - Managing logs files 
   * - **phys.py**
     - some functions to compute physical variables as wind stress or converting temperature to Kelvin
   * - **time.py**
     - time utilities to convert time in various format 

It also contain this two directories:

.. list-table:: Sloop source core code 
   :header-rows: 1

   * - Name of the directory 
     - Description
   * - **cli**
     - All the routines that can be launched with sloop commands (ini,constants,compile,run)
   * - **models**
     - Model specific routines. There is one directory per model (Croco and Hycom) 


Detail of cli commands
----------------------

Detail of Croco specific routines
----------------------------------