<commit_before>Installation
===============

This is a quick guide to getting the PyRate software up and running in various platforms.
Step by step guide to install Pyrate and run toy example.

.. include:: ubuntu.rst
.. include:: docker.rst
.. include:: hpc.rst


Verify Installation
-------------------

To verify PyRate has been successfully installed, run the workflow with the
included example config file and data:

::

    pyrate prepifg input_parameters.conf
    pyrate process input_parameters.conf
    pyrate postprocess input_parameters.conf

On Raijin and other HPC systems, you can utilise MPI to run PyRate in parallel:
    
::

    # Modify 'n' based on the number of processors available.
    mpirun -n 4 pyrate prepifg input_parameters.conf
    mpirun -n 4 pyrate process input_parameters.conf -c 2 -r 2
    mpirun -n 4 pyrate postprocess input_parameters.conf -c 2 -r 2

If the installation has been successful, this workflow will complete without 
errors and results will be available in:

:: 
    <commit_msg>Add geotiff conversion to installation verification.<commit_after>Installation
===============

This is a quick guide to getting the PyRate software up and running in various platforms.
Step by step guide to install Pyrate and run toy example.

.. include:: ubuntu.rst
.. include:: docker.rst
.. include:: hpc.rst


Verify Installation
-------------------

To verify PyRate has been successfully installed, run the workflow with the
included example config file and data:

::
    pyrate converttogeotiff input_parameters.conf
    pyrate prepifg input_parameters.conf
    pyrate process input_parameters.conf
    pyrate postprocess input_parameters.conf

On Raijin and other HPC systems, you can utilise MPI to run PyRate in parallel:
    
::

    # Modify 'n' based on the number of processors available.
    mpirun -n 4 pyrate converttogeotiff input_parameters.conf
    mpirun -n 4 pyrate prepifg input_parameters.conf
    mpirun -n 4 pyrate process input_parameters.conf -c 2 -r 2
    mpirun -n 4 pyrate postprocess input_parameters.conf -c 2 -r 2

If the installation has been successful, this workflow will complete without 
errors and results will be available in:

:: 
    
{'fraction_non_alphanumeric': 0.0769927536231884, 'fraction_numerical': 0.006793478260869565, 'mean_word_length': 3.47165991902834, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1510190', 'n_tokens_mistral': 648, 'n_tokens_neox': 587, 'n_words': 276}