<commit_before>Configuration
=============

A configuration file is needed to run the gypsy simulation

A template configuration can be generated as follows:

::

    pygypsy generate_config

The configuration file is a json file and must follow `json syntax <http://www.w3schools.com/js/js_json_syntax.asp>`__.

It is generally safe to replace values in the configuration files with new
values of the same type (e.g. replace integers with integers).

The schema, against which the configuration file is validated, is available
`here
<https://github.com/tesera/pygypsy/blob/dev/pygypsy/scripts/config/conf.schema>`__.

Simulations
===========

With the output directory and configuration file prepared, the next steps are
to:

- prepare the plot data for use with pygypsy
- run the simulation on the prepared plot data


Preparing plot data
-------------------

Prepare your plot data as follows

::

   pygypsy prep --config-file ./pygypsy-output/config.json /path/to/your/plot-data.csv

Take note of the console output to see where the prepared plot data is created.

Running simulation
------------------

Run the gypsy simulation as follows

::

   pygypsy simulate --config-file ./pygypsy-output/config.json /pygypsy-output/plot-data-prepped.csv

Data Management
===============

Output for each pygypsy command is created at a fixed path relative to a
configurable output directory

The output directory can be specified after the pygypsy command and before
subcommands, i.e.
<commit_msg>Use default config file name in docs<commit_after>Configuration
=============

A configuration file is needed to run the gypsy simulation

A template configuration can be generated as follows:

::

    pygypsy generate_config

The configuration file is a json file and must follow `json syntax <http://www.w3schools.com/js/js_json_syntax.asp>`__.

It is generally safe to replace values in the configuration files with new
values of the same type (e.g. replace integers with integers).

The schema, against which the configuration file is validated, is available
`here
<https://github.com/tesera/pygypsy/blob/dev/pygypsy/scripts/config/conf.schema>`__.

Simulations
===========

With the output directory and configuration file prepared, the next steps are
to:

- prepare the plot data for use with pygypsy
- run the simulation on the prepared plot data


Preparing plot data
-------------------

Prepare your plot data as follows

::

   pygypsy prep --config-file ./pygypsy-output/pygypsy-config.json /path/to/your/plot-data.csv

Take note of the console output to see where the prepared plot data is created.

Running simulation
------------------

Run the gypsy simulation as follows

::

   pygypsy simulate --config-file ./pygypsy-output/config.json /pygypsy-output/plot-data-prepped.csv

Data Management
===============

Output for each pygypsy command is created at a fixed path relative to a
configurable output directory

The output directory can be specified after the pygypsy command and before
subcommands, e.g.

{'fraction_non_alphanumeric': 0.10632659821132825, 'fraction_numerical': 0.000662471016893011, 'mean_word_length': 3.778481012658228, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 2, 'lorem ipsum': 0, 'www.': 2, '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': '2091417', 'n_tokens_mistral': 820, 'n_tokens_neox': 788, 'n_words': 356}