<commit_before>ReMU - Response Matrix Utilities
================================

A framework for likelihood calculations and hypothesis testing using binned events and response matrices.

[![Build Status](https://travis-ci.org/ast0815/remu.svg?branch=master)](https://travis-ci.org/ast0815/remu)
[![Coverage Status](https://coveralls.io/repos/github/ast0815/remu/badge.svg?branch=master)](https://coveralls.io/github/ast0815/remu?branch=master)

Setup
-----

It is recommended to run this software in a virtual Python environment
(virtualenv).  This ensures that all required packages are present in the
tested version and do not interfere with other packages installed on the
system.

    $ # Create a new virtual environment
    $ virtualenv ENV
    $ # Activate the environment
    $ . ENV/bin/activate
    $ # Upgrade pip to the latest version (optional)
    $ pip install --upgrade pip
    $ # Install all required packages
    $ pip install -r requirements.txt
    $ pip install -r pymc-requirements.txt
    $ pip install -r multiprocess-requirements.txt
    $ # Install actual package
    $ pip install -e .

You might need to install additional system libraries to compile all packages.
PyMC needs to be installed in a separate step, because it requires numpy
already being installed to work. The `multiprocess-requirements` are optional
and only need to be installed, if one wants to use parallel computing.

Tests
-----

Run all test cases of the framework:<commit_msg>Add instructions to install via pip.<commit_after>ReMU - Response Matrix Utilities
================================

A framework for likelihood calculations and hypothesis testing using binned events and response matrices.

[![Build Status](https://travis-ci.org/ast0815/remu.svg?branch=master)](https://travis-ci.org/ast0815/remu)
[![Coverage Status](https://coveralls.io/repos/github/ast0815/remu/badge.svg?branch=master)](https://coveralls.io/github/ast0815/remu?branch=master)

Setup
-----

### Installing development version from source

It is recommended to run this software in a virtual Python environment
(virtualenv).  This ensures that all required packages are present in the
tested version and do not interfere with other packages installed on the
system.

    $ # Create a new virtual environment
    $ virtualenv ENV
    $ # Activate the environment
    $ . ENV/bin/activate
    $ # Upgrade pip to the latest version (optional)
    $ pip install --upgrade pip
    $ # Install all required packages
    $ pip install -r requirements.txt
    $ pip install -r pymc-requirements.txt
    $ pip install -r multiprocess-requirements.txt
    $ # Install actual package
    $ pip install -e .

You might need to install additional system libraries to compile all packages.
PyMC needs to be installed in a separate step, because it requires numpy
already being installed to work. The `multiprocess-requirements` are optional
and only need to be installed, if one wants to use parallel computing.

### Installing official releases with `pip`

Alternatively you can install official releases directly with `pip`:

    $ # Create a new virtual environment
    $ virtualenv ENV
    $ # Activate the environment
    $ . ENV/bin/activate
    $ # Upgrade pip to the latest version (optional)
    $ pip install --upgrade pip
    $ # Install remu and its dependencies
    $ pip install remu==1.0.0

Tests
-----

Run all test cases of the framework:
{'fraction_non_alphanumeric': 0.09783878504672897, 'fraction_numerical': 0.01022196261682243, 'mean_word_length': 3.823943661971831, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 8, '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': '2906114', 'n_tokens_mistral': 933, 'n_tokens_neox': 889, 'n_words': 369}