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**flintyPy**
====================================

This is the homepage of **flintyPy**, the Python version of the software **flinty** (Flexible and Interpretable Non-parametric Tests of Exchangeability). The R version is available `here <https://alanaw1.github.io/flintyR>`_. 

What does this package offer?
-----------------------------

**flintyPy** provides exact tests of exchangeability in multivariate datasets.

- It is *non-parametric* (i.e., makes no distributional assumptions of the features), which makes it suitable for settings where the user might prefer not to make distributional assumptions about their data.
- It is *flexible*, meaning that the practitioner can specify feature dependencies based on their knowledge of the problem, or can simply provide summary statistics in the form of pairwise distance data. See Examples for details.
- It is *scalable*, so the user does not have to worry about the sample size :math:`N` or the number of features :math:`P` of the data.
- It is *robust*, meaning that it controls for false positive rate (FPR) and remains powerful in realistic settings including uneven representation of subpopulations, sparsity of discriminative features, and small sample sizes.

Here is a schema of how **flintyPy** works.

.. image:: standalone_6.jpg

How to install?
---------------

**flintyPy** requires Python >= 3.7.10, and for now we recommend the following installation procedures for native Python and for Anaconda users. 

Using both ``conda`` and ``pip`` (Recommended)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Download `anaconda <https://www.anaconda.com/download/>`_ or `miniconda <https://conda.io/miniconda.html>`_. 
2. Create a separate conda environment and activate it.

.. code-block:: console

    conda create -n flinty python==3.7.10
    conda activate flinty

3. *(Optional)* Install dependencies / required packages.

.. code-block:: console
    
    conda install numpy==1.21.1
    conda install numba==0.53.1
    conda install scipy==1.7.1
    conda install gmpy2=2.0.8

4. Install **flintyPy** using pip.

.. code-block:: console

    pip install flintypy

Run Steps 1,2 and 4. If Step 4 fails, go back to Step 3 and proceed with Step 4. 

Using only ``pip`` (Native Python Users with Homebrew)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Install `virtualenv <https://virtualenv.pypa.io/en/latest/>`_ if you don't already use it.

.. code-block:: console
    
    brew install virtualenv

2. Create a new virtual environment under the working directory. 

.. code-block:: console
    
    python3 -m virtualenv --python [PATH-TO-PYTHON>=3.7.10] [ENVIRONMENT-NAME]
    # Example: python3 -m virtualenv --python /usr/local/bin/python3.9 flinty

3. Activate the virtual environment

.. code-block:: console
    
    source flinty/bin/activate

4. Install **flintyPy** using pip.

.. code-block:: console

    pip install flintypy

Note that if Step 4 fails, a practical workaround solution is to ``pip install`` **numpy** (==1.21.1), **numba** (==0.53.1), **scipy** (==1.7.1) and **gmpy2** (=2.0.8) right after Step 3. 

Using the Tarball (Not Recommended)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Download the `package <https://pypi.org/project/flintypy/>`_ tar ball.
2. Use tar to unzip the tar ball.
3. Enter the directory containing ``setup.py`` and run ``python setup.py install``.


For guidance on running our exchangeability test, please click on the "Examples" tab.

API reference
------------------

Our :ref:`flintypy` contains detailed descriptions of the main and auxiliary functions.

Indices
-------

* :ref:`genindex`
* :ref:`search`