|PyPI version shields.io| |Build status| |Website pypop.org| |GitHub license| |Citations| |DOI|

PyPop: Python for Population Genomics
=====================================

PyPop is a framework for processing genotype and allele data and
running population genetic analyses, including conformity to
Hardy-Weinberg expectations; tests for balancing or directional
selection; estimates of haplotype frequencies and measures and tests
of significance for linkage disequilibrium (LD). Full documentation is
available in the `PyPop User Guide <http://pypop.org/docs>`__.

.. _guide-include-pypop-cite-start:
		       
**How to cite PyPop**

If you write a paper that uses PyPop in your analysis, please cite
**both**:

* our `2024 article
  <https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1378512/full>`__
  in *Frontiers in Immunology*:

      Lancaster AK, Single RM, Mack SJ, Sochat V, Mariani MP, Webster
      GD. (2024) "PyPop: A mature open-source software pipeline for
      population genomics."  *Front. Immunol.* **15**:1378512 doi:
      `10.3389/fimmu.2024.1378512
      <https://doi.org/10.3389/fimmu.2024.1378512>`__

* **and** the `Zenodo record <https://zenodo.org/records/10080667>`__
  for the software. To cite the correct version, follow these steps:

  1) First visit the DOI for the overall Zenodo record:
     `10.5281/zenodo.10080667
     <https://zenodo.org/doi/10.5281/zenodo.10080667>`__. This DOI
     represents **all versions**, and will always resolve to the
     latest one.

  2) When you are viewing the record, look for the **Versions** box
     in the right-sidebar. Here are listed all versions (including
     older versions).

  3) Select and click the version-specific DOI that matches the
     specific version of PyPop that you used for your analysis.

  4) Once you are visiting the Zenodo record for the specific version,
     under the **Citation** box in the right-sidebar, select the
     citation format you wish to use and click to copy the citation.
     It will contain link to the version-specific DOI, and be of the
     form:

       Lancaster, AK et al. (YYYY) "PyPop: Python for Population
       Genomics" (Version X.Y.Z) [Computer
       software]. Zenodo. https://doi.org/10.5281/zenodo.XXXXX

  Note that citation metadata for the current Zenodo record is also
  stored in `CITATION.cff
  <https://github.com/alexlancaster/pypop/blob/main/CITATION.cff>`__
   
.. _guide-include-pypop-cite-end:

.. _guide-include-start:

.. ATTENTION:: 

   The package name for installation purposes is |pkgname| - to avoid
   conflicting with an unrelated package with the name ``pypop``
   already on `PyPI <https://pypi.org>`__.

Quickstart Guide
================

**Installing** |pkgname|

If you already have Python and ``pip`` installed, install using the following:

.. code-block:: shell

   pip install pypop-genomics

Otherwise, follow `these instructions <Install Python 3 and pip_>`_ to install Python 3 and pip.

Once |pkgname| is installed, depending on your platform, you may also
need to `adjust <Post-install PATH adjustments_>`_ your ``PATH``
environment variable.  

**Upgrading** |pkgname|

.. code-block:: shell

   pip install -U pypop-genomics

**Uninstalling** |pkgname|

.. code-block:: shell

   pip uninstall pypop-genomics

**For more, including handling common installation issues, see the** `detailed installation instructions`_ **.**
   
Once you have installed |pkgname|, you can move on to try some
`example runs <Examples_>`__.
   
   
.. _guide_readme_examples:

Examples
========

These are examples of how to check that the program is installed and
some minimal use cases.

Checking version and installation
---------------------------------

.. code-block:: shell

   pypop --version

This simply reports the version number and other information about
PyPop, and indirectly checks that the program is installed. If all is
well, you should see something like:

.. code-block:: text

   pypop 1.0.0
   [Python 3.10.9 | Linux.x86_64-x86_64 | x86_64]
   Copyright (C) 2003-2006 Regents of the University of California.
   Copyright (C) 2007-2023 PyPop team.
   This is free software.  There is NO warranty; not even for
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

You can also run ``pypop --help`` to see a full list and explanation
of all the options available.

Run a minimal dataset:
----------------------

Download test ``.ini`` and ``.pop`` files: `minimal.ini
<https://raw.githubusercontent.com/alexlancaster/pypop/main/tests/data/minimal.ini>`_
and `USAFEL-UchiTelle-small.pop
<https://raw.githubusercontent.com/alexlancaster/pypop/main/tests/data/USAFEL-UchiTelle-small.pop>`_.
You can then run them

.. code-block:: shell

   pypop -c  minimal.ini USAFEL-UchiTelle-small.pop

If you have already cloned the git repository and it is your working
directory, you can simply run

.. code-block:: shell

   pypop -c  tests/data/minimal.ini tests/data/USAFEL-UchiTelle-small.pop


This will generate the following two files, an XML output file and a
plain text version:

::

   USAFEL-UchiTelle-small-out.xml
   USAFEL-UchiTelle-small-out.txt


Detailed installation instructions
==================================

There are three main steps:

1. install Python and ``pip``
2. install package from Test PyPI
3. adjusting your ``PATH`` variable after installation


Install Python 3 and ``pip``
----------------------------

A full description of installing Python and ``pip`` on your system is
beyond the scope of this guide, we recommend starting here:

   https://wiki.python.org/moin/BeginnersGuide/Download

Here are some additional platform-specific notes that may be helpful:
   
- Most Linux distributions come with Python 3 preinstalled. On most
  modern systems, ``pip`` and ``python`` will default to Python 3.

- MacOS 10.9 (Jaguar) up until 12.3 (Catalina), used to ship with
  Python 2 pre-installed, but it now has to be manually installed.
  See the `MacOS quick-start guide
  <https://docs.python.org/3/using/mac.html>`__ in the official
  documentation for how to install Python 3. (Note that if Python is
  installed on Mac via the MacOS developer tools, it may include the
  version ``3`` suffix on commands, e.g. ``python3`` and ``pip3``, so
  modify the below, accordingly).

- For Windows, see also the `Windows quick-start guide
  <https://docs.python.org/3/using/windows.html>`__ in the official
  documentation. Running ``python`` in the Windows command terminal
  in Windows 11 and later will launch the installer for the
  Microsoft-maintained Windows package of Python 3.

Install package from PyPI
-------------------------

Once you have both python and ``pip`` installed, you can use ``pip``
to install pre-compiled binary "wheels" of |pkgname|
directly from  `PyPI <https://pypi.org/>`__.

.. code-block:: shell

   pip install pypop-genomics

.. note::

   If, for whatever reason, you cannot use the these binaries
   (e.g. the pre-compiled binaries are not available for your
   platform), you may need to follow the `developer installation
   instructions <http://pypop.org/docs/guide-chapter-contributing.html#installation-for-developers>`_ in the contributors
   guide.
		
**Upgrade an existing PyPop installation**

To update an existing installation to a newer version, use the same
command as above, but add the ``--upgrade`` (short version: ``-U``)
flag, i.e.

.. code-block:: shell

   pip install -U pypop-genomics

**Installing from Test PyPI**

From time to time, we may make available packages on the `Test PyPI
<https://test.pypi.org/>`__ instance, rather than the through the main
instance. The above installation and updating instructions can be
used, by appending the following:

.. code-block:: shell

   --extra-index-url https://test.pypi.org/simple/

to the above ``pip`` commands.
   
**Issues with installation permission**

By default, ``pip`` will attempt to install the |pkgname|
package wherever the current Python installation is installed.  This
location may be a user-specific virtual environment (like ``conda``,
see below), or a system-wide installation. On many Unix-based systems,
Python will generally already be pre-installed in a "system-wide"
location (e.g. under ``/usr/lib``) which is read-only for regular
users. (This can also be true for system-installed versions of Python
on Windows and MacOS.)

When ``pip install`` cannot install in a read-only system-wide
location , ``pip`` will gracefully "fall-back" to installing just for
you in your home directory (typically ``~/.local/lib/python<VER>``
where ``<VER>`` is the version number of your current Python). In
general, this is what is wanted, so the above instructions are
normally sufficient.

However, you can also explicitly set installation to be in the user
directory, by adding the ``--user`` command-line option to the ``pip install``
command, i.e.:

.. code-block:: shell

   pip install pypop-genomics --user

This may be necessary in certain cases where ``pip install`` doesn't
install into the expected user directory.
   
.. admonition:: Installing within a ``conda`` environment

   In the special case that you installing from within an activated
   user-specific ``conda`` virtual environment that provides Python,
   then you should **not** add the ``--user`` because it will install
   it in ``~/.local/lib/`` rather than under the user-specific conda
   virtual environment in ``~/.conda/envs/``.
		
Post-install ``PATH`` adjustments
---------------------------------
   
You may need to adjust the ``PATH`` settings (especially on Windows)
for the ``pypop`` scripts to be visible when run from your console
application, without having to supply the full path to the ``pypop``
executable file.

.. warning::

   Pay close attention to the "WARNINGS" that are shown during the
   ``pip`` installation, they will often note which directories need to
   be added to the ``PATH``.

- On Linux and MacOS, systems this is normally fairly simple and only
  requires edit of the shell ``.profile``, or similar and addition of
  the ``$HOME/.local/bin`` to the ``PATH`` variable, followed by a
  restart of the terminal.

- For Windows, however, as noted in most online `instructions
  <https://www.computerhope.com/issues/ch000549.htm>`_, this may need
  additional help from your system administrator if your user doesn't
  have the right permissions, and also require a system reboot.
   
Uninstalling PyPop
------------------

To uninstall the current version of |pkgname|:

.. code-block:: shell

   pip uninstall pypop-genomics

  
   
Support and development
=======================

Please submit any bug reports, feature requests or questions, via our
GitHub issue tracker (see our `bug reporting guidelines
<http://pypop.org/docs/guide-chapter-contributing.html#reporting-and-requesting>`_
for more details on how to file a good bug report):

   https://github.com/alexlancaster/pypop/issues
   
**Please do not report bugs via private email to developers.**

The development of the code for PyPop is via our GitHub project:

   https://github.com/alexlancaster/pypop

.. _guide-include-end:

For a detailed description on bug reporting as well as how to
contribute to PyPop, please consult our `CONTRIBUTING.rst
<https://github.com/alexlancaster/pypop/blob/main/CONTRIBUTING.rst>`_
guide. For reporting security vulnerabilities visit `SECURITY.md
<https://github.com/alexlancaster/pypop/blob/main/SECURITY.md>`__.

We also have additional notes and background relevant for developers
in `DEV_NOTES.md
<https://github.com/alexlancaster/pypop/blob/main/DEV_NOTES.md>`__. Source
for the website and the documentation is located in the `website
<https://github.com/alexlancaster/pypop/blob/main/website>`__
subdirectory.

Copyright and License
=====================

PyPop is Copyright (C) 2003-2006. The Regents of the University of
California (Regents)

Copyright (C) 2007-2023 PyPop team.

PyPop is distributed under the terms of GPLv2


.. |pkgname| replace:: ``pypop-genomics``

.. |PyPI version fury.io| image:: https://badge.fury.io/py/pypop-genomics.svg
   :target: https://pypi.python.org/pypi/pypop-genomics/

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   :target: https://pypi.python.org/pypi/pypop-genomics/	    
	    
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   :target: https://github.com/alexlancaster/pypop/releases/

.. |Build status| image:: https://github.com/alexlancaster/pypop/actions/workflows/build_wheels.yml/badge.svg?branch=main
    :target: https://github.com/alexlancaster/pypop/actions/workflows/build_wheels.yml

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.. |Citations| image:: https://api.juleskreuer.eu/citation-badge.php?doi=10.1111/j.1399-0039.2006.00769.x
   :target: https://juleskreuer.eu/projekte/citation-badge/

.. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.10080667.svg
   :target: https://doi.org/10.5281/zenodo.10080667
      
.. |GitHub version| image:: https://badge.fury.io/gh/alexlancaster%2Fpypop.svg
   :target: https://github.com/alexlancaster/pypop/

.. |GitHub tag| image:: https://img.shields.io/github/tag/alexlancaster/pypop.svg
   :target: https://github.com/alexlancaster/pypop/tags/	    

.. |Website pypop.org| image:: https://img.shields.io/website-up-down-green-red/http/pypop.org.svg
   :target: http://pypop.org/	    
