|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, currently in review, available as a `Zenodo
preprint <https://doi.org/10.5281/zenodo.10602940>`__:
Lancaster AK, Single RM, Mack SJ, Sochat V, Mariani MP, Webster
GD. (2024) "PyPop: A mature open-source software pipeline for
population genomics" (Preprint v1). Zenodo.
DOI:`10.5281/zenodo.10602940
<https://doi.org/10.5281/zenodo.10602940>`__.
* **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/
.. |PyPI version shields.io| image:: https://img.shields.io/pypi/v/pypop-genomics.svg
:target: https://pypi.python.org/pypi/pypop-genomics/
.. |PyPI pyversions| image:: https://img.shields.io/pypi/pyversions/pypop-genomics.svg
:target: https://pypi.python.org/pypi/pypop-genomics/
.. |GitHub release| image:: https://img.shields.io/github/release/alexlancaster/pypop.svg
: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
.. |GitHub license| image:: https://img.shields.io/github/license/alexlancaster/pypop.svg
:target: https://github.com/alexlancaster/pypop/blob/main/LICENSE
.. |GitHub issues| image:: https://img.shields.io/github/issues/alexlancaster/pypop.svg
:target: https://github.com/alexlancaster/pypop/issues
.. |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/
Raw data
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"home_page": "http://www.pypop.org/",
"name": "pypop-genomics",
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"docs_url": null,
"requires_python": "",
"maintainer_email": "",
"keywords": "bioinformatics,population-genomics,evolutionary-biology,population-genetics",
"author": "Alex Lancaster",
"author_email": "",
"download_url": "https://files.pythonhosted.org/packages/43/5b/abd98e41f4a7299b7a81fe4f10a59e6f5c026cd9dcb91534c3975692b7bc/pypop-genomics-1.0.2.tar.gz",
"platform": "GNU/Linux",
"description": "|PyPI version shields.io| |Build status| |Website pypop.org| |GitHub license| |Citations| |DOI|\n\nPyPop: Python for Population Genomics\n=====================================\n\nPyPop is a framework for processing genotype and allele data and\nrunning population genetic analyses, including conformity to\nHardy-Weinberg expectations; tests for balancing or directional\nselection; estimates of haplotype frequencies and measures and tests\nof significance for linkage disequilibrium (LD). Full documentation is\navailable in the `PyPop User Guide <http://pypop.org/docs>`__.\n\n.. _guide-include-pypop-cite-start:\n\t\t \n**How to cite PyPop**\n\nIf you write a paper that uses PyPop in your analysis, please cite\n**both**:\n\n* our 2024 article, currently in review, available as a `Zenodo\n preprint <https://doi.org/10.5281/zenodo.10602940>`__:\n\n Lancaster AK, Single RM, Mack SJ, Sochat V, Mariani MP, Webster\n GD. (2024) \"PyPop: A mature open-source software pipeline for\n population genomics\" (Preprint v1). Zenodo.\n DOI:`10.5281/zenodo.10602940\n <https://doi.org/10.5281/zenodo.10602940>`__.\n\n* **and** the `Zenodo record <https://zenodo.org/records/10080667>`__\n for the software. To cite the correct version, follow these steps:\n\n 1) First visit the DOI for the overall Zenodo record:\n `10.5281/zenodo.10080667\n <https://zenodo.org/doi/10.5281/zenodo.10080667>`__. This DOI\n represents **all versions**, and will always resolve to the\n latest one.\n\n 2) When you are viewing the record, look for the **Versions** box\n in the right-sidebar. Here are listed all versions (including\n older versions).\n\n 3) Select and click the version-specific DOI that matches the\n specific version of PyPop that you used for your analysis.\n\n 4) Once you are visiting the Zenodo record for the specific version,\n under the **Citation** box in the right-sidebar, select the\n citation format you wish to use and click to copy the citation.\n It will contain link to the version-specific DOI, and be of the\n form:\n\n Lancaster, AK et al. (YYYY) \"PyPop: Python for Population\n Genomics\" (Version X.Y.Z) [Computer\n software]. Zenodo. https://doi.org/10.5281/zenodo.XXXXX\n\n Note that citation metadata for the current Zenodo record is also\n stored in `CITATION.cff\n <https://github.com/alexlancaster/pypop/blob/main/CITATION.cff>`__\n \n.. _guide-include-pypop-cite-end:\n\n.. _guide-include-start:\n\n.. ATTENTION:: \n\n The package name for installation purposes is |pkgname| - to avoid\n conflicting with an unrelated package with the name ``pypop``\n already on `PyPI <https://pypi.org>`__.\n\nQuickstart Guide\n================\n\n**Installing** |pkgname|\n\nIf you already have Python and ``pip`` installed, install using the following:\n\n.. code-block:: shell\n\n pip install pypop-genomics\n\nOtherwise, follow `these instructions <Install Python 3 and pip_>`_ to install Python 3 and pip.\n\nOnce |pkgname| is installed, depending on your platform, you may also\nneed to `adjust <Post-install PATH adjustments_>`_ your ``PATH``\nenvironment variable. \n\n**Upgrading** |pkgname|\n\n.. code-block:: shell\n\n pip install -U pypop-genomics\n\n**Uninstalling** |pkgname|\n\n.. code-block:: shell\n\n pip uninstall pypop-genomics\n\n**For more, including handling common installation issues, see the** `detailed installation instructions`_ **.**\n \nOnce you have installed |pkgname|, you can move on to try some\n`example runs <Examples_>`__.\n \n \n.. _guide_readme_examples:\n\nExamples\n========\n\nThese are examples of how to check that the program is installed and\nsome minimal use cases.\n\nChecking version and installation\n---------------------------------\n\n.. code-block:: shell\n\n pypop --version\n\nThis simply reports the version number and other information about\nPyPop, and indirectly checks that the program is installed. If all is\nwell, you should see something like:\n\n.. code-block:: text\n\n pypop 1.0.0\n [Python 3.10.9 | Linux.x86_64-x86_64 | x86_64]\n Copyright (C) 2003-2006 Regents of the University of California.\n Copyright (C) 2007-2023 PyPop team.\n This is free software. There is NO warranty; not even for\n MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n\nYou can also run ``pypop --help`` to see a full list and explanation\nof all the options available.\n\nRun a minimal dataset:\n----------------------\n\nDownload test ``.ini`` and ``.pop`` files: `minimal.ini\n<https://raw.githubusercontent.com/alexlancaster/pypop/main/tests/data/minimal.ini>`_\nand `USAFEL-UchiTelle-small.pop\n<https://raw.githubusercontent.com/alexlancaster/pypop/main/tests/data/USAFEL-UchiTelle-small.pop>`_.\nYou can then run them\n\n.. code-block:: shell\n\n pypop -c minimal.ini USAFEL-UchiTelle-small.pop\n\nIf you have already cloned the git repository and it is your working\ndirectory, you can simply run\n\n.. code-block:: shell\n\n pypop -c tests/data/minimal.ini tests/data/USAFEL-UchiTelle-small.pop\n\n\nThis will generate the following two files, an XML output file and a\nplain text version:\n\n::\n\n USAFEL-UchiTelle-small-out.xml\n USAFEL-UchiTelle-small-out.txt\n\n\nDetailed installation instructions\n==================================\n\nThere are three main steps:\n\n1. install Python and ``pip``\n2. install package from Test PyPI\n3. adjusting your ``PATH`` variable after installation\n\n\nInstall Python 3 and ``pip``\n----------------------------\n\nA full description of installing Python and ``pip`` on your system is\nbeyond the scope of this guide, we recommend starting here:\n\n https://wiki.python.org/moin/BeginnersGuide/Download\n\nHere are some additional platform-specific notes that may be helpful:\n \n- Most Linux distributions come with Python 3 preinstalled. On most\n modern systems, ``pip`` and ``python`` will default to Python 3.\n\n- MacOS 10.9 (Jaguar) up until 12.3 (Catalina), used to ship with\n Python 2 pre-installed, but it now has to be manually installed.\n See the `MacOS quick-start guide\n <https://docs.python.org/3/using/mac.html>`__ in the official\n documentation for how to install Python 3. (Note that if Python is\n installed on Mac via the MacOS developer tools, it may include the\n version ``3`` suffix on commands, e.g. ``python3`` and ``pip3``, so\n modify the below, accordingly).\n\n- For Windows, see also the `Windows quick-start guide\n <https://docs.python.org/3/using/windows.html>`__ in the official\n documentation. Running ``python`` in the Windows command terminal\n in Windows 11 and later will launch the installer for the\n Microsoft-maintained Windows package of Python 3.\n\nInstall package from PyPI\n-------------------------\n\nOnce you have both python and ``pip`` installed, you can use ``pip``\nto install pre-compiled binary \"wheels\" of |pkgname|\ndirectly from `PyPI <https://pypi.org/>`__.\n\n.. code-block:: shell\n\n pip install pypop-genomics\n\n.. note::\n\n If, for whatever reason, you cannot use the these binaries\n (e.g. the pre-compiled binaries are not available for your\n platform), you may need to follow the `developer installation\n instructions <http://pypop.org/docs/guide-chapter-contributing.html#installation-for-developers>`_ in the contributors\n guide.\n\t\t\n**Upgrade an existing PyPop installation**\n\nTo update an existing installation to a newer version, use the same\ncommand as above, but add the ``--upgrade`` (short version: ``-U``)\nflag, i.e.\n\n.. code-block:: shell\n\n pip install -U pypop-genomics\n\n**Installing from Test PyPI**\n\nFrom time to time, we may make available packages on the `Test PyPI\n<https://test.pypi.org/>`__ instance, rather than the through the main\ninstance. The above installation and updating instructions can be\nused, by appending the following:\n\n.. code-block:: shell\n\n --extra-index-url https://test.pypi.org/simple/\n\nto the above ``pip`` commands.\n \n**Issues with installation permission**\n\nBy default, ``pip`` will attempt to install the |pkgname|\npackage wherever the current Python installation is installed. This\nlocation may be a user-specific virtual environment (like ``conda``,\nsee below), or a system-wide installation. On many Unix-based systems,\nPython will generally already be pre-installed in a \"system-wide\"\nlocation (e.g. under ``/usr/lib``) which is read-only for regular\nusers. (This can also be true for system-installed versions of Python\non Windows and MacOS.)\n\nWhen ``pip install`` cannot install in a read-only system-wide\nlocation , ``pip`` will gracefully \"fall-back\" to installing just for\nyou in your home directory (typically ``~/.local/lib/python<VER>``\nwhere ``<VER>`` is the version number of your current Python). In\ngeneral, this is what is wanted, so the above instructions are\nnormally sufficient.\n\nHowever, you can also explicitly set installation to be in the user\ndirectory, by adding the ``--user`` command-line option to the ``pip install``\ncommand, i.e.:\n\n.. code-block:: shell\n\n pip install pypop-genomics --user\n\nThis may be necessary in certain cases where ``pip install`` doesn't\ninstall into the expected user directory.\n \n.. admonition:: Installing within a ``conda`` environment\n\n In the special case that you installing from within an activated\n user-specific ``conda`` virtual environment that provides Python,\n then you should **not** add the ``--user`` because it will install\n it in ``~/.local/lib/`` rather than under the user-specific conda\n virtual environment in ``~/.conda/envs/``.\n\t\t\nPost-install ``PATH`` adjustments\n---------------------------------\n \nYou may need to adjust the ``PATH`` settings (especially on Windows)\nfor the ``pypop`` scripts to be visible when run from your console\napplication, without having to supply the full path to the ``pypop``\nexecutable file.\n\n.. warning::\n\n Pay close attention to the \"WARNINGS\" that are shown during the\n ``pip`` installation, they will often note which directories need to\n be added to the ``PATH``.\n\n- On Linux and MacOS, systems this is normally fairly simple and only\n requires edit of the shell ``.profile``, or similar and addition of\n the ``$HOME/.local/bin`` to the ``PATH`` variable, followed by a\n restart of the terminal.\n\n- For Windows, however, as noted in most online `instructions\n <https://www.computerhope.com/issues/ch000549.htm>`_, this may need\n additional help from your system administrator if your user doesn't\n have the right permissions, and also require a system reboot.\n \nUninstalling PyPop\n------------------\n\nTo uninstall the current version of |pkgname|:\n\n.. code-block:: shell\n\n pip uninstall pypop-genomics\n\n \n \nSupport and development\n=======================\n\nPlease submit any bug reports, feature requests or questions, via our\nGitHub issue tracker (see our `bug reporting guidelines\n<http://pypop.org/docs/guide-chapter-contributing.html#reporting-and-requesting>`_\nfor more details on how to file a good bug report):\n\n https://github.com/alexlancaster/pypop/issues\n \n**Please do not report bugs via private email to developers.**\n\nThe development of the code for PyPop is via our GitHub project:\n\n https://github.com/alexlancaster/pypop\n\n.. _guide-include-end:\n\nFor a detailed description on bug reporting as well as how to\ncontribute to PyPop, please consult our `CONTRIBUTING.rst\n<https://github.com/alexlancaster/pypop/blob/main/CONTRIBUTING.rst>`_\nguide. For reporting security vulnerabilities visit `SECURITY.md\n<https://github.com/alexlancaster/pypop/blob/main/SECURITY.md>`__.\n\nWe also have additional notes and background relevant for developers\nin `DEV_NOTES.md\n<https://github.com/alexlancaster/pypop/blob/main/DEV_NOTES.md>`__. Source\nfor the website and the documentation is located in the `website\n<https://github.com/alexlancaster/pypop/blob/main/website>`__\nsubdirectory.\n\nCopyright and License\n=====================\n\nPyPop is Copyright (C) 2003-2006. The Regents of the University of\nCalifornia (Regents)\n\nCopyright (C) 2007-2023 PyPop team.\n\nPyPop is distributed under the terms of GPLv2\n\n\n.. |pkgname| replace:: ``pypop-genomics``\n\n.. |PyPI version fury.io| image:: https://badge.fury.io/py/pypop-genomics.svg\n :target: https://pypi.python.org/pypi/pypop-genomics/\n\n.. |PyPI version shields.io| image:: https://img.shields.io/pypi/v/pypop-genomics.svg\n :target: https://pypi.python.org/pypi/pypop-genomics/\n\n.. |PyPI pyversions| image:: https://img.shields.io/pypi/pyversions/pypop-genomics.svg\n :target: https://pypi.python.org/pypi/pypop-genomics/\t \n\t \n.. |GitHub release| image:: https://img.shields.io/github/release/alexlancaster/pypop.svg\n :target: https://github.com/alexlancaster/pypop/releases/\n\n.. |Build status| image:: https://github.com/alexlancaster/pypop/actions/workflows/build_wheels.yml/badge.svg?branch=main\n :target: https://github.com/alexlancaster/pypop/actions/workflows/build_wheels.yml\n\n.. |GitHub license| image:: https://img.shields.io/github/license/alexlancaster/pypop.svg\n :target: https://github.com/alexlancaster/pypop/blob/main/LICENSE\t \n\n.. |GitHub issues| image:: https://img.shields.io/github/issues/alexlancaster/pypop.svg\n :target: https://github.com/alexlancaster/pypop/issues\n\n.. |Citations| image:: https://api.juleskreuer.eu/citation-badge.php?doi=10.1111/j.1399-0039.2006.00769.x\n :target: https://juleskreuer.eu/projekte/citation-badge/\n\n.. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.10080667.svg\n :target: https://doi.org/10.5281/zenodo.10080667\n \n.. |GitHub version| image:: https://badge.fury.io/gh/alexlancaster%2Fpypop.svg\n :target: https://github.com/alexlancaster/pypop/\n\n.. |GitHub tag| image:: https://img.shields.io/github/tag/alexlancaster/pypop.svg\n :target: https://github.com/alexlancaster/pypop/tags/\t \n\n.. |Website pypop.org| image:: https://img.shields.io/website-up-down-green-red/http/pypop.org.svg\n :target: http://pypop.org/\t \n",
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