INSTALL

Supported Python versions
-------------------------

Pyteomics supports Python 2.7 and Python 3.3+.


Install with pip
----------------

The main way to obtain Pyteomics is via `pip Python package manager <https://pip.pypa.io/>`_::

    pip install pyteomics


Install with conda
------------------

You can also install Pyteomics from `Bioconda <https://bioconda.github.io/index.html>`_
using `conda <https://docs.conda.io/projects/conda/en/latest/index.html>`_::

    conda install -c bioconda pyteomics


Arch-based distros
..................

On Arch Linux and related distros, you can install Pyteomics from AUR:
`python-pyteomics <https://aur.archlinux.org/packages/python-pyteomics/>`_

Project dependencies
--------------------

Some functionality in Pyteomics relies on other packages:

 - `numpy <https://numpy.org/>`_;
 - `matplotlib <https://matplotlib.org/>`_ (used by :py:mod:`pyteomics.pylab_aux`);
 - `lxml <https://lxml.de/>`_ (used by XML parsing modules and :py:class:`pyteomics.mass.mass.Unimod`);
 - `pandas <https://pandas.pydata.org/>`_ (can be used with :py:mod:`pyteomics.pepxml`,
   :py:mod:`pyteomics.tandem`, :py:mod:`pyteomics.mzid`, :py:mod:`pyteomics.auxiliary`);
 - `sqlalchemy <https://www.sqlalchemy.org/>`_ (used by :py:mod:`pyteomics.mass.unimod`);
 - `pynumpress <https://pypi.org/project/pynumpress/>`_ (adds support for Numpress compression in mzML);
 - `h5py <https://www.h5py.org/>`_ and optionally `hdf5plugin <https://hdf5plugin.readthedocs.io/en/latest/>`_
   (used by :py:mod:`pyteomics.mzmlb`);
 - `psims <https://mobiusklein.github.io/psims/docs/build/html/>`_ (used py :py:mod:`pyteomics.proforma`);
 - `spectrum_utils <https://spectrum-utils.readthedocs.io/en/latest/>`_ (optionally used for spectrum annotation in
   :py:mod:`pyteomics.pylab_aux`).

All dependencies are optional.

Installing a subset of dependencies with pip
............................................

You can quickly install just the dependencies you need by specifying an
`"extra" <https://setuptools.pypa.io/en/latest/userguide/dependency_management.html#optional-dependencies>`_. For example::

    pip install pyteomics[XML]

This will install Pyteomics, NumPy and lxml, which are needed to read XML format. Currently provided identifiers are:
`XML`, `TDA`, `graphics`, `DF`, `Unimod`, `numpress`, `mzMLb`, `proforma`.

You can also use these specs as dependencies in your own packages which require specific Pyteomics functionality.