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updated installation instructions for Python 3 only
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orbeckst committed Aug 17, 2021
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31 changes: 13 additions & 18 deletions INSTALL.rst
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Quick installation instructions for *MDPOW*
=============================================

MDPOW is compatible with Python 2.7 and 3.7+ and tested
on Ubuntu and Mac OS. Python 2.7 is rock-stable and frozen but
not officially supported anymore by the Python developers.
MDPOW is compatible with Python 3.7+ and tested
on Ubuntu and Mac OS.

We recommend that you install MDPOW in a virtual environment.

Expand All @@ -29,28 +28,26 @@ GROMACS_.
Conda environment with pre-requisites
-------------------------------------

To make a conda environment with the latest packages for Python 2.7
and name it *mdpow*; this installs the larger dependencies that are
Make a conda environment with the latest packages for Python 3.7 and
higher with the name *mdpow*; this installs the larger dependencies that are
pre-requisites for MDPOW::

conda create -c conda-forge -n mdpow python=2.7 numpy scipy 'matplotlib<3.3' 'mdanalysis<2' 'mdanalysistests<2' pyyaml six
conda activate mdpow
pip install gromacswrapper
conda create -c conda-forge -n mdpow numpy scipy matplotlib mdanalysis pyyaml 'pandas>1.3.0'
conda activate mdpow
pip install gromacswrapper

Install MDPOW with ``pip``::

For Python 3.7 and up.
pip install mdpow

*Note:* with Pandas version 1.3 there is an error with `Alchemlyb <https://github.com/alchemistry/alchemlyb>`_
(see `issue #147 <https://github.com/alchemistry/alchemlyb/issues/147>`_) which will be fixed in Alchemlyb 0.5.::
(This will install additional dependencies such as alchemlyb, which in turns
needs pandas > 1.3.0.)

conda create -c conda-forge -n mdpow python=3.7 numpy scipy 'matplotlib' 'mdanalysis' 'mdanalysistests' pyyaml six
conda activate mdpow
pip install gromacswrapper

Installation from source
------------------------
Install from source::

Instead of the pip-installation of MDPOW, you can also install from source::

conda activate mdpow
git clone https://github.com/Becksteinlab/MDPOW.git
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cd MDPOW
pip install -e .

14 changes: 7 additions & 7 deletions README.rst
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===================
===================
README for MDPOW
===================
===================

|build| |cov| |docs|

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* https://mdpow.readthedocs.io
* `Tutorial`_ : computing the octanol-water partition coefficient of
benzene (uses the `example files`_)


.. _Tutorial: http://mdpow.readthedocs.io/en/latest/init.html#tutorial-using-the-mdpow-scripts-to-compute-logpow-of-benzene
.. _example files: https://github.com/Becksteinlab/MDPOW/tree/develop/doc/examples

Installation
------------

See `INSTALL`_ for detailed instructions. MDPOW currently supports Python 2.7 and Python 3.7 to 3.9.
See `INSTALL`_ for detailed instructions. MDPOW currently supports Python 3.7 to 3.9.

You will also need `Gromacs`_ (currently tested with versions 4.6.5,
2018, 2020, 2021 but 2016 and 2019 should also work).
Expand All @@ -55,7 +55,7 @@ Development version
If you want to install the development version, get the sources from
GitHub (the development branch) ::

git clone https://github.com/Becksteinlab/MDPOW.git
git clone https://github.com/Becksteinlab/MDPOW.git

and Install from the checked out source::

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*MDPOW* is open source and published under the `GNU General Public License
v3`_. Source code is available at https://github.com/Becksteinlab/MDPOW .

.. _`GNU General Public License v3`:
.. _`GNU General Public License v3`:
http://www.gnu.org/licenses/gpl-3.0.html

Footnotes
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.. |docs| image:: https://readthedocs.org/projects/mdpow/badge/?version=latest
:target: http://mdpow.readthedocs.org/en/latest/?badge=latest
:alt: Documentation

.. _INSTALL: INSTALL.rst

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