diff --git a/INSTALL.rst b/INSTALL.rst index 0d769817..20381963 100644 --- a/INSTALL.rst +++ b/INSTALL.rst @@ -2,9 +2,8 @@ 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. @@ -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 `_ -(see `issue #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 @@ -91,5 +88,3 @@ A development install is useful while hacking away on the code:: cd MDPOW pip install -e . - - diff --git a/README.rst b/README.rst index 21f90abf..2657250e 100644 --- a/README.rst +++ b/README.rst @@ -1,6 +1,6 @@ -=================== +=================== README for MDPOW -=================== +=================== |build| |cov| |docs| @@ -35,7 +35,7 @@ Documentation * 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 @@ -43,7 +43,7 @@ Documentation 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). @@ -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:: @@ -71,7 +71,7 @@ Source code *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 @@ -91,5 +91,5 @@ Footnotes .. |docs| image:: https://readthedocs.org/projects/mdpow/badge/?version=latest :target: http://mdpow.readthedocs.org/en/latest/?badge=latest :alt: Documentation - + .. _INSTALL: INSTALL.rst