Merge pull request #268 from Becksteinlab/fix-rtd

updated CI environments

ci/conda-envs/test_env.yaml

@@ -3,7 +3,6 @@ channels:
 - conda-forge
 dependencies:
 - python
-- six
 - numpy>=1.0
 - matplotlib
 - pandas>=0.17

ci/readthedocs/environment.yml

@@ -4,9 +4,9 @@ channels:
 - defaults
 dependencies:
 - python=3.11
-- six
 - numpy>=1.0
 - matplotlib-base
 - pandas
 - numkit>=1.0
 - gromacs==2023.1
+- sphinx_rtd_theme

ci/readthedocs/requirements.txt

@@ -1,4 +1,3 @@
-six
 numpy>=1.0
 matplotlib
 pandas

doc/sphinx/source/alternatives.txt

@@ -24,11 +24,20 @@ gmxapi_ (M.E. Irrgang, J.M. Hays, and P.M. Kasson)
    `10.1093/bioinformatics/bty484
    <https://doi.org/10.1093/bioinformatics/bty484>`_
 
+`gromacs_py`_ (Samuel Murail, Maxence Delaunay, Damien Espana)
+   Gromacs_py is a Python library allowing a simplified use of the
+   Gromacs MD simulation software. Gromacs_py can build a system
+   topologie based on a pdb file, create the simulation system (pbc
+   box, adding water and ions) and run minimisation, equilibration and
+   production runs. One of the main objective of the Gromacs_py
+   wrapper is to automatize routine operations for MD simulation of
+   multiple systems.
+
 MDAnalysis_ (N. Michaud-Agrawal, E. J. Dennning, and O. Beckstein)
   Reads various trajectories (dcd, xtc, trr) and makes coordinates
   available as numpy_ arrays. It also has a fairly sophisticated
   selection language, similar to Charmm_ or VMD_.
-
+  
 ParmEd_
   A general tool for working with topology files for all the popular
   MD codes, including the `parmed.gromacs`_ module for ITP and TOP
@@ -160,3 +169,4 @@ they can be added here. Thanks.
 .. _issue tracker: https://github.com/Becksteinlab/GromacsWrapper/issues
 .. _ParmEd: http://parmed.github.io/ParmEd/html/index.html
 .. _parmed.gromacs: http://parmed.github.io/ParmEd/html/api/parmed/parmed.gromacs.html
+.. _`gromacs_py`: https://github.com/samuelmurail/gromacs_py

doc/sphinx/source/index.txt

@@ -2,30 +2,30 @@
 .. GromacsWrapper documentation master file, created by sphinx-quickstart on Tue Jun 23 19:38:56 2009.
 
 ====================================================
-  GromacsWrapper --- a Python framework for Gromacs
+  GromacsWrapper --- a Python framework for GROMACS
 ====================================================
 
 :Release: |release|
 :Date: |today|
 
 
-**GromacsWrapper** is a Python package (Python 2.7.x and Python ≥ 3.6)
-that wraps system calls to GROMACS_ tools into thin classes. This
-allows for fairly seamless integration of the gromacs tools into
-Python_ scripts. This is generally superior to shell scripts because
-of Python's better error handling and superior data structures. It
-also allows for modularization and code re-use. In addition, commands,
-warnings and errors are logged to a file so that there exists a
-complete history of what has been done.
+**GromacsWrapper** is a pure Python package that wraps system calls to
+GROMACS_ tools into thin classes. This allows for fairly seamless
+integration of the GROMACS tools into Python_ scripts. This is
+generally superior to shell scripts because of Python's better error
+handling and superior data structures. It also allows for
+modularization and code re-use. In addition, commands, warnings and
+errors are logged to a file so that there exists a complete history of
+what has been done.
 
 GROMACS_ versions 4.6.x, 2016.x, 2018.x, 2019.x, 2020.x, 2021.x,
 2022.x, and 2023.x are all supported. GromacsWrapper detects your
 Gromacs tools and provides them as :func:`gromacs.grompp`,
 :func:`gromacs.mdrun`, etc, regardless of your Gromacs version, which
 allows one to write scripts that are broadly Gromacs-version
 agnostic. Source your ``GMXRC`` file or make the :program:`gmx` binary
-(for versions ≥ 5.x) or all the Gromacs tools available on your
-:envvar:`PATH` for GromacsWrapper to find the Gromacs installation.
+(for versions ≥ 5.x) or all the GROMACS tools available on your
+:envvar:`PATH` for GromacsWrapper to find the GROMACS installation.
 
 .. warning::
 
@@ -51,9 +51,9 @@ you're fixing.
 Getting started
 ===============
 
-See :ref:`installation` for download and installation instructions. The
-:ref:`quickstart` provides a brief example of how to use
-GromacsWrapper in the most basic fashion.
+See :ref:`installation` for supported versions of Python and download
+and installation instructions. The :ref:`quickstart` provides a brief
+example of how to use GromacsWrapper in the most basic fashion.
 
 The source code itself is available in the `GromacsWrapper git
 repository`_.