From 440667690dc7bf7f89fb7c45cb30eab0fb766969 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Fri, 10 Mar 2023 10:21:13 -0700 Subject: [PATCH] doc updates - supported python and gromacs versions - main instead of master - link to GH Discussions forum --- README.rst | 8 +++---- doc/sphinx/source/index.txt | 35 +++++++++++++++++------------- doc/sphinx/source/installation.txt | 14 ++++++------ 3 files changed, 31 insertions(+), 26 deletions(-) diff --git a/README.rst b/README.rst index 1f183824..3fbef3d7 100644 --- a/README.rst +++ b/README.rst @@ -128,12 +128,12 @@ or as a `bioconda package`_ with ``conda`` from the *bioconda* channel :: Development version ------------------- -The *master* branch in the GitHub source repository generally +The *main* branch in the GitHub source repository generally contains useful code but nevertheless, things can break in weird and wonderful ways. Please report issues through the `Issue Tracker`_ and mention that you used the *develop branch*. -To use the *development code base*: checkout the ``master`` branch:: +To use the *development code base*: checkout the ``main`` branch:: git clone https://github.com/Becksteinlab/GromacsWrapper.git cd GromacsWrapper @@ -172,7 +172,7 @@ and feature requests. **Pull requests** for bug fixes and enhancements are very welcome. See http://makeapullrequest.com for a general introduction on how make a pull request and contribute to open source projects. -.. _Issue Tracker: http://github.com/Becksteinlab/GromacsWrapper/issues +.. _Issue Tracker: https://github.com/Becksteinlab/GromacsWrapper/issues Building Documentation @@ -207,5 +207,5 @@ or in the Acknowledgements section. Thank you. .. _AUTHORS: - https://raw.githubusercontent.com/Becksteinlab/GromacsWrapper/master/AUTHORS + https://raw.githubusercontent.com/Becksteinlab/GromacsWrapper/main/AUTHORS diff --git a/doc/sphinx/source/index.txt b/doc/sphinx/source/index.txt index 5917d51a..c13e4e64 100644 --- a/doc/sphinx/source/index.txt +++ b/doc/sphinx/source/index.txt @@ -18,14 +18,14 @@ 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, and 2021.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. +GROMACS_ versions 4.6.x, 2016.x, 2018.x, 2019.x, 2020.x, 2021.x, and +2022.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. .. warning:: @@ -37,8 +37,12 @@ Gromacs installation. simulations with sensible parameters.** Provide appropriate template files instead of the bundled defaults and check the logger output! -Any `feedback, bug reports, suggestions`_ and contributions are very -welcome. +Please report bugs in the `issue tracker`_ and go to the +`discussions`_ forum for questions. + +Contributions are very welcome --- start by raising an issue in the +`issue tracker`_ to describe what feature you're adding or what bug +you're fixing. .. SeeAlso:: Other approaches to interfacing Python_ and GROMACS_ are listed under :doc:`alternatives`. @@ -63,9 +67,10 @@ You also need to have a version of GROMACS_ installed. .. _Documentation: https://gromacswrapper.readthedocs.io/ .. _GromacsWrapper git repository: https://github.com/Becksteinlab/GromacsWrapper -.. _feedback, bug reports, suggestions: +.. _issue tracker: https://github.com/Becksteinlab/GromacsWrapper/issues - +.. _discussions: + https://github.com/Becksteinlab/GromacsWrapper/discussions License ======= @@ -106,10 +111,10 @@ Thank you. Contact ======= -Please use the `Issue Tracker`_ to report bugs, installation problems, -and feature requests (mention ``@orbeckst`` in the issue report). +Please use the `issue tracker`_ to report bugs, installation problems, +and feature requests (mention ``@orbeckst`` in the issue report) and +use the `discussions`_ forum for general questions. -.. _Issue Tracker: https://github.com/Becksteinlab/GromacsWrapper/issues .. Contents diff --git a/doc/sphinx/source/installation.txt b/doc/sphinx/source/installation.txt index 5c9dbca5..d6572b47 100644 --- a/doc/sphinx/source/installation.txt +++ b/doc/sphinx/source/installation.txt @@ -10,9 +10,11 @@ This document should help you to install the **GromacsWrapper** package. Please raise and issue in the `Issue Tracker`_ if problems occur or if you have suggestions on how to improve the package or -these instructions. +these instructions. Ask for help in the `discussions`_ forum. .. _Issue Tracker: https://github.com/Becksteinlab/GromacsWrapper/issues +.. _discussions: + https://github.com/Becksteinlab/GromacsWrapper/discussions .. _setuptools: https://pypi.org/project/setuptools/ @@ -84,7 +86,7 @@ contains a full source code distribution. In order to follow code development you can also browse the code **git** repository at https://github.com/Becksteinlab/GromacsWrapper -and checkout the *master* branch:: +and checkout the *main* branch:: git clone https://github.com/Becksteinlab/GromacsWrapper.git cd GromacsWrapper @@ -94,10 +96,8 @@ Requirements ============ Python_ 2.7.x or Python >= 3.6 and GROMACS_ (4.6.x, 2016, 2018, 2019, -2020, 2021) must be installed. ipython_ is very much -recommended. These packages might already be available through your -local package manager such as ``aptitude/apt``, ``yum``, ``yast``, -``fink`` or ``macports``. +2020, 2021, 2022) must be installed. ipython_ is very much +recommended. .. _Python: http://www.python.org .. _ipython: http://ipython.scipy.org @@ -106,7 +106,7 @@ local package manager such as ``aptitude/apt``, ``yum``, ``yast``, System requirements ------------------- -Tested with Python 2.7.x and Python 3.6--3.9 on Linux and Mac +Tested with Python 2.7.x and Python 3.6--3.11 on Linux and Mac OS X. Earlier Python versions are not supported.