From f1efb6cd5edda7685c034f3a0875ab18d465599d Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Tue, 28 Dec 2021 18:18:39 -0700 Subject: [PATCH] add link to GitHub Discussions forum - in docs - in README (update with the Getting Involved section from docs) --- README.rst | 43 +++++++++++++++++++++++++++++++------------ docs/index.rst | 13 ++++++++++--- 2 files changed, 41 insertions(+), 15 deletions(-) diff --git a/README.rst b/README.rst index 51fca4b4..3ade4108 100644 --- a/README.rst +++ b/README.rst @@ -11,15 +11,41 @@ includes: molecular dynamics engines such as `GROMACS`_, `AMBER`_, `NAMD`_ and `other simulation codes`_. -2. Subsamplers for obtaining uncorrelated samples from timeseries data. +2. Subsamplers for obtaining uncorrelated samples from timeseries data + (including extracting independent, equilibrated samples + [Chodera2016]_ as implemented in the pymbar_ package). 3. Estimators for obtaining free energies directly from this data, using best-practices approaches for multistate Bennett acceptance ratio (MBAR) - [Shirts2008]_ and thermodynamic integration (TI). + [Shirts2008]_ and BAR (from pymbar_) and thermodynamic integration (TI). -In particular, it uses internally the excellent `pymbar -`_ library for performing MBAR and extracting -independent, equilibrated samples [Chodera2016]_. +.. _GROMACS: http://www.gromacs.org/ +.. _AMBER: http://ambermd.org/ +.. _NAMD: http://www.ks.uiuc.edu/Research/namd/ +.. _`other simulation codes`: https://alchemlyb.readthedocs.io/en/latest/parsing.html +.. _`pymbar`: http://pymbar.readthedocs.io/ + + +Getting involved +---------------- + +Contributions of all kinds are very welcome. + +If you have questions or want to discuss alchemlyb please post in the `alchemlyb Discussions`_. + +If you have bug reports or feature requests then please get in touch with us through the `Issue Tracker`_. + +We also welcome code contributions: have a look at our `Developer Guide`_. Open an issue with the proposed fix or change in the `Issue Tracker`_ and submit a pull request against the `alchemistry/alchemlyb`_ GitHub repository. + +.. _`alchemlyb Discussions`: https://github.com/alchemistry/alchemlyb/discussions +.. _`Developer Guide`: https://github.com/alchemistry/alchemlyb/wiki/Developer-Guide +.. _`Issue Tracker`: https://github.com/alchemistry/alchemlyb/issues +.. _`alchemistry/alchemlyb`: https://github.com/alchemistry/alchemlyb + + + +References +---------- .. [Shirts2008] Shirts, M.R., and Chodera, J.D. (2008). Statistically optimal analysis of samples from multiple equilibrium states. The Journal of Chemical @@ -29,14 +55,7 @@ independent, equilibrated samples [Chodera2016]_. Equilibration Detection in Molecular Simulations. Journal of Chemical Theory and Computation 12, 1799–1805. -.. _GROMACS: http://www.gromacs.org/ -.. _AMBER: http://ambermd.org/ - -.. _NAMD: http://www.ks.uiuc.edu/Research/namd/ - -.. _`other simulation codes`: https://alchemlyb.readthedocs.io/en/latest/parsing.html - .. |doi| image:: https://zenodo.org/badge/68669096.svg :alt: Zenodo DOI :scale: 100% diff --git a/docs/index.rst b/docs/index.rst index f9b36240..6d42c6a3 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -54,10 +54,17 @@ The pandas_ package (one of our other primary dependencies) also follows `NEP 29 .. _contact: -Contributing ------------- -Contributions are very welcome. If you have bug reports or feature requests or questions then please get in touch with us through the `Issue Tracker`_. We also welcome code contributions: have a look at our `Developer Guide`_ and submit a pull request against the `alchemistry/alchemlyb`_ GitHub repository. +Getting involved +---------------- +Contributions of all kinds are very welcome. +If you have questions or want to discuss alchemlyb please post in the `alchemlyb Discussions`_. + +If you have bug reports or feature requests then please get in touch with us through the `Issue Tracker`_. + +We also welcome code contributions: have a look at our `Developer Guide`_. Open an issue with the proposed fix or change in the `Issue Tracker`_ and submit a pull request against the `alchemistry/alchemlyb`_ GitHub repository. + +.. _`alchemlyb Discussions`: https://github.com/alchemistry/alchemlyb/discussions .. _`Developer Guide`: https://github.com/alchemistry/alchemlyb/wiki/Developer-Guide .. _`Issue Tracker`: https://github.com/alchemistry/alchemlyb/issues .. _`alchemistry/alchemlyb`: https://github.com/alchemistry/alchemlyb