Merge branch 'master' into lammps

CITATION.cff

@@ -221,6 +221,9 @@ preferred-citation:
   year: 2024
   journal: 'Journal of Open Source Software'
   doi: '10.21105/joss.06934'
+  pages: '6934'
+  volume: '9'
+  number: '101'
 references:
   - title: Statistically optimal analysis of samples from multiple equilibrium states
     authors:

README.md

@@ -1,6 +1,6 @@
 # alchemlyb: the simple alchemistry library
 
-[![Zenodo DOI](https://zenodo.org/badge/68669096.svg)](https://zenodo.org/badge/latestdoi/68669096) [![Documentation](https://readthedocs.org/projects/alchemlyb/badge/?version=latest)](http://alchemlyb.readthedocs.io/en/latest/) [![Build Status](https://github.com/alchemistry/alchemlyb/actions/workflows/ci.yaml/badge.svg?branch=master)](https://github.com/alchemistry/alchemlyb/actions/workflows/ci.yaml) [![Code coverage](https://codecov.io/gh/alchemistry/alchemlyb/branch/master/graph/badge.svg)](https://codecov.io/gh/alchemistry/alchemlyb) [![anaconda package](https://anaconda.org/conda-forge/alchemlyb/badges/version.svg)](https://anaconda.org/conda-forge/alchemlyb)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.06934/status.svg)](https://doi.org/10.21105/joss.06934)[![Zenodo DOI](https://zenodo.org/badge/68669096.svg)](https://zenodo.org/badge/latestdoi/68669096) [![Documentation](https://readthedocs.org/projects/alchemlyb/badge/?version=latest)](http://alchemlyb.readthedocs.io/en/latest/) [![Build Status](https://github.com/alchemistry/alchemlyb/actions/workflows/ci.yaml/badge.svg?branch=master)](https://github.com/alchemistry/alchemlyb/actions/workflows/ci.yaml) [![Code coverage](https://codecov.io/gh/alchemistry/alchemlyb/branch/master/graph/badge.svg)](https://codecov.io/gh/alchemistry/alchemlyb) [![anaconda package](https://anaconda.org/conda-forge/alchemlyb/badges/version.svg)](https://anaconda.org/conda-forge/alchemlyb)
 
 **alchemlyb** makes alchemical free energy calculations easier to do by leveraging the full power and flexibility of the PyData stack. It includes:
 
@@ -10,6 +10,17 @@
 
 3. Estimators for obtaining free energies directly from this data, using best-practices approaches for multistate Bennett acceptance ratio (MBAR) [Shirts2008](#shirts2008) and BAR (from [pymbar](http://pymbar.readthedocs.io/)) and thermodynamic integration (TI).
 
+## How to Cite
+
+If you use this software in your research, please cite it as follows:
+
+Wu, Z., Dotson, D. L., Alibay, I., Allen, B. K., Barhaghi, M. S., Hénin, J., Joseph, T. T.,  
+Kenney, I. M., Lee, H., Li, H., Lim, V., Liu, S., Marson, D., Merz, P. T., Schlaich, A.,  
+Mobley, D., Shirts, M. R., Beckstein, O. (2024).  
+**alchemlyb: the simple alchemistry library.**  
+*Journal of Open Source Software, 9*(101), 6934.  
+[https://doi.org/10.21105/joss.06934](https://doi.org/10.21105/joss.06934)
+
 ## Documentation
 
 The documentation is hosted on [Read the Docs](https://alchemlyb.readthedocs.io/en/latest/).

docs/index.rst

@@ -29,6 +29,17 @@ See :ref:`contact` for how to get in touch if you have questions or find problem
 .. _`discussion #205`: https://github.com/alchemistry/alchemlyb/discussions/205
 .. _`issue #207`: https://github.com/alchemistry/alchemlyb/issues/207
 
+How to Cite
+===========
+
+If you use this software in your research, please cite it as follows:
+
+Wu, Z., Dotson, D. L., Alibay, I., Allen, B. K., Barhaghi, M. S., Hénin, J., Joseph, T. T.,
+Kenney, I. M., Lee, H., Li, H., Lim, V., Liu, S., Marson, D., Merz, P. T., Schlaich, A.,
+Mobley, D., Shirts, M. R., Beckstein, O. (2024).
+**alchemlyb: the simple alchemistry library.**
+*Journal of Open Source Software, 9*(101), 6934.
+https://doi.org/10.21105/joss.06934
 
 Core philosophy
 ---------------