From d131ae7aba301585ffe344b862a4ef4211aaff9a Mon Sep 17 00:00:00 2001 From: Zhiyi Wu Date: Sat, 7 Dec 2024 14:37:47 +0000 Subject: [PATCH 1/3] add badge and how to cite --- README.md | 2 +- docs/index.rst | 11 +++++++++++ 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 1082f210..e362e6cc 100644 --- a/README.md +++ b/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: diff --git a/docs/index.rst b/docs/index.rst index 70cda583..8993efbf 100644 --- a/docs/index.rst +++ b/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 --------------- From 32fc1c1cac254986951075a34d4fe6afa65bffdd Mon Sep 17 00:00:00 2001 From: Zhiyi Wu Date: Sat, 7 Dec 2024 14:40:13 +0000 Subject: [PATCH 2/3] add to readme --- README.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/README.md b/README.md index e362e6cc..3a94b472 100644 --- a/README.md +++ b/README.md @@ -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/). From f87f58342e73378722b1c5fe866e0461991dc6f7 Mon Sep 17 00:00:00 2001 From: Zhiyi Wu Date: Sat, 14 Dec 2024 22:20:28 +0000 Subject: [PATCH 3/3] updtae --- CITATION.cff | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 5105ba83..ab8ccea4 100644 --- a/CITATION.cff +++ b/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: