From 3a597810049d45966bbb39e388c6dbd0464e635e Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 12 Sep 2024 13:12:12 -0700 Subject: [PATCH 1/2] replaced whitepaper with paper DOI in README - fix #87 - some more README clean-up --- README.rst | 44 ++++++++++++++++++++++++++++++-------------- 1 file changed, 30 insertions(+), 14 deletions(-) diff --git a/README.rst b/README.rst index a6e725bf..af2af8c0 100644 --- a/README.rst +++ b/README.rst @@ -8,34 +8,36 @@ Contents ======== -This repository contains the source code for the MDAKits registry. -The registry hosts a list of MDAKits which it then both documents -and continually validate. +This repository contains the source code for the `MDAKits registry`_. -For more details about the MDAKit registry, see Section 4 of the -`MDAKit Whitepaper`_. +The registry hosts a list of MDAKits which it then both documents and +continually validate. For more details about the MDAKit registry, please see +the `MDAKit paper`_ in the section *The MDAKit registry*. + +For detailed documentation and tutorials about MDAKits see the MDAKits site +https://mdakits.mdanalysis.org/ Creating a new MDAKit ===================== -The minimum specification for an MDAKit is defined under Section 3 of the -`MDAKit Whitepaper`_. To developers in creating best practices adhering -projects, a `cookiecutter`_ has been made available. +The minimum specification for an MDAKit is defined in the `MDAKit +paper`_ under *The MDAKit framework*. To developers in creating best +practices adhering projects, a `cookiecutter`_ has been made +available. Adding a new MDAKit =================== -The registry is currently in development, the way by which new MDAKits -are added is likely to change significantly over time. If you have any -concerns or questions about the process, please reach out by raising an -issue! - Adding a new MDAKit involves making a PR against this repository and adding a new `metadata`_ file within it's own respective directory under `mdakits`. +*The registry is currently in development, the way by which new MDAKits are +added may change over time. If you have any concerns or questions about the +process, please reach out by raising an issue!* + License ======= @@ -48,9 +50,23 @@ Acknowledgements The development of this repository is supported by a grant from the Chan Zuckerberg Initiative under an EOSS4 award. +References +========== + +1. Irfan Alibay, Lily Wang, Fiona Naughton, Ian Kenney, Jonathan Barnoud, + Richard J Gowers, and Oliver Beckstein. **MDAKits: A framework for + FAIR-compliant molecular simulation analysis.** In Meghann Agarwal, Chris + Calloway, and Dillon Niederhut, editors, *Proceedings of the 22nd Python in + Science Conference (SCIPY 2023)*, pages 76-84, Austin, TX, 2023. doi: + `10.25080/gerudo-f2bc6f59-00a`_. + +.. _`MDAKits registry`: https://mdakits.mdanalysis.org/mdakits.html + .. _`metadata`: mdakits/template/metadata.yaml -.. _`MDAKit Whitepaper`: paper/whitepaper/MDAKits_whitepaper.pdf +.. _`MDAKit paper`: https://doi.org/10.25080/gerudo-f2bc6f59-00a + +.. _`10.25080/gerudo-f2bc6f59-00a`: https://doi.org/10.25080/gerudo-f2bc6f59-00a .. _`cookiecutter`: https://github.com/MDAnalysis/cookiecutter-mdakit From f8e0f756f1f44e2a46422d2fbba20c24c597ff0f Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Mon, 16 Sep 2024 09:27:31 -0700 Subject: [PATCH 2/2] Update README.rst Co-authored-by: Fiona Naughton --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index af2af8c0..2ce349b7 100644 --- a/README.rst +++ b/README.rst @@ -11,7 +11,7 @@ Contents This repository contains the source code for the `MDAKits registry`_. The registry hosts a list of MDAKits which it then both documents and -continually validate. For more details about the MDAKit registry, please see +continually validates. For more details about the MDAKit registry, please see the `MDAKit paper`_ in the section *The MDAKit registry*. For detailed documentation and tutorials about MDAKits see the MDAKits site