diff --git a/AUTHORS b/AUTHORS index 80df4495..53219da2 100644 --- a/AUTHORS +++ b/AUTHORS @@ -16,6 +16,9 @@ GitHub handle are preferred. The repository history at https://github.com/alchemistry/alchemlyb and the CHANGES file show individual code contributions. +New contributors should add themselves to the end of this file AND to +the file CITATION.cff at the end of the top-level authors list. + Chronological list of authors ----------------------------- @@ -53,3 +56,6 @@ Chronological list of authors 2023 - Haoxi Li (@hl2500) + +2024 + - Jennifer A. Clark (@jaclark5) diff --git a/CHANGES b/CHANGES index 62fd9cea..11e9e307 100644 --- a/CHANGES +++ b/CHANGES @@ -12,15 +12,17 @@ The rules for this file: * accompany each entry with github issue/PR number (Issue #xyz) * release numbers follow "Semantic Versioning" https://semver.org ------------------------------------------------------------------------------- -??/??/2024 jaclark5 +??/??/2024 jaclark5, orbeckst * 2.4.0 Enhancements - Addition of `block_average` function in both `convergence` and `visualization` (Issue #380, PR #381) + +Enhancements: + - add CITATION.cff file with all authors from AUTHORS (issue #394, PR #395) 08/24/2024 xiki-tempula diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000..f9030c7b --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,244 @@ +# -*- coding: utf-8 -*- +# This CITATION.cff file was initially generated with cffinit. +# Visit https://bit.ly/cffinit to generate yours today! + +cff-version: 1.2.0 +title: alchemlyb +message: >- + If you use this software, please cite it using the + preferred citation together with any other references. +type: software +authors: + - email: david@datryllic.com + given-names: David L. + family-names: Dotson + orcid: 'https://orcid.org/0000-0001-5879-2942' + affiliation: Datryllic LLC + - given-names: Ian M. + family-names: Kenney + orcid: 'https://orcid.org/0000-0002-9749-8866' + affiliation: Kenney Consulting, LLC + - given-names: Oliver + family-names: Beckstein + email: obeckste@asu.edu + affiliation: Arizona State University + orcid: 'https://orcid.org/0000-0003-1340-0831' + - given-names: Shuai + family-names: Liu + orcid: 'https://orcid.org/0000-0002-8632-633X' + affiliation: Silicon Therapeutics LLC + - given-names: Travis + family-names: Jensen + - given-names: Bryce + family-names: Allen + orcid: 'https://orcid.org/0000-0002-0804-8127' + affiliation: Differentiated Therapeutics + - given-names: Dominik + family-names: Wille + affiliation: Freie Universität Berlin + - given-names: Victoria + family-names: Lim + orcid: 'https://orcid.org/0000-0003-4030-9312' + affiliation: University of California Irvine + - given-names: Hyungro + family-names: Lee + orcid: 'https://orcid.org/0000-0002-4221-7094' + affiliation: Pacific Northwest National Laboratory + - given-names: Mohammad Soroush + family-names: Barhaghi + orcid: 'https://orcid.org/0000-0001-8226-7347' + affiliation: Wayne State University + - given-names: Zhiyi + family-names: Wu + affiliation: Exscientia plc + orcid: 'https://orcid.org/0000-0002-7615-7851' + email: william@zhiyiwu.me + - given-names: Wei-Tse + family-names: Hsu + orcid: https://orcid.org/0000-0001-6167-5480 + affiliation: University of Colorado Boulder + - given-names: Alexander + family-names: Schlaich + orcid: 'https://orcid.org/0000-0002-4250-363X' + affiliation: University of Stuttgart + - given-names: Jérôme + family-names: Hénin + orcid: 'https://orcid.org/0000-0003-2540-4098' + affiliation: CNRS + - given-names: Thomas T. + family-names: Joseph + orcid: 'https://orcid.org/0000-0003-1323-3244' + affiliation: University of Pennsylvania + - given-names: Irfan + family-names: Alibay + orcid: 'https://orcid.org/0000-0001-5787-9130' + affiliation: Open Molecular Software Foundation + - given-names: Pascal T. + family-names: Merz + affiliation: PM Scientific Consulting + orcid: 'https://orcid.org/0000-0002-7045-8725' + - given-names: Domenico + family-names: Marson + orcid: 'https://orcid.org/0000-0003-1839-9868' + affiliation: University of Trieste + - given-names: Shujie + family-names: Fan + orcid: 'https://orcid.org/0000-0002-0271-2760' + affiliation: Arizona State University + - given-names: Jan + family-names: Janssen + affiliation: Max-Planck-Institut for Sustainable Materials + orcid: 'https://orcid.org/0000-0001-9948-7119' + - given-names: Haoxi + family-names: Li + orcid: 'https://orcid.org/0009-0004-8369-1042' + affiliation: University of North Carolina + - given-names: Helmut + family-names: Carter + orcid: https://orcid.org/0000-0003-0273-4107 + affiliation: City University of New York + - given-names: David + family-names: Mobley + orcid: 'https://orcid.org/0000-0002-1083-5533' + affiliation: University of California Irvine + - given-names: Michael R. + family-names: Shirts + orcid: 'https://orcid.org/0000-0003-3249-1097' + affiliation: University of Colorado Boulder + - given-names: Jennifer A. + family-names: Clark + orcid: https://orcid.org/0000-0003-4897-5651 + affiliation: National Institute of Standards and Technology +identifiers: + - type: swh + value: 'swh:1:dir:4cd266754be413312ee7ef3f1f7fbe05b38192cf' + description: >- + The Software Heritage identifier for the top level + directory of the repository. +repository-code: 'https://github.com/alchemistry/alchemlyb' +url: 'https://alchemlyb.readthedocs.io' +abstract: >- + alchemlyb is an open-source Python software package for + the analysis of alchemical free energy calculations. Its + functionality contains individual composable building + blocks for all aspects of a full typical free energy + analysis workflow, starting with the extraction of raw + data from the output of diverse molecular simulation + packages, moving on to data preprocessing tasks such as + decorrelation of time series, using various estimators to + derive free energy estimates from simulation samples, and + finally providing quality analysis tools for data + convergence checking and visualization. alchemlyb also + contains high-level end-to-end workflows that combine + multiple building blocks into a user-friendly analysis + pipeline from the initial data input stage to the final + results. +keywords: + - Python + - free energy + - molecular dynamics + - alchemistry +license: BSD-3-Clause +preferred-citation: + title: 'alchemlyb: the simple alchemistry library' + authors: + - given-names: Zhiyi + family-names: Wu + affiliation: Exscientia plc + orcid: 'https://orcid.org/0000-0002-7615-7851' + email: william@zhiyiwu.me + - given-names: David L. + family-names: Dotson + orcid: 'https://orcid.org/0000-0001-5879-2942' + affiliation: Arizona State University + - given-names: Irfan + family-names: Alibay + orcid: 'https://orcid.org/0000-0001-5787-9130' + affiliation: Open Molecular Software Foundation + - given-names: Bryce + family-names: Allen + orcid: 'https://orcid.org/0000-0002-0804-8127' + affiliation: Differentiated Therapeutics + - given-names: Mohammad Soroush + family-names: Barhaghi + orcid: 'https://orcid.org/0000-0001-8226-7347' + affiliation: Wayne State University + - given-names: Jérôme + family-names: Hénin + orcid: 'https://orcid.org/0000-0003-2540-4098' + affiliation: CNRS + - given-names: Thomas T. + family-names: Joseph + orcid: 'https://orcid.org/0000-0003-1323-3244' + affiliation: University of Pennsylvania + - given-names: Ian M. + family-names: Kenney + orcid: 'https://orcid.org/0000-0002-9749-8866' + affiliation: Arizona State University + - given-names: Hyungro + family-names: Lee + orcid: 'https://orcid.org/0000-0002-4221-7094' + affiliation: Pacific Northwest National Laboratory + - given-names: Haoxi + family-names: Li + orcid: 'https://orcid.org/0009-0004-8369-1042' + affiliation: University of North Carolina + - given-names: Victoria + family-names: Lim + orcid: 'https://orcid.org/0000-0003-4030-9312' + affiliation: University of California Irvine + - given-names: Shuai + family-names: Liu + orcid: 'https://orcid.org/0000-0002-8632-633X' + affiliation: Silicon Therapeutics LLC + - given-names: Domenico + family-names: Marson + orcid: 'https://orcid.org/0000-0003-1839-9868' + affiliation: University of Trieste + - given-names: Pascal T. + family-names: Merz + affiliation: PM Scientific Consulting + orcid: 'https://orcid.org/0000-0002-7045-8725' + - given-names: Alexander + family-names: Schlaich + orcid: 'https://orcid.org/0000-0002-4250-363X' + affiliation: University of Stuttgart + - given-names: David + family-names: Mobley + orcid: 'https://orcid.org/0000-0002-1083-5533' + affiliation: University of California Irvine + - given-names: Michael R. + family-names: Shirts + orcid: 'https://orcid.org/0000-0003-3249-1097' + affiliation: University of Colorado Boulder + - given-names: Oliver + family-names: Beckstein + email: obeckste@asu.edu + affiliation: Arizona State University + orcid: 'https://orcid.org/0000-0003-1340-0831' + type: 'article' + year: 2024 + journal: 'Journal of Open Source Software' + doi: '10.21105/joss.06934' +references: + - title: Statistically optimal analysis of samples from multiple equilibrium states + authors: + - family-names: Shirts + given-names: Michael R + - family-names: Chodera + given-names: John D + type: 'article' + pages: '124105' + year: '2008' + journal: Journal of Chemical Physics + doi: '10.1063/1.2978177' + - title: A Simple Method for Automated Equilibration Detection in Molecular Simulations + authors: + - family-names: Chodera + given-names: John D. + type: 'article' + pages: '1799–1805' + year: '2016' + journal: 'Journal of Chemical Theory and Computation' + doi: '10.1021/acs.jctc.5b00784' +