From b5ffe13bb24f5847ad02e09b70df9f9fc7f8834c Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 11 Sep 2024 14:29:40 -0700 Subject: [PATCH 1/7] initial CITATION.cff file - generated with https://bit.ly/cffinit - authors and order from AUTHORS - affiliations and ORCID from JOSS paper - emails from paper or individuals Co-authored-by: David L. Dotson --- CITATION.cff | 113 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 113 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000..33ac0025 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,113 @@ +# -*- 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 + metadata from this file. +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: 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 + 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: Haoxi + family-names: Li + orcid: 'https://orcid.org/0009-0004-8369-1042' + affiliation: University of North Carolina +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 From 50bbbab6e67afa23757719e3d6c4defb67f4f19b Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 11 Sep 2024 15:24:15 -0700 Subject: [PATCH 2/7] add JOSS paper as preferred citation to CITATION - inferred DOI from proof - assume final acceptance in 2024... --- CITATION.cff | 84 +++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 83 insertions(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index 33ac0025..5482ecd3 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -69,7 +69,7 @@ authors: family-names: Alibay orcid: 'https://orcid.org/0000-0001-5787-9130' affiliation: Open Molecular Software Foundation - - given-names: Pascal + - given-names: Pascal T. family-names: Merz affiliation: PM Scientific Consulting orcid: 'https://orcid.org/0000-0002-7045-8725' @@ -111,3 +111,85 @@ keywords: - 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-name: David + family-name: 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 + From b0a5965c6a8baa243daf178f8ff3d546b1bb3073 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 11 Sep 2024 15:39:15 -0700 Subject: [PATCH 3/7] added references for MBAR and equilibration detection --- CITATION.cff | 35 ++++++++++++++++++++++++++++------- 1 file changed, 28 insertions(+), 7 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 5482ecd3..15a6e9fd 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -6,7 +6,7 @@ cff-version: 1.2.0 title: alchemlyb message: >- If you use this software, please cite it using the - metadata from this file. + preferred citation together with any other references. type: software authors: - email: david@datryllic.com @@ -175,8 +175,8 @@ preferred-citation: family-names: Schlaich orcid: 'https://orcid.org/0000-0002-4250-363X' affiliation: University of Stuttgart - - given-name: David - family-name: Mobley + - given-names: David + family-names: Mobley orcid: 'https://orcid.org/0000-0002-1083-5533' affiliation: University of California Irvine - given-names: Michael R. @@ -188,8 +188,29 @@ preferred-citation: email: obeckste@asu.edu affiliation: Arizona State University orcid: 'https://orcid.org/0000-0003-1340-0831' - type: "Article" + type: 'article' year: 2024 - journal: "Journal of Open Source Software" - doi: 10.21105/joss.06934 - + 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' + From ba2561853e1624af7ec2f44b6a6059e5335c11ba Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 11 Sep 2024 16:22:29 -0700 Subject: [PATCH 4/7] inserted additional JOSS paper authors in software author list - added David Mobley @davidlmobley (original conception and design of alchemlyb) - added Michael Shirts @mrshirts (original conception and design of alchemlyb) --- CITATION.cff | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 15a6e9fd..54f10405 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -81,6 +81,14 @@ authors: family-names: Li orcid: 'https://orcid.org/0009-0004-8369-1042' affiliation: University of North Carolina + - 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 identifiers: - type: swh value: 'swh:1:dir:4cd266754be413312ee7ef3f1f7fbe05b38192cf' From f94f6ebb1128f1dc6035147b1b55f8f45e174e95 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 11 Sep 2024 16:38:41 -0700 Subject: [PATCH 5/7] updated CHANGES and AUTHORS for 2.3.3 - CHANGES: bump to 2.3.3 - add reminder to AUTHORS to also update CITATION.cff --- AUTHORS | 3 +++ CHANGES | 10 +++++++++- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/AUTHORS b/AUTHORS index 80df4495..89d7fde1 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 ----------------------------- diff --git a/CHANGES b/CHANGES index 993ac8d8..3e401096 100644 --- a/CHANGES +++ b/CHANGES @@ -12,7 +12,15 @@ The rules for this file: * accompany each entry with github issue/PR number (Issue #xyz) * release numbers follow "Semantic Versioning" https://semver.org ------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +09/??/2024 orbeckst + + * 2.3.3 + +Enhancements: + - add CITATION.cff file with all authors from AUTHORS (issue #394, PR #395) + + 08/24/2024 xiki-tempula * 2.3.2 From 8dcd2d438236183f7287d9c47361480178c4fbcd Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 11 Sep 2024 17:09:08 -0700 Subject: [PATCH 6/7] add authors to CITATION who had NOT been in AUTHORS Added all authors that were mentioned in the Acknowledgements of the JOSS paper but were not in AUTHORS - Wei-Tse Hsu @wehs7661 (2020) for code clean-up in a732380cc6b9571eca7eb694e3acd8adeda4ed78 - Jan Janssen @jan-janssen (2022) for creating the conda-forge package - Shujie Fan @VOD555 (2022) for initial code for fractional equilibration time - Helmut Carter @helmutcarter (2024) for doc fix in #356 --- CITATION.cff | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 54f10405..d25b1e2c 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -53,6 +53,10 @@ authors: 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' @@ -77,10 +81,22 @@ authors: 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' From e2d73dcff31f26ab64230a1b226c535ad552d945 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Mon, 16 Sep 2024 13:00:26 -0700 Subject: [PATCH 7/7] add @jaclark5 to AUTHORS and CITATION.cff AUTHORS entry had been forgotten in PR #381 --- AUTHORS | 3 +++ CITATION.cff | 4 ++++ 2 files changed, 7 insertions(+) diff --git a/AUTHORS b/AUTHORS index 89d7fde1..53219da2 100644 --- a/AUTHORS +++ b/AUTHORS @@ -56,3 +56,6 @@ Chronological list of authors 2023 - Haoxi Li (@hl2500) + +2024 + - Jennifer A. Clark (@jaclark5) diff --git a/CITATION.cff b/CITATION.cff index d25b1e2c..f9030c7b 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -105,6 +105,10 @@ authors: 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'