Merge branch '71-joss-paper' of github.com:alchemistry/alchemlyb into…

… 71-joss-paper

CHANGES

@@ -13,6 +13,14 @@ The rules for this file:
  * release numbers follow "Semantic Versioning" https://semver.org
 
 ------------------------------------------------------------------------------
+??/??/2024 orbeckst
+
+ * 2.3.1
+
+Changes:
+ - alchemlyb adopts SPEC 0 (replaces NEP 29)
+ https://scientific-python.org/specs/spec-0000/
+
 
 21/05/2024 xiki-tempula
 

docs/index.rst

@@ -52,14 +52,12 @@ Development is done in the open on `GitHub`_.
 Software engineering best-practices are used throughout, including continuous integration testing via Github Actions, up-to-date documentation, and regular releases.
 
 .. Note::
- With release 0.5.0, the alchemlyb project adopted `NEP 29`_ to determine which versions of Python and NumPy_ will be supported.
- When we release a new major or minor version, alchemlyb will support *at least all minor versions of Python introduced and released in the prior 42 months from the release date with a minimum of 2 minor versions of Python*, and *all minor versions of NumPy released in the prior 24 months from the anticipated release date with a minimum of 3 minor versions of NumPy*.
-
-The pandas_ package (one of our other primary dependencies) also follows `NEP 29`_ so this support policy will make it easier to maintain **alchemlyb** in the future.
+ The alchemlyb project uses `SPEC 0`_ to determine which versions of Python, NumPy_, and pandas_ will be supported.
+ When we release a new major or minor version, alchemlyb will support *at least all minor versions of Python introduced and released in the prior 3 years from the release date*, and *all minor versions of NumPy and pandas released in the prior 2 years from the anticipated release date*.
 
 
 .. _`GitHub`: https://github.com/alchemistry/alchemlyb
-.. _`NEP 29`: https://numpy.org/neps/nep-0029-deprecation_policy.html
+.. _`SPEC 0`: https://scientific-python.org/specs/spec-0000/
 .. _NumPy: https://numpy.org
 .. _pandas: https://pandas.pydata.org/
 

joss_paper/paper.md

@@ -14,14 +14,17 @@ authors:
  orcid: 0000-0001-5879-2942
  equal-contrib: true
  affiliation: "2, 3"
+ - name: Irfan Alibay
+ orcid: 0000-0001-5787-9130
+ affiliation: 13
  - name: Jérôme Hénin
  orcid: 0000-0003-2540-4098
  affiliation: 4
  - name: Thomas T. Joseph
  orcid: 0000-0003-1323-3244
  affiliation: 5
  - name: Ian M. Kenney
- orchid: 0000-0002-9749-8866
+ orcid: 0000-0002-9749-8866
  affiliation: 2
  - name: Hyungro Lee
  orcid: 0000-0002-4221-7094
@@ -70,6 +73,8 @@ affiliations:
  index: 11
  - name: Center for Biological Physics, Arizona State University, Tempe, AZ, USA
  index: 12
+ - name: Open Free Energy, Open Molecular Software Foundation, Davis, 95616 California, United States
+ index: 13
 
 date: 31 May 2024
 bibliography: paper.bib
@@ -187,11 +192,11 @@ It can directly estimate quantities such as solvation free energies and makes it
 Some work on alchemlyb was supported by grants from the National Institutes of Health (Award No R01GM118772 to O.B., K08GM139031 to T.T.J.) and the National Science Foundation (award ACI-1443054 to O.B.). A.S. acknowledges funding by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy - EXC 2075 – 390740016 and support by the Stuttgart Center for Simulation Science (SimTech).
 The sponsors were not involved in any aspects of the research or the writing of the manuscript.
 
-Shuai Liu, Travis Jensen, Bryce Allen, Dominik Wille, Victoria Lim, Mohammad S. Barhaghi, Irfan Alibay, and Pascal Merz contributed code to *alchemlyb*.
+Shuai Liu, Travis Jensen, Bryce Allen, Dominik Wille, Victoria Lim, Mohammad S. Barhaghi, and Pascal Merz contributed code to *alchemlyb*.
 
 # Author contributions
 
-D.L.D., M.R.S., D.M., and O.B. designed the project. Z.W., D.L.D., J.H., T.T.J., I.M.K., H.L., H.L., D.M., A.S. contributed to new features. Z.W., D.L.D., O.B. maintained the code base. Z.W., D.L.D., M.R.S, A.S., O.B. wrote the manuscript.
+D.L.D., M.R.S., D.M., and O.B. designed the project. Z.W., D.L.D., I.A., J.H., T.T.J., I.M.K., H.L., H.L., D.M., A.S. contributed to new features. Z.W., D.L.D., O.B. maintained the code base. Z.W., D.L.D., M.R.S, A.S., O.B. wrote the manuscript.
 
 # References