[REVIEW]: alchemlyb: the simple alchemistry library #6934

editorialbot · 2024-06-27T07:31:48Z

Submitting author: @orbeckst (Oliver Beckstein)
Repository: https://github.com/alchemistry/alchemlyb
Branch with paper.md (empty if default branch): 71-joss-paper
Version: 2.4.1
Editor: @srmnitc
Reviewers: @glycodynamics, @ryankzhu
Archive: 10.5281/zenodo.13799342

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/86fe561edfcc3bd3e40339b3b7513a97"><img src="https://joss.theoj.org/papers/86fe561edfcc3bd3e40339b3b7513a97/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/86fe561edfcc3bd3e40339b3b7513a97/status.svg)](https://joss.theoj.org/papers/86fe561edfcc3bd3e40339b3b7513a97)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@glycodynamics & @mikemhenry & @philbiggin, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @srmnitc know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @glycodynamics

📝 Checklist for @ryankzhu

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-06-27T07:31:51Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot · 2024-06-27T07:32:10Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (1054.2 files/s, 172073.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          50           2311           3704           6697
reStructuredText                34            502            370           1087
TeX                              1             40              0            280
Markdown                         1             41              0            186
YAML                             7             36             13            183
DOS Batch                        1              8              1             27
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                            95           2942           4094           8470
-------------------------------------------------------------------------------

Commit count by author:

   139	Oliver Beckstein
    96	David Dotson
    82	Zhiyi Wu
    24	harlor
    12	Domenico Marson
     9	Ian Kenney
     7	Hyungro Lee
     6	trje3733
     5	shuai
     4	Jérôme Hénin
     4	Pascal Merz
     4	Victoria Lim
     3	Michael Shirts
     2	Irfan Alibay
     2	Mohammad Soroush Barhaghi
     2	Shuai Liu
     2	Tom Joseph
     2	hl2500
     1	Alexander Schlaich
     1	Bryce Allen
     1	David Mobley
     1	Wei-Tse Hsu
     1	brycestx
     1	helmut carter

editorialbot · 2024-06-27T07:32:14Z

Paper file info:

📄 Wordcount for paper.md is 2661

✅ The paper includes a Statement of need section

editorialbot · 2024-06-27T07:32:17Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/0021-9991(76)90078-4 is OK
- 10.1002/jcc.20290 is OK
- 10.1021/ct0502864 is OK
- 10.1016/j.softx.2020.100627 is OK
- 10.1021/jp807701h is OK
- 10.1021/acs.jcim.2c01052 is OK
- 10.21105/joss.01831 is OK
- 10.1063/1.1749657 is OK
- 10.1007/s10822-015-9840-9 is OK
- 10.1021/ct2003995 is OK
- 10.1063/1.3607597 is OK
- 10.1063/5.0014475 is OK
- 10.1021/jp102971x is OK
- 10.1016/j.softx.2015.06.001 is OK
- 10.1063/1.2978177 is OK
- 10.1063/1.1638996 is OK
- 10.1063/1.1740409 is OK
- 10.1007/s10822-019-00267-z is OK
- 10.33011/livecoms.2.1.18378 is OK
- 10.1021/acs.jctc.5b00784 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1021/acs.jctc.8b00447 is OK
- 10.33011/livecoms.5.1.2067 is OK

MISSING DOIs

- No DOI given, and none found for title: Drug design: structure-and ligand-based approaches
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: API design for machine learning software: experien...
- No DOI given, and none found for title: Simulation techniques for solvation-induced surfac...

INVALID DOIs

- None

editorialbot · 2024-06-27T07:32:17Z

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

editorialbot · 2024-06-27T07:33:03Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

srmnitc · 2024-06-27T07:34:45Z

👋🏼 @orbeckst @glycodynamics, @mikemhenry, @philbiggin this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of just judging this submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#REVIEW_NUMBER so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@srmnitc ) if you have any questions/concerns, thanks again for the submission, and for the reviews

glycodynamics · 2024-06-27T12:21:36Z

Review checklist for @glycodynamics

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/alchemistry/alchemlyb?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@orbeckst) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

glycodynamics · 2024-06-27T12:23:28Z

@srmnitc is there a due date?

srmnitc · 2024-06-27T13:06:22Z

It would be ideal to complete the review within about 2-4 weeks. If you need more time, please let me know.

@srmnitc is there a due date?

mikemhenry · 2024-06-27T20:08:42Z

@srmnitc So sorry but I will have to withdraw as a reviewer, I didn't look at the author list closely when I agreed to review (my bad!) and I have a COI from publishing with one of the authors in the last 4 years

philbiggin · 2024-06-27T20:44:25Z

If this is an issue (ie publishing with one of the authors in the last four years) then I would also have to withdrawn Best wishes, Phil

…

-------------------------------------------- Prof Phil Biggin T: 01865 613305 W: sbcb.bioch.ox.ac.uk/biggin.php E: ***@***.*** On 27 Jun 2024, at 21:09, Mike Henry ***@***.***> wrote: @srmnitc<https://github.com/srmnitc> So sorry but I will have to withdraw as a reviewer, I didn't look at the author list closely when I agreed to review (my bad!) and I have a COI from publishing with one of the authors in the last 4 years — Reply to this email directly, view it on GitHub<#6934 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMMKVGQUDWR5C2XR23UIMSDZJRWODAVCNFSM6AAAAABJ7KO7RGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJVGU4DMNJXHE>. You are receiving this because you were mentioned.Message ID: ***@***.***>

mikemhenry · 2024-06-28T00:14:26Z

@philbiggin This is the policy https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#joss-conflict-of-interest-policy fyi

philbiggin · 2024-06-28T05:31:50Z

In that case I am definitely conflicted as having published with several of the authors. Phil

…

----------------------------------------------------------- Prof Phil Biggin Professor of Computational Biochemistry Chair of the Molecular Graphics and Modelling Society Fellow and Tutor at Lady Margaret Hall, Oxford Department of Biochemistry South Parks Road Oxford OX1 3QU E: ***@***.*** W: sbcb.bioch.ox.ac.uk/biggin.php T: +44 1865 613305 On 28 Jun 2024, at 01:14, Mike Henry ***@***.***> wrote: @philbiggin<https://github.com/philbiggin> This is the policy https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#joss-conflict-of-interest-policy fyi — Reply to this email directly, view it on GitHub<#6934 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMMKVGW2FJJKN75DHBMIHLTZJSTHRAVCNFSM6AAAAABJ7KO7RGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJVHA3DEMZTGY>. You are receiving this because you were mentioned.Message ID: ***@***.***>

srmnitc · 2024-06-28T08:17:34Z

@mikemhenry and @philbiggin thank you for bringing this up. I will unassign you as reviewers. Thanks for your efforts nevertheless!

srmnitc · 2024-06-28T08:18:19Z

@editorialbot remove @mikemhenry from reviewers

editorialbot · 2024-06-28T08:18:22Z

@mikemhenry removed from the reviewers list!

srmnitc · 2024-06-28T08:18:41Z

@editorialbot remove @philbiggin from reviewers

editorialbot · 2024-06-28T08:18:43Z

@philbiggin removed from the reviewers list!

srmnitc · 2024-06-28T10:27:03Z

@editorialbot add @ryankzhu as reviewer

editorialbot · 2024-06-28T10:27:05Z

@ryankzhu added to the reviewers list!

srmnitc · 2024-06-28T10:29:38Z

@ryankzhu thanks for agreeing to be reviewer. You can start you review by using @editorialbot generate my checklist. Here, you can find some information about the checklist. Of course, feel fre e to ping/email me if you need any help. We aim to finish the review in 2-4 weeks. If you need more time, please let me know.

ryankzhu · 2024-07-07T13:03:48Z

Review checklist for @ryankzhu

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/alchemistry/alchemlyb?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@orbeckst) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

srmnitc · 2024-09-20T09:38:25Z

@editorialbot set 2.4.1 as version

editorialbot · 2024-09-20T09:38:27Z

Done! version is now 2.4.1

srmnitc · 2024-09-20T09:38:57Z

@editorialbot generate pdf

editorialbot · 2024-09-20T09:40:24Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

srmnitc · 2024-09-20T13:13:11Z

@editorialbot check references

editorialbot · 2024-09-20T13:13:42Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1016/0021-9991(76)90078-4 is OK
- 10.1002/jcc.20290 is OK
- 10.1021/ct0502864 is OK
- 10.1016/j.softx.2020.100627 is OK
- 10.1021/jp807701h is OK
- 10.1021/acs.jcim.2c01052 is OK
- 10.21105/joss.01831 is OK
- 10.1063/1.1749657 is OK
- 10.1007/s10822-015-9840-9 is OK
- 10.48550/arXiv.1309.0238 is OK
- 10.1021/ct2003995 is OK
- 10.1063/1.3607597 is OK
- 10.1063/5.0014475 is OK
- 10.1021/jp102971x is OK
- 10.1016/j.softx.2015.06.001 is OK
- 10.1063/1.2978177 is OK
- 10.1063/1.1638996 is OK
- 10.1063/1.1740409 is OK
- 10.1007/s10822-019-00267-z is OK
- 10.33011/livecoms.2.1.18378 is OK
- 10.1021/acs.jctc.5b00784 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.48550/arXiv.1309.0238 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1021/acs.jctc.8b00447 is OK
- 10.33011/livecoms.5.1.2067 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: Simulation techniques for solvation-induced surfac...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

srmnitc · 2024-09-20T14:25:43Z

@editorialbot recommend-accept

editorialbot · 2024-09-20T14:25:47Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-09-20T14:26:10Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1016/0021-9991(76)90078-4 is OK
- 10.1002/jcc.20290 is OK
- 10.1021/ct0502864 is OK
- 10.1016/j.softx.2020.100627 is OK
- 10.1021/jp807701h is OK
- 10.1021/acs.jcim.2c01052 is OK
- 10.21105/joss.01831 is OK
- 10.1063/1.1749657 is OK
- 10.1007/s10822-015-9840-9 is OK
- 10.48550/arXiv.1309.0238 is OK
- 10.1021/ct2003995 is OK
- 10.1063/1.3607597 is OK
- 10.1063/5.0014475 is OK
- 10.1021/jp102971x is OK
- 10.1016/j.softx.2015.06.001 is OK
- 10.1063/1.2978177 is OK
- 10.1063/1.1638996 is OK
- 10.1063/1.1740409 is OK
- 10.1007/s10822-019-00267-z is OK
- 10.33011/livecoms.2.1.18378 is OK
- 10.1021/acs.jctc.5b00784 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.48550/arXiv.1309.0238 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1021/acs.jctc.8b00447 is OK
- 10.33011/livecoms.5.1.2067 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: Simulation techniques for solvation-induced surfac...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-09-20T14:27:48Z

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5896, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

srmnitc · 2024-09-20T14:29:48Z

@orbeckst Thank you for your patience, our editor in charge will take a look and finish the rest of the steps. Thanks a lot for making all the changes, and for this nice submission to JOSS.

orbeckst · 2024-09-20T17:25:38Z

Thank you very much, especially for the excellent review process!

Kevin-Mattheus-Moerman · 2024-09-23T09:26:48Z

address openjournals/joss-reviews#6934 (comment)

orbeckst · 2024-09-24T00:50:20Z

@Kevin-Mattheus-Moerman I spelled out USA in the affiliations.

However, I do not know how to address the point about the authorship list in the zenodo archive. The author list of the paper differs from the list of contributors on the software. Not all software authors chose to be authors on the paper or their contributions did not warrant authorship (as already discussed with @srmnitc ). However, every author on the zenodo archive is either an author of the paper or mentioned in the Acknowledgements of the paper. I cannot change the author list on the zenodo archive to conform to the paper list.

If JOSS insists on these two lists being identical I will have to manually create a zenodo submission with a release tar ball included. (I was happy that I could use the automatic zenodo archive, that is tightly linked to the GitHub repo, for the JOSS paper submission but if needed will create a manual dump archive.)

Kevin-Mattheus-Moerman · 2024-09-24T05:37:42Z

@editorialbot generate pdf

editorialbot · 2024-09-24T05:39:36Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

Kevin-Mattheus-Moerman · 2024-09-26T11:43:10Z

@orbeckst thanks for updating the affiliations. On the contributors being listed on the archive, that is okay. We can keep that the way it is. I will now proceed to process this work for acceptance.

Kevin-Mattheus-Moerman · 2024-09-26T11:43:28Z

@editorialbot accept

editorialbot · 2024-09-26T11:43:31Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-09-26T11:50:52Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Wu
  given-names: Zhiyi
  orcid: "https://orcid.org/0000-0002-7615-7851"
- family-names: Dotson
  given-names: David L.
  orcid: "https://orcid.org/0000-0001-5879-2942"
- family-names: Alibay
  given-names: Irfan
  orcid: "https://orcid.org/0000-0001-5787-9130"
- family-names: Allen
  given-names: Bryce K.
  orcid: "https://orcid.org/0000-0002-0804-8127"
- family-names: Barhaghi
  given-names: Mohammad Soroush
  orcid: "https://orcid.org/0000-0001-8226-7347"
- family-names: Hénin
  given-names: Jérôme
  orcid: "https://orcid.org/0000-0003-2540-4098"
- family-names: Joseph
  given-names: Thomas T.
  orcid: "https://orcid.org/0000-0003-1323-3244"
- family-names: Kenney
  given-names: Ian M.
  orcid: "https://orcid.org/0000-0002-9749-8866"
- family-names: Lee
  given-names: Hyungro
  orcid: "https://orcid.org/0000-0002-4221-7094"
- family-names: Li
  given-names: Haoxi
  orcid: "https://orcid.org/0009-0004-8369-1042"
- family-names: Lim
  given-names: Victoria
  orcid: "https://orcid.org/0000-0003-4030-9312"
- family-names: Liu
  given-names: Shuai
  orcid: "https://orcid.org/0000-0002-8632-633X"
- family-names: Marson
  given-names: Domenico
  orcid: "https://orcid.org/0000-0003-1839-9868"
- family-names: Merz
  given-names: Pascal T.
  orcid: "https://orcid.org/0000-0002-7045-8725"
- family-names: Schlaich
  given-names: Alexander
  orcid: "https://orcid.org/0000-0002-4250-363X"
- family-names: Mobley
  given-names: David
  orcid: "https://orcid.org/0000-0002-1083-5533"
- family-names: Shirts
  given-names: Michael R.
  orcid: "https://orcid.org/0000-0003-3249-1097"
- family-names: Beckstein
  given-names: Oliver
  orcid: "https://orcid.org/0000-0003-1340-0831"
contact:
- family-names: Beckstein
  given-names: Oliver
  orcid: "https://orcid.org/0000-0003-1340-0831"
doi: 10.5281/zenodo.13799342
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Wu
    given-names: Zhiyi
    orcid: "https://orcid.org/0000-0002-7615-7851"
  - family-names: Dotson
    given-names: David L.
    orcid: "https://orcid.org/0000-0001-5879-2942"
  - family-names: Alibay
    given-names: Irfan
    orcid: "https://orcid.org/0000-0001-5787-9130"
  - family-names: Allen
    given-names: Bryce K.
    orcid: "https://orcid.org/0000-0002-0804-8127"
  - family-names: Barhaghi
    given-names: Mohammad Soroush
    orcid: "https://orcid.org/0000-0001-8226-7347"
  - family-names: Hénin
    given-names: Jérôme
    orcid: "https://orcid.org/0000-0003-2540-4098"
  - family-names: Joseph
    given-names: Thomas T.
    orcid: "https://orcid.org/0000-0003-1323-3244"
  - family-names: Kenney
    given-names: Ian M.
    orcid: "https://orcid.org/0000-0002-9749-8866"
  - family-names: Lee
    given-names: Hyungro
    orcid: "https://orcid.org/0000-0002-4221-7094"
  - family-names: Li
    given-names: Haoxi
    orcid: "https://orcid.org/0009-0004-8369-1042"
  - family-names: Lim
    given-names: Victoria
    orcid: "https://orcid.org/0000-0003-4030-9312"
  - family-names: Liu
    given-names: Shuai
    orcid: "https://orcid.org/0000-0002-8632-633X"
  - family-names: Marson
    given-names: Domenico
    orcid: "https://orcid.org/0000-0003-1839-9868"
  - family-names: Merz
    given-names: Pascal T.
    orcid: "https://orcid.org/0000-0002-7045-8725"
  - family-names: Schlaich
    given-names: Alexander
    orcid: "https://orcid.org/0000-0002-4250-363X"
  - family-names: Mobley
    given-names: David
    orcid: "https://orcid.org/0000-0002-1083-5533"
  - family-names: Shirts
    given-names: Michael R.
    orcid: "https://orcid.org/0000-0003-3249-1097"
  - family-names: Beckstein
    given-names: Oliver
    orcid: "https://orcid.org/0000-0003-1340-0831"
  date-published: 2024-09-26
  doi: 10.21105/joss.06934
  issn: 2475-9066
  issue: 101
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6934
  title: "alchemlyb: the simple alchemistry library"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06934"
  volume: 9
title: "alchemlyb: the simple alchemistry library"

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editorialbot · 2024-09-26T11:50:57Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-09-26T11:50:58Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06934 joss-papers#5914
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06934
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2024-09-26T12:42:12Z

@orbeckst congratulations on this JOSS publication!

Thanks for editing @srmnitc !

And a special thanks to the reviewers: @glycodynamics, @ryankzhu !!!

editorialbot · 2024-09-26T12:42:14Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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editorialbot added Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Jun 27, 2024

editorialbot assigned srmnitc Jun 27, 2024

editorialbot mentioned this issue Jun 27, 2024

[PRE REVIEW]: alchemlyb: the simple alchemistry library #6845

Closed

orbeckst mentioned this issue Jul 18, 2024

JOSS paper alchemistry/alchemlyb#328

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Sep 20, 2024

orbeckst added a commit to alchemistry/alchemlyb that referenced this issue Sep 24, 2024

paper affiliations: spell out USA

27caba8

address openjournals/joss-reviews#6934 (comment)

editorialbot added accepted published Papers published in JOSS labels Sep 26, 2024

Kevin-Mattheus-Moerman closed this as completed Sep 26, 2024

orbeckst mentioned this issue Sep 26, 2024

JOSS paper alchemistry/alchemlyb#71

Closed

[REVIEW]: alchemlyb: the simple alchemistry library #6934

[REVIEW]: alchemlyb: the simple alchemistry library #6934

Comments

editorialbot commented Jun 27, 2024 • edited Loading

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srmnitc commented Jun 27, 2024 • edited Loading

glycodynamics commented Jun 27, 2024 • edited Loading

Review checklist for @glycodynamics

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

glycodynamics commented Jun 27, 2024

srmnitc commented Jun 27, 2024 • edited Loading

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srmnitc commented Jun 28, 2024

ryankzhu commented Jul 7, 2024 • edited Loading

Review checklist for @ryankzhu

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

srmnitc commented Sep 20, 2024

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srmnitc commented Sep 20, 2024

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orbeckst commented Sep 20, 2024

Kevin-Mattheus-Moerman commented Sep 23, 2024 • edited Loading

Checks on repository

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Remaining points:

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editorialbot commented Jun 27, 2024 •

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ryankzhu commented Jul 7, 2024 •

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