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

Closed editorialbot closed 2 months ago

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@orbeckst<!--end-author-handle-- (Oliver Beckstein) Repository: https://github.com/alchemistry/alchemlyb Branch with paper.md (empty if default branch): 71-joss-paper Version: 2.3.0 Editor: !--editor-->@srmnitc<!--end-editor-- Reviewers: @glycodynamics, @mikemhenry, @philbiggin Managing EiC: Kevin M. Moerman

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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)

Author instructions

Thanks for submitting your paper to JOSS @orbeckst. Currently, there isn't a JOSS editor assigned to your paper.

@orbeckst if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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editorialbot commented 3 months ago

Hello human, 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 commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (1053.3 files/s, 171878.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          50           2311           3704           6697
reStructuredText                34            502            370           1087
TeX                              1             40              0            276
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           8466
-------------------------------------------------------------------------------

Commit count by author:

   135  Oliver Beckstein
    96  David Dotson
    81  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 commented 3 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 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
- 10.1007/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
- 10.1007/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
- 10.1021/acs.jctc.8b00447 is OK
- 10.33011/livecoms.5.1.2067 is OK

MISSING DOIs

- 10.1016/0021-9991(76)90078-4 may be a valid DOI for title: Efficient estimation of free energy differences fr...
- No DOI given, and none found for title: Statistical mechanics of fluid mixtures
- No DOI given, and none found for title: Drug design: structure-and ligand-based approaches
- 10.1063/1.1740409 may be a valid DOI for title: High‐temperature equation of state by a perturbati...
- 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...
- 10.1016/j.cpc.2021.108171 may be a valid DOI for title: LAMMPS - a flexible simulation tool for particle-b...

INVALID DOIs

- None
editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 2657

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

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

editorialbot commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot generate pdf

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot check references

editorialbot commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 3 months ago 
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
Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot invite @srmnitc as editor

editorialbot commented 3 months ago

Invitation to edit this submission sent!

srmnitc commented 3 months ago

@editorialbot assign me as editor

editorialbot commented 3 months ago

Assigned! @srmnitc is now the editor

srmnitc commented 3 months ago

Hi @orbeckst, I will be the handling editor for this submission. The next step would be to find some reviewers for the submission. Please feel free to give any suggestions for reviewers that you might have, and, feel free to ask me any questions here.

srmnitc commented 3 months ago

👋🏽 @ttjoseph @glycodynamics @thesketh @mizu-bai , would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html. Thanks!

ttjoseph commented 3 months ago

@srmnitc I think this paper is absolutely amazing, but I am also one of the authors :) Accordingly I must decline to review.

orbeckst commented 3 months ago

@editorialbot generate pdf

orbeckst commented 3 months ago

(Please regenerate the PDF because a couple of days ago I fixed a name in the acknowledgements. Thanks!)

editorialbot commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

orbeckst commented 3 months ago

@srmnitc here are some potential reviewers: @jvilseck @oostenbrink @philbiggin

srmnitc commented 3 months ago

@srmnitc I think this paper is absolutely amazing, but I am also one of the authors :) Accordingly I must decline to review.

Turns out I found too good of a reviewer! sorry about the mistake!

glycodynamics commented 3 months ago

@srmnitc Yes, I can.

srmnitc commented 3 months ago

@srmnitc Yes, I can.

Thanks a lot!

srmnitc commented 3 months ago

@editorialbot add @glycodynamics as reviewer

editorialbot commented 3 months ago

@glycodynamics added to the reviewers list!

srmnitc commented 3 months ago

@jvilseck @dwhswenson , would either of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html. Thanks!

srmnitc commented 3 months ago

👋🏽 @oostenbrink @philbiggin, would either of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html. Thanks!

srmnitc commented 3 months ago

👋🏽 @mikemhenry @SimonBoothroyd, would either of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html. Thanks!

srmnitc commented 2 months ago

@orbeckst I am also trying to find some reviewers through email, if you have any suggestions, feel free to add them here.

orbeckst commented 2 months ago

Ok, it may well be that some of the people that I suggested don't read GitHub pings and I'd also try email. If you need email addresses I am happy to provide them if you let me know how — I just don't want to put other people's emails into the public.

srmnitc commented 2 months ago

Ok, it may well be that some of the people that I suggested don't read GitHub pings and I'd also try email. If you need email addresses I am happy to provide them if you let me know how — I just don't want to put other people's emails into the public.

I will reach out to some of them through email, thanks! I will reach out if I need any help in finding the emails.

mikemhenry commented 2 months ago

So sorry for missing the ping! Yes I can review this!

philbiggin commented 2 months ago

I can do this, but do I have to operate through GitHub?

If you send a standard email I am more likely to pick things up ;-)

Best wishes, Phil

Prof Phil Biggin T: 01865 613305 W: sbcb.bioch.ox.ac.uk/biggin.php E: @.***

On 26 Jun 2024, at 16:53, Oliver Beckstein @.***> wrote:



Ok, it may well be that some of the people that I suggested don't read GitHub pings and I'd also try email. If you need email addresses I am happy to provide them if you let me know how — I just don't want to put other people's emails into the public.

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/6845#issuecomment-2192049311, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AMMKVGR3HDCNRV47XNGJZNDZJLPV3AVCNFSM6AAAAABI2KUGT6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJSGA2DSMZRGE. You are receiving this because you were mentioned.Message ID: @.***>

srmnitc commented 2 months ago

So sorry for missing the ping! Yes I can review this!

Thanks a lot @mikemhenry, I will now add you as reviewer.

srmnitc commented 2 months ago

@editorialbot add @mikemhenry as reviewer

editorialbot commented 2 months ago

@mikemhenry added to the reviewers list!

srmnitc commented 2 months ago

@mikemhenry and @glycodynamics thanks for agreeing to be reviewers once again. I will start a separate issue for the review itself, where you would be able to generate the checklist.

@orbeckst I would still give some time for some the people I reached out through email to reply, we will get the review started tomorrow. Thanks for your patience :)

srmnitc commented 2 months ago

@editorialbot add @philbiggin as reviewer

editorialbot commented 2 months ago

@philbiggin added to the reviewers list!

srmnitc commented 2 months ago

@editorialbot start review

editorialbot commented 2 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6934.