[PRE REVIEW]: PsiRESP: calculating RESP charges with Psi4

[whedon]

Submitting author: @lilyminium (Lily Wang)
Repository: https://github.com/lilyminium/psiresp
Version: v0.3.1
Editor: @pdebuyl
Reviewers: @ptmerz
Managing EiC: Kyle Niemeyer

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e9da64635833d70c0efe66da34b682b0"><img src="https://joss.theoj.org/papers/e9da64635833d70c0efe66da34b682b0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e9da64635833d70c0efe66da34b682b0/status.svg)](https://joss.theoj.org/papers/e9da64635833d70c0efe66da34b682b0)

Author instructions

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

The author's suggestion for the handling editor is @pdebuyl.

@lilyminium if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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

@whedon commands

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

@whedon commands

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1317

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.15 s (771.7 files/s, 161516.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          46           1301           1582           4610
TeX                              3             49              0            813
XML                              1              0              0            586
YAML                             9             58             51            510
reStructuredText                38            277            275            450
Markdown                        12            137              0            394
Jupyter Notebook                 3              0          13492            146
TOML                             1              3              0             44
Bourne Shell                     3              5              8             41
DOS Batch                        1              8              1             27
make                             1              7              8             20
CSS                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                           119           1845          15417           7644
-------------------------------------------------------------------------------


Statistical information for the repository 'a89f4b6c81344534ad5e2508' was
gathered on 2021/12/17.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Lily Wang                       31         24698          17245          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Lily Wang                  7453           30.2          1.8                9.78

[whedon]

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

OK DOIs

- 10.1002/jcc.21787 is OK
- 10.25080/Majora-629e541a-00e is OK
- 10.1021/ct200196m is OK
- 10.1002/jcc.540161106 is OK
- 10.1021/ja00074a030 is OK
- 10.1021/j100142a004 is OK
- 10.1039/c0cp00111b is OK
- 10.1093/nar/gkm887 is OK
- 10.1038/s42004-020-0291-4 is OK
- 10.1002/qua.26035 is OK
- 10.1002/jcc.540050204 is OK
- 10.1063/1.1740588 is OK
- 10.1021/jp0667442 is OK
- 10.1021/ja00049a045 is OK
- 10.1063/5.0059356 is OK
- 10.5281/zenodo.5601736 is OK
- 10.1063/5.0005188 is OK
- 10.5281/zenodo.4107869 is OK
- 10.1063/1.1747632 is OK
- 10.1007/BF00549096 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/jcc.540141013 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/wcms.1491 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/jcc.540110311 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1107/S0021889883010985 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/wcms.93 is INVALID because of 'https://doi.org/' prefix

[whedon]

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

[kyleniemeyer]

@whedon invite @pdebuyl as editor

Hi @pdebuyl, could you edit this submission?

[whedon]

@pdebuyl has been invited to edit this submission.

[kyleniemeyer]

Hi @lilyminium, while we are getting started assigning an editor and finding reviewers, could you please take a look at those DOI issues raised above and resolve them in your paper?

[lilyminium]

@whedon generate pdf

[whedon]

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

[lilyminium]

Thanks @kyleniemeyer -- I've fixed those now.

For reviewers, could I please suggest the following from the list:

• hannahbrucemacdonald
• mkhorton
• ptmerz
• blakeaw
• chryswoods

[kthyng]

@pdebuyl Adding a ping here now that it is the new year — would you like to edit this submission? Thanks!

[pdebuyl]

Hi @kthyng indeed. I will gladly edit the submission starting next week :-)

[kthyng]

@pdebuyl Awesome! I'll assign you to it now with the understanding you'll start next week. Thanks!

[kthyng]

@whedon assign @pdebuyl as editor

[whedon]

OK, the editor is @pdebuyl

[lilyminium]

@pdebuyl I just made a new release of psiresp 0.3 -- would it be possible to change the version to that instead? It contains minor improvements: making some dependencies optional and renaming some ambiguously-named variables.

[lilyminium]

Hi there, just checking in on the progress of this submission.

[pdebuyl]

Hi @lilyminium sorry about this. I was getting another submission started and will look for reviewers quickly.

[pdebuyl]

@hannahbrucemacdonald @ptmerz would you review the article "PsiRESP: calculating RESP charges with Psi4" for the Journal of Open Source Software?

[ptmerz]

@pdebuyl Yes, I'd be happy to review!

[pdebuyl]

Thank you very much @ptmerz The review will only start once a second reviewer is onboard.

[pdebuyl]

@whedon assign @ptmerz as reviewer

[whedon]

OK, @ptmerz is now a reviewer

[pdebuyl]

@whedon set v0.3 as version

[whedon]

OK. v0.3 is the version.

[pdebuyl]

@whedon set v0.3.1 as version

[whedon]

OK. v0.3.1 is the version.

[hannahbrucemacdonald]

Hey - the paper looks interesting, happy to review!

[pdebuyl]

Thank you very much @hannahbrucemacdonald !

[pdebuyl]

@whedon start review

[whedon]

OK, I've started the review over in #4100.