[REVIEW]: PsiRESP: calculating RESP charges with Psi4 #4100

whedon · 2022-01-26T18:02:57Z

Submitting author: @lilyminium (Lily Wang)
Repository: https://github.com/lilyminium/psiresp
Branch with paper.md (empty if default branch):
Version: 0.3.2
Editor: @pdebuyl
Reviewers: @ptmerz, @hannahbrucemacdonald
Archive: 10.5281/zenodo.6501898

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General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@lilyminium) 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

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 and who the target audience is?
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?

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

whedon · 2022-01-26T18:03:00Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ptmerz it looks like you're currently assigned to review this paper 🎉.

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whedon · 2022-01-26T18:03:11Z

Wordcount for paper.md is 1317

whedon · 2022-01-26T18:03:15Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.27 s (348.3 files/s, 126263.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          47           1357           1617           4955
TeX                              3             49              0            813
XML                              1              0              0            586
YAML                            10             67             56            534
reStructuredText                11            300            308            510
Markdown                        12            145              0            410
Jupyter Notebook                 3              0          22442            160
Bourne Shell                     3              5              8             41
DOS Batch                        1              8              1             27
make                             1              7              8             20
TOML                             1              0              0              4
CSS                              1              0              0              3
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            95           1938          24440           8064
-------------------------------------------------------------------------------


Statistical information for the repository '1330ea95e6d8730261fd24a0' was
gathered on 2022/01/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Lily Wang                       34         25388          17499          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                  7889           31.1          2.3                9.33

whedon · 2022-01-26T18:03:33Z

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
- 10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P is OK
- 10.1002/jcc.540141013 is OK
- 10.1021/jp0667442 is OK
- 10.1021/ja00049a045 is OK
- 10.1063/5.0059356 is OK
- 10.1002/wcms.1491 is OK
- 10.5281/zenodo.5601736 is OK
- 10.1063/5.0005188 is OK
- 10.1002/jcc.540110311 is OK
- 10.1107/S0021889883010985 is OK
- 10.5281/zenodo.4107869 is OK
- 10.1002/wcms.93 is OK
- 10.1063/1.1747632 is OK
- 10.1007/BF00549096 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2022-01-26T18:03:39Z

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

pdebuyl · 2022-01-26T18:07:48Z

@ptmerz @hannahbrucemacdonald thanks for accepting to review for JOSS! Make sure to accept the invitation to the reviewers group and to have a look at the reviewer guidelines linked to at the top of this review page.

The review process will happen in this issue page, so questions to the author or to me can be added as comments here.

hannahbrucemacdonald · 2022-01-26T23:07:16Z

Hey @pdebuyl - I think I was missed off at the top as a reviewer, do I need this to get an editable checklist?

thanks!

pdebuyl · 2022-01-27T08:08:44Z

Hi @hannahbrucemacdonald indeed, I started the review without adding you as a reviewer in the pre-review stage. Sorry about this. I'll add you and duplicate the the checklist.

pdebuyl · 2022-01-27T08:08:54Z

@whedon add @hannahbrucemacdonald as reviewer

whedon · 2022-01-27T08:09:01Z

OK, @hannahbrucemacdonald is now a reviewer

pdebuyl · 2022-01-27T08:09:05Z

@whedon reinvite @hannahbrucemacdonald

whedon · 2022-01-27T08:09:08Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

pdebuyl · 2022-01-27T08:09:59Z

@whedon commands

whedon · 2022-01-27T08:10:01Z

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pdebuyl · 2022-01-27T08:10:23Z

@whedon re-invite @hannahbrucemacdonald as reviewer

whedon · 2022-01-27T08:10:26Z

The reviewer already has a pending invite.

@hannahbrucemacdonald please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

ptmerz · 2022-01-28T18:39:29Z

Hi @lilyminium, I started the review today. I didn't have time yet to review the package in all details, so I won't comment on it yet, but it definitely looks to be in great shape!

I did review the paper already, and I think it's very well written. A few things I noted:

The author instructions (https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain) ask to start the paper with "a summary of the high-level functionality of your software for a non-specialist reader". This section is missing in your paper.
I think the Statement of Need section could be split into two sections. Most of this section (from the second paragraph on) actually describes the functionality of the software and isn't a statement of need, so this could be split off in a new section titled "Functionality" or something similar.
I think you could extend the Statement of Need section to include some real-world use cases. You are doing a great job at explaining the existing packages, and how your package improves upon them, so it would be interesting to add some real-world examples of what these improvements can achieve (or make easier) compared to the existing solutions.
You are repeatedly adding citations for the same concepts or methods in the different sections. I think that adding citations at the first mentioning is enough and could improve the readability of the remaining text, but maybe @pdebuyl can chime in if there are some editorial recommendations regarding this.

pdebuyl · 2022-04-19T14:16:05Z

Solving environment: ...

I'll provide an update but so far conda and mamba are slow.

lilyminium · 2022-04-20T00:41:53Z

Thanks @pdebuyl. I didn't find mamba so bad, but conda can take forever -- so far as I can tell that's out of my control. I think adding the --debug flag can give you low level information on what it's doing.

pdebuyl · 2022-04-22T13:10:48Z

Hi @lilyminium

Status: I could install with mamba install -n tmpenv3.9 -c conda-forge psiresp==0.3.1 "qcfractal>0.15". I understand that psiresp is especially complex to install as it relies on quite elaborate packages that are not otherwise bundled.

I have only two requests before confirming the paper:

When running the examples, the user learns about the dependency on psi4 or mdanalysis, has to install and restart the kernel. Can you mention those dependencies visibly at the top of the example file?
The example "04_example_rest_minimal.ipynb" is not running because of missing input files.

lilyminium · 2022-04-23T15:28:39Z

Hi @pdebuyl, I've done the first change! Unfortunately with regards to the second, that's because I added that example as a response to this review. 04_example_rest_minimal.ipynb is not actually in version 0.3.1 of the repository, but the next release 0.4.0. That's why the input files are also missing, as they were created specifically for the example.

I looked into a bit and I can't patch a release I've already put on pip or conda -- however, I could make a new 0.3.2 that includes those examples as the only change from 0.3.1, and update the version in this review?

pdebuyl · 2022-04-26T13:25:24Z

HI @lilyminium yes, a 0.3.2 release with only the minimal fixes to be able to run the examples properly would be totally ok.

lilyminium · 2022-04-29T17:16:20Z

Great @pdebuyl, I've made a version 0.3.2 and put it on Zenodo here: https://zenodo.org/record/6501898 :)

pdebuyl · 2022-05-03T21:47:31Z

@editorialbot set 0.3.2 as version

editorialbot · 2022-05-03T21:47:33Z

Done! version is now 0.3.2

pdebuyl · 2022-05-03T21:47:57Z

@editorialbot set 10.5281/zenodo.6501898 as archive

editorialbot · 2022-05-03T21:47:59Z

Done! Archive is now 10.5281/zenodo.6501898

pdebuyl · 2022-05-03T21:48:54Z

@editorialbot recommend-accept

editorialbot · 2022-05-03T21:48:55Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-05-03T21:49:02Z

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
- 10.1002/jcc.540141013 is OK
- 10.1021/jp0667442 is OK
- 10.1021/ja00049a045 is OK
- 10.1063/5.0059356 is OK
- 10.1002/wcms.1491 is OK
- 10.5281/zenodo.5601736 is OK
- 10.1063/5.0005188 is OK
- 10.1002/jcc.540110311 is OK
- 10.1107/S0021889883010985 is OK
- 10.5281/zenodo.4107869 is OK
- 10.1002/wcms.93 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-05-03T21:50:32Z

⚠️ Error prepararing paper acceptance. The generated XML metadata file is invalid.

Element issn: [facet 'maxLength'] The value has a length of '20'; this exceeds the allowed maximum length of '9'.
Element issn: [facet 'pattern'] The value '1549-9618, 1549-9626' is not accepted by the pattern '\d{4}-?\d{3}[\dX]'.
Element issn: [facet 'maxLength'] The value has a length of '20'; this exceeds the allowed maximum length of '9'.
Element issn: [facet 'pattern'] The value '0192-8651, 1096-987X' is not accepted by the pattern '\d{4}-?\d{3}[\dX]'.
Element issn: [facet 'maxLength'] The value has a length of '20'; this exceeds the allowed maximum length of '9'.
Element issn: [facet 'pattern'] The value '0002-7863, 1520-5126' is not accepted by the pattern '\d{4}-?\d{3}[\dX]'.
Element issn: [facet 'maxLength'] The value has a length of '20'; this exceeds the allowed maximum length of '9'.
Element issn: [facet 'pattern'] The value '0022-3654, 1541-5740' is not accepted by the pattern '\d{4}-?\d{3}[\dX]'.
Element issn: [facet 'maxLength'] The value has a length of '20'; this exceeds the allowed maximum length of '9'.
Element issn: [facet 'pattern'] The value '1463-9076, 1463-9084' is not accepted by the pattern '\d{4}-?\d{3}[\dX]'.
Element issn: [facet 'maxLength'] The value has a length of '20'; this exceeds the allowed maximum length of '9'.
Element issn: [facet 'pattern'] The value '0305-1048, 1362-4962' is not accepted by the pattern '\d{4}-?\d{3}[\dX]'.
Element issn: [facet 'maxLength'] The value has a length of '20'; this exceeds the allowed maximum length of '9'.
Element issn: [facet 'pattern'] The value '0021-9606, 1089-7690' is not accepted by the pattern '\d{4}-?\d{3}[\dX]'.

pdebuyl · 2022-05-04T07:38:25Z

There can be only one ISSN per bib entry. You have to pick one of "online" or "print" only.

lilyminium · 2022-05-04T10:30:59Z

Ohh, thanks for that. I've gone through them now :)

pdebuyl · 2022-05-04T10:47:58Z

@editorialbot recommend-accept

editorialbot · 2022-05-04T10:47:59Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-05-04T10:48:05Z

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
- 10.1002/jcc.540141013 is OK
- 10.1021/jp0667442 is OK
- 10.1021/ja00049a045 is OK
- 10.1063/5.0059356 is OK
- 10.1002/wcms.1491 is OK
- 10.5281/zenodo.5601736 is OK
- 10.1063/5.0005188 is OK
- 10.1002/jcc.540110311 is OK
- 10.1107/S0021889883010985 is OK
- 10.5281/zenodo.4107869 is OK
- 10.1002/wcms.93 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-05-04T10:49:23Z

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

Check final proof 👉 openjournals/joss-papers#3188

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3188, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kyleniemeyer · 2022-05-04T15:01:21Z

@editorialbot accept

editorialbot · 2022-05-04T15:01:22Z

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

editorialbot · 2022-05-04T15:03:21Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-05-04T15:03:22Z

🚨🚨🚨 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.04100 joss-papers#3190
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04100
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2022-05-04T15:09:51Z

Congratulations @lilyminium on your article's publication in JOSS!

Many thanks to @ptmerz and @hannahbrucemacdonald for reviewing this, and @pdebuyl for editing.

editorialbot · 2022-05-04T15:09:52Z

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

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whedon added Python review Shell TeX labels Jan 26, 2022

whedon assigned pdebuyl Jan 26, 2022

whedon mentioned this issue Jan 26, 2022

[PRE REVIEW]: PsiRESP: calculating RESP charges with Psi4 #4005

Closed

whedon assigned ptmerz Jan 27, 2022

whedon assigned hannahbrucemacdonald, pdebuyl and ptmerz and unassigned pdebuyl and ptmerz Jan 27, 2022

lilyminium mentioned this issue Jan 28, 2022

Update paper per review lilyminium/psiresp#68

Merged

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editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label May 4, 2022

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kyleniemeyer closed this as completed May 4, 2022

[REVIEW]: PsiRESP: calculating RESP charges with Psi4 #4100

[REVIEW]: PsiRESP: calculating RESP charges with Psi4 #4100

Comments

whedon commented Jan 26, 2022 • edited by editorialbot Loading

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Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @hannahbrucemacdonald

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Jan 26, 2022

whedon commented Jan 26, 2022

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whedon commented Jan 26, 2022 •

edited by editorialbot

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