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[REVIEW]: AutoGAMESS: A Python package for automation of GAMESS(us) Raman calculations #1612

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whedon opened this issue Jul 31, 2019 · 108 comments

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commented Jul 31, 2019

Submitting author: @Cavenfish (Brian Ferrari)
Repository: https://github.com/Cavenfish/autogamess
Version: v1.1.1
Editor: @jedbrown
Reviewer: @arosen93, @shivupa, @colleeneb
Archive: 10.5281/zenodo.3385236

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/794a5294c44ee66fb210760db10353f9"><img src="http://joss.theoj.org/papers/794a5294c44ee66fb210760db10353f9/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/794a5294c44ee66fb210760db10353f9/status.svg)](http://joss.theoj.org/papers/794a5294c44ee66fb210760db10353f9)

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

@arosen93 & @shivupa & @colleeneb, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Please try and complete your review in the next two weeks

Review checklist for @arosen93

Conflict of interest

Code of Conduct

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?
  • Version: v1.1.1
  • Authorship: Has the submitting author (@Cavenfish) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @shivupa

Conflict of interest

Code of Conduct

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?
  • Version: v1.1.1
  • Authorship: Has the submitting author (@Cavenfish) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @colleeneb

Conflict of interest

Code of Conduct

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?
  • Version: v1.1.1
  • Authorship: Has the submitting author (@Cavenfish) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
@whedon

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commented Jul 31, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @arosen93, @shivupa, @colleeneb it looks like you're currently assigned to review this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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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
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commented Jul 31, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 31, 2019

@jedbrown

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commented Jul 31, 2019

@arosen93, @shivupa, and @colleeneb 👋 Welcome and thanks for agreeing to review! The comments from @whedon above outline the review process, which takes place in this thread (possibly with issues filed in the AutoGAMESS repository). I'll be watching this thread if you have any questions.

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commented Aug 1, 2019

Hi the version has progressed to 1.0.33. Is it possible to update the submission to reflect this?

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commented Aug 1, 2019

@shivupa We can set the version at acceptance. It's common for the review to result in a new release.

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commented Aug 1, 2019

@whedon set 1.0.33 as version

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commented Aug 1, 2019

OK. 1.0.33 is the version.

@shivupa shivupa referenced this issue Aug 1, 2019
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commented Aug 1, 2019

Yeah that makes sense, and also thanks! (Thanks @whedon)

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commented Aug 2, 2019

@whedon generate pdf

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commented Aug 2, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Aug 2, 2019

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commented Aug 2, 2019

An issue with AutoGAMESS angle calculations has recently been pointed out to me. I should have this fixed in less than a day, the changes will be reflected in the paper as well.
I apologize for not catching this sooner.

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commented Aug 2, 2019

@Cavenfish Good to know. Just FYI, I plan to get to this review over the weekend (by Monday at the latest).

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commented Aug 2, 2019

Okay, I have committed the edits to the code and paper.

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commented Aug 2, 2019

@whedon generate pdf

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commented Aug 2, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Aug 2, 2019

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commented Aug 4, 2019

@arosen93 Your comments on the paper were greatly appreciated! I have made revisions to the paper taking your comments into account, and I believe it has strengthened the paper.

I look forward to hearing more comments from you all.

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commented Aug 4, 2019

@whedon generate pdf

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commented Aug 4, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Aug 4, 2019

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commented Sep 3, 2019


OK DOIs

- 10.1002/jcc.540141112 is OK
- 10.1016/B978-044451719-7/50084-6 is OK
- 10.1016/j.theochem.2004.06.013 is OK
- 10.1002/jcc.23415 is OK
- 10.1051/0004-6361:20052658 is OK
- 10.1088/0004-637x/782/2/63 is OK
- 10.1023/A:1008193805436 is OK
- 10.1016/S1093-3263(99)00002-9 is OK
- 10.1002/jcc.21600 is OK
- 10.1016/j.tcb.2005.05.001 is OK
- 10.1002/jcc.20823 is OK
- 10.1002/(SICI)1096-987X(199610)17:13<1571::AID-JCC9>3.0.CO;2-P is OK
- 10.1021/ci600510j is OK
- 10.1021/acs.jpca.7b07361 is OK
- 10.1016/j.commatsci.2017.07.030 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.1016/j.cpc.2015.08.012 is OK
- 10.1021/jp960976r is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Sep 3, 2019

Another small PR, then I think we'll be ready. We only need DOIs for references that have them.

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commented Sep 3, 2019

@whedon generate pdf

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commented Sep 3, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Sep 3, 2019

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commented Sep 3, 2019

Thanks! Looks good to me now, so please tag a release (annotated tags preferred). Presumably this will be v1.1.1, but it's your choice. Then please archive on Zenodo or a similar service and report the DOI back in this thread.

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commented Sep 3, 2019

v1.1.1 sounds good to me! I made the tag and here is the DOI: 10.5281/zenodo.3385177.

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commented Sep 3, 2019

@Cavenfish Can you please push your tag?

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commented Sep 3, 2019

@jedbrown sorry about that, just pushed it.

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commented Sep 3, 2019

@whedon set v1.1.1 as version

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commented Sep 3, 2019

OK. v1.1.1 is the version.

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commented Sep 3, 2019

Thanks.

Sorry, my instructions may have been unclear: You should archive your repository with Zenodo, not the paper. JOSS handles the paper DOI, with reference to the DOI for your repository.

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commented Sep 3, 2019

@jedbrown
Oh, that makes more sense. I apologize for the inconvenience.

Do you by any chance know how to go about removing the previous upload or should i just leave it be and simply archive the repository?

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commented Sep 3, 2019

DOI are intended to be permanent so either leave it or add a new version (https://help.zenodo.org/#versioning).

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commented Sep 3, 2019

I left alone for now, here is the new repository DOI: 10.5281/zenodo.3385236.

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commented Sep 3, 2019

@whedon set 10.5281/zenodo.3385236 as archive

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commented Sep 3, 2019

OK. 10.5281/zenodo.3385236 is the archive.

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commented Sep 3, 2019

@whedon accept

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commented Sep 3, 2019

Attempting dry run of processing paper acceptance...
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commented Sep 3, 2019

Check final proof 👉 openjournals/joss-papers#942

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#942, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

@jedbrown jedbrown added the accepted label Sep 3, 2019

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commented Sep 3, 2019

@openjournals/joss-eics This paper is accepted; over to you.

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commented Sep 4, 2019

@whedon accept deposit=true

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commented Sep 4, 2019

Doing it live! Attempting automated processing of paper acceptance...
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commented Sep 4, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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commented Sep 4, 2019

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#943
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01612
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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commented Sep 4, 2019

@arosen93, @shivupa, @colleeneb - many thanks for your reviews here and to @jedbrown for editing this submission

@Cavenfish - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Sep 4, 2019

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commented Sep 4, 2019

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01612/status.svg)](https://doi.org/10.21105/joss.01612)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01612">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01612/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01612/status.svg
   :target: https://doi.org/10.21105/joss.01612

This is how it will look in your documentation:

DOI

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