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

whedon · 2019-07-31T03:39:32Z

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

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Markdown: [![status](http://joss.theoj.org/papers/794a5294c44ee66fb210760db10353f9/status.svg)](http://joss.theoj.org/papers/794a5294c44ee66fb210760db10353f9)

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

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✨ Please try and complete your review in the next two weeks ✨

Review checklist for @arosen93

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 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

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 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

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 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)?

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

whedon · 2019-07-31T03:39:35Z

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:

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

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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

whedon · 2019-07-31T03:39:36Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-07-31T03:39:56Z

👉 Check article proof 📄 👈

jedbrown · 2019-07-31T03:41:22Z

@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.

shivupa · 2019-08-01T17:19:21Z

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

jedbrown · 2019-08-01T17:21:25Z

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

jedbrown · 2019-08-01T17:21:46Z

@whedon set 1.0.33 as version

whedon · 2019-08-01T17:21:49Z

OK. 1.0.33 is the version.

shivupa · 2019-08-01T17:25:01Z

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

Cavenfish · 2019-08-02T00:19:51Z

@whedon generate pdf

whedon · 2019-08-02T00:19:53Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-08-02T00:20:17Z

👉 Check article proof 📄 👈

Cavenfish · 2019-08-02T03:23:53Z

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.

Andrew-S-Rosen · 2019-08-02T03:27:16Z

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

Cavenfish · 2019-08-02T21:31:25Z

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

Cavenfish · 2019-08-02T21:31:40Z

@whedon generate pdf

whedon · 2019-08-02T21:31:42Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-08-02T21:32:06Z

👉 Check article proof 📄 👈

Cavenfish · 2019-08-04T18:17:06Z

@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.

Cavenfish · 2019-08-04T18:17:22Z

@whedon generate pdf

whedon · 2019-08-04T18:17:25Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-08-04T18:17:50Z

👉 Check article proof 📄 👈

jedbrown · 2019-09-03T18:43:19Z

@whedon generate pdf

whedon · 2019-09-03T18:43:22Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-09-03T18:43:54Z

👉 Check article proof 📄 👈

jedbrown · 2019-09-03T18:50:58Z

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.

Cavenfish · 2019-09-03T19:04:26Z

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

jedbrown · 2019-09-03T19:08:11Z

@Cavenfish Can you please push your tag?

Cavenfish · 2019-09-03T19:10:54Z

@jedbrown sorry about that, just pushed it.

jedbrown · 2019-09-03T20:14:11Z

@whedon set v1.1.1 as version

whedon · 2019-09-03T20:14:15Z

OK. v1.1.1 is the version.

jedbrown · 2019-09-03T20:16:20Z

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.

Cavenfish · 2019-09-03T20:24:37Z

@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?

jedbrown · 2019-09-03T20:30:01Z

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

Cavenfish · 2019-09-03T20:33:08Z

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

jedbrown · 2019-09-03T20:45:00Z

@whedon set 10.5281/zenodo.3385236 as archive

whedon · 2019-09-03T20:45:04Z

OK. 10.5281/zenodo.3385236 is the archive.

jedbrown · 2019-09-03T20:45:22Z

@whedon accept

whedon · 2019-09-03T20:45:24Z

Attempting dry run of processing paper acceptance...

whedon · 2019-09-03T20:46:01Z

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 · 2019-09-03T20:48:50Z

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

arfon · 2019-09-04T00:17:26Z

@whedon accept deposit=true

whedon · 2019-09-04T00:17:29Z

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

whedon · 2019-09-04T00:18:26Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2019-09-04T00:18:26Z

🚨🚨🚨 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.01612 joss-papers#943
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01612
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

arfon · 2019-09-04T00:21:31Z

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

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

whedon · 2019-09-04T00:21:34Z

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

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whedon assigned jedbrown Jul 31, 2019

whedon added the review label Jul 31, 2019

whedon mentioned this issue Jul 31, 2019

[PRE REVIEW]: AutoGAMESS: A Python package for automation of GAMESS(us) Raman calculations #1602

Closed

whedon assigned Andrew-S-Rosen, colleeneb and shivupa Aug 1, 2019

shivupa mentioned this issue Aug 1, 2019

Paper DOIs Cavenfish/autogamess#1

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Andrew-S-Rosen mentioned this issue Aug 3, 2019

Comments on the JOSS paper Cavenfish/autogamess#2

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jedbrown added the accepted label Sep 3, 2019

arfon closed this as completed Sep 4, 2019

whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

editorialbot mentioned this issue Oct 1, 2023

[PRE REVIEW]: MAHOS: Measurement Automation Handling and Orchestration System #5720

Closed

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

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

Comments

whedon commented Jul 31, 2019 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @arosen93

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @shivupa

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @colleeneb

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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