Joss-reviews: [PRE REVIEW]: AutoGAMESS: A Python package for automation of GAMESS(us) Raman calculations
Submitting author: @Cavenfish (Brian Ferrari)
Repository: https://github.com/Cavenfish/autogamess
Version: 1.0.31
Editor: @jedbrown
Reviewers: @arosen93, @shivupa, @colleeneb
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whedon
on 28 Jul 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #1602 with the following error:
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:115:in check_fields': Paper YAML header is missing expected fields: authors, affiliations (RuntimeError)
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whedon
on 28 Jul 2019
Hi @Cavenfish, thanks for your interest in JOSS. Before we move forward with your submission, I have a few concerns based on our submission requirements and review criteria:
The biggest issue is that, while useful, the software appears (to me) to be more of a utility for interacting with another software package, AutoGAMESS, rather than fully fledged research software in its own right. One common test for this is: if used towards a research paper, would it be cited? (Due to contributing meaningfully to the results.)
In addition, your submission is missing some of the major things we look for:
- I don't see any test suite, making it impossible for reviewers to assess whether the software works correctly.
- I don't see any documentation, or examples.
- I don't see any sort of community guidelines.
kyleniemeyer
on 28 Jul 2019
Hello Dr. Niemeyer,
This is my first submission to JOSS, so I am not sure how to continue from here. I understand rebuttals are typical in other journals, I’m not sure if this is the same in JOSS.
To address your concerns:
-AutoGAMESS is in fact a utility for interacting with another software package, however since it expedites the process of completing computational chemistry research it would certainly be cited, most likely within the acknowledgements section. It has already been acknowledged at conferences for aiding in the research progress. I’m also in contact with other researchers that plan on citing AutoGAMESS, once able to, In their future work.
-I will make and commit the test suit as soon as possible.
-The current level of documentation and guidelines is the doc strings for each function. If this is not sufficient I can write up documentation and community guidelines in the GitHub markdown as soon as possible.
Thank you for you time.
Thanks,
Brian Ferrari
From: Kyle Niemeyer notifications@github.com
Sent: Sunday, July 28, 2019 3:00:55 AM
To: openjournals/joss-reviews joss-reviews@noreply.github.com
Cc: Brian Ferrari brianf1996@Knights.ucf.edu; Mention mention@noreply.github.com
Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: AutoGAMESS: A Python package for automation of GAMESS(us) Raman calculations (#1602)
Hi @Cavenfishhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCavenfish&data=02%7C01%7Cbrianf1996%40knights.ucf.edu%7Cca0883268a6749534b9c08d71329572e%7C5b16e18278b3412c919668342689eeb7%7C0%7C0%7C636998940582758341&sdata=MkVvepuV1z4YLn1psEixcFB1Q1QKJMtftFf2JexmpHk%3D&reserved=0, thanks for your interest in JOSS. Before we move forward with your submission, I have a few concerns based on our submission requirementshttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjoss.readthedocs.io%2Fen%2Flatest%2Fsubmitting.html%23submission-requirements&data=02%7C01%7Cbrianf1996%40knights.ucf.edu%7Cca0883268a6749534b9c08d71329572e%7C5b16e18278b3412c919668342689eeb7%7C0%7C0%7C636998940582758341&sdata=euVHNq6zj0YSBkwzupW%2ByPRqffSaUCvU8hhT4z7Pwr8%3D&reserved=0 and review criteriahttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjoss.readthedocs.io%2Fen%2Flatest%2Freview_criteria.html&data=02%7C01%7Cbrianf1996%40knights.ucf.edu%7Cca0883268a6749534b9c08d71329572e%7C5b16e18278b3412c919668342689eeb7%7C0%7C0%7C636998940582768349&sdata=eZ7km%2BbGxrnlr1uzAPAKSCNGj3deCwYSfd%2FNVKNkUrk%3D&reserved=0:
The biggest issue is that, while useful, the software appears (to me) to be more of a utility for interacting with another software package, AutoGAMESS, rather than fully fledged research software in its own right. One common test for this is: if used towards a research paper, would it be cited? (Due to contributing meaningfully to the results.)
In addition, your submission is missing some of the major things we look for:
- I don't see any test suite, making it impossible for reviewers to assess whether the software works correctly.
- I don't see any documentation, or examples.
- I don't see any sort of community guidelines.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHubhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fopenjournals%2Fjoss-reviews%2Fissues%2F1602%3Femail_source%3Dnotifications%26email_token%3DALULTPIQDWTU4UK5CHCBZ53QBU72PA5CNFSM4IHLYSXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD26YW7Y%23issuecomment-515738495&data=02%7C01%7Cbrianf1996%40knights.ucf.edu%7Cca0883268a6749534b9c08d71329572e%7C5b16e18278b3412c919668342689eeb7%7C0%7C0%7C636998940582768349&sdata=ItJKa34%2B4zPrlNrBeH1vdVaFpJJ8KegnoSOLQ6MzFRw%3D&reserved=0, or mute the threadhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALULTPK32NCBDMTXYPWIYWTQBU72PANCNFSM4IHLYSXA&data=02%7C01%7Cbrianf1996%40knights.ucf.edu%7Cca0883268a6749534b9c08d71329572e%7C5b16e18278b3412c919668342689eeb7%7C0%7C0%7C636998940582778357&sdata=Hz5q1YdMIc2ylj8rnKd4qcpBk8jHCdxpPv3wggjjk24%3D&reserved=0.
Cavenfish
on 28 Jul 2019
@Cavenfish with JOSS all interactions with editors and reviewers are more like conversations rather than the more formal step-by-step process of older journals. In this case, the Associate Editor-in-Chief on duty (me) does a quick filter of new submissions before assigning to an editor. We look to ensure submissions are in scope, and aren't missing any major items.
For documentation, software packages should come with enough information such that a new user could come across the package and begin using it. At minimum, this could be in a README, but frequently more detailed documentation (like that generated via Sphinx) also accompanies software. This also generally includes installation info and examples.
kyleniemeyer
on 29 Jul 2019
👋 @Cavenfish — I am the Associate Editor-in-Chief on rotation this week. Given the major issues identified by the previous AEiC, this submission is not ready to be assigned an editor and proceed to review. I will thus add the "paused" label now, and wait for your updates. If you decide to withdraw your submission and re-submit at a later date, do let me know by a reply here.
labarba
on 29 Jul 2019
@labarba I believe I have fully satisfied all the previously addressed concerns. I have added documentation and examples to the README.md and added community guidelines to a CONTRIBUTE.md. A test suite was also added for the package.
Is this ready to proceed to the review stage, or should i make more updates first?
Thanks!
Cavenfish
on 30 Jul 2019
@whedon generate pdf
Cavenfish
on 30 Jul 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #1602 with the following error:
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:115:in check_fields': Paper YAML header is missing expected fields: authors, affiliations (RuntimeError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:80:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:inset_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:116:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in
whedon
on 30 Jul 2019
@whedon generate pdf
labarba
on 30 Jul 2019
Attempting PDF compilation. Reticulating splines etc...
👋 @jedbrown — Could you handle this new JOSS submission as editor? Thanks!
labarba
on 30 Jul 2019
@whedon assign @jedbrown as editor
jedbrown
on 30 Jul 2019
OK, the editor is @jedbrown
whedon
on 30 Jul 2019
@arosen93 @goerz @shivupa @robertodr @KEIPERTK :wave: Would you be willing to review this submission for JOSS?
jedbrown
on 30 Jul 2019
@jedbrown. This is in my area. I would be happy to review.
arosen93
on 30 Jul 2019
I’d feel comfortable and would enjoy reviewing this as well!
shivupa
on 31 Jul 2019
@whedon add @arosen93 as reviewer
jedbrown
on 31 Jul 2019
OK, @arosen93 is now a reviewer
whedon
on 31 Jul 2019
@whedon add @shivupa as reviewer
jedbrown
on 31 Jul 2019
OK, @shivupa is now a reviewer
whedon
on 31 Jul 2019
@whedon add @colleeneb as reviewer
jedbrown
on 31 Jul 2019
OK, @colleeneb is now a reviewer
whedon
on 31 Jul 2019
@whedon start review
jedbrown
on 31 Jul 2019
OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1612. Feel free to close this issue now!
whedon
on 31 Jul 2019
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