[REVIEW]: stingray: A modern Python library for spectral timing #1393

whedon · 2019-04-18T12:05:00Z

Submitting author: @dhuppenkothen (Daniela Huppenkothen)
Repository: https://github.com/StingraySoftware/stingray
Version: v0.1.3
Editor: @arfon
Reviewer: @Cadair
Archive: 10.5281/zenodo.3242835

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@Cadair, 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 @Cadair

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: v0.1.3
Authorship: Has the submitting author (@dhuppenkothen) 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 · 2019-04-18T12:05:02Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Cadair it looks like you're currently assigned as the reviewer for this paper 🎉.

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whedon · 2019-04-18T12:05:03Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-18T12:05:27Z

👉 Check article proof 📄 👈

arfon · 2019-04-18T12:14:38Z

@Cadair - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Any questions/concerns please let me know.

arfon · 2019-05-01T17:22:33Z

👋 @Cadair - how are you getting along here? Do you think you might be able to complete your review in the next week?

Cadair · 2019-05-01T17:33:51Z

Hey, sorry for the delay I should be able to get to this hopefully by the end of the week 😄

Cadair · 2019-05-03T12:35:12Z

@dhuppenkothen Really glad to stingray hit a major milestone 😄

A couple of notes from the review:

Should the citation for Astropy be the second paper from 2018, either instead of or in addition to the 2013 paper?
A few of your references in the paper seem to be missing links to DOIs.
I am not sure all your dependencies are installed automatically by pip so I opened Unify dependencies into setup.cfg StingraySoftware/stingray#397

I will have a play around with the code and complete my review as soon as I can (my train is about to arrive and I want to push send on this before it does 😆)

Cadair · 2019-05-03T12:35:46Z

Oh also, do you plan to release the final 0.1 version before this paper is completed?

arfon · 2019-05-29T17:42:28Z

👋 @Cadair - did you manage to complete your review yet?

1313e · 2019-05-31T00:41:40Z

@dhuppenkothen For some reason, I was sent the DOI of the AAS Journals submission of the Stingray paper instead of you.
So, here you go: 10.3847/1538-4357/ab258d

If you want, I can also send the entire email to you.

crawfordsm · 2019-06-03T23:53:55Z

Thanks @1313e for posting it and letting us know it was sent to the wrong person -- I'll follow up with why that might have happened.

arfon · 2019-06-08T21:15:22Z

@dhuppenkothen - could you please add the following two fields to the paper.md YAML header:

aas-doi: 10.3847/1538-4357/ab258d
aas-journal: Astrophysical Journal

arfon · 2019-06-09T14:47:41Z

@crawfordsm @dhuppenkothen - is the associated AAS paper in ApJ?

Cadair · 2019-06-09T17:12:43Z

This all looks great, apart from the queries I have above about dependencies, missing DOIs and the Astropy citation. 😄

dhuppenkothen · 2019-06-10T18:44:12Z

I had a response all typed out and then somehow forgot to actually send it. Thank you @Cadair for the comments!

To respond:

We have fixed the citation (we now cite both, as per recommendation from one of the Astropy developers)
We have added DOIs where we could. One is a paper in Astronomy and Astrophysics Supplements from 1993, which seems to not have a DOI I can find (the publisher points back to ADS for issues before 1996), and a couple of others are entries in ASCL, which also seem to not have DOIs associated with them.
We're iterating with @Cadair on the dependencies, which I think is pretty close to merging.
We have released Version 0.1 officially: https://zenodo.org/record/3239519#.XP6iky-ZMWo
We have added the reference to the ApJ paper (and yes, the paper is indeed slated to be published in ApJ)

I realized I don't know whether the JOSS paper gets automatically updated from our master branch. Do I need to complete a separate step to make sure everything gets updated?

arfon · 2019-06-10T19:04:30Z

@whedon generate pdf

whedon · 2019-06-10T19:04:33Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-06-10T19:05:00Z

👉 Check article proof 📄 👈

arfon · 2019-06-10T19:05:54Z

@whedon check references

whedon · 2019-06-10T19:05:56Z

Attempting to check references...

whedon · 2019-06-10T19:06:13Z


OK DOIs

- 10.1109/MCSE.2011.36 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1088/0004-637X/770/2/103 is OK
- 10.1117/12.2231304 is OK
- 10.5281/zenodo.3239519 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Cadair · 2019-06-10T20:45:27Z

👍 looks good to me.

arfon · 2019-06-10T21:29:03Z

We're iterating with @Cadair on the dependencies, which I think is pretty close to merging.

@dhuppenkothen - once this is merged, I think we're good to accept here.

dhuppenkothen · 2019-06-10T22:01:22Z

Ok, @Cadair's PR has been merged. :)

arfon · 2019-06-10T23:17:01Z

Great! @dhuppenkothen - at this point could you:

Make a new release of Stingray that includes all of the changes from this review
Make an archive of the reviewed software in Zenodo/figshare/other service making sure that the Zenodo archive name matches the title of your paper and that the authors are the same as the paper?
Then update this thread with the DOI of the archive.

I can then move forward with accepting the submission.

dhuppenkothen · 2019-06-11T00:20:15Z

@whedon generate pdf

whedon · 2019-06-11T00:20:18Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-06-11T00:20:22Z

PDF failed to compile for issue #1393 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon/author.rb:23:in strip_footnotes': undefined method []' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon/author.rb:13:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon.rb:141:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon.rb:141:in block in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon.rb:138:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon.rb:138:in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon.rb:84:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon/processor.rb:36:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
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:in dispatch'
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-18b9a37e7f54/bin/whedon:116:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

dhuppenkothen · 2019-06-11T00:23:09Z

Eek, I broke something. As I was preparing the Zenodo archive, I realized that I'd messed up the co-authors compared to the ApJ version. Trying to fix this, I apparently broke the paper? Any advice, @arfon?

arfon · 2019-06-11T00:24:30Z

@dhuppenkothen - this PR should fix it StingraySoftware/stingray#412

dhuppenkothen · 2019-06-11T00:27:44Z

@whedon generate pdf

whedon · 2019-06-11T00:27:47Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-06-11T00:28:08Z

👉 Check article proof 📄 👈

dhuppenkothen · 2019-06-11T00:38:21Z

Thank you, @arfon! I hope this is all correct this time around. I made a new release and synched it to Zenodo.

The Zenodo DOI is 10.5281/zenodo.3242835.

arfon · 2019-06-11T11:57:18Z

@whedon set v0.1.3 as version

whedon · 2019-06-11T11:57:22Z

OK. v0.1.3 is the version.

arfon · 2019-06-11T11:57:30Z

@whedon set 10.5281/zenodo.3242835 as archive

whedon · 2019-06-11T11:57:33Z

OK. 10.5281/zenodo.3242835 is the archive.

arfon · 2019-06-11T11:58:04Z

@whedon generate pdf

whedon · 2019-06-11T11:58:06Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-06-11T11:58:27Z

👉 Check article proof 📄 👈

arfon · 2019-06-11T12:04:43Z

@Cadair many thanks for your review here ✨

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

whedon · 2019-06-11T12:04:46Z

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whedon assigned arfon Apr 18, 2019

whedon added the review label Apr 18, 2019

whedon mentioned this issue Apr 18, 2019

[PRE REVIEW]: stingray: A modern Python library for spectral timing #1391

Closed

arfon added the AAS Papers being published together with a AAS submission label Apr 20, 2019

Cadair mentioned this issue May 3, 2019

Unify dependencies into setup.cfg StingraySoftware/stingray#397

Merged

whedon assigned Cadair May 6, 2019

arfon added the accepted label Jun 11, 2019

arfon closed this as completed Jun 11, 2019

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

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[REVIEW]: stingray: A modern Python library for spectral timing #1393

[REVIEW]: stingray: A modern Python library for spectral timing #1393

Comments

whedon commented Apr 18, 2019 • edited Loading

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