[REVIEW]: SunPy: A Python package for Solar Physics #1832

whedon · 2019-10-23T10:48:58Z

Submitting author: @Cadair (Stuart Mumford)
Repository: https://github.com/sunpy/sunpy
Version: v1.0.0
Editor: @arfon
Reviewer: @mwcraig, @ceb8
Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/55b4af87caa5fb93377308b8bb0b2cea/status.svg)](https://joss.theoj.org/papers/55b4af87caa5fb93377308b8bb0b2cea)

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Reviewer instructions & questions

@mwcraig & @ceb8, 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 @mwcraig

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
Contribution and authorship: Has the submitting author (@Cadair) 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 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: Do the authors clearly state 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?

Review checklist for @ceb8

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
Contribution and authorship: Has the submitting author (@Cadair) 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 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: Do the authors clearly state 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?

whedon · 2019-10-23T10:49:01Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @mwcraig, @ceb8 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:

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

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 · 2019-10-23T10:49:02Z

Attempting PDF compilation. Reticulating splines etc...

arfon · 2019-10-23T10:50:10Z

@whedon generate pdf from branch joss_paper

whedon · 2019-10-23T10:50:13Z

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

whedon · 2019-10-23T10:50:24Z

PDF failed to compile for issue #1832 with the following error:

ORCID looks to be the wrong length
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon.rb:143:in block in check_orcids': Problem with ORCID (000-0003-4747-4329) for Tiago M. D. Pereira (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon.rb:141:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon.rb:141:in check_orcids' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon.rb:88:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon/processor.rb:36:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/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-1e4ee47b240d/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

'

arfon · 2019-10-23T10:51:10Z

@Cadair - could you fix that ORCID please ☝️?

arfon · 2019-10-23T10:56:14Z

@mwcraig, @ceb8 - one thing I forgot to mention when inviting you both to review is that this JOSS submission/paper is a joint publication with AAS Journals, i.e. this JOSS paper will be published together with another paper in one of the AAS journals. As part of this collaboration, AAS publishing makes a small donation to the running costs of JOSS.

If this is unacceptable to you, please let me know and I can look for alternative reviewers.

Some related links:

Blog post describing the collaboration: https://blog.joss.theoj.org/2018/12/a-new-collaboration-with-aas-publishing
Summary of JOSS financial model: https://joss.theoj.org/about#costs

Cadair · 2019-10-23T13:17:37Z

The author list is currently not in the right format. I am still soliciting ORCIDs and Affiliations from people, I will reformat the author list and create a zenodo author file at some point soon. I can do this at whatever point you feel is most appropriate, but am stalling to give people time to give me their info.

Cadair · 2019-10-23T13:20:46Z

@whedon generate pdf from branch joss_paper

whedon · 2019-10-23T13:20:49Z

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

whedon · 2019-10-23T13:21:11Z

PDF failed to compile for issue #1832 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon/author.rb:56:in build_affiliation_string': undefined method split' for #Array:0x00000000066aaf58 (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon/author.rb:17:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon.rb:191:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon.rb:191:in block in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon.rb:188:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon.rb:188:in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon.rb:91:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/lib/whedon/processor.rb:36:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-1e4ee47b240d/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-1e4ee47b240d/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

'

Cadair · 2019-10-23T13:21:43Z

I fixed the ORCID, but that error is because the author list is just in the wrong format.

arfon · 2019-10-23T13:48:49Z

@mwcraig, @ceb8 - for now, please use this copy of the paper for your review for now: https://github.com/openjournals/joss-papers/blob/joss.01789/joss.01789/10.21105.joss.01789.pdf

arfon · 2019-11-10T17:05:28Z

@mwcraig, @ceb8 - how are you both getting along with your reviews?

mwcraig · 2019-11-11T00:36:54Z

@arfon -- sorry for the delay. I'll get the review done on Monday.

mwcraig · 2019-11-11T00:38:50Z

@mwcraig, @ceb8 - for now, please use this copy of the paper for your review for now:
https://github.com/openjournals/joss-papers/blob/joss.01789/joss.01789/10.21105.joss.01789.pdf

@arfon -- this link is a 404...

arfon · 2019-11-11T00:54:33Z

@whedon generate pdf

whedon · 2019-11-11T00:54:36Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-11-11T00:54:49Z

PDF failed to compile for issue #1832 with the following error:

Can't find any papers to compile :-(

arfon · 2019-11-11T00:58:38Z

@mwcraig - this paper should work for now: 10.21105.joss.01832.pdf

arfon · 2019-11-11T00:59:23Z

@Cadair - please fix up your paper authors and affiliations ASAP so that the reviewers can check it out. As it currently stands, the paper won't compile.

mwcraig · 2019-11-11T15:55:43Z

this paper should work for now: 10.21105.joss.01832.pdf

🤣 that second author, with the correct affiliation

Cadair · 2019-11-12T14:14:26Z

@whedon generate pdf from branch joss_paper

whedon · 2019-11-12T14:14:29Z

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

whedon · 2019-11-12T14:15:27Z

👉 Check article proof 📄 👈

Cadair · 2019-11-12T14:18:56Z

Well I made it compile by doing that particular hack. My author list is being generated by a yaml translation script now, so it's easy enough to edit 😁

Cadair · 2019-11-12T14:33:30Z

@whedon generate pdf from branch joss_paper

whedon · 2019-11-12T14:33:33Z

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

whedon · 2019-11-12T14:34:31Z

👉 Check article proof 📄 👈

arfon · 2019-11-12T16:54:53Z

Well I made it compile by doing that particular hack. My author list is being generated by a yaml translation script now, so it's easy enough to edit 😁

You can also have an affiliation of 'None' for some of the people (where None is listed as one of the affiliations)

Cadair · 2019-11-12T17:01:22Z

@whedon generate pdf from branch joss_paper

whedon · 2019-11-12T17:01:25Z

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

Cadair · 2019-11-12T17:01:32Z

Well I made it compile by doing that particular hack. My author list is being generated by a yaml translation script now, so it's easy enough to edit grin

You can also have an affiliation of 'None' for some of the people (where None is listed as one of the affiliations)

Done 😄

whedon · 2019-11-12T17:02:49Z

👉 Check article proof 📄 👈

mwcraig · 2019-11-13T04:08:33Z

@arfon -- I made a comment on the sunpy JOSS paper that they hadn't addressed the state of the field in the JOSS paper. @mbobra mentioned that it is addressed in the accompanying ApJ paper:

We address this in the introduction section of the accompanying ApJ Paper. Does this satisfy the review criteria or would you like us to explicitly address this in the JOSS paper?

I've read that section of the ApJ paper and it is very good and probably too long for the JOSS paper. Does it need to be addressed in the JOSS paper? Would a reference to the ApJ paper suffice?

My leaning would be towards a reference in the JOSS paper to the discussion in the ApJ paper but I haven't reviewed a JOSS/ApJ combination before.

arfon · 2019-11-13T11:53:10Z

I've read that section of the ApJ paper and it is very good and probably too long for the JOSS paper. Does it need to be addressed in the JOSS paper? Would a reference to the ApJ paper suffice?

I think this is OK, we just need to make sure it's cited properly in the body of the text.

mwcraig · 2019-11-14T04:56:29Z

@whedon generate pdf from branch joss_paper

whedon · 2019-11-14T04:56:32Z

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

whedon · 2019-11-14T04:57:25Z

👉 Check article proof 📄 👈

mwcraig · 2019-11-14T05:02:52Z

Aside from a couple of cosmetic issues with the new references (commented on the paper PR) this is ready to go. The reference to the ApJ paper isn't complete yet, but I assume that will be worked out. Thanks for the quick responses to the review comments @Cadair and @mbobra!

Cadair · 2019-11-14T09:47:16Z

Thanks for the review @mwcraig 😄

ceb8 · 2019-11-15T20:05:53Z

Aside from the incomplete ApJ paper reference issue noted by @mwcraig this is ready.

arfon · 2019-11-15T20:21:04Z

Thanks @ceb8 and @mwcraig.

@Cadair - I don't think we can finalize the ApJ citation until we have a DOI for this paper. @crawfordsm - do we have a DOI yet for the accompanying ApJ paper?

Cadair · 2019-11-18T20:34:48Z

Thanks @ceb8 😊

Cadair · 2019-11-18T22:21:55Z

@whedon generate pdf from branch joss_paper

whedon · 2019-11-18T22:21:58Z

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

whedon · 2019-11-18T22:22:42Z

👉 Check article proof 📄 👈

Cadair · 2019-11-19T14:25:15Z

@arfon We would like to document how we have sorted our author list somewhere, in the name of transparency and clarity. Do you have any suggestions about where we should put that information?

arfon · 2019-11-21T12:27:49Z

@arfon We would like to document how we have sorted our author list somewhere, in the name of transparency and clarity. Do you have any suggestions about where we should put that information?

Something like this will allow you to have a footnote in the paper: sunpy/sunpy@joss_paper...arfon:patch-1

danielskatz · 2019-12-05T10:54:04Z

👋 @arfon - it looks like this is waiting for the ApJ paper's DOI, correct? Assuming so, I'm going to mark it as paused for now.

whedon added the review label Oct 23, 2019

whedon assigned arfon Oct 23, 2019

whedon mentioned this issue Oct 23, 2019

[PRE REVIEW]: SunPy: A Python package for Solar Physics #1789

Closed

openjournals deleted a comment from whedon Oct 23, 2019

arfon added the AAS label Oct 23, 2019

Cadair mentioned this issue Oct 23, 2019

Submit SunPy to the Journal of Open Source Software #3391

Open

1 of 2 tasks complete

whedon assigned ceb8 and mwcraig Oct 25, 2019

arfon added the accepted label Nov 15, 2019

danielskatz added the paused label Dec 5, 2019

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[REVIEW]: SunPy: A Python package for Solar Physics #1832

Comments

whedon commented Oct 23, 2019 • edited by ceb8

Status

Reviewer instructions & questions

Review checklist for @mwcraig

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @ceb8

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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whedon commented Oct 23, 2019 •

edited by ceb8