Joss-reviews: [REVIEW]: SunPy: A Python package for Solar Physics

[whedon]

Submitting author: @Cadair (Stuart Mumford)
Repository: https://github.com/sunpy/sunpy
Version: v1.0.0
Editor: @arfon
Reviewer: @mwcraig, @ceb8
Archive: 10.5281/zenodo.3666625

Status

Status badge code:

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

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

@mwcraig & @ceb8, 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 @arfon know.

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

Review checklist for @mwcraig

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] 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

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] 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

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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]

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 :tada:.

:star: Important :star:

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:

1. 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]

Attempting PDF compilation. Reticulating splines etc...

[arfon]

@whedon generate pdf from branch joss_paper

[whedon]

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

[whedon]

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:ineach'
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:ininitialize'
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:inset_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: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-1e4ee47b240d/bin/whedon:116:in 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]

@Cadair - could you fix that ORCID please ☝️?

[arfon]

@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]

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]

@whedon generate pdf from branch joss_paper

[whedon]

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

[whedon]

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 methodsplit' for # (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:innew'
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:ineach'
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:ininitialize'
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:inset_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: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-1e4ee47b240d/bin/whedon:116:in 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]

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

[arfon]

@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]

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

[mwcraig]

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

[mwcraig]

@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]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

Can't find any papers to compile :-(

[arfon]

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

[arfon]

@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]

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

🤣 that second author, with the correct affiliation

[mwcraig]

Left some minor comments

• On references at https://github.com/sunpy/sunpy/pull/3391#pullrequestreview-315211867
• On "State of the field" at https://github.com/sunpy/sunpy/pull/3391#issuecomment-552664103

otherwise, this is good to go.

[Cadair]

@whedon generate pdf from branch joss_paper

[whedon]

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

[whedon]

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

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/lib/whedon.rb:190:in block in parse_authors': Author (Florian Mayer) is missing affiliation (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/lib/whedon.rb:188:ineach'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/lib/whedon.rb:188:in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/lib/whedon.rb:91:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/lib/whedon/processor.rb:36:inset_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/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-74bc29a6a731/bin/whedon:116:in 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]

:eyes: Do all the authors really require an affiliation? At least one has explicitly stated they don't have one they want to put on there. Also a lot of people contribute to OSS projects while explicitly not wearing their employers hat, so it might feel in appropriate to put affiliations down. @arfon Has this come up before?

[Cadair]

@whedon generate pdf from branch joss_paper

[whedon]

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

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[Cadair]

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:

[Cadair]

@whedon generate pdf from branch joss_paper

[whedon]

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

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[arfon]

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]

@whedon generate pdf from branch joss_paper

[whedon]

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

[Cadair]

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 :smile:

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[mwcraig]

@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]

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]

@whedon generate pdf from branch joss_paper

[whedon]

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

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[mwcraig]

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]

Thanks for the review @mwcraig :smile:

[ceb8]

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

[arfon]

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]

Thanks @ceb8 😊

[Cadair]

@whedon generate pdf from branch joss_paper

[whedon]

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

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[Cadair]

@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]

@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: https://github.com/sunpy/sunpy/compare/joss_paper...arfon:patch-1

[danielskatz]

👋 @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.

[danielskatz]

👋 Hi all - just checking that we are still waiting for the ApJ paper's DOI?

[arfon]

👋 Hi all - just checking that we are still waiting for the ApJ paper's DOI?

Yes, I believe so. Any news on this front @crawfordsm ?

[Cadair]

As far as I know we have seen some proofs of the ApJ paper, but not a DOI yet.

[Cadair]

@whedon generate pdf from branch joss_paper

[whedon]

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

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[arfon]

@Cadair - apparently the AAS DOI is 10.3847/1538-4357/ab4f7a. I've opened a PR adding this in https://github.com/sunpy/sunpy/pull/3771

[Cadair]

Thanks @arfon what is the procedure now? I need to make a release with the paper in and the author list on Zenodo needs to match the paper?

[arfon]

I need to make a release with the paper in and the author list on Zenodo needs to match the paper?

Ideally yes.

[Cadair]

Ok I need to write a script to generate the zenodo metadata from the paper metadata. I will try and get that sorted in the next couple of days.

[Cadair]

@whedon generate pdf from branch joss_paper

[whedon]

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

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[Cadair]

@arfon other than the author list breaking the sidebar, it also seems the footer with the author names in etc has got the [ from the footnote syntax after my name?

[crawfordsm]

In case you still need it, the ApJ Doi is:

DOI: 10.3847/1538-4357/ab4f7a

[arfon]

@Cadair - this PR should fix the footnote: https://github.com/sunpy/sunpy/pull/3774

[Cadair]

@crawfordsm or @arfon the bibtex for the AAS reference is also incomplete. Now we have a DOI do we have access to the full reference bibtex?

[arfon]

@Cadair - looks like the AAS paper is published now, can you figure out the details from this: https://iopscience.iop.org/article/10.3847/1538-4357/ab4f7a ?

[arfon]

@Cadair because I'm feeling nice today 😸 https://github.com/sunpy/sunpy/pull/3795

[Cadair]

Thanks! The ApJ site was giving me a 500 when I tried to download the bibtex :angry:

[Cadair]

@whedon generate pdf from branch master

[whedon]

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

[arfon]

@Cadair - does this Zenodo release include all of the changes that resulted from this JOSS review?

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[Cadair]

@arfon Probably. I was planning on doing a 1.0.8 with the correct author info etc shortly.

[Cadair]

@arfon 1.0.8 has been released the zenodo record is here: https://zenodo.org/record/3666625

[arfon]

@whedon set 10.5281/zenodo.3666625 as archive

[whedon]

OK. 10.5281/zenodo.3666625 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.21105/joss.01614 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1051/0004-6361:20021326 is OK
- 10.1051/0004-6361:20054262 is OK
- 10.5281/zenodo.2529131 is OK
- 10.3847/1538-4357/ab4f7a is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:321:in block (4 levels) in crossref_authors': undefined methodencode' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.10.4/lib/nokogiri/xml/builder.rb:394:in insert' from /app/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.10.4/lib/nokogiri/xml/builder.rb:377:inmethod_missing'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:319:in block (3 levels) in crossref_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:310:ineach'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:310:in each_with_index' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:310:inblock (2 levels) in crossref_authors'
from /app/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.10.4/lib/nokogiri/xml/builder.rb:394:in insert' from /app/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.10.4/lib/nokogiri/xml/builder.rb:377:inmethod_missing'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:309:in block in crossref_authors' from /app/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.10.4/lib/nokogiri/xml/builder.rb:295:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:308:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:308:incrossref_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/compilers.rb:246:in crossref_from_markdown' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/compilers.rb:21:ingenerate_crossref'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:95:in compile' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:79:incompile'
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:ininvoke_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:instart'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

[arfon]

Gonna need to debug what's going here. Pls hold...

[arfon]

@Cadair - please reformat the YAML header of your paper.md to match the documented example.

Specifically, your affiliations block is currently empty. Affiliations in JOSS papers need to be described separately and then referenced by their index which allows for more reuse of affiliations between authors.

[Cadair]

@arfon What version of the paper.md is it pulling? The version on master and on the 1.0 both have a filled in affiliations block with references to the indexes etc. I think everything is spelt correctly and nothing is missing. :confused:

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.21105/joss.01614 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1051/0004-6361:20021326 is OK
- 10.1051/0004-6361:20054262 is OK
- 10.5281/zenodo.2529131 is OK
- 10.3847/1538-4357/ab4f7a is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1303

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1303, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/1304
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01832
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...

[arfon]

@mwcraig, @ceb8 - thanks again for your reviews here ✨

@Cadair - your paper is now accepted into JOSS :zap::rocket::boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.01832/status.svg)](https://doi.org/10.21105/joss.01832)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01832">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01832/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01832/status.svg
   :target: https://doi.org/10.21105/joss.01832

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[Cadair]

Thank you very much @arfon @ceb8 @mwcraig and everyone else :smile: :rocket:

[arfon]

BTW @Cadair, the formatting of the PDF (margin on second page) is as good as I could get the layout without completely rebuilding our LaTeX template. I hope this is acceptable :-)

[Cadair]

it looks good :) Happy to be causing chaos with a long author list :grinning: