Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[REVIEW]: dfitspy #1249

Closed
whedon opened this Issue Feb 12, 2019 · 109 comments

Comments

Projects
None yet
4 participants
@whedon
Copy link
Collaborator

whedon commented Feb 12, 2019

Submitting author: @astrom-tom (Romain Thomas)
Repository: https://github.com/astrom-tom/dfitspy
Version: v19.3.3
Editor: @arfon
Reviewer: @taldcroft
Archive: 10.5281/zenodo.2592698

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/6a3d39d2fcb6c44965e203527f276c8a"><img src="http://joss.theoj.org/papers/6a3d39d2fcb6c44965e203527f276c8a/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/6a3d39d2fcb6c44965e203527f276c8a/status.svg)](http://joss.theoj.org/papers/6a3d39d2fcb6c44965e203527f276c8a)

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) 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

@taldcroft, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @arfon know.

Please try and complete your review in the next two weeks

Review checklist for @taldcroft

Conflict of interest

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: v19.3.3
  • Authorship: Has the submitting author (@astrom-tom) 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)?
@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Feb 12, 2019

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

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

watching

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

notifications

For a list of things I can do to help you, just type:

@whedon commands
@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Feb 12, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Feb 12, 2019

@arfon

This comment has been minimized.

Copy link
Member

arfon commented Feb 12, 2019

@taldcroft - 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

This comment has been minimized.

Copy link
Member

arfon commented Mar 11, 2019

👋 @taldcroft - a friendly reminder that you said you thought you'd be able to complete your review by the 12th March 😄

@taldcroft

This comment has been minimized.

Copy link
Collaborator

taldcroft commented Mar 11, 2019

Yup, it's on my calendar!

@taldcroft

This comment has been minimized.

Copy link
Collaborator

taldcroft commented Mar 11, 2019

Minor comments on the article proof:

  • fits is an acronym and should always be capitalized as FITS.
  • usefull => useful.
  • used natively inside a another program (extra a)
  • strenghth => strength
  • Not sure of JOSS standards, but I believe Python should always be capitalized.
  • Therefore fits file can => Therefore FITS files can (plural files)
  • There is a space in the URL for the www.eso.org/... link. Note also that this link goes to a page that provides man page links for the original dfits and fitsort standalone tools, but both those links are broken. Can you dig up any working links for the dfits and fitsort man pages?
@taldcroft

This comment has been minimized.

Copy link
Collaborator

taldcroft commented Mar 11, 2019

@arfon @astrom-tom - Review completed.

I opened a number of issues that I think should be addressed (by fixing or discussion). These issues are the source of unchecked boxes in the review checklist.

Overall I see the utility in this package as a standalone package, separate from astropy or fitsio. (For astropy there is a GPL / BSD license problem anyway). When we've ironed the issues I opened then I'll be happy to recommend inclusion to JOSS. 😄

@arfon

This comment has been minimized.

Copy link
Member

arfon commented Mar 11, 2019

👍 thanks @taldcroft. Over to you @astrom-tom

@astrom-tom

This comment has been minimized.

Copy link

astrom-tom commented Mar 11, 2019

Thanks you very much @taldcroft! I will be working on a revision in the next few days and get back to you with a revised version!

I will close the issue as I fix them. @arfon, Can I submit a new version number after the corrections?

@astrom-tom

This comment has been minimized.

Copy link

astrom-tom commented Mar 11, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 11, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 11, 2019

@astrom-tom

This comment has been minimized.

Copy link

astrom-tom commented Mar 13, 2019

Dear @arfon ,

What is the process to resubmit the code?

Thanks!

@taldcroft

This comment has been minimized.

Copy link
Collaborator

taldcroft commented Mar 13, 2019

@astrom-tom - still 3 open issues that you should address prior to resubmitting. None of them are difficult. 😄

@arfon

This comment has been minimized.

Copy link
Member

arfon commented Mar 13, 2019

What is the process to resubmit the code?

Please just let me know here once you've updated your code based on @taldcroft's feedback. There's no need to resubmit - you simply have to update this issue letting us know you've made the changes.

@astrom-tom

This comment has been minimized.

Copy link

astrom-tom commented Mar 13, 2019

@taldcroft, @arfon The remaining issues have been adressed and the code have been updated and moved to the main pypi repository. The new version is 19.3.3.

@taldcroft

This comment has been minimized.

Copy link
Collaborator

taldcroft commented Mar 13, 2019

All good now, I've reviewed and closed the outstanding issues and have now checked off the remaining review boxes.

From my perspective I'm pleased to recommend to @arfon and the editors that dfitspy be accepted to JOSS.

🎉

@arfon

This comment has been minimized.

Copy link
Member

arfon commented Mar 13, 2019

@whedon set v19.3.3 as version

@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 13, 2019

OK. v19.3.3 is the version.

@arfon

This comment has been minimized.

Copy link
Member

arfon commented Mar 13, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 13, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 13, 2019

@arfon

This comment has been minimized.

Copy link
Member

arfon commented Mar 13, 2019

Thanks @taldcroft!

@astrom-tom - your paper is currently very short. Do you think it would be possible to add a little more detail for example discussing the need for this software and some examples of usage? https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain

@astrom-tom

This comment has been minimized.

Copy link

astrom-tom commented Mar 13, 2019

Thanks so much @taldcroft & @arfon !

@arfon I will try to add some more in the paper today and I will let you know when I think it is ready.
Also, is it ok to put dfitspy to ASCL when the final paper is made?

@astrom-tom

This comment has been minimized.

Copy link

astrom-tom commented Mar 13, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 13, 2019

Attempting PDF compilation. Reticulating splines etc...
@astrom-tom

This comment has been minimized.

Copy link

astrom-tom commented Mar 14, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 14, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 14, 2019

@astrom-tom

This comment has been minimized.

Copy link

astrom-tom commented Mar 14, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 14, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 14, 2019

@arfon

This comment has been minimized.

Copy link
Member

arfon commented Mar 14, 2019

@arfon Here it is: DOI: 10.5281/zenodo.2592698

👍

@astrom-tom - before I proceed with accepting this paper can you confirm you've finished iterating on the paper?

One question, can I put dfitspy in ASCL?

Definitely, although you probably want to make sure you're filling in the 'preferred citation' field to make sure that authors are citing the thing you want to be cited (presumably this paper). See for example Astropy's entry: http://ascl.net/1304.002

@astrom-tom

This comment has been minimized.

Copy link

astrom-tom commented Mar 14, 2019

@arfon Yes, the paper is ok for me and I will not modify it.
As for ASCL I will wait that this paper is ready on ADS.

@arfon

This comment has been minimized.

Copy link
Member

arfon commented Mar 14, 2019

@whedon set 10.5281/zenodo.2592698 as archive

@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 14, 2019

OK. 10.5281/zenodo.2592698 is the archive.

@arfon

This comment has been minimized.

Copy link
Member

arfon commented Mar 14, 2019

@whedon accept

@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 14, 2019

Attempting dry run of processing paper acceptance...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 14, 2019

PDF failed to compile for issue #1249 with the following error:

Can't find any papers to compile :-(

@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 14, 2019


OK DOIs

- 10.1051/0004-6361:20010923 is OK

MISSING DOIs

- None

INVALID DOIs

- None
@arfon

This comment has been minimized.

Copy link
Member

arfon commented Mar 14, 2019

@whedon accept

@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 14, 2019

Attempting dry run of processing paper acceptance...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 14, 2019

Check final proof 👉 openjournals/joss-papers#554

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#554, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 14, 2019


OK DOIs

- 10.1051/0004-6361:20010923 is OK

MISSING DOIs

- None

INVALID DOIs

- None
@arfon

This comment has been minimized.

Copy link
Member

arfon commented Mar 14, 2019

@whedon accept deposit=true

@whedon whedon added the accepted label Mar 14, 2019

@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 14, 2019

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

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 14, 2019

🚨🚨🚨 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 👉 openjournals/joss-papers#555
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01249
  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

This comment has been minimized.

Copy link
Member

arfon commented Mar 14, 2019

@taldcroft - many thanks for your review here

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

@arfon arfon closed this Mar 14, 2019

@whedon

This comment has been minimized.

Copy link
Collaborator Author

whedon commented Mar 14, 2019

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01249/status.svg)](https://doi.org/10.21105/joss.01249)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01249">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01249/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01249/status.svg
   :target: https://doi.org/10.21105/joss.01249

This is how it will look in your documentation:

DOI

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:

@astrom-tom

This comment has been minimized.

Copy link

astrom-tom commented Mar 14, 2019

Thank you so much for your work @arfon and @taldcroft. It is really awesome!
(I just signed up for being a reviewer :D ).

@arfon One very last question, when will it be available in ADS? Is there any timeline?

@arfon

This comment has been minimized.

Copy link
Member

arfon commented Mar 14, 2019

(I just signed up for being a reviewer :D ).

Thanks!

@arfon One very last question, when will it be available in ADS? Is there any timeline?

I think ADS typically index us every few weeks. It's not immediate.

@astrom-tom

This comment has been minimized.

Copy link

astrom-tom commented Mar 14, 2019

@arfon Thanks a lot!
For the future version, should I resubmit them or can I just cite the paper for the version that was just accepted?

@arfon

This comment has been minimized.

Copy link
Member

arfon commented Mar 14, 2019

For the future version, should I resubmit them or can I just cite the paper for the version that was just accepted?

Future versions of this package? If there have been major updates then it's possible to resubmit and publish another JOSS paper but this has only happened for a couple of packages in the past and the changes were very large. Basically unless you feel like you need to publish a new paper, I'd encourage people to cite this paper.

@astrom-tom

This comment has been minimized.

Copy link

astrom-tom commented Mar 14, 2019

@arfon Perfect! Thanks again for all this work!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.