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[REVIEW]: DataDepsGenerators.jl: making reusing data easy by automatically generating DataDeps.jl registration code #921

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whedon opened this Issue Aug 31, 2018 · 44 comments

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whedon commented Aug 31, 2018

Submitting author: @oxinabox (Lyndon White)
Repository: https://github.com/oxinabox/DataDepsGenerators.jl/
Version: v0.4.0
Editor: @arfon
Reviewer: @ninjin
Archive: 10.5281/zenodo.1478705

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/f52340014957dc0e74d5935162221c29"><img src="http://joss.theoj.org/papers/f52340014957dc0e74d5935162221c29/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/f52340014957dc0e74d5935162221c29/status.svg)](http://joss.theoj.org/papers/f52340014957dc0e74d5935162221c29)

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

@ninjin, 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 @ninjin

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: Does the release version given match the GitHub release (v0.4.0)?
  • Authorship: Has the submitting author (@oxinabox) 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)?
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whedon commented Aug 31, 2018

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

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whedon commented Aug 31, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Aug 31, 2018

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arfon commented Sep 10, 2018

👋 @ninjin - when do you think you might be able to complete your review by?

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ninjin commented Sep 26, 2018

Apologies for the delays, here is the current state of my review.

Formatting:

  1. The citations look a bit odd to me, should “((Bezanson et al. 2014))” not be “(Bezanson et al. 2014)”?
  2. A period is missing at the end of the third bullet in the first bullet list.
  3. In the second to last paragraph there is what I think is a failed listing with hyphens following dots, this should probably be fixed.
  4. I suspect that both of the cited works have DOIs assigned to them, Bezanson et al. (2014) I think was accepted by some IEEE journal. These DOIs should be added.

Content:

  1. Are there not other similar packages for other programming languages? There is currently a bit of a lack of a wider context of open science, etc. and I think one or two sentences with a few cites would be very helpful for the readers.

Other than the above comments, the submitted paper reads very well.

Documentation:

  1. No clear statement of need.
  2. Misspellings: “consitantly”, “webbrowser”, “targetted”, etc. run a spell checker.
  3. Awkward grammar in a number of places, just give it another read through.
  4. While this is a small package, having at least a rudimentary CONTRIBUTING.md would be a good idea.

Functionality:

Currently blocked by #62.

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oxinabox commented Sep 26, 2018

Thanks, I will attend to these in the next couple of days.

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oxinabox commented Sep 26, 2018

I suspect that both of the cited works have DOIs assigned to them, Bezanson et al. (2014) I think was accepted by some IEEE journal. These DOIs should be added.

the DataDeps work is still under-review (and is taking a truly long time) and does not yet have a DOI.
I have searched IEEE
and I can not find 2014 julia paper there.
But it appears now the 2017 SIAM paper is now the preferred citation for Julia, so I will update it to that,
that one does have a DOI.

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ninjin commented Sep 26, 2018

Your are indeed correct, it was a SIAM paper and not IEEE.

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oxinabox commented Sep 27, 2018

For my own records:
Formatting issues are fixed.

Content issues are fixed, at least for R I added a section.
I don't know much about this space for Python.

@whedon generate pdf

Documentation:
Will be fixed once oxinabox/DataDepsGenerators.jl#64
is merged

No clear statement of need.

I took the first paragraph from the paper and added it to the docs,
since I think that sums it up pretty well.

Misspellings: “consitantly”, “webbrowser”, “targetted”, etc. run a spell checker.

Done

Awkward grammar in a number of places, just give it another read through.

Done

While this is a small package, having at least a rudimentary CONTRIBUTING.md would be a good idea

Done


Re Functionality being blocked.
That is now resolved for julia 0.7+/1.0 in the newly released DataDepsGenerators v0.5.0
The DataDepsGenerators 0.4.0 release can be used on 0.6, but I agree with @ninjin it is better for him to review the julia 1.0 compatible version since that will become the version most people will use.

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arfon commented Sep 27, 2018

@whedon generate pdf

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whedon commented Sep 27, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Sep 27, 2018

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SebastinSanty commented Oct 14, 2018

Any updates on this?

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arfon commented Oct 14, 2018

👋 @ninjin - it looks like you're nearly done with the review here. Any chance you could check on the last few items in the checklist?

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ninjin commented Oct 17, 2018

My apologies, will sort it out in the morning.

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ninjin commented Oct 22, 2018

I think GitHub is back online…

Writing

Nothing major, but some issues that should be addressed.

  1. “leavages”
  2. The CKAN entry has a bullet point split across two bullet points.
  3. Same for JSON-LD.
  4. “Julia” should always be capitalised.
  5. “By generating code that the user may edit they may tweak the details as required.”, this one is a bit hard to parse, reformulate?
  6. “If these APIs were to be access directly by a project, …”, not native, but “accessed”?
  7. Maybe not use “things” in academic writing.
  8. “the was proposed package (doidata) to acquire data based on a DOI.”, grammar.

Code

Pretty much works as intended, just some minor syntax issues in the README and some examples that were borked. Overall, I would say the code is good to go.

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oxinabox commented Oct 23, 2018

@whedon generate pdf

Fixed the paper. thank you for the feedback.
(At some point I misread the guidance on the capitalization of julia, getting it literally backwards,
and thought it was julia for the language, and Julia for the compiler.
But indeed it is the other way round (which makes much more sense since lowercase matches the executable name).

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whedon commented Oct 23, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 23, 2018

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ninjin commented Oct 23, 2018

As far as I can see, there are only two issues with spelling left – do turn on the spell checker as these are super easy to spot automatically. “leavages” and “editting”.

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arfon commented Nov 4, 2018

Thanks @ninjin. @oxinabox - could you please do a final check of the spelling in your paper?

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oxinabox commented Nov 5, 2018

@arfon I fixed up those spelling issues (though, I'll give it a 3rd check),
I was just waiting to fix up an issue @ninjin identified with one of our data providers,
oxinabox/DataDepsGenerators.jl#67
Something in the DataONE API, or in the SSL client we use to access it changed in a breaking way in the last few months.
I am talking with the devs on both sides there.

@whedon generate pdf

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ninjin commented Nov 5, 2018

@whedon generate pdf

Please…?

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whedon commented Nov 5, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Nov 5, 2018

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ninjin commented Nov 5, 2018

Fix “lavages” – fun fact. Other than that is looks solid.

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oxinabox commented Nov 5, 2018

@whedon generate pdf

(sorry didn't do the 3rd check yet)

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whedon commented Nov 5, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Nov 5, 2018

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ninjin commented Nov 5, 2018

Looks good to me, @arfon do I sign off on the final version by closing this issue?

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arfon commented Nov 5, 2018

@oxinabox - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

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arfon commented Nov 5, 2018

Looks good to me, @arfon do I sign off on the final version by closing this issue?

Thanks @ninjin - I'll take it from here.

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oxinabox commented Nov 6, 2018

Done.

DOI: 10.5281/zenodo.1478705

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arfon commented Nov 6, 2018

@whedon set 10.5281/zenodo.1478705 as archive

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whedon commented Nov 6, 2018

OK. 10.5281/zenodo.1478705 is the archive.

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arfon commented Nov 6, 2018

@whedon accept

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whedon commented Nov 6, 2018

Attempting dry run of processing paper acceptance...

@whedon whedon added the accepted label Nov 6, 2018

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whedon commented Nov 6, 2018

Check final proof 👉 openjournals/joss-papers#57

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#57, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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arfon commented Nov 6, 2018

@whedon accept deposit=true

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whedon commented Nov 6, 2018

Doing it live! Attempting automated processing of paper acceptance...
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whedon commented Nov 6, 2018

🚨🚨🚨 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#58
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.00921
  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...

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arfon commented Nov 6, 2018

@ninjin - many thanks for your review here

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

@arfon arfon closed this Nov 6, 2018

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whedon commented Nov 6, 2018

🎉🎉🎉 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.00921/status.svg)](https://doi.org/10.21105/joss.00921)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00921">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00921/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00921/status.svg
   :target: https://doi.org/10.21105/joss.00921

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:

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oxinabox commented Nov 6, 2018

@SebastinSanty woot we did the thing.

@ninjin thanks again

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