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[REVIEW]: Pooch: A friend to fetch your data files #1943

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @leouieda (Uieda, L) Repository: https://github.com/fatiando/pooch Version: v0.7.1 Editor: @danielskatz Reviewer: @hmaarrfk, @martindurant Archive: 10.5281/zenodo.3611376

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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

@hmaarrfk & @martindurant, 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 @danielskatz know.

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

Review checklist for @hmaarrfk

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @martindurant

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @hmaarrfk, @martindurant it looks like you're currently assigned to review this paper :tada:.

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whedon commented 4 years ago 
Attempting to check references...
whedon commented 4 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 4 years ago 

OK DOIs

- 10.7717/peerj.453 is OK
- 10.5065/D6WW7G29 is OK
- 10.21105/joss.00957 is OK
- 10.5281/ZENODO.3086002 is OK
- 10.5281/ZENODO.3542092 is OK
- 10.5281/ZENODO.1450596 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 4 years ago

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

danielskatz commented 4 years ago

👋 @hmaarrfk & @martindurant - here we are in the review thread

As I think you know you, your job now is go through the paper and repository and check off boxes in your checklist

Also please be sure to read the prior comments in this issue

danielskatz commented 4 years ago

Also, thanks for agreeing to review!

martindurant commented 4 years ago

What is the usual timeframe for this process?

danielskatz commented 4 years ago

normally a couple of weeks for the initial passes is requested, but with the December holidays, a bit longer is fine

martindurant commented 4 years ago

Note that the links are not clickable in the github-rendered version of the PDF, only in the download. This is doubtless not a fault of the authors.

I find that the paper does indeed convey that Pooch exists, is and says how and when it might be used. It completes the purpose, therefore, of submitting to JOSS. I am still disappointed by the comparison with the rest of the field and Intake in particular. Obviously, again, I am biased here and perhaps some of the points that follow have more to do with Intake's documentation than with Pooch's, and I do not insist on any changes. However:

hmaarrfk commented 4 years ago

Looks good. I think a few numbers and facts can be given to accentuate the impact of the paper.

Paragraph 2:

Paragraph 3:

Paragraph 4:

Paragraph 5:

hmaarrfk commented 4 years ago

Truthfully, if pinged, I will accept for JOSS, but I think a few extra words could go a long way.

danielskatz commented 4 years ago

Note that the links are not clickable in the github-rendered version of the PDF, only in the download. This is doubtless not a fault of the authors.

Yes, this is a function of GitHub - and some of the links in the paper will not fully work until the paper is closer to being accepted, such as the link to the archived software.

danielskatz commented 4 years ago

Thanks @martindurant & @hmaarrfk!

It looks to me like a bit more work would really help this paper, particularly in terms of the state of the field part.

Also, I notice both of you have not checked off the functionality box - Can you let us know what you think is still needed to enable you to check this off?

hmaarrfk commented 4 years ago

I would like a checkbox for Functionality to be incldued in the Software Paper section. My comments mostly refer to that.

danielskatz commented 4 years ago

I'm confused by your comment.

The software paper section includes

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?

This is intended to ask if the paper sufficiently describes the functionality of the software at a high-level.

The functionality section includes

Functionality: Have the functional claims of the software been confirmed?

This is intended to ask if the software does what it says it does.

Can you explain what you would like again?

hmaarrfk commented 4 years ago

I guess the question is:

Do you want a deeper discussion of the functionality in the paper for a more technical audience as well?

If so, some of the comments I made refer to that.

danielskatz commented 4 years ago

JOSS papers are not intended to be long, and they are really intended to support/introduce the software itself and its documentation, so the paper should be more of a high-level introduction to what the software does, and the software documentation should include the deeper discussion

danielskatz commented 4 years ago

@hmaarrfk - To continue our discussion, if the functionality of the software is as claimed, please check off the functionality box. If you have further thoughts on the software paper or documentation, let's talk about them as well.

danielskatz commented 4 years ago

👋 @leouieda - I think we are also waiting for you to address some of @martindurant's comments on the state of the field description in the paper. Please let us know how this is going.

martindurant commented 4 years ago

(just to reiterate: my comments were friendly suggestions only, and if the authors decide not to change anything, they are welcome to say so)

leouieda commented 4 years ago

:wave: @danielskatz just catching up with notifications from the holidays and will start working on replies/fixes.

@martindurant @hmaarrfk thank you for the reviews! They are all appreciated and I'll provide detailed replies soon.

(just to reiterate: my comments were friendly suggestions only, and if the authors decide not to change anything, they are welcome to say so)

@martindurant your comments are more than welcome and that is precisely why I suggested you as a reviewer :slightly_smiling_face:

leouieda commented 4 years ago

the library fsspec contains local-file-cache implementations that could be seen as implementing what Pooch does, also by changing only a single line of code. I would argue that it is indeed more flexible, having many file-system backends and allowing for partial downloads of large files. It can also check the source for changes on backends that support checksum or at least write-date metadata, or general cache expiry.

@martindurant I had seen fsspec while investigating Intake but to be honest, I didn't understand that this is what it does after reading the README or the documentation front page. In hind sight, I should have dug deeper as using fsspec would have simplified some of the work we did on Pooch.

You're right that fsspec is a much more flexible and comprehensive tool and people should definitely use it if they need this flexibility. What Pooch offers is a more limited scope and because of that it's probably easier to understand for non-specialists.

I'll include a section about fsspec in the paper as well.

Intake does not require you to rewrite any code at all in the simplest case such as the pandas example, but only change one line (pd.read_csv -> intake.open_csv; same arguments) with or without local caching

Right, that is what we meant but didn't do a good job in conveying it in the text. Sorry about that. I'll revise this part to make it clear that you only need this for non-standard formats.

Intake does many other things too, such as read from sources which are not files, from remote servers and services; metadata and visualisation and data-source browsing. In this, I agree that Pooch does one job and does it well.

I'll make sure to mention more of this in the text. We should probably also include something like this in the documentation pointing people to Intake if they need these other features.

Indeed, Intake and Pooch should have integration points, and I think this is the biggest and saddest missing point. The Pooch registry (which files) and an Intake catalog (how to load which files) clearly have overlap. Pooch could be one way of obtaining files for Intake.

I completely agree. This has come down to a lack of time on my part to invest in really learning Intake. I'm happy to keep the door open for collaboration but given the time constraints it can't be a priority of mine (but that doesn't mean someone else couldn't take this on).

At the very least, Pooch may want to investigate fsspec and its backends, to enable downloading from a variety of file stores, not just HTTP/FTP. https://github.com/intake/filesystem_spec/blob/master/fsspec/registry.py#L12

Right now, Pooch is pretty much a finished product since it solves the problem we initially set out to solve. But it would make a lot of sense to replace our download code with fsspec in the future and use it as our backend. That way, we can contribute back new backends to fsspec instead.

leouieda commented 4 years ago

Hopefully all reviewer comments have been addressed in fatiando/pooch#132 and fatiando/pooch#134

leouieda commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

danielskatz commented 4 years ago

👋 @martindurant & @hmaarrfk - please let us know if you think this is now ready to accept or if anything else is needed. (@martindurant - specifically, there is one review criterion that you have not checked)

martindurant commented 4 years ago

yes, all go

danielskatz commented 4 years ago

@hmaarrfk - your opinion please?

hmaarrfk commented 4 years ago

Just waking up. Good on my end. I was following up in their repo and tracking there progress there :+1:

danielskatz commented 4 years ago

👋 @leouieda - At this point could you:

I can then move forward with accepting the submission. Please also proofread the submission, including the references, which I will also do.

leouieda commented 4 years ago

@danielskatz will do. Just waiting on any editorial fixes to the paper before releasing and archiving.

danielskatz commented 4 years ago

The only things I see are potentially that some of the "python"s in reference titles could be "Python"s instead.

leouieda commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

leouieda commented 4 years ago

Should be fixed now. The bibtex was poorly formatted.

leouieda commented 4 years ago

@danielskatz done. Release version 0.7.1 and archive DOI 10.5281/zenodo.3611376

danielskatz commented 4 years ago

@whedon set v0.7.1 as version

whedon commented 4 years ago

OK. v0.7.1 is the version.

danielskatz commented 4 years ago

@whedon set 10.5281/zenodo.3611376 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3611376 is the archive.

danielskatz commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.7717/peerj.453 is OK
- 10.5065/D6WW7G29 is OK
- 10.21105/joss.00957 is OK
- 10.5281/ZENODO.3086002 is OK
- 10.5281/ZENODO.3542092 is OK
- 10.5281/ZENODO.1450596 is OK
- 10.21105/joss.01450 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1234

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1234, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
danielskatz commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years ago

🚨🚨🚨 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/1235
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01943
  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...

danielskatz commented 4 years ago

Thanks to @hmaarrfk & @martindurant for editing! And congratulations to @leouieda and co-authors!