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[REVIEW]: SemanticModels.jl: A Julia Package for Scientific Model Augmentation #57

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: !--author-handle-->@mehalter<!--end-author-handle-- (Micah Halter) Repository: https://github.com/mehalter/juliacon2019-submission Branch with paper.md (empty if default branch): Version: Editor: !--editor-->@vchuravy<!--end-editor-- Reviewers: @MasonProtter, @ChrisRackauckas Archive:

Status

status

Status badge code:

HTML: <a href="https://submissions.juliacon.org/papers/33aac8bcc9f413f18cc1cb3894ad7b57"><img src="https://submissions.juliacon.org/papers/33aac8bcc9f413f18cc1cb3894ad7b57/status.svg"></a>
Markdown: [![status](https://submissions.juliacon.org/papers/33aac8bcc9f413f18cc1cb3894ad7b57/status.svg)](https://submissions.juliacon.org/papers/33aac8bcc9f413f18cc1cb3894ad7b57)

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

@MasonProtter & @ChrisRackauckas, 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/JuliaCon/proceedings-reviews/invitations

The reviewer guidelines are available here: https://proceedings.juliacon.org/guide/reviewers. Any questions/concerns please let @vchuravy know.

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

Review checklist for @MasonProtter

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Paper format

Content

Review checklist for @ChrisRackauckas

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Paper format

Content

whedon commented 4 years ago

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

:star: Important :star:

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@whedon generate pdf
whedon commented 4 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 4 years ago

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

vchuravy commented 4 years ago

@ChrisRackauckas @MasonProtter are you still willing to perform reviews?

ChrisRackauckas commented 4 years ago

I recently took a pretty deep dive through the package and its documentation. The documentation is extremely thorough, especially things like https://aske.gtri.gatech.edu/docs/latest/examples/html/malaria.html . I have nothing to add and think this can be accepted as is. It might finally make a category theorist out of me.

vchuravy commented 4 years ago

@ChrisRackauckas good to hear that the package is in a good state. Anuthing about the submitted paper?

ChrisRackauckas commented 4 years ago

The paper is mostly good. It should really be citing a lot more of the tools that it's using an some of the category theory background. Maybe a full example that's from scratch and not reading from a file? That's about it.

vchuravy commented 4 years ago

@whedon check references

whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1137/141000671 is OK

MISSING DOIs

- None

INVALID DOIs

- None
MasonProtter commented 4 years ago

I'm very sorry to say that I forgot about this, my apologies to Valentin and the submission authors.

@vchuravy It appears all the Juliacon related links are currently broken. What is the page limit for the paper? If it's more than a page, I think it'd be good if the paper was expanded a bit, but also this is fine. People can see the every extensive and well written docs / notebooks if they want to see more.

I will need a bit more time before I can say I feel that I understand the package well enough to sign off on functionality claims, but what I have seen and understand of the package so far is very impressive, novel to the julia ecosystem and interesting.

The test suite on their latest tagged release failed for me on 1.5.0-beta1 and 1.4.2 due to internal Julia errors and also some Cassette weirdness.

One area I'm a little unsure about, and I also don't know what the requirements / expectations are on the JuliaCon side, would be "Are there any comparable or similar packages in other programming languages?" So far as I can tell, other than saying that this package takes a different approach from Jump, Stan and ModellingToolkit it's hard for me to know how novel this work is in the wider world of scientific domain modelling.

vchuravy commented 4 years ago

Thank you Mason for your comments.

@mehalter thank you for your patience, can you address the reviewer comments? And is there an archival DOI for the associated code that you would like to associate with the publication? https://joss.readthedocs.io/en/latest/editing.html#after-reviewers-recommend-acceptance

mehalter commented 4 years ago

I have just tagged a new release on SemanticModels to address the notes from @MasonProtter about the test suite, this now works again in Julia v1.0-1.4.2. Julia v1.5.0-beta1 does not work, but the error comes from being unable to precompile Cassette with the new version. Given it is an unreleased version of Julia for now, we are alright with it not working quite yet until Cassette updates their package.

In regards to the paper length and adding more content, the paper was submitted as an extended abstract with a 1 page limit. As @ChrisRackauckas mentioned, with the short page limit, we were expecting to build interest in the package with the abstract and have people go check out it's documentation which we have spent a lot of time on to have full fledge examples and thorough usage notes.

Thank you to both @MasonProtter and @ChrisRackauckas for taking time to review the paper and your great feedback.

@vchuravy We do not have an archival DOI to be associated with the publication.

vchuravy commented 4 years ago

@vchuravy We do not have an archival DOI to be associated with the publication.

Can you create one for SemanticsModels.jl see https://joss.readthedocs.io/en/latest/editing.html#after-reviewers-recommend-acceptance

mehalter commented 4 years ago

@whedon set 10.5281/zenodo.3961696 as archive

whedon commented 4 years ago

I'm sorry @mehalter, I'm afraid I can't do that. That's something only editors are allowed to do.

mehalter commented 4 years ago

ah sorry, also I misunderstood. We do have a DOI for SemanticModels (this is for the new v0.4.0): 10.5281/zenodo.3961696

vchuravy commented 4 years ago

@whedon set 10.5281/zenodo.3961696 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3961696 is the archive.

vchuravy commented 4 years ago

@whedon set 0.4.0 as version

whedon commented 4 years ago

OK. 0.4.0 is the version.

vchuravy 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

- 10.1137/141000671 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 4 years ago

:wave: @JuliaCon/jcon-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/JuliaCon/proceedings-papers/pull/21

If the paper PDF and Crossref deposit XML look good in https://github.com/JuliaCon/proceedings-papers/pull/21, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
mehalter commented 4 years ago

The paper PDF looks good. Thanks for your help @vchuravy

vchuravy 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

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JCON! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/JuliaCon/proceedings-papers/pull/22
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/jcon.00057
  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...

whedon commented 4 years ago

: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://proceedings.juliacon.org/papers/10.21105/jcon.00057/status.svg)](https://doi.org/10.21105/jcon.00057)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jcon.00057">
  <img src="https://proceedings.juliacon.org/papers/10.21105/jcon.00057/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://proceedings.juliacon.org/papers/10.21105/jcon.00057/status.svg
   :target: https://doi.org/10.21105/jcon.00057

This is how it will look in your documentation:

DOI

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mehalter commented 4 years ago

@vchuravy I just checked the page and the software repository links to the paper repository, could we get that moved to https://github.com/jpfairbanks/SemanticModels.jl

vchuravy commented 4 years ago

@arfon On we had the case that some folks submitted their papers in independent repositories from the actual software: As an example https://proceedings.juliacon.org/papers/10.21105/jcon.00057 points to https://github.com/mehalter/juliacon2019-submission

Is it possible to add an alias?

arfon commented 3 years ago

I've updated this submission to point to https://github.com/jpfairbanks/SemanticModels.jl on the JCON website.