[REVIEW]: Caliban: Docker-based job manager for reproducible workflows

whedon commented 4 years ago

Submitting author: @sritchie (Sam Ritchie) Repository: https://github.com/google/caliban Version: 0.4.1 Editor: @diehlpk Reviewer: @lukasheinrich, @arokem Archive: 10.5281/zenodo.4026612

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c33c8b464103b2fb3b641878722bf8f3"><img src="https://joss.theoj.org/papers/c33c8b464103b2fb3b641878722bf8f3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c33c8b464103b2fb3b641878722bf8f3/status.svg)](https://joss.theoj.org/papers/c33c8b464103b2fb3b641878722bf8f3)

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

@lukasheinrich & @arokem, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
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 @diehlpk know.

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

Review checklist for @lukasheinrich

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 (@sritchie) 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 @arokem

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 (@sritchie) 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?

diehlpk commented 4 years ago

@sritchie How are things going? When do you estimate to finalize the submission?

sritchie commented 4 years ago

Hey @diehlpk , apologies, I had seen the first item but not the checklist. I should be able to finalize this in the next couple of days!

sritchie commented 4 years ago

[x] Make a tagged release of your software, and list the version tag of the archived version here: 0.4.1, https://github.com/google/caliban/releases/tag/0.4.1
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository):
[x] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[x] Please list the DOI of the archived version here: 10.5281/zenodo.4026612,

@diehlpk , I'm not going to take the suggestion at the moment to mirror the tutorial from the README to the readthedocs page, as it's slightly more involved, and I need to think through a proper publishing workflow to guarantee that users who find the README can get started right away without the information falling out of sync.

Let me know if I can do anything else here!

diehlpk commented 4 years ago

@whedon set 0.4.1 as version

whedon commented 4 years ago

OK. 0.4.1 is the version.

diehlpk commented 4 years ago

@whedon set 10.5281/zenodo.4026612 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.4026612 is the archive.

diehlpk commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1145/2889160.2891057 is OK
- 10.1109/cvpr.2009.5206848 is OK
-  10.25080/Majora-4af1f417-001  is OK

MISSING DOIs

- None

INVALID DOIs

- None

diehlpk commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

diehlpk commented 4 years ago

Hi, @sritchie please check the final paper, before I accept it and publish it.

sritchie commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

sritchie commented 4 years ago

@diehlpk okay, now we're looking good! I found a single typo and pushed a fix.

diehlpk 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 (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1145/2889160.2891057 is OK
- 10.1109/cvpr.2009.5206848 is OK
-  10.25080/Majora-4af1f417-001  is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1727

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1727, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

diehlpk commented 4 years ago

@sritchie Congratulations to the accepted paper. @lukasheinrich and @arokem thanks for your review.

sritchie commented 4 years ago

Thanks all!!

kyleniemeyer commented 4 years ago

Hi @sritchie, I'm doing some final checks on your submission. In the paper, it looks like the Forde et al. and Zaharia et al. references may be missing some details. Also, please look at the other references, and add curly braces {} around words to enforce capitalization where appropriate (e.g., "IEEE", "Linux").

sritchie commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

sritchie commented 4 years ago

@kyleniemeyer , just took another pass and I think we're set here.

diehlpk commented 4 years ago

@sritchie For the second reference ieee should be IEEE.

sritchie commented 4 years ago

@whedon generate pdf

sritchie commented 4 years ago

@diehlpk I'll figure this out someday... nice catch, fixed!

whedon commented 4 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

kyleniemeyer commented 4 years ago

Hey @sritchie, looks like the Forde et al. reference is still missing something. Where was that published—a journal, or on a website, or something?

sritchie commented 4 years ago

@kyleniemeyer , I took the bibtex entry from here: https://scholar.google.com/scholar?q=Reproducing+%7BMachine+%7BLearning+%7BResearch+on+%7BBinder&hl=en&as_sdt=0&as_vis=1&oi=scholart:

@article{forde2018reproducing,
  title={Reproducing Machine Learning Research on Binder},
  author={Forde, Jessica and Bussonnier, Matthias and Fortin, F{\'e}lix-Antoine and Granger, Brian and Head, Tim and Holdgraf, Chris and Ivanov, Paul and Kelley, Kyle and Pacer, M and Panda, Yuvi and others},
  year={2018}
}

It lives on OpenReview.net: https://openreview.net/forum?id=BJlR6KTE3X

and was published at NIPS 2018 Workshop MLOSS; you're right that even though that isn't in the bibtex entry Scholar generates it needs to be here. Adding now.

sritchie commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

kyleniemeyer commented 4 years ago

@sritchie yeah, unfortunately Google Scholar's BiBTeX generation only seems to work consistently for regular journal articles.

kyleniemeyer 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 (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1145/2889160.2891057 is OK
- 10.1109/cvpr.2009.5206848 is OK
-  10.25080/Majora-4af1f417-001  is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1734

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1734, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kyleniemeyer 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:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1735
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02403
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 4 years ago

Congrats @sritchie on your article's publication in JOSS!

Many thanks to @lukasheinrich and @arokem for reviewing this, and @diehlpk for editing it.

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://joss.theoj.org/papers/10.21105/joss.02403/status.svg)](https://doi.org/10.21105/joss.02403)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02403">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02403/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02403/status.svg
   :target: https://doi.org/10.21105/joss.02403

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

openjournals / joss-reviews