Joss-reviews: [REVIEW]: Singularity Compose: Orchestration for Singularity Instances

[whedon]

Submitting author: @vsoch (Vanessa Sochat)
Repository: https://github.com/singularityhub/singularity-compose
Version: 0.0.16
Editor: @gkthiruvathukal
Reviewer: @daissi, @cole-brokamp
Archive: 10.5281/zenodo.3376793

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/1fc2593b11b5e18df12efb59ed8757a0/status.svg)](http://joss.theoj.org/papers/1fc2593b11b5e18df12efb59ed8757a0)

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

@daissi, 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 @gkthiruvathukal know.

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

Review checklist for @daissi

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: 0.0.16
• [x] Authorship: Has the submitting author (@vsoch) 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

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] 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)?

Review checklist for @cole-brokamp

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: 0.0.16
• [x] Authorship: Has the submitting author (@vsoch) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

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

:star: Important :star:

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:

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

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

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[vsoch]

Thanks whedon! The content of the paper looks good, but there are "nd-(a-c)" that likely I can fix by adding a date.

[vsoch]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[cole-brokamp]

@gkthiruvathukal -- should I be using this issue to review in also? i think @whedon forgot to add me? 🤷‍♂

[gkthiruvathukal]

@cole-brokamp Hmm, I thought I assigned you as a reviewer but you are not showing up on the list of reviewers (and therefore don't have a checklist). I am not sure why you're not showing up. I am going to see if someone from @openjournals/joss-eics can add you.

In the meantime, you can go ahead and list any issues here as I definitely want you involved in this review.

[kyleniemeyer]

Hi @cole-brokamp, I added you as a reviewer manually, including your reviewer checklist.

cc @gkthiruvathukal

[gkthiruvathukal]

Thanks, @kyleniemeyer!

[gkthiruvathukal]

@daissi, @cole-brokamp: Just nudging this a bit to get a progress update on your review.

[cole-brokamp]

working on it now, should be done today!

[cole-brokamp]

FYI... @vsoch is currently helping me through some of my own issues with running the example (totally my own fault!) over here: https://github.com/singularityhub/singularity-compose/issues/22

...I'll report back soon

[vsoch]

Totally not his fault! Singularity changes so fast that nobody can really keep up.

[gkthiruvathukal]

Thanks, @cole-brokamp and all. Just wanted to get an idea of where we stand.

[cole-brokamp]

I completed my review and have checked off everything on my reviewer checklist. @vsoch has done an outstanding job on this one, as usual! :clap:

[gkthiruvathukal]

@cole-brokamp and @daissi, Thanks for the help in reviewing this submission.

@vsoch, I am ready to move toward acceptance. Please do the following:

• [ ] Make a tagged release of your software, and list the version tag of the archived version here.
• [ ] Archive the reviewed software in Zenodo
• [ ] Check the Zenodo deposit 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.
• [ ] List the Zenodo DOI of the archived version here.

[vsoch]

On it!

[vsoch]

• [x] The tagged release is for version 0.0.16, available here
• [x] The archive on Zenodo is here
• [x] For metadata, I made sure my full name was used, affiliation, orcid id, the title corresponds with the name of the paper, and the release is 0.0.16
• [x] The zenodo DOI (along with other metadata) is provided below!

Vanessa Sochat. (2019, August 25). Singularity Compose: Orchestration for Singularity Instances (Version 0.0.16). Zenodo. http://doi.org/10.5281/zenodo.3376793

I updated the version in the first comment here too.

[gkthiruvathukal]

@whedon set 0.0.16 as release

[gkthiruvathukal]

@whedon set 10.5281/zenodo.3376793 as archive

[whedon]

OK. 10.5281/zenodo.3376793 is the archive.

[gkthiruvathukal]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to accept the paper and deposit with Crossref
@whedon accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

[gkthiruvathukal]

@whedon set 0.0.16 as version

[whedon]

OK. 0.0.16 is the version.

[gkthiruvathukal]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• None

MISSING DOIs

• https://doi.org/10.1007/978-1-4842-3936-0_6 may be missing for title: Docker Compose

INVALID DOIs

• journal.pone.0177459 is INVALID
  ```

[gkthiruvathukal]

Hi @vsoch Can you take a look at the invalid DOIs in the references? I think the problem is that you don't have the full DOI: 10.1371/journal.pone.0177459

[vsoch]

Sure thing.

[vsoch]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1578 with the following error:

Error reading bibliography ./paper.bib (line 60, column 3):
unexpected "d"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[vsoch]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[vsoch]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• https://doi.org/10.1371/journal.pone.0177459 is OK

MISSING DOIs

• https://doi.org/10.1007/978-1-4842-3936-0_6 may be missing for title: Docker Compose

INVALID DOIs

• None
  ```

[vsoch]

The Docker Compose entry shouldn't have a DOI, it's for a software page (so I think safe to ignore).

[gkthiruvathukal]

@vsoch Thanks for your follow up. I'm ready to move forward with accepting your submission.

@openjournals/joss-editors I recommend acceptance, pending any additional input you may have.

[kthyng]

@gkthiruvathukal You want to use @openjournals/joss-eics here!

[kyleniemeyer]

Hi @vsoch, just a few edits needed on the paper:

• Could you add more-complete affiliation info?
• For the "Running services — singularity container 3.2 documentation." reference, I think you can add "Sylabs Inc" as the author
• For the Kurtzer reference, could you strip the "https://doi.org/" from the DOI in the bib file? Our template only expects the DOI itself

[vsoch]

Could you clarify where you would like the affiliation info? I have it in the paper and zenodo record.

For the second point, I'm happy to do this, but for historical correctness I need to point out that the majority of content for that page was copy pasted verbatim from https://github.com/singularityware/singularityware.github.io/blob/master/pages/docs/user-docs/docs-instances.md, which was written well before the existence of Sylabs, by community members too.

[vsoch]

Changes made - I chose "Singularity contributors" to the authors to be more correct, and stripped the DOI. I will wait for feedback about the affiliation.

[vsoch]

I changed "Stanford University" to "Stanford University Research Computing Center" in case that is what you are wanting.

[kyleniemeyer]

@vsoch For the affiliation, I just want more-complete info, like what you'd see on a typical article: department, institution, city, state, country (or similar).

For that reference, the choice of author is fine, I just wanted someone listed in the author field.

[kyleniemeyer]

@vsoch (for the affiliation field in the paper)

[vsoch]

okay just added a bunch of Stanfords to it :)

[vsoch]

Just a comment - the example paper only has the university title for the affiliation, https://joss.readthedocs.io/en/latest/submitting.html?highlight=affiliation#example-paper-and-bibliography which is what I've done for the last (maybe 6?) papers. If the requirement is to have these extraneous fields, it should be clearly stated... somewhere, and then the criteria checked consistently across reviewers / editors.

[kyleniemeyer]

@vsoch thanks. We aren't very consistent about this, and in fact I may be the only one who asks for this at the final checks stage.

[kyleniemeyer]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[vsoch]

I appreciate the detail! I did a PR to the docs -> https://github.com/openjournals/joss/pull/598 but I'm not sure if Travis isn't working or if the changes to the text triggered the error.

[kyleniemeyer]

Sorry, one final thing- could you merge this: https://github.com/singularityhub/singularity-compose/pull/23

[vsoch]

Yes! Apologies for the delay, was doing some d3 stuffs.

[kyleniemeyer]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/929

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/929, 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]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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/930
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01578
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...

[kyleniemeyer]

Hey @arfon, for some reason the PDF isn't showing up at https://joss.theoj.org/papers/10.21105/joss.01578, even though the paper build fine in the PR. Any ideas?

[kyleniemeyer]

@arfon nvm... it just showed up. 🤦‍♂

[kyleniemeyer]

Congrats @vsoch on your article's publication in JOSS! Many thanks to @daissi and @cole-brokamp for reviewing, and @gkthiruvathukal for editing.

[whedon]

: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.01578/status.svg)](https://doi.org/10.21105/joss.01578)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01578">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01578/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01578/status.svg
   :target: https://doi.org/10.21105/joss.01578

This is how it will look in your documentation:

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[vsoch]

Thanks everyone! I'm really grateful for your help. If I can ever be of help, please poke away!

[gkthiruvathukal]

Thanks, @vsoch. We always can use help with reviews, especially in systems areas. Congratulations on reaching the accept state!