[REVIEW]: funsies: A minimalist, distributed and dynamic workflow engine

[whedon]

Submitting author: @clavigne (Cyrille Lavigne)
Repository: https://github.com/aspuru-guzik-group/funsies
Version: 0.8.1
Editor: @diehlpk
Reviewer: @gflofst, @vijaysm
Archive: 10.5281/zenodo.5528107

⚠️ JOSS reduced service mode ⚠️

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:

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Markdown: [![status](https://joss.theoj.org/papers/e5c1e6bf39474021f548f0f0aefd9cb8/status.svg)](https://joss.theoj.org/papers/e5c1e6bf39474021f548f0f0aefd9cb8)

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

@camillescott & @gflofst & @vijaysm, 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 @diehlpk know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @gflofst

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@clavigne) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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 @vijaysm

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@clavigne) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

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.

⭐ 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:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. 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]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.29 s (270.4 files/s, 54489.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            10            639              0           6867
Python                          57           1304           1324           4879
Markdown                         6             75              0            380
TeX                              1             27              0            294
YAML                             1              0              0             40
INI                              2              3              0             29
Bourne Shell                     1             11             23             14
Mako                             1              0              0              8
-------------------------------------------------------------------------------
SUM:                            79           2059           1347          12511
-------------------------------------------------------------------------------


Statistical information for the repository 'faecd364a3f68a5fe5aff86a' was
gathered on 2021/05/11.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Cyrille Lavigne                317         23835          14394          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Cyrille Lavigne            7316           30.7          2.2               12.40

[whedon]

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

OK DOIs

- 10.1063/5.0006002 is OK
- 10.1063/5.0004835 is OK
- 10.1063/5.0007045 is OK
- 10.1063/5.0004997 is OK
- 10.1063/5.0005188 is OK
- 10.1063/1.5144261 is OK
- 10.1016/j.matt.2021.02.017 is OK
- 10.1145/1330017.1330019 is OK
- 10.1093/bioinformatics/bts480 is OK
- 10.12688/f1000research.29032.2 is OK
- 10.1145/2807591.2807623 is OK
- 10.1007/10968987_3 is OK
- 10.1007/978-3-319-63688-7_19 is OK

MISSING DOIs

- 10.26434/chemrxiv.13008500.v1 may be a valid DOI for title: Automatic discovery of chemical reactions using imposed activation
- 10.21276/ijre.2018.5.5.4 may be a valid DOI for title: MapReduce: Simplified Data Processing on Large Clusters

INVALID DOIs

- None

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[diehlpk]

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

OK DOIs

- 10.1063/5.0006002 is OK
- 10.1063/5.0004835 is OK
- 10.1063/5.0007045 is OK
- 10.1063/5.0004997 is OK
- 10.1063/5.0005188 is OK
- 10.1063/1.5144261 is OK
- 10.1016/j.matt.2021.02.017 is OK
- 10.1145/1330017.1330019 is OK
- 10.1093/bioinformatics/bts480 is OK
- 10.12688/f1000research.29032.2 is OK
- 10.1145/2807591.2807623 is OK
- 10.1007/10968987_3 is OK
- 10.1007/978-3-319-63688-7_19 is OK

MISSING DOIs

- 10.26434/chemrxiv.13008500.v1 may be a valid DOI for title: Automatic discovery of chemical reactions using imposed activation
- 10.21276/ijre.2018.5.5.4 may be a valid DOI for title: MapReduce: Simplified Data Processing on Large Clusters

INVALID DOIs

- None

@clavigne please add the missing DOIs to the paper and recompile the paper.

[clavigne]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[clavigne]

I added the DOI for the Chemrxiv pre-print. The other paper, (which is available here https://research.google/pubs/pub62/ ) does not have a DOI, as far as I can tell.

The ACM which compiles the USENIX proceedings doesn't have the OSDI '04 one https://dl.acm.org/conference/osdi/proceedings .

[diehlpk]

@whedon check references

[whedon]

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

OK DOIs

- 10.26434/chemrxiv.13008500.v2 is OK
- 10.1063/5.0006002 is OK
- 10.1063/5.0004835 is OK
- 10.1063/5.0007045 is OK
- 10.1063/5.0004997 is OK
- 10.1063/5.0005188 is OK
- 10.1063/1.5144261 is OK
- 10.1016/j.matt.2021.02.017 is OK
- 10.1145/1330017.1330019 is OK
- 10.1093/bioinformatics/bts480 is OK
- 10.12688/f1000research.29032.2 is OK
- 10.1145/2807591.2807623 is OK
- 10.1007/10968987_3 is OK
- 10.1007/978-3-319-63688-7_19 is OK

MISSING DOIs

- 10.21276/ijre.2018.5.5.4 may be a valid DOI for title: MapReduce: Simplified Data Processing on Large Clusters

INVALID DOIs

- None

[diehlpk]

@clavigne Can you please add this one missing DOI

MISSING DOIs

• 10.21276/ijre.2018.5.5.4 may be a valid DOI for title: MapReduce: Simplified Data Processing on Large Clusters

[clavigne]

I added the DOI for the Chemrxiv pre-print. The other paper, (which is available here https://research.google/pubs/pub62/ ) does not have a DOI, as far as I can tell.

The ACM which compiles the USENIX proceedings doesn't have the OSDI '04 one https://dl.acm.org/conference/osdi/proceedings .

@diehlpk as above, there are no DOI for this reference, as far as I know.

[diehlpk]

@whedon check references

[whedon]

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

OK DOIs

- 10.26434/chemrxiv.13008500.v2 is OK
- 10.1063/5.0006002 is OK
- 10.1063/5.0004835 is OK
- 10.1063/5.0007045 is OK
- 10.1063/5.0004997 is OK
- 10.1063/5.0005188 is OK
- 10.1063/1.5144261 is OK
- 10.1016/j.matt.2021.02.017 is OK
- 10.1145/1330017.1330019 is OK
- 10.1093/bioinformatics/bts480 is OK
- 10.12688/f1000research.29032.2 is OK
- 10.1145/2807591.2807623 is OK
- 10.1007/10968987_3 is OK
- 10.1007/978-3-319-63688-7_19 is OK

MISSING DOIs

- 10.21276/ijre.2018.5.5.4 may be a valid DOI for title: MapReduce: Simplified Data Processing on Large Clusters

INVALID DOIs

- None

[diehlpk]

@clavigne

MISSING DOIs

• 10.21276/ijre.2018.5.5.4 may be a valid DOI for title: MapReduce: Simplified Data Processing on Large Clusters

@whedon still complains about this missing DOI. Can you have a look?

[whedon]

👋 @gflofst, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @camillescott, please update us on how your review is going (this is an automated reminder).

[gflofst]

added issue for making community guidelines more apparent. Continuing other testing.

[gflofst]

Everything works for me. The last bit of testing on Windows getting an up to date Redis working is going to take time. As it is the last bit, and everything else is good, I am ok signing off on it for now and I'll raise an issue later if it isn't working. Windows is a marginal platform for this field, but it is what I have for my desktop machine for testing.

[diehlpk]

@camillescott How is your review going?

[diehlpk]

@camillescott How is your review going?

[diehlpk]

@whedon remind @camillescott in one week

[whedon]

Reminder set for @camillescott in one week

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2611

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2611, 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]

@gflofst, @vijaysm thanks again for your review.

[danielskatz]

@clavigne - I've suggested some small changes in aspuru-guzik-group/funsies#5
(Note that removing the abstracts simply cleans up the XML file that we submit to Crossref - it has no effect on generated paper).

Let me know when you've merged these changes, and we can proceed to the final publishing step.

Also, and just FYI, this work is interesting to read in the context of the Parsl project to which I contribute.

[danielskatz]

👋 @clavigne - note that this is basically ready to proceed, once you merge the PR...

[clavigne]

@danielskatz @diehlpk Thanks a lot for your help! I merged in the changes. I think the paper is ready for publication.

[clavigne]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[clavigne]

@whedon accept deposit=true

[whedon]

I'm sorry @clavigne, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

[danielskatz]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.26434/chemrxiv.13008500.v2 is OK
- 10.1063/5.0006002 is OK
- 10.1063/5.0004835 is OK
- 10.1063/5.0007045 is OK
- 10.1063/5.0004997 is OK
- 10.1063/5.0005188 is OK
- 10.1063/1.5144261 is OK
- 10.1016/j.matt.2021.02.017 is OK
- 10.1145/1330017.1330019 is OK
- 10.1093/bioinformatics/bts480 is OK
- 10.12688/f1000research.29032.2 is OK
- 10.1145/2807591.2807623 is OK
- 10.1007/10968987_3 is OK
- 10.1007/978-3-319-63688-7_19 is OK

MISSING DOIs

- 10.21276/ijre.2018.5.5.4 may be a valid DOI for title: MapReduce: Simplified Data Processing on Large Clusters

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2640

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2640, 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]

@clavigne - sorry, there's one more thing I missed initially and then just caught: aspuru-guzik-group/funsies#6

[clavigne]

@danielskatz no need to apologize for making the paper better :D Thanks again!

[danielskatz]

@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:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03274 joss-papers#2641
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03274
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Note that at least, for me, the DOI is not yet resolving, so I'll keep this open until it does, the close the issue.

[danielskatz]

Congratulations to @clavigne (Cyrille Lavigne) and co-author!!

And thanks to @gflofst and @vijaysm for reviewing, and @diehlpk for editing!
We couldn't do this without you!

[arfon]

DOI is resolving now.

[whedon]

🎉🎉🎉 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](https://joss.theoj.org/papers/10.21105/joss.03274/status.svg)](https://doi.org/10.21105/joss.03274)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03274">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03274/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03274/status.svg
   :target: https://doi.org/10.21105/joss.03274

This is how it will look in your documentation:

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[danielskatz]

The DOI now resolves, so we're done!!