[REVIEW]: Curifactory: A research experiment manager

[editorialbot]

Submitting author: @WildfireXIII (Nathan Martindale)
Repository: https://github.com/ORNL/curifactory
Branch with paper.md (empty if default branch):
Version: v0.16.1
Editor: @kellyrowland
Reviewers: @abhishektiwari, @deniederhut
Archive: 10.5281/zenodo.10035496

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Checklists

📝 Checklist for @abhishektiwari

📝 Checklist for @deniederhut

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Software report:

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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1409

[editorialbot]

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

OK DOIs

- 10.25080/majora-212e5952-01b is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[abhishektiwari]

Review checklist for @abhishektiwari

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 https://github.com/ORNL/curifactory?
• 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 (@WildfireXIII) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[abhishektiwari]

@WildfireXIII A few questions/improvements to meet JOSS guidelines

Contribution and authorship:

• I was unable to see code contributions of Jason Hite for this software. Can you please provide more context on Jason Hite contributions for this Software and paper?

Community guidelines:

• I was also unable to find explicitly stated community guidelines for anyone wishing to contribute to the software, raise issues, or seek support. I assume people for raising issue or seeking support people can raise Github issue.

Installation instructions:

• It will be worth calling out the dependencies (Python, although mentioned as badge on repository) and prerequisite (Conda, Pip, Docker, etc). Also, unclear hardware and OS requirements for someone using in a lab setting.

State of the field:

• How Curifactory compares with generic DAG/workflow frameworks like Apache Airflow and Luigi? Paper did cover some tools like Kedro and Tango with similar goals which is great.

Quality of writing:
Some minor corrections,

“reusability” not “reusablility”

“This is often a result of” not “This often is a result of”

This leads to the next core concept of Curifactory, which are "parameters”. not This leads to the next core concept of Curifactory, which are "parameters."

Lastly, a suggestion for future versions of curifactory,

• Consider providing interface to run DAG validation tests (curifactory.dag.tests()) so user can check if their DAGs fulfill a list of basic criteria like no import errors, etc.

[deniederhut]

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[deniederhut]

Review checklist for @deniederhut

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 https://github.com/ORNL/curifactory?
• 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 (@WildfireXIII) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[deniederhut]

Okay I've got some issues opened regarding some of the functionality in the getting started guide:

• Lazy values are not shown if they get cached across trials ORNL/curifactory#78
• Curifactory assumes that it is being run inside a git repository ORNL/curifactory#79
• Curifactory logger might be eating my logging settings? ORNL/curifactory#80

@kellyrowland as Nathan mentioned in the other ticket, a paper about this software was published at SciPy. Will that be a problem?

[WarmCyan]

@editorialbot generate pdf

[editorialbot]

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

[WarmCyan]

@abhishektiwari thanks for your review!

Contribution and authorship:

I was unable to see code contributions of Jason Hite for this software. Can you please provide more context on Jason Hite contributions for this Software and paper?

Jason's contributions have largely been internal, he has been invaluable throughout Curifactory's development in discussing/proposing features and ideas, making implementation suggestions, testing the tool, and code review.

Community guidelines:

I was also unable to find explicitly stated community guidelines for anyone wishing to contribute to the software, raise issues, or seek support. I assume people for raising issue or seeking support people can raise Github issue.

Ahh yeah I forgot about that, I added a CONTRIBUTING.md to the project root

Installation instructions:

It will be worth calling out the dependencies (Python, although mentioned as badge on repository) and prerequisite (Conda, Pip, Docker, etc). Also, unclear hardware and OS requirements for someone using in a lab setting.

I added a requirements section to the README.md

State of the field:

How Curifactory compares with generic DAG/workflow frameworks like Apache Airflow and Luigi? Paper did cover some tools like Kedro and Tango with similar goals which is great.

Good point, we actually looked into Luigi a bit back in the beginning, I added a few sentences in the Statement of Need section comparing it to that.

Quality of writing: Some minor corrections,

“reusability” not “reusablility”

“This is often a result of” not “This often is a result of”

This leads to the next core concept of Curifactory, which are "parameters”. not This leads to the next core concept of Curifactory, which are "parameters."

I updated the paper with these corrections.

Lastly, a suggestion for future versions of curifactory,

Consider providing interface to run DAG validation tests (curifactory.dag.tests()) so user can check if their DAGs fulfill a list of basic criteria like no import errors, etc.

Yeah that's a really good idea, informally you can sort of already do this to some degree: running experiment [...] --map executes just the mapping portion of the DAG code, so trivial issues like syntax (outside of the stages), imports, and incorrect artifact names would be caught here, but I think it would be good to make a "verification" step be more explicit and expand it to check for more basic issues. I've created a feature issue for it (ORNL/curifactory#81)

[abhishektiwari]

Thanks @WildfireXIII for making those revisions. Updated my checklist.

[deniederhut]

@WildfireXIII bit of a meta-question for you -- there are a few things in the curifactory API design that feel unexpected to me. I'm not sure any of them are actually bugs, they could all just be my mental model not matching reality.

What's the best way to give you that feedback? The issue template feels very focused on actual bugs so I've felt a bit bad about opening "I don't understand why it works this way" tickets there.

[WarmCyan]

@deniederhut no worries, feel free to still just open them as issues, for now I use issues pretty informally as my brainstorming, todo list, and design concept ideas I need to discuss with others, so you're welcome to just delete the issue template text and put whatever for the purposes of this review

[WarmCyan]

@kellyrowland as Nathan mentioned in the other ticket, a paper about this software was published at SciPy. Will that be a problem?

Just so it's here, I'll mention what I put in my message to the editors on the submission to clarify our intent, the paper we submitted to SciPy was meant more as a discussion of the "theory", a set of design aspects that can be used to compare/analyze experiment workflow tools (we did go on to spend a couple pages covering how Curifactory meets those), while this submission is meant to focus just on the Curifactory package itself and to get more of a formal external review of the tool. (It's also worth noting we've updated Curifactory pretty substantially since our SciPy work)

[kellyrowland]

I think this is okay based on the separation of the theory versus the software package itself, but I'll ask @danielskatz to weigh in here.

[deniederhut]

Thanks for the updates @WildfireXIII ! Here's what I've got after taking a second look:

• Rendering of SciPy title in references section of paper ORNL/curifactory#87
• manager.generate_report fails in CLI mode ORNL/curifactory#88
• Default artifact manager in procedure generates empty report ORNL/curifactory#89
• Question about Stage API design ORNL/curifactory#90
• Why is pytables in the requirements file? ORNL/curifactory#91
• Two failing tests in test_experiment ORNL/curifactory#92

[stewartsl]

@editorialbot generate pdf

[editorialbot]

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

[kellyrowland]

thanks for all of the work here, everyone. @deniederhut just checking in if you're able to take a look at this again with the latest updates.

[WarmCyan]

@kellyrowland a new release has been created (v0.16.1), and I've put it on zenodo: https://zenodo.org/records/10035496 (DOI: 10.5281/zenodo.10035496)

@deniederhut and @abhishektiwari thanks so much for the reviews! I appreciate your all's time!

[kellyrowland]

@editorialbot set 10.5281/zenodo.10035496 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10035496

[kellyrowland]

@editorialbot set v0.16.1 as version

[editorialbot]

Done! version is now v0.16.1

[kellyrowland]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.25080/majora-212e5952-01b is OK

MISSING DOIs

- None

INVALID DOIs

- None

[kellyrowland]

@editorialbot generate pdf

[editorialbot]

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

[kellyrowland]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.25080/majora-212e5952-01b is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4723, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@WildfireXIII - I'm the track editor who will handle the rest of the process for your submission. I've suggested some minor changes in ORNL/curifactory#112 (adding the country to the affiliation, fixing capitalization to match JOSS's style, removing an extra period in a title). Please merge this, or let me know what you disagree with, then we can proceed to acceptance and publication.

[WarmCyan]

@danielskatz great, thanks! I merged your changes

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.25080/majora-212e5952-01b is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4726, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Martindale
  given-names: Nathan
  orcid: "https://orcid.org/0000-0002-5036-5433"
- family-names: Stewart
  given-names: Scott L.
  orcid: "https://orcid.org/0000-0003-4320-5818"
- family-names: Hite
  given-names: Jason
  orcid: "https://orcid.org/0000-0001-8931-5815"
- family-names: Adams
  given-names: Mark B.
  orcid: "https://orcid.org/0000-0002-5414-2800"
contact:
- family-names: Martindale
  given-names: Nathan
  orcid: "https://orcid.org/0000-0002-5036-5433"
doi: 10.5281/zenodo.10035496
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Martindale
    given-names: Nathan
    orcid: "https://orcid.org/0000-0002-5036-5433"
  - family-names: Stewart
    given-names: Scott L.
    orcid: "https://orcid.org/0000-0003-4320-5818"
  - family-names: Hite
    given-names: Jason
    orcid: "https://orcid.org/0000-0001-8931-5815"
  - family-names: Adams
    given-names: Mark B.
    orcid: "https://orcid.org/0000-0002-5414-2800"
  date-published: 2023-10-25
  doi: 10.21105/joss.05793
  issn: 2475-9066
  issue: 90
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5793
  title: "Curifactory: A research experiment manager"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05793"
  volume: 8
title: "Curifactory: A research experiment manager"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

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[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.05793 joss-papers#4727
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05793
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]

Congratulations to @WildfireXIII (Nathan Martindale) and co-authors on your publication!!

And thanks to @abhishektiwari and @deniederhut for reviewing, and to @kellyrowland for editing!
JOSS depends on volunteers and we couldn't be successful without you

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