[REVIEW]: Jobflow: Computational Workflows Made Simple

[editorialbot]

Submitting author: @Andrew-S-Rosen (Andrew S. Rosen)
Repository: https://github.com/materialsproject/jobflow
Branch with paper.md (empty if default branch): main
Version: v0.1.16
Editor: @arfon
Reviewers: @rashatwi, @jherasdo
Archive: 10.5281/zenodo.10466868

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/fe6c0ab0721b3271728a35e69d02c538"><img src="https://joss.theoj.org/papers/fe6c0ab0721b3271728a35e69d02c538/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/fe6c0ab0721b3271728a35e69d02c538/status.svg)](https://joss.theoj.org/papers/fe6c0ab0721b3271728a35e69d02c538)

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

@rashatwi & @jherasdo, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arfon 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 ✨

Checklists

📝 Checklist for @jherasdo

📝 Checklist for @rashatwi

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (980.2 files/s, 159490.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          49           2517           2711           6311
Markdown                        10            262              0            693
YAML                            13             61              6            355
Jupyter Notebook                 7              0           1993            225
TOML                             1             13              4            155
TeX                              1              0              0            130
reStructuredText                13             95            220            104
CSS                              1              9              3             58
SVG                              1              0              1             16
HTML                             1              0              0              3
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            98           2957           4938           8051
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2361

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.7720998 is OK
- 10.1063/1.4812323 is OK
- 10.1016/j.commatsci.2015.09.013 is OK
- 10.1038/s41467-021-23339-x is OK
- 10.1002/cpe.3505 is OK
- 10.1109/p3hpc51967.2020.00011 is OK
- 10.1109/works54523.2021.00012 is OK
- 10.5281/zenodo.5903364 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[arfon]

@rashatwi, @jherasdo – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/5995 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[jherasdo]

Review checklist for @jherasdo

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/materialsproject/jobflow?
• 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 (@Andrew-S-Rosen) 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?

[jherasdo]

The manuscript “Jobflow: Computational Workflows Made Simple” by Andrew S. Rosen and co-workers present the software application called Jobflow as an open source Python package for writing computational workflows tailored for high-throughput computing applications. This application abstracts a lot of complexities in the field by using a decorator-based approach which is able to transform pythonic functions and classes into more complex workflows. Furthermore, Jobflow also supports dynamic workflows and different ways to store the results both locally and cloud-based databases. Finally, this application can be coupled with FireWorks package to easily manage computational resources in typical HPC cluster architectures.

I have completed my first review of the code and the paper. The software looks very good. The paper is well written with a clear statement of need and state of the field. There are only few things to solve in the manuscript:

• There is a minor typo in line 80: A missing comma after e.g. (for consistency with the other “e.g.”, I would add it).

I encourage the authors to revise the references since there are some issues:

• It is a bit weird the use of “& others” since there is more than enough space to include all authors in each reference.
• For the Covalent software package reference, the authors provide the zenodo link but didn’t include any author or the format of citation suggested in the zenodo link.
• For the reference “Existing workflow systems. (2023).” The README file from the github has a different way of citing this work. Seems like should be cited through the following work https://dl.acm.org/doi/10.1145/3486897