[REVIEW]: PhaseFieldX: An Open-Source Framework for Advanced Phase-Field Simulations

[editorialbot]

Submitting author: @CastillonMiguel (Miguel Castillón de Miguel)
Repository: https://github.com/CastillonMiguel/phasefieldx
Branch with paper.md (empty if default branch):
Version: v0.0.2
Editor: @zhubonan
Reviewers: @finsberg, @IgorBaratta
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/7111b621625200b3d2c4b199ea9568c0/status.svg)](https://joss.theoj.org/papers/7111b621625200b3d2c4b199ea9568c0)

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

@finsberg & @IgorBaratta, 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 @zhubonan 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 @finsberg

📝 Checklist for @IgorBaratta

[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]

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

✅ OK DOIs

- 10.5281/zenodo.10447666 is OK
- 10.1145/3524456 is OK
- 10.21105/joss.03982 is OK
- 10.1145/2566630 is OK
- 10.1016/j.cma.2010.04.011 is OK
- 10.1016/j.jmps.2009.04.011 is OK
- 10.1007/s00466-014-1109-y is OK
- 10.1016/j.cma.2019.112731 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.15 s (862.1 files/s, 74807.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          72           1772           3521           3230
reStructuredText                36            431            384            347
CSV                              3              2              0            189
GLSL                             4            134            477            156
XML                              6              0              0            150
Markdown                         2             50              0            127
TeX                              1              9              2             86
YAML                             2              3              0             47
DOS Batch                        1              8              1             26
TOML                             1              2              0             20
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           129           2415           4392           4387
-------------------------------------------------------------------------------

Commit count by author:

    37	CastillonMiguel

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 393

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[zhubonan]

Hello @finsberg & @IgorBaratta 👏 , thanks for agreeing to review this submission. The review process is checklist based. Each of you will have a separate checklist that you should update when carrying out your review.

To get started, please 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. If you have any question, please let me know.

If you want to make comments and suggestions in the review process, you can open issues in the project repo and mention this review issue to keep things in track.

Please finish the initial review in two weeks time, if possible, but do let me know if you think more time is needed. Thanks in advance!

[finsberg]

Review checklist for @finsberg

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/CastillonMiguel/phasefieldx?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@CastillonMiguel) 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?

[zhubonan]

Hi @IgorBaratta, I am wondering if you have started reviewing the package. Please let me or the author know if you have any difficulties installing/testing/reviewing. Thanks in advance!

[IgorBaratta]

Hi @zhubonan, I've already started my review. I'll make some issues in their repo soon.

[zhubonan]

Great! Thanks for letting us know.

[finsberg]

@editorialbot generate pdf

[editorialbot]

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

[finsberg]

@editorialbot generate pdf

[editorialbot]

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

[zhubonan]

Hi @IgorBaratta, How is it going reviewing the package? It would be used to generate the checklist in order to track the progress.
You can do this by making a comment under this issue with

@editorialbot generate my checklist

Please let me or the author know if you have any difficulties installing/testing/reviewing. Thanks in advance!

[IgorBaratta]

Review checklist for @IgorBaratta

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/CastillonMiguel/phasefieldx?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@CastillonMiguel) 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?

[zhubonan]

Hi @finsberg, how is the reviewing process going? I can see there are still a few opened issues. Have they being addressed by @CastillonMiguel and wonder if there is anything that got stuck in the meantime.

[zhubonan]

Hi @IgorBaratta, I can see quite a few unchecked items in your checklist. If you have finished the review, could you please give some generate comments about the package and if changes that need to be done? Thanks a lot.

[finsberg]

Hi @zhubonan, thank for pinging me. I will get this done next week.

[finsberg]

@editorialbot generate pdf

[editorialbot]

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

[finsberg]

@zhubonan I have completed my review and can recommend PhaseFieldX for publication in JOSS. PhaseFieldX is very well documented software with a lot to good material to learn about phasefield modeling. The author has been very responsive and addressed the issues being raised. I would, however encourage the author to run a linter / formatter as part of the continous integration to be consistent about formatting and to remove unused code (such as unused imports). Also, I would encourage the author to use pull requests rather than committing and pushing directly to the main branch. However, in my opinion, these issues (as well as CastillonMiguel/phasefieldx#2) should not be blocking it from acceptance in JOSS.

[zhubonan]

Hi @IgorBaratta, happy new year! How is the review going? We are looking forward to hearing from you. Thanks a lot.

[zhubonan]

Hi @IgorBaratta are you still up to completing the review? Please let me know. Thanks!