[REVIEW]: f3dasm: Framework for Data-Driven Design and Analysis of Structures and Materials

[editorialbot]

Submitting author: !--author-handle-->@mpvanderschelling<!--end-author-handle-- (Martin van der Schelling) Repository: https://github.com/bessagroup/f3dasm Branch with paper.md (empty if default branch): Version: v1.5.3 Editor: !--editor-->@RMeli<!--end-editor-- Reviewers: @AntObi, @idocx Archive: 10.5281/zenodo.13227915

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b0a25f75a32ae95a0a75bf3118952a5d"><img src="https://joss.theoj.org/papers/b0a25f75a32ae95a0a75bf3118952a5d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b0a25f75a32ae95a0a75bf3118952a5d/status.svg)](https://joss.theoj.org/papers/b0a25f75a32ae95a0a75bf3118952a5d)

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

@AntObi & @idocx, 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 @RMeli 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 @AntObi

📝 Checklist for @idocx

[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 1.90  T=0.15 s (862.2 files/s, 129719.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          79           3486           5138           8357
Markdown                         9            220              0            588
YAML                            15             32             25            543
reStructuredText                18            198            201            360
make                             2             37              5            175
DOS Batch                        1             23              1            166
CSS                              2             26             40             78
TeX                              1              5              0             69
TOML                             1              2              0             16
Bourne Shell                     1             16             35             13
CSV                              3              0              0              5
-------------------------------------------------------------------------------
SUM:                           132           4045           5445          10370
-------------------------------------------------------------------------------

Commit count by author:

   816  Martin van der Schelling
     6  Guillaume Broggi
     1  llguo95

[editorialbot]

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

OK DOIs

- 10.1016/j.cma.2017.03.037 is OK
- 10.21105/joss.04364 is OK
- 10.21105/joss.04719 is OK
- 10.21105/joss.02338 is OK
- 10.21105/joss.05594 is OK

MISSING DOIs

- No DOI given, and none found for title: Optuna: A next-generation hyperparameter optimizat...

INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 651

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[RMeli]

@editorialbot remind @idocx in 2 weeks

[editorialbot]

Reminder set for @idocx in 2 weeks

[RMeli]

@editorialbot remind @AntObi in 2 weeks

[editorialbot]

Reminder set for @AntObi in 2 weeks

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[AntObi]

Review checklist for @AntObi

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (CI) 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

• [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 https://github.com/bessagroup/f3dasm?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@mpvanderschelling) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[editorialbot]

:wave: @idocx, please update us on how your review is going (this is an automated reminder).

[editorialbot]

:wave: @AntObi, please update us on how your review is going (this is an automated reminder).

[idocx]

Review checklist for @idocx

Conflict of interest

• [x] 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

• [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 https://github.com/bessagroup/f3dasm?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@mpvanderschelling) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[RMeli]

Thank you @AntObi and @idocx for starting the review!

[RMeli]

👋 @mpvanderschelling, @AntObi, and @idocx

I hope you are all doing well. Could you please all provide a short few sentences/bullet points on how things are going with this review?

Thanks and keep up the great work!

[mpvanderschelling]

Hey everyone! First of all thanks for taking up the review of my work! I'll be happy to resolve any feedback you might have. I'll be traveling for a conference until the 31st of July, but after that I'm available!

[idocx]

Hey Martin! Thank you for the great work!

I will try to get the review ready by the end of this week. So far it looks good except for the annoying numpy 2.0 issue. The Pypi registry has not been updated to numpy < 2.0 to avoid autograd package failure. (https://github.com/HIPS/autograd/issues/622#issue-2371900518)

Do you have plan to update the pypi registry some time? I notice that you have updated the version on the github. Thanks!

[mpvanderschelling]

@idocx ; I have updated the PyPI registry to version 1.5.2; which fixes the numpy 2.0 issue

[AntObi]

Hey Martin!

This is some great work! I've been working through my review and should hopefully have it complete within the next couple of days!

[idocx]

Hey Martin @mpvanderschelling,

Thank you for sharing the great work! I have gone through the package and had several questions/comments regarding the package. Since my background is mostly on high-throughput screening and experimentation, my questions are mostly based on my understanding of how to apply this package to HT screening workflows.

• Documentation: In the tutorial doc part, all the tutorial pages go into the last section. Could you update it?

  

• Project structure: In your source code, the actual code is placed inside a _src folder. According to Python's naming convention, it means it is a private namespace. All the public functions are exported by making a new name. Since it seems harder to add/remove a function/class, I wonder why you decide to use this kind of project structure? I guess one reason is that this can make public APIs from different modules look neat. But it should be even better if you can classify the APIs inside the package directly.

• Non-vectorizable parameters: In material science, sometimes the parameters are not vectorizable. For example, if I would like to input a CIF structure to the VASP program and get some energy as the output, how I could do this? Or is this an unrealistic problem for the package?

• Data generator: Is there a way to link the data generator's parameters to the experiment data? Sometimes I may have different definitions of data generator and different parameters (e.g., different config for VASP during calculation). How can I record this kind of information and link them to the experiment data

• Database support: is there any plan for supporting database-backend data storage. We found this very useful if you would like to run a project across various computation resources. You don't have to copy the data folder everywhere to sync the data.

Thank you and look forward to knowing your thoughts!

Best, Yuxing

[mpvanderschelling]

Hey Yuxing @idocx,

Thank you for your feedback, I'll address each of your points individually

Documentation Yes, this is definitely a bug from my part (created a new issue here), and might be due to some header issues when generating the Sphinx Gallery. Will take a look at it!

Project structure The reason that I put all the source code of the Python package in a separate _src directory is precisely what you mentioned: since I put the actual implementations behind a private submodule, I can structure the public API separately [^1]. It indeed creates overhead when implementing new public functions/classes, but I have more control over the public API and notice earlier in the development process when I (accidentally) cause an API change when renaming methods.

Non-vectorizable parameters At the moment, this is not implemented yet but on the backlog. This behaviour is already implemented for large objects or array-like data, and makes it possible to store any output that is non-vectorizable to disk and store a reference link in the ExperimentData object. I am planning on implementing the same behaviour for the input parameters in the near future.

Data generator Yes, for that you will have to use the class approach of creating a custom DataGenerator. You can create any class and store object parameters (e.g., different config for VASP) via the self attribute. In your execute function, you can use those. Whenever you call the evaluate method on your ExperimentData object, you can determine which custom DataGenerator object you want to use on the experiments.

[^1]: Similar practices are shown for the numpy with the _core directory and jax source code

Database support Yes, there is the idea to support database access to the ExperimentData object, but this is not a priority at the moment. However, I have no experience with databases and Python, so if you have any suggestions or pointers for this, please let me know!

Best, Martin

[mpvanderschelling]

Hey everyone,

• @idocx ; I have resolved the Sphing Gallery proble with TOC headers issue
• @AntObi ; do you have an estimation when you are able to finish your review :)

[RMeli]

Thanks @mpvanderschelling for the update. @idocx and @AntObi thank you very much for your reviews. I see the checklists are now complete; are you happy with the latest changes by @mpvanderschelling? If you could quickly summarize your review status it would be fantastic.

[idocx]

Hi @RMeli and @mpvanderschelling, the author's response has resolved all my concerns. I agree to publish the software package to JOSS as it is.

For the database support, you can refer to pandas.DataFrame.to_sql if you would like to support SQL database. If you would like to use MongoDB, then you can directly call df.to_dict("record") to get the record you would like to save. One tricky thing I can imagine is to retrieve large result - you will have to link the local file to the database somehow. But it should be doable.

Thanks, Yuxing

[AntObi]

Hi @RMeli and @mpvanderschelling , this is some great work that has been produced! It's well documented, great coverage with unit tests and the integration of experiments with Hydra is a very great addition to the package.

I'm happy to accept the paper and package as is.

Yours truly, Anthony

[RMeli]

Thank you @AntObi and @idocx for completing your reviews. @mpvanderschelling I'll now start the final checks.

[RMeli]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• [x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
• [x] Check that the archive title, author list, version tag, and the license are correct
• [x] Set archive DOI with @editorialbot set <DOI here> as archive
• [x] Set version with @editorialbot set <version here> as version
• [x] Double check rendering of paper with @editorialbot generate pdf
• [x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• [x] Recommend acceptance with @editorialbot recommend-accept

[RMeli]

@editorialbot generate pdf

[RMeli]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.cma.2017.03.037 is OK
- 10.21105/joss.04364 is OK
- 10.21105/joss.04719 is OK
- 10.21105/joss.02338 is OK
- 10.21105/joss.05594 is OK

MISSING DOIs

- No DOI given, and none found for title: Optuna: A next-generation hyperparameter optimizat...

INVALID DOIs

- None

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[RMeli]

@mpvanderschelling can you please add the DOI for Optuna? I thin it should be https://doi.org/10.1145/3292500.333070

[mpvanderschelling]

Latest release: 1.5.3 Zenodo DOI: 10.5281/zenodo.13227916

[RMeli]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.cma.2017.03.037 is OK
- 10.21105/joss.04364 is OK
- 10.21105/joss.04719 is OK
- 10.21105/joss.02338 is OK
- 10.1145/3292500.3330701 is OK
- 10.21105/joss.05594 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[RMeli]

@editorialbot set 10.5281/zenodo.13227915 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.13227915

[RMeli]

@editorialbot set v1.5.3 as version

[editorialbot]

Done! version is now v1.5.3

[RMeli]

@editorialbot set 1.5.3 as version

[editorialbot]

Done! version is now 1.5.3

[RMeli]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[RMeli]

@mpvanderschelling I read the paper again and left a few very minor suggestions as a PR. Otherwise LGTM.

[mpvanderschelling]

Thank you! I have approved the minor suggestions and merged the PR with the main branch

[RMeli]

@editorialbot recommend-accept

Thank you @mpvanderschelling for the fast final fix. Based on the extensive comments from the reviewers (and my own assessment), I'm happy to recommend this paper for acceptance! The EiC will now perform the final checks. Thank you for engaging so well with the review process.

Thank you very much again @idocx and @AntObi for doing the hard work!

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1016/j.cma.2017.03.037 is OK
- 10.21105/joss.04364 is OK
- 10.21105/joss.04719 is OK
- 10.21105/joss.02338 is OK
- 10.1145/3292500.3330701 is OK
- 10.21105/joss.05594 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5758, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept