Hi All, Happy New Year!
@ascourtas Thanks for your updates.
@marshallmcdonnell would you please finish the checklist? Thanks for your time.

from joss-reviews.

Hi @marshallmcdonnell, would please generate your checklist at your convenience? Please let me know if you need any help. Thanks for your time.

from joss-reviews.

Review checklist for @marshallmcdonnell

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/MLMI2-CSSI/foundry?
• 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 (@blaiszik) 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?

from joss-reviews.

Hello @blaiszik and @duhd1993

I have started going over the code but still need more time to test it out and write up notes.
I'll try to update the checklist as I go.

Thanks

from joss-reviews.

from joss-reviews.

Overall, Foundry-ML seems like a great contribution to JOSS. I have left my review comments above.

For the source code, I've opened the following Issues:

• MLMI2-CSSI/foundry#372
• MLMI2-CSSI/foundry#373
• MLMI2-CSSI/foundry#375
• MLMI2-CSSI/foundry#376

And opened a small PR:

• MLMI2-CSSI/foundry#374

I hope these are helpful!

That is currently all I have.
Happy to help in any way I can, just let me know.
And thanks for your patience!

from joss-reviews.

@duhd1993, @marshallmcdonnell please can you resume your review and give us an update? Thanks

from joss-reviews.

Hello @Fei-Tao ! We have addressed all of the opened issues:

• MLMI2-CSSI/foundry#372
• MLMI2-CSSI/foundry#373
• MLMI2-CSSI/foundry#375
• MLMI2-CSSI/foundry#376

Please let us know how we can assist with next steps. I will continue to go through the review comments in this thread and see if there's anything we missed.

from joss-reviews.

Thank you @ascourtas (and others) for working through the issues I opened.
@Fei-Tao I completed my checklist and happy with the current state of the manuscript / repo.

Let me know if there is any further action I need to take.

Otherwise, great work and thanks for letting me be part of the review!

from joss-reviews.

@marshallmcdonnell great. Thanks for your time and help in improving this submission.

@ascourtas @blaiszik At this point could you make a new release of this software that includes the changes resulting from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive. For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

from joss-reviews.

@ascourtas It seems there are several papers' DOIs are not correct. Can you verify it?

from joss-reviews.

@ascourtas thanks for your quick response. By the way, after you correct all missing DOIs, please follow the previous thread to make a new release and archive the software.

from joss-reviews.

@ascourtas the joss branch would be good.

from joss-reviews.

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

OK DOIs

- 10.1557/mrc.2019.118 is OK
- 10.1007/s11837-016-2001-3 is OK
- 10.1093/micmic/ozac043 is OK
- 10.1063/5.0066009 is OK
- 10.1126/science.abh3350 is OK
- 10.1021/acs.jctc.2c01058 is OK
- 10.1039/D2ME00137C is OK
- 10.1038/s41524-020-00406-3 is OK
- 10.3389/fphar.2020.565644 is OK
- 10.48550/arXiv.2102.09548 is OK
- 10.1039/C7SC02664A is OK
- 10.1038/s41524-019-0173-4 is OK
- 10.1145/3219104.3219127 is OK
- 10.1109/eScience.2015.68 is OK

MISSING DOIs

- Errored finding suggestions for "Strengthening and Democratizing the U.S. Artificia...", please try later

INVALID DOIs

- None

from joss-reviews.

@Fei-Tao Good evening!

1. I resolved all DOI and reference issues -- editorialbot has only one warning, but it's for an article that does not possess a DOI.
2. The most up-to-date code release can be found here: v0.7.3
3. The new archive of the code at the joss branch can be found here: 10.5281/zenodo.10494644

Please let us know if any other changes need to be made. Thank you!

from joss-reviews.

Hi @ascourtas, it seems there are still two errors associated with the citation. Can you fix them at your convenience? Thanks.

from joss-reviews.

Hi @ascourtas Thanks for your quick response. I have recommended to accept this submission.

Hi @openjournals/bcm-eics, the paper looks good to me now. Would you please take it from here?

from joss-reviews.

@blaiszik Congratulations on this JOSS publication !

Thanks for editing @Fei-Tao !!

And a special thanks to the reviewers: @duhd1993, @marshallmcdonnell !

from joss-reviews.

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

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (966.5 files/s, 172224.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                        25            730              0           1578
Python                           9            261            297            834
Jupyter Notebook                10              0           5392            567
TeX                              1             20              0            158
YAML                             4             16              3             89
JSON                             3              0              0             30
SVG                              4              0              0              4
-------------------------------------------------------------------------------
SUM:                            56           1027           5692           3260
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

from joss-reviews.

Wordcount for paper.md is 1335

from joss-reviews.

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

OK DOIs

- None

MISSING DOIs

- 10.1007/s11837-016-2001-3 may be a valid DOI for title: The materials data facility: data services to advance materials science research
- 10.1093/micmic/ozac043 may be a valid DOI for title: Benchmark tests of atom segmentation deep learning models with a consistent dataset
- 10.1126/science.abh3350 may be a valid DOI for title: A priori control of zeolite phase competition and intergrowth with high-throughput simulations
- 10.3389/fphar.2020.565644 may be a valid DOI for title: Molecular sets (MOSES): a benchmarking platform for molecular generation models
- 10.1039/c7sc02664a may be a valid DOI for title: MoleculeNet: a benchmark for molecular machine learning
- 10.1145/3219104.3219127 may be a valid DOI for title: Globus platform services for data publication
- 10.1145/3219104.3219127 may be a valid DOI for title: Globus platform services for data publication
- 10.1109/escience.2015.68 may be a valid DOI for title: Globus data publication as a service: Lowering barriers to reproducible science

INVALID DOIs

- None

from joss-reviews.

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

from joss-reviews.

Review checklist for @duhd1993

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/MLMI2-CSSI/foundry?
• 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 (@blaiszik) 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?

from joss-reviews.

Hi @duhd1993 and @marshallmcdonnell! Is there anything we can do to facilitate the review process for you? Let us know if you have any questions or need clarifications.

from joss-reviews.

Hi @duhd1993 @marshallmcdonnell, any updates on the review? Please let us know if you need any help. Thanks again for your time.

from joss-reviews.

Thank you @marshallmcdonnell! There are a series of examples in the examples folder that should run easily on Google Colab. If you run locally and don't want to install the Globus Connect personal endpoint just set the variable globus=False. We will go back and make this the default ASAP since it gets people up and running without additional installs or reliance on Colab.

https://github.com/MLMI2-CSSI/foundry/tree/main/examples

from joss-reviews.

Quick note:

For contributions:

Contribution and authorship: Has the submitting author (@blaiszik) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

I wanted to check on something.
I went to the contributors list for Foundry here.

I checked this against the author list.
There are contributors on the GitHub list not added as authors on this list:

• Steve Wangen: https://github.com/blue442
• Braeden Cullen: https://github.com/BraedenCu
• Nathaniel Martinez: https://github.com/nmartinez233
• Eric Blau (sp?): https://github.com/ericblau
• Sterling G. Baird: https://github.com/sgbaird
• Cora Schneck: https://github.com/cyschneck
• Nathan Pruyne: https://github.com/NathanPruyne
• Ryan Chard: https://github.com/ryanchard

There are also authors included in the author list that are not contributors. Yet, I'm not so worried about that.

My main concern is should the contributors to the source code listed above not be added to the author list?

from joss-reviews.

Quick note:

Functionality: Have the functional claims of the software been confirmed?
I'm hesitant to check this off since I was having trouble running the notebooks in Google Collab (mainly the DefectTrack).

I let it spin for 30 minutes on the result = f.run("jwei74_wisc/DefectTrack_in_situ_TEM_videos", {'images':imgs_original}) cell but finally gave up.

I can assume that these notebooks work since the output is saved and stored in the current main branch source code files.

Since the authors heavily rely on notebooks for the examples, have you considered using a tool like nbdev to run actual tests on these notebooks to ensure the software examples can be sustained with continuing development?

• https://github.com/fastai/nbdev

Disclaimer: I haven't used nbdev extensively so only suggesting this if it helps.

from joss-reviews.

I do feel this needs to be addressed in the paper:

State of the field: Do the authors describe how this software compares to other commonly-used packages?

I did not see comparisons of Foundry-ML to other such tools or frameworks.
The paper reads more to just explain Foundry-ML and what it interacts with (Globus services and Materials Data Facility)

I'd like to see a statement (just a few sentences even) to explain the other similar tools and how Foundry-ML might differ.

from joss-reviews.

For this:

Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

I see that GitHub Actions is used for CI testing. I also see that there are GitHub secrets used for what looks like Globus credentials to run the tests.

I did try to run the tests locally but have the following errors:

FAILED tests/test_foundry.py::test_download_globus - globus_sdk.exc.base.GlobusSDKUsageError: destination_endpoint is required
FAILED tests/test_foundry.py::test_globus_dataframe_load - globus_sdk.exc.base.GlobusSDKUsageError: destination_endpoint is required
FAILED tests/test_foundry.py::test_publish_with_https - assert False
FAILED tests/test_foundry.py::test_publish_with_globus - assert False

Yet it appears all of these tests are decorated with:

@pytest.mark.skipif(bool(is_gha), reason="Not run as part of GHA CI")

This is fine. But there is no documentation in the tests/README to explain how one would run these tests or that they will fail locally without a globus endpoint enabled (I assume).

Finally, since these tests require a third-party application (Globus), perhaps these should be move to "integration tests"? And leave the current tests as proper "unit tests"? That way they can be run separately.

Just a suggestion for new developers.

from joss-reviews.

For this:

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?

I am using the proofs from #5467 (comment) and these show that the citations are "broken" (i.e. (yearofopendata?) in the first paragraph of "Summary" on page 1, (Li67 et al., 2021; wei2021benchmark?), MIT (Schwalbe-Koda et al., 2021) ??, in "Usage" section on page 3

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@Fei-Tao can you pick this up again?

from joss-reviews.

@Kevin-Mattheus-Moerman sure. Thanks for your reminder.

from joss-reviews.

@duhd1993 would you please start your reviewing at your convenience?

@blaiszik can you address the issues opened by marshallmcdonnell.

from joss-reviews.

@Fei-Tao – I think both @duhd1993 and @blaiszik might need a bit of a nudge here as this review seems to have gone pretty stale.

from joss-reviews.

@arfon thanks arfon.
@duhd1993 can you start the review at your convenience?
@blaiszik can you address the issues opened by marshallmcdonnell? Please let me know if you need any help.

from joss-reviews.

@Kevin-Mattheus-Moerman Thanks for the heads-up. I'm working on it now.

from joss-reviews.

Foundry-ML provides a hub with ready-to-use research datasets from various sources. Combined to DLHub, it provides a simple click-to-run experience. I have run several examples on Colab. Overall, this can facilitate the ML for science community. I have some concerns

1. The API document is not comprehensive. https://ai-materials-and-chemistry.gitbook.io/foundry/advanced-usage/methods
2. Some references are broken in the pdf.
3. Can you add descriptions on how to run the unit tests properly?

FAILED test_foundry.py::test_publish_with_https - assert False
FAILED test_foundry.py::test_publish_with_globus - assert False

I got error due to authentication issues: Error 403 submitting dataset: You cannot access this service or organization.

4. I did install the globus client. But if it is not necessary, could you disable it by default so users can get started faster?
5. If there are alternative hubs for ML datasets for materials science, please provide a comparison. If not, I think it's worthwhile to compare against successful hubs from broader ML community, for instance, the huggingface.

from joss-reviews.

@Fei-Tao please check in here ~once a week (but at least one every 2 weeks), the reviewers need reminders here. It would be good to check in regularly and remind them.

from joss-reviews.

@blaiszik can you respond to the issues raised by the reviewer? ☝️

from joss-reviews.

@Kevin-Mattheus-Moerman Sure. Thanks for the reminder.

from joss-reviews.

Hi @blaiszik, can you address the issues raised by the reviewer? Since both reviewers have given their comments. If you can address their issues, we can move forward to the next step.

from joss-reviews.

@Fei-Tao Please check in once every 2 weeks if you can.

from joss-reviews.

@blaiszik please can you respond to the reviewer/editor queries in a timely manor, or otherwise let us know when you can provide an update? Thanks.

from joss-reviews.

@Kevin-Mattheus-Moerman sure. I will try my best. Thanks for the reminder.

from joss-reviews.

Yes, sorry we will address these ASAP.

from joss-reviews.

@blaiszik great. we are looking forward to your changes.

from joss-reviews.

Hello @Fei-Tao , the code changes have been released in v0.7.2 (with an additional release of v0.7.3 to complete the Zenodo integration).

The Zenodo archive has been created with the DOI 10.5281/zenodo.10480757 (associated with the latest release).

Please let me know if any updates or other content is required. Thanks!

EDIT: Actually a brief author naming discrepancy just came to my attention -- please stand by, fixing it now!
EDIT 2: Resolved author discrepancy

from joss-reviews.

@editorialbot check references

from joss-reviews.

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

OK DOIs

- None

MISSING DOIs

- 10.1007/s11837-016-2001-3 may be a valid DOI for title: The materials data facility: data services to advance materials science research
- 10.1093/micmic/ozac043 may be a valid DOI for title: Benchmark tests of atom segmentation deep learning models with a consistent dataset
- 10.1126/science.abh3350 may be a valid DOI for title: A priori control of zeolite phase competition and intergrowth with high-throughput simulations
- 10.3389/fphar.2020.565644 may be a valid DOI for title: Molecular sets (MOSES): a benchmarking platform for molecular generation models
- 10.1039/c7sc02664a may be a valid DOI for title: MoleculeNet: a benchmark for molecular machine learning
- 10.1145/3219104.3219127 may be a valid DOI for title: Globus platform services for data publication
- 10.1145/3219104.3219127 may be a valid DOI for title: Globus platform services for data publication
- 10.1109/escience.2015.68 may be a valid DOI for title: Globus data publication as a service: Lowering barriers to reproducible science

INVALID DOIs

- None

from joss-reviews.

Ah will do, thank you for the check

from joss-reviews.

@Fei-Tao quick question, do you want me to create an archive of the main branch of the software, or the joss branch (which contains the markdown paper submission)?

from joss-reviews.

@editorialbot check references

from joss-reviews.

@editorialbot generate pdf

from joss-reviews.

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

from joss-reviews.

@editorialbot set 10.5281/zenodo.10494644 as archive

from joss-reviews.

Done! archive is now 10.5281/zenodo.10494644

from joss-reviews.

@editorialbot recommend-accept

from joss-reviews.

Attempting dry run of processing paper acceptance...

from joss-reviews.

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

OK DOIs

- 10.1557/mrc.2019.118 is OK
- 10.1007/s11837-016-2001-3 is OK
- 10.1093/micmic/ozac043 is OK
- 10.1063/5.0066009 is OK
- 10.1126/science.abh3350 is OK
- 10.1021/acs.jctc.2c01058 is OK
- 10.1039/D2ME00137C is OK
- 10.1038/s41524-020-00406-3 is OK
- 10.3389/fphar.2020.565644 is OK
- 10.48550/arXiv.2102.09548 is OK
- 10.1039/C7SC02664A is OK
- 10.1038/s41524-019-0173-4 is OK
- 10.1145/3219104.3219127 is OK
- 10.1109/eScience.2015.68 is OK

MISSING DOIs

- None

INVALID DOIs

- None

from joss-reviews.

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

citation wei2021benchmark not found

citation yearofopendata not found

from joss-reviews.

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

IDREFS attribute rid references an unknown ID "ref-yearofopendata"
IDREFS attribute rid references an unknown ID "ref-wei2021benchmark"
IDREFS attribute rid references an unknown ID "figU00202"
IDREFS attribute rid references an unknown ID "figU00202"

from joss-reviews.

@Fei-Tao we have fixed the identified errors to the best of our knowledge -- all changes have been merged. I have updated the Zenodo archive, which can still be found at 10.5281/zenodo.10494644 (resolves to latest version).

Please let me know if anything else remains, thank you!

from joss-reviews.

@editorialbot recommend-accept

from joss-reviews.

Attempting dry run of processing paper acceptance...

from joss-reviews.

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

OK DOIs

- 10.1557/mrc.2019.118 is OK
- 10.1007/s11837-016-2001-3 is OK
- 10.1017/S1431927621008989 is OK
- 10.1093/micmic/ozac043 is OK
- 10.1063/5.0066009 is OK
- 10.1126/science.abh3350 is OK
- 10.1021/acs.jctc.2c01058 is OK
- 10.1039/D2ME00137C is OK
- 10.1038/s41524-020-00406-3 is OK
- 10.3389/fphar.2020.565644 is OK
- 10.48550/arXiv.2102.09548 is OK
- 10.1039/C7SC02664A is OK
- 10.1038/s41524-019-0173-4 is OK
- 10.1145/3219104.3219127 is OK
- 10.1109/eScience.2015.68 is OK

MISSING DOIs

- None

INVALID DOIs

- None

from joss-reviews.

👋 @openjournals/bcm-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#4931, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

from joss-reviews.

@Fei-Tao thanks for editing here. It looks like you called @editoralbot recommed-accept a bit prematurely. Please first call @editorialbot create post-review checklist and ensure all final steps are completed first. In addition:

• The version is not set here.
• Above, I see comments asking if the joss or main branch should be archived. The archived version should be for the tagged release and need not include paper files. It is about the software reviewed and the subsequent tagged-release for this. Therefore please check that the archived version, they may need to create a new one, reflects the correct/latest reviewed software.
• Once the tagged release version is created and archived you should check that the same version tag is used on ZENODO (it currently isn't).
• The authors should add state, city, and country, to their affiliations. In addition, they should spell out USA as United States of America.

from joss-reviews.

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

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

from joss-reviews.

@editorialbot check references

from joss-reviews.

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

OK DOIs

- 10.1557/mrc.2019.118 is OK
- 10.1007/s11837-016-2001-3 is OK
- 10.1017/S1431927621008989 is OK
- 10.1093/micmic/ozac043 is OK
- 10.1063/5.0066009 is OK
- 10.1126/science.abh3350 is OK
- 10.1021/acs.jctc.2c01058 is OK
- 10.1039/D2ME00137C is OK
- 10.1038/s41524-020-00406-3 is OK
- 10.3389/fphar.2020.565644 is OK
- 10.48550/arXiv.2102.09548 is OK
- 10.1039/C7SC02664A is OK
- 10.1038/s41524-019-0173-4 is OK
- 10.1145/3219104.3219127 is OK
- 10.1109/eScience.2015.68 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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@editorialbot generate pdf

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

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@Kevin-Mattheus-Moerman Thanks for letting me know the update on the review process.

@ascourtas sorry for the back-and-forth changes. 1. Could you make a new release of this software that includes the changes from this review? 2. Please rearchive the software in Zenodo/figshare/other service and update this thread with the DOI of the archive. 3. In addition, please spell out USA as United States of America as requested by EIC. Thanks for your time.

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@ascourtas in addition, please check the "Additional Author Tasks After Review is Complete" in the above thread. Thanks for your time.

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Hello @Fei-Tao ! Per your request, I have completed the following:

• updated the Zenodo archive to v0.7.4 with the latest code from main; it can still be found at the DOI 10.5281/zenodo.10494644 (resolves to latest)
• updated all author affiliations to include city, state, and unabbreviated country name in both paper.md and the Zenodo archive
• confirmed all author names and Orcid IDs
• confirmed the correct license is set in Zenodo
• confirmed the correct title is used in Zenodo

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@ascourtas great! Thanks for your prompt response.

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@editorialbot set 10.5281/zenodo.10494644 as archive

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Done! archive is now 10.5281/zenodo.10494644

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@editorialbot set v0.7.4 as version

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Done! version is now v0.7.4

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@editorialbot generate pdf

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

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.1557/mrc.2019.118 is OK
- 10.1007/s11837-016-2001-3 is OK
- 10.1017/S1431927621008989 is OK
- 10.1093/micmic/ozac043 is OK
- 10.1063/5.0066009 is OK
- 10.1126/science.abh3350 is OK
- 10.1021/acs.jctc.2c01058 is OK
- 10.1039/D2ME00137C is OK
- 10.1038/s41524-020-00406-3 is OK
- 10.3389/fphar.2020.565644 is OK
- 10.48550/arXiv.2102.09548 is OK
- 10.1039/C7SC02664A is OK
- 10.1038/s41524-019-0173-4 is OK
- 10.1145/3219104.3219127 is OK
- 10.1109/eScience.2015.68 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @openjournals/bcm-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#4940, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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@blaiszik @Fei-Tao all looks good now. We will now process this for acceptance. Thanks.

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@editorialbot accept

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

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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:

cff-version: "1.2.0"
authors:
- family-names: Schmidt
  given-names: KJ
  orcid: "https://orcid.org/0000-0002-9373-0058"
- family-names: Scourtas
  given-names: Aristana
  orcid: "https://orcid.org/0000-0002-3917-605X"
- family-names: Ward
  given-names: Logan
  orcid: "https://orcid.org/0000-0002-1323-5939"
- family-names: Wangen
  given-names: Steve
- family-names: Schwarting
  given-names: Marcus
  orcid: "https://orcid.org/0000-0001-6817-7265"
- family-names: Darling
  given-names: Isaac
- family-names: Truelove
  given-names: Ethan
- family-names: Ambadkar
  given-names: Aadit
- family-names: Bose
  given-names: Ribhav
- family-names: Katok
  given-names: Zoa
- family-names: Wei
  given-names: Jingrui
- family-names: Li
  given-names: Xiangguo
- family-names: Jacobs
  given-names: Ryan
  orcid: "https://orcid.org/0000-0003-2229-6730"
- family-names: Schultz
  given-names: Lane
- family-names: Kim
  given-names: Doyeon
- family-names: Ferris
  given-names: Michael
  orcid: "https://orcid.org/0000-0002-7652-6776"
- family-names: Voyles
  given-names: Paul M.
  orcid: "https://orcid.org/0000-0001-9438-4284"
- family-names: Morgan
  given-names: Dane
  orcid: "https://orcid.org/0000-0002-4911-0046"
- family-names: Foster
  given-names: Ian
  orcid: "https://orcid.org/0000-0003-2129-5269"
- family-names: Blaiszik
  given-names: Ben
  orcid: "https://orcid.org/0000-0002-5326-4902"
doi: 10.5281/zenodo.10494644
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Schmidt
    given-names: KJ
    orcid: "https://orcid.org/0000-0002-9373-0058"
  - family-names: Scourtas
    given-names: Aristana
    orcid: "https://orcid.org/0000-0002-3917-605X"
  - family-names: Ward
    given-names: Logan
    orcid: "https://orcid.org/0000-0002-1323-5939"
  - family-names: Wangen
    given-names: Steve
  - family-names: Schwarting
    given-names: Marcus
    orcid: "https://orcid.org/0000-0001-6817-7265"
  - family-names: Darling
    given-names: Isaac
  - family-names: Truelove
    given-names: Ethan
  - family-names: Ambadkar
    given-names: Aadit
  - family-names: Bose
    given-names: Ribhav
  - family-names: Katok
    given-names: Zoa
  - family-names: Wei
    given-names: Jingrui
  - family-names: Li
    given-names: Xiangguo
  - family-names: Jacobs
    given-names: Ryan
    orcid: "https://orcid.org/0000-0003-2229-6730"
  - family-names: Schultz
    given-names: Lane
  - family-names: Kim
    given-names: Doyeon
  - family-names: Ferris
    given-names: Michael
    orcid: "https://orcid.org/0000-0002-7652-6776"
  - family-names: Voyles
    given-names: Paul M.
    orcid: "https://orcid.org/0000-0001-9438-4284"
  - family-names: Morgan
    given-names: Dane
    orcid: "https://orcid.org/0000-0002-4911-0046"
  - family-names: Foster
    given-names: Ian
    orcid: "https://orcid.org/0000-0003-2129-5269"
  - family-names: Blaiszik
    given-names: Ben
    orcid: "https://orcid.org/0000-0002-5326-4902"
  date-published: 2024-01-23
  doi: 10.21105/joss.05467
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5467
  title: Foundry-ML - Software and Services to Simplify Access to
    Machine Learning Datasets in Materials Science
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05467"
  volume: 9
title: Foundry-ML - Software and Services to Simplify Access to Machine
  Learning Datasets in Materials Science

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.

Find more information on .cff files here and here.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 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 👉 openjournals/joss-papers#4942
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05467
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...

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🎉🎉🎉 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.05467/status.svg)](https://doi.org/10.21105/joss.05467)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05467">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05467/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05467/status.svg
   :target: https://doi.org/10.21105/joss.05467

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

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