[REVIEW]: ATHENA: A Fortran package for neural networks

[editorialbot]

Submitting author: @nedtaylor (Ned Thaddeus Taylor)
Repository: https://github.com/nedtaylor/athena
Branch with paper.md (empty if default branch): paper
Version: 1.3.3
Editor: @HaoZeke
Reviewers: @milancurcic, @awvwgk, @jrybarczyk
Archive: 10.6084/m9.figshare.26158630

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/7806cc51a998f872034abfe0bb24bc24/status.svg)](https://joss.theoj.org/papers/7806cc51a998f872034abfe0bb24bc24)

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

@milancurcic & @awvwgk & @jrybarczyk, 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 @HaoZeke 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 @awvwgk

📝 Checklist for @jrybarczyk

📝 Checklist for @milancurcic

[editorialbot]

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

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (1572.1 files/s, 405276.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Fortran 90                     107           4808           6220          19570
make                             6            138            138            664
CMake                            3            111            270            647
YAML                             4             69             57            408
Markdown                         3            115              0            271
Python                           4             55             55            235
TeX                              1              4              0             79
TOML                             2             15              0             58
JSON                             2              0              0             42
-------------------------------------------------------------------------------
SUM:                           132           5315           6740          21974
-------------------------------------------------------------------------------

Commit count by author:

   771	Ned Taylor
    37	ntt203
     5	Ned Thaddeus Taylor

[editorialbot]

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

OK DOIs

- 10.1145/3323057.3323059 is OK
- 10.1145/3206214.3206215 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.5555/3327546.3327732 is INVALID
- 10.5555/3045118.3045167 is INVALID
- 10.5555/2627435.2670313 is INVALID

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 625

✅ 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 📄 👈

[awvwgk]

Review checklist for @awvwgk

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/nedtaylor/athena?
• 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 (@nedtaylor) 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?

[nedtaylor]

Hi @HaoZeke, a few questions. Firstly, the paper version is now 1.3.0 (updated around 2-3 days ago, so before the paper went into review). Can this be updated here?

Second, I notice that there are still some issues with DOIs for references. I assume I should fix them:
https://dl.acm.org/doi/10.5555/3327546.3327732
https://dl.acm.org/doi/10.5555/3045118.3045167
https://dl.acm.org/doi/10.5555/2627435.2670313

Should I add them to the paper.bib as urls (it appears they don’t work exactly as DOIs from the journal)? Or should I wait for review to be over now?

[HaoZeke]

Hi @HaoZeke, a few questions. Firstly, the paper version is now 1.3.0 (updated around 2-3 days ago, so before the paper went into review). Can this be updated here?

Second, I notice that there are still some issues with DOIs for references. I assume I should fix them: https://dl.acm.org/doi/10.5555/3327546.3327732 https://dl.acm.org/doi/10.5555/3045118.3045167 https://dl.acm.org/doi/10.5555/2627435.2670313

Should I add them to the paper.bib as urls (it appears they don’t work exactly as DOIs from the journal)? Or should I wait for review to be over now?

Hi @nedtaylor, great questions. I wouldn't worry about the version for now, at the end of the review we'll set the version to the latest (which should also include changes in response to the reviewers, if any).

Modifying the paper.bib should be alright, but can also wait until the first round of reviews are in (you can mention it in the response / changes made, if any).

[jrybarczyk]

Review checklist for @jrybarczyk

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/nedtaylor/athena?
• 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 (@nedtaylor) 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?

[HaoZeke]

Hi @milancurcic, @awvwgk, @jrybarczyk, just wanted to check in / provide a reminder regarding the reviews.

[milancurcic]

Thanks @HaoZeke. I don't see my checklist in this thread, can you take a look?

[HaoZeke]

Thanks @HaoZeke. I don't see my checklist in this thread, can you take a look?

Ah, sorry, if you comment @editorialbot generate my checklist it will be created for you.

[milancurcic]

Review checklist for @milancurcic

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/nedtaylor/athena?
• 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 (@nedtaylor) 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?

[crvernon]

👋 @HaoZeke - this one has been still for a while, could you check in to see how things are going? Thanks!

[HaoZeke]

@nedtaylor could you take a look at the issues raised by the reviewers and provide an ETA?

[awvwgk]

I finished my review, the paper and the repo look all good for JOSS.

[nedtaylor]

@nedtaylor could you take a look at the issues raised by the reviewers and provide an ETA?

Hi @HaoZeke. From what I can see, the three issues opened are:

• gfortran-11.4 Internal Compiler Error building test_network.f90 nedtaylor/athena#20
• Error compiling mod_base_layer.f90 with ifort and ifx nedtaylor/athena#21
• CONTRIBUTING.md was largely copied from neural-fortran nedtaylor/athena#23

From what I can see, these have been resolved. All issues have been kept open as requested for the review process until approved for the new paper branch version.

• Issue 20 is for bookkeeping (i.e. gfortran 11 does not work with the library, which is already documented in the README)
• Issue 21 has been fixed
• I believe I have addressed issue 23 and am awaiting a response from @milancurcic regarding a related issue (issue 24).

If I haven't addressed these issues properly and there is more to do on my end, then please let me know. I'm eager to do whatever I can to continue the process.

If there are other issues I have missed, please point me to them.

[milancurcic]

@nedtaylor can you merge the updates into main and I'll continue the review?

[editorialbot]

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

OK DOIs

- 10.1145/3323057.3323059 is OK
- 10.1145/3206214.3206215 is OK

MISSING DOIs

- No DOI given, and none found for title: DropBlock: a regularization method for convolution...
- No DOI given, and none found for title: Batch normalization: accelerating deep network tra...
- No DOI given, and none found for title: Dropout: a simple way to prevent neural networks f...

INVALID DOIs

- None

[editorialbot]

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

[HaoZeke]

@nedtaylor it seems like all the NeurIPS ones are to be coded as inproceedings as I understand, since they don't have a usable DOI, but I'll ping a few more editors, maybe @crvernon has an opinion as well?

Also the Missing ones are a suggestion, so I can also just let is slide as is.

[nedtaylor]

@nedtaylor it seems like all the NeurIPS ones are to be coded as inproceedings as I understand, since they don't have a usable DOI, but I'll ping a few more editors, maybe @crvernon has an opinion as well?

Also the Missing ones are a suggestion, so I can also just let is slide as is.

@HaoZeke

Maybe this information will help for clarity and in determining how to handle these.

I've set both DropBlock and Batchnorm papers as inproceedings (they've been that for a whiles) and the editor bot is still bringing them up as "missing DOIs". I'm happy to change Dropout to an inproceedings, but that's not what it says it is published in and their website when exporting that specific citation returns a bib article format (unlike the previous two, which export as inproceedings.

[crvernon]

@nedtaylor and @HaoZeke - it is fine to have a justification here for the missing DOI. If there is none available for the record, regardless of the specification, then we will be OK with publishing it as such. The more critical notices are those that get labeled as invalid, which it looks like you don't have any of those in your listing. Thanks!

[HaoZeke]

@editorialbot recommend-accept

Thanks for the additional context and quick turnaround @nedtaylor and @crvernon!!
I'm happy to recommend accepting this, after all the excellent effort put in by the reviewers (@awvwgk, @milancurcic and @jrybarczyk) and author (@nedtaylor).

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1145/3323057.3323059 is OK
- 10.1145/3206214.3206215 is OK

MISSING DOIs

- No DOI given, and none found for title: DropBlock: a regularization method for convolution...
- No DOI given, and none found for title: Batch normalization: accelerating deep network tra...
- No DOI given, and none found for title: Dropout: a simple way to prevent neural networks f...

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-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#5573, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[crvernon]

🔍 checking out the following:

• reviewer checklists are completed or addressed
• version set
• archive set
• archive names (including order) and title in archive matches those specified in the paper
• archive uses the same license as the repo and is OSI approved as open source
• archive DOI and version match or redirect to those set by editor in review thread
• paper is error free - grammar and typos
• paper is error free - test links in the paper and bib
• paper is error free - refs preserve capitalization where necessary
• paper is error free - no invalid refs without justification

[crvernon]

@editorialbot generate pdf

[editorialbot]

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

[nedtaylor]

@editorialbot recommend-accept

Thanks for the additional context and quick turnaround @nedtaylor and @crvernon!! I'm happy to recommend accepting this, after all the excellent effort put in by the reviewers (@awvwgk, @milancurcic and @jrybarczyk) and author (@nedtaylor).

I've had a quick look through the final proof and am happy with it.

Thanks very much, @HaoZeke and @crvernon for the fantastic editorial work! 😄

And thanks to the reviewers, (@awvwgk, @jrybarczyk, and @milancurcic ) for the massive amount of work and dedication put towards reviewing this paper and the code! I greatly appreciate it! 😄

[crvernon]

👋 @nedtaylor - You are almost there before we are ready to accept this submission for publication. Please correct the following (no need to make a new release for these):

In the paper:

• LINE 26: "neural-fortran (Curcic (2019)), address" should read "neural-fortran (Curcic, 2019), address" please fix the formatting of this citation in the paper file.
• LINE 28: "batchnormalisation" needs a space between "batch" and "normalisation"
• LINES 31-32: "Finally, more features convolutional techniques are supported in the ATHENA library, including various data padding types, and stride." This sentence needs some work. Perhaps the following, "Finally, more features for convolutional techniques are supported in the ATHENA library, including various data padding types and stride." Note the addition of "for" and the removal of the comma before "and stride".
• LINE 45: The citation "Ioffe & Szegedy (2015))" should appear as "Ioffe & Szegedy, 2015)" in this case. Please fix the formatting in the paper.
• LINE 46: The citation "Ghiasi et al. (2018))" should appear as "Ghiasi et al., 2018)" in the paper.
• LINE 54: Preserve capitalization for the "F" in "fortran". This can be done in your bib file using curly brackets around how you want the case to appear in the paper.
• LINE 73: the "F" in "fortran" should be capitalized.

Let me know when these have been addressed. Thanks!

[nedtaylor]

Thanks @crvernon, I'll get on with that right away. :)

[nedtaylor]

@crvernon I’m having issue finding documentation on how to remove brackets around citations inside bracketed statements. Do you know how to tackle that? If not, I might just rephrase it to move it outside of brackets instead. Fixed it.

Also, just to confirm, I think the second to last issue is line 64, not 54. Am I correct?

I cannot tick off the list, so I’ll make my own comment with them.

• LINE 26: "neural-fortran (Curcic (2019)), address" should read "neural-fortran (Curcic, 2019), address" please fix the formatting of this citation in the paper file.
• LINE 28: "batchnormalisation" needs a space between "batch" and "normalisation"
• LINES 31-32: "Finally, more features convolutional techniques are supported in the ATHENA library, including various data padding types, and stride." This sentence needs some work. Perhaps the following, "Finally, more features for convolutional techniques are supported in the ATHENA library, including various data padding types and stride." Note the addition of "for" and the removal of the comma before "and stride".
• LINE 45: The citation "Ioffe & Szegedy (2015))" should appear as "Ioffe & Szegedy, 2015)" in this case. Please fix the formatting in the paper.
• LINE 46: The citation "Ghiasi et al. (2018))" should appear as "Ghiasi et al., 2018)" in the paper.
• LINE 64: Preserve capitalization for the "F" in "fortran". This can be done in your bib file using curly brackets around how you want the case to appear in the paper.
• LINE 73: the "F" in "fortran" should be capitalized.

[nedtaylor]

@crvernon I have addressed the errors in the paper and the corrections can be found in the paper branch.

[crvernon]

@editorialbot generate pdf

[editorialbot]

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

[crvernon]

@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: Taylor
  given-names: Ned Thaddeus
  orcid: "https://orcid.org/0000-0002-9134-9712"
contact:
- family-names: Taylor
  given-names: Ned Thaddeus
  orcid: "https://orcid.org/0000-0002-9134-9712"
doi: 10.6084/m9.figshare.26158630
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Taylor
    given-names: Ned Thaddeus
    orcid: "https://orcid.org/0000-0002-9134-9712"
  date-published: 2024-07-04
  doi: 10.21105/joss.06492
  issn: 2475-9066
  issue: 99
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6492
  title: "ATHENA: A Fortran package for neural networks"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06492"
  volume: 9
title: "ATHENA: A Fortran package for neural networks"

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.

[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.06492 joss-papers#5574
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06492
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...

[crvernon]

🥳 Congratulations on your new publication @nedtaylor! Many thanks to @HaoZeke for editing and @milancurcic, @awvwgk, and @jrybarczyk for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

[editorialbot]

🎉🎉🎉 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.06492/status.svg)](https://doi.org/10.21105/joss.06492)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06492">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06492/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06492/status.svg
   :target: https://doi.org/10.21105/joss.06492

This is how it will look in your documentation:

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