editorialbot commented 6 months ago

Submitting author: !--author-handle-->@Sm00thix@boisgera<!--end-editor-- Reviewers: @parmentelat, @basileMarchand Archive: 10.5281/zenodo.12794521

Status

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Markdown: [![status](https://joss.theoj.org/papers/ac559cbcdc6e6551f58bb3e573a73afc/status.svg)](https://joss.theoj.org/papers/ac559cbcdc6e6551f58bb3e573a73afc)

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Checklists

📝 Checklist for @parmentelat

📝 Checklist for @basileMarchand

editorialbot commented 6 months ago

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editorialbot commented 6 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (779.5 files/s, 168165.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          18            988           2107           4300
CSV                              1              0              0            607
TeX                              1             20              0            188
YAML                             7             24             14            150
reStructuredText                10             73             67            123
Markdown                         1             30              0             76
DOS Batch                        1              8              1             26
TOML                             1              2              0             21
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            41           1149           2196           5500
-------------------------------------------------------------------------------

Commit count by author:

    54  Ole Engstrøm
    13  Ole-Christian Galbo Engstrøm
     2  Sm00thix

editorialbot commented 6 months ago

Paper file info:

📄 Wordcount for paper.md is 1471

✅ The paper includes a Statement of need section

editorialbot commented 6 months ago

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

editorialbot commented 6 months ago

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

editorialbot commented 6 months ago

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

OK DOIs

- None

MISSING DOIs

- No DOI given, and none found for title: Estimation of principal components and related mod...
- No DOI given, and none found for title: Food research and data analysis
- 10.1016/s0169-7439(01)00155-1 may be a valid DOI for title: PLS-regression: a basic tool of chemometrics
- No DOI given, and none found for title: Partial least squares for discrimination
- 10.1002/(sici)1099-128x(199701)11:1<73::aid-cem435>3.0.co;2-# may be a valid DOI for title: Improved PLS algorithms
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- 10.1016/j.trac.2009.07.007 may be a valid DOI for title: Review of the most common pre-processing technique...
- 10.1007/978-981-15-8648-4_7 may be a valid DOI for title: NIR Data Exploration and Regression by Chemometric...
- 10.1111/1541-4337.12958 may be a valid DOI for title: Quantitative assessment of wheat quality using nea...
- 10.1007/s00362-009-0251-7 may be a valid DOI for title: Comparison of PLS algorithms when number of object...
- 10.1002/cem.1248 may be a valid DOI for title: A comparison of nine PLS1 algorithms
- 10.1109/iccvw60793.2023.00055 may be a valid DOI for title: Improving Deep Learning on Hyperspectral Images of...
- No DOI given, and none found for title: Analyzing Near-Infrared Hyperspectral Imaging for ...
- No DOI given, and none found for title: Array programming with NumPy
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Autograd: Effortless gradients in numpy
- 10.1177/09670335221078356 may be a valid DOI for title: Hyperspectral imaging for classification of bulk g...
- 10.1002/cem.3141 may be a valid DOI for title: Orders of magnitude speed increase in partial leas...
- 10.1002/cem.3201 may be a valid DOI for title: Much faster cross-validation in PLSR-modelling by ...
- 10.21105/joss.01190 may be a valid DOI for title: Multiblock PLS: Block dependent prediction modelin...
- No DOI given, and none found for title: Shortcutting Cross-Validation: Efficiently Derivin...

INVALID DOIs

- None

parmentelat commented 6 months ago

Review checklist for @parmentelat

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/Sm00thix/IKPLS?
[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 (@Sm00thix) 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?

parmentelat commented 6 months ago

I have a very first and obvious concern about authorship, given that only the corresponding author seems to have contributed to this work and given the nature of the work, which is primarily of an implementation nature, I am questioning the appearance of 3 ! other people in the authors list, and wonder what exactly were their respective contributions ?

Sm00thix commented 6 months ago

I have a very first and obvious concern about authorship, given that only the corresponding author seems to have contributed to this work and given the nature of the work, which is primarily of an implementation nature, I am questioning the appearance of 3 ! other people in the authors list, and wonder what exactly were their respective contributions ?

Hi @parmentelat I appreciate your concern. My co-authors have contributed in writing the paper - even though I am the one who committed it to the repository. They have contributed with discussion and ideas regarding how to communicate the performance of the different algorithms - resulting in the figure in the paper. In general, they have contributed by providing me with guidance throughout the project.

boisgera commented 5 months ago

I have a very first and obvious concern about authorship, given that only the corresponding author seems to have contributed to this work and given the nature of the work, which is primarily of an implementation nature, I am questioning the appearance of 3 ! other people in the authors list, and wonder what exactly were their respective contributions ?

Hi @parmentelat I appreciate your concern. My co-authors have contributed in writing the paper - even though I am the one who committed it to the repository. They have contributed with discussion and ideas regarding how to communicate the performance of the different algorithms - resulting in the figure in the paper. In general, they have contributed by providing me with guidance throughout the project.

Hi @Sm00thix & @parmentelat,

I have asked my co-editors what the JOSS policy was wrt authorship. And there is actually a paragraph in the journal documentation that mentions that "active project direction and other forms of non-code contributions are considered sufficient for co-authorship of JOSS submissions". (Source: https://joss.readthedocs.io/en/latest/submitting.html#authorship)

So given the details provided by @Sm00thix, I'd say that the list of co-authors is fine! 👍

Sm00thix commented 5 months ago

I have a very first and obvious concern about authorship, given that only the corresponding author seems to have contributed to this work and given the nature of the work, which is primarily of an implementation nature, I am questioning the appearance of 3 ! other people in the authors list, and wonder what exactly were their respective contributions ?

Hi @parmentelat I appreciate your concern. My co-authors have contributed in writing the paper - even though I am the one who committed it to the repository. They have contributed with discussion and ideas regarding how to communicate the performance of the different algorithms - resulting in the figure in the paper. In general, they have contributed by providing me with guidance throughout the project.

Hi @Sm00thix & @parmentelat,

I have asked my co-editors what the JOSS policy was wrt authorship. And there is actually a paragraph in the journal documentation that mentions that "active project direction and other forms of non-code contributions are considered sufficient for co-authorship of JOSS submissions". (Source: https://joss.readthedocs.io/en/latest/submitting.html#authorship)

So given the details provided by @Sm00thix, I'd say that the list of co-authors is fine! 👍

Hi @boisgera,

Thank you for the clarification! Given this information, I will keep the list of co-authors as is.

parmentelat commented 5 months ago

So given the details provided by @Sm00thix, I'd say that the list of co-authors is fine! 👍

I abide by the decision of the editor, however I can't help but think that as phrased above, this rationale can apply to any contribution in any environment, and personally I would have appreciated a little more explicit list of contributions !

boisgera commented 4 months ago

Hi @Sm00thix,

To let you know what's going on:

I have exchanged some e-mails with @parmentelat wrt the review progress (basically: 👍).
@basileMarchand is not currently online, but I'll try to have an exchange with him next week.

Sm00thix commented 4 months ago

Hi @boisgera,

Thank you for the update and for your effort. I appreciate it. I look forward to hearing from you or the reviewers again :-)

boisgera commented 3 months ago

Hi @Sm00thix,

My apologies for the delay. I finally managed to meet in person with the 2nd reviewer (@basileMarchand) today. We'll get some inputs from him next week!

Sm00thix commented 3 months ago

Hi @boisgera ,

It is perfectly fine - I appreciate the work you guys do! Sounds good, and I look forward to his review!

basileMarchand commented 3 months ago

Review checklist for @basileMarchand

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/Sm00thix/IKPLS?
[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 (@Sm00thix) 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?

parmentelat commented 3 months ago

about reproducibility, and for the record

as per https://github.com/Sm00thix/IKPLS/pull/23 the repo now comes with a utility notebook that lets users recompute the runtime of the various runs that appear in the main figure in the paper - except for the ones that are estimated

parmentelat commented 3 months ago

I have now checked all the boxes, pending a few minor changes that will be raised by @basileMarchand with whom we had a meeting together with @boisgera earlier today

here's a couple general comments/reservations that I'd like to make before closing my contribution to his review

About contribution and authorship:

Contributions to the project, in practical terms and in particular with respect to commits in the repo, have been exclusively made by the submitting author @Sm00thix; the contributions of the 3 other authors mentioned in the paper are far more fuzzy, and have been described in very vague terms as "discussions and feedback on the project", as reported by the main author upon our request for clarification; nor have they taken any part during the paper review.

Although this seems to be in line with the authorship guidelines of the journal, and this has been deemed acceptable by the editor, I must admit that I find this practice to be somewhat questionable, as it is not clear to me how the contributions of the 3 other authors have been substantial enough to warrant their inclusion in the author list.

About functionality:

For practical reasons I have only been able to run the code on a CPU, and have not been able to verify the GPU / TPU functionality, that is advertised as a side-effect of the JAX implementation. However, the code seems to be well-structured and well-documented, and I have no reason to doubt that the GPU functionality works as intended.

basileMarchand commented 3 months ago

Hello @Sm00thix

first of all, sorry for the excessive delay for my review

In the JOSS paper, it would be good in my opinion to have a more "simplified" introduction in the summary so that a less experienced reader can easily understand what need the package is addressing. Also, the first paragraph of the README (which is also the first paragraph of the documentation) should be made more engaging to catch the attention of readers who might be searching without really knowing what they need. This would help attract more users and build a more diverse community.

Sm00thix commented 3 months ago

Hello @Sm00thix

first of all, sorry for the excessive delay for my review

In the JOSS paper, it would be good in my opinion to have a more "simplified" introduction in the summary so that a less experienced reader can easily understand what need the package is addressing. Also, the first paragraph of the README (which is also the first paragraph of the documentation) should be made more engaging to catch the attention of readers who might be searching without really knowing what they need. This would help attract more users and build a more diverse community.

Hi @basileMarchand

No worries. Life happens :-)

Thank you for your feedback. I will make sure to incorporate it. I created an issue on the IKPLS repo and will address the feedback from there.

basileMarchand commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

boisgera commented 3 months ago

Hi everyone!

I see that @parmentelat has checked all the items from his list ; there are still a few unchecked items for @basileMarchand. Anything I can do to help about these items?

All issues opened so far have been adressed and closed, except for https://github.com/Sm00thix/IKPLS/issues/29. @basileMarchand, did the change https://github.com/Sm00thix/IKPLS/commit/36b10aedb42de483d89c3b9adf24723840401439 address your concern? Can you close the issue?

Kind regards,

Sébastien

basileMarchand commented 2 months ago

Hi @boisgera, @parmentelat @Sm00thix

I have now completed my review and now checked all the boxes.

I have two general comments to make before closing my contribution to this review:

Performance Evaluation:

Unfortunately, I was unable to evaluate the performance on GPU as I could not successfully install JAX. Thus, my review only covers the CPU version.

References:

The references cited in the paper appear to be relevant. However, I am not an expert in this specific field, so my judgment is limited to the extent of my current knowledge.

Thank you for the opportunity to review this submission.

Basile

boisgera commented 2 months ago

@editorialbot generate pdf

boisgera commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago

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

OK DOIs

- None

MISSING DOIs

- No DOI given, and none found for title: Estimation of principal components and related mod...
- No DOI given, and none found for title: Food research and data analysis
- 10.1016/s0169-7439(01)00155-1 may be a valid DOI for title: PLS-regression: a basic tool of chemometrics
- No DOI given, and none found for title: Partial least squares for discrimination
- 10.1002/(sici)1099-128x(199701)11:1<73::aid-cem435>3.0.co;2-# may be a valid DOI for title: Improved PLS algorithms
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- 10.1016/j.trac.2009.07.007 may be a valid DOI for title: Review of the most common pre-processing technique...
- 10.1007/978-981-15-8648-4_7 may be a valid DOI for title: NIR Data Exploration and Regression by Chemometric...
- 10.1111/1541-4337.12958 may be a valid DOI for title: Quantitative assessment of wheat quality using nea...
- 10.1007/s00362-009-0251-7 may be a valid DOI for title: Comparison of PLS algorithms when number of object...
- 10.1002/cem.1248 may be a valid DOI for title: A comparison of nine PLS1 algorithms
- 10.1109/iccvw60793.2023.00055 may be a valid DOI for title: Improving Deep Learning on Hyperspectral Images of...
- No DOI given, and none found for title: Analyzing Near-Infrared Hyperspectral Imaging for ...
- No DOI given, and none found for title: Array programming with NumPy
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Autograd: Effortless gradients in numpy
- 10.1177/09670335221078356 may be a valid DOI for title: Hyperspectral imaging for classification of bulk g...
- 10.1002/cem.3141 may be a valid DOI for title: Orders of magnitude speed increase in partial leas...
- 10.1002/cem.3201 may be a valid DOI for title: Much faster cross-validation in PLSR-modelling by ...
- 10.21105/joss.01190 may be a valid DOI for title: Multiblock PLS: Block dependent prediction modelin...
- No DOI given, and none found for title: Shortcutting Cross-Validation: Efficiently Derivin...

INVALID DOIs

- None

editorialbot commented 2 months ago

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

boisgera commented 2 months ago

@editorialbot commands

editorialbot commented 2 months ago

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boisgera commented 2 months ago

Hi everyone,

Everything looks good at this stage, thanks @parmentelat, @basileMarchand and @Sm00thix for your efforts 🙏 We are now entering the "post-review" stage!

@Sm00thix can you make a new release of ikpls (if it's necessary/appropriate) and deposit a new archive of the software with Zenodo/figshare? I'll need the corresponding archive DOI to proceed.

Cheers

Sébastien

Sm00thix commented 2 months ago

Hi @parmentelat, @basileMarchand, and @boisgera

Thank you so much for your help in reviewing IKPLS!

@boisgera I tried using Zenodo and believe I have succeeded. The doi is 10.5281/zenodo.12794521. Please let me know if you need anything else! :-)

Best, Ole

boisgera commented 2 months ago

@editorialbot set 10.5281/zenodo.12794521 as archive

editorialbot commented 2 months ago

Done! archive is now 10.5281/zenodo.12794521

boisgera commented 2 months ago

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

boisgera commented 2 months ago

@editorialbot set v1.2.4 as version

editorialbot commented 2 months ago

Done! version is now v1.2.4

boisgera commented 2 months ago

Hi @Sm00thix,

It seems that there are a small number of minor issues with the current Zenodo archive:

[x] The title of the archive does not match the (full) title of the JOSS paper,
[x] The list of authors does not match the declared list of authors for the JOSS paper (and the ORCID tags are not included),
[x] The license of the archive does not match the sofware license.

See e.g. https://joss.theoj.org/papers/10.21105/joss.06566 and the archive https://zenodo.org/records/12775561 to see how these metadata should match.

I guess that these metadata are immutable and that you will need to make a new Zenodo archive (?). Sorry for the inconvenience...

Sm00thix commented 2 months ago

Hi @boisgera,

I apologize for the oversights. I have taken care of all three points. Interestingly, I was able to edit the metadata without changing the DOI. In fact, Zenodo notified me that I can not change the files in the archive, but I can always change the metadata.

Please let me know if I need to do anything else! :-)

boisgera commented 2 months ago

@editorialbot recommend-accept

editorialbot commented 2 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 months ago

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

OK DOIs

- None

MISSING DOIs

- No DOI given, and none found for title: Estimation of principal components and related mod...
- No DOI given, and none found for title: Food research and data analysis
- 10.1016/s0169-7439(01)00155-1 may be a valid DOI for title: PLS-regression: a basic tool of chemometrics
- No DOI given, and none found for title: Partial least squares for discrimination
- 10.1002/(sici)1099-128x(199701)11:1<73::aid-cem435>3.0.co;2-# may be a valid DOI for title: Improved PLS algorithms
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- 10.1016/j.trac.2009.07.007 may be a valid DOI for title: Review of the most common pre-processing technique...
- 10.1007/978-981-15-8648-4_7 may be a valid DOI for title: NIR Data Exploration and Regression by Chemometric...
- 10.1111/1541-4337.12958 may be a valid DOI for title: Quantitative assessment of wheat quality using nea...
- 10.1007/s00362-009-0251-7 may be a valid DOI for title: Comparison of PLS algorithms when number of object...
- 10.1002/cem.1248 may be a valid DOI for title: A comparison of nine PLS1 algorithms
- 10.1109/iccvw60793.2023.00055 may be a valid DOI for title: Improving Deep Learning on Hyperspectral Images of...
- No DOI given, and none found for title: Analyzing Near-Infrared Hyperspectral Imaging for ...
- No DOI given, and none found for title: Array programming with NumPy
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Autograd: Effortless gradients in numpy
- 10.1177/09670335221078356 may be a valid DOI for title: Hyperspectral imaging for classification of bulk g...
- 10.1002/cem.3141 may be a valid DOI for title: Orders of magnitude speed increase in partial leas...
- 10.1002/cem.3201 may be a valid DOI for title: Much faster cross-validation in PLSR-modelling by ...
- 10.21105/joss.01190 may be a valid DOI for title: Multiblock PLS: Block dependent prediction modelin...
- No DOI given, and none found for title: Shortcutting Cross-Validation: Efficiently Derivin...

INVALID DOIs

- None

editorialbot commented 2 months ago

:wave: @openjournals/dsais-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/5662, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

crvernon commented 2 months ago

🔍 checking out the following:

[x] reviewer checklists are completed or addressed
[x] version set
[x] archive set
[x] archive names (including order) and title in archive matches those specified in the paper
[x] archive uses the same license as the repo and is OSI approved as open source
[x] 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 commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

crvernon commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago

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

OK DOIs

- None

MISSING DOIs

- No DOI given, and none found for title: Estimation of principal components and related mod...
- No DOI given, and none found for title: Food research and data analysis
- 10.1016/s0169-7439(01)00155-1 may be a valid DOI for title: PLS-regression: a basic tool of chemometrics
- No DOI given, and none found for title: Partial least squares for discrimination
- 10.1002/(sici)1099-128x(199701)11:1<73::aid-cem435>3.0.co;2-# may be a valid DOI for title: Improved PLS algorithms
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- 10.1016/j.trac.2009.07.007 may be a valid DOI for title: Review of the most common pre-processing technique...
- 10.1007/978-981-15-8648-4_7 may be a valid DOI for title: NIR Data Exploration and Regression by Chemometric...
- 10.1111/1541-4337.12958 may be a valid DOI for title: Quantitative assessment of wheat quality using nea...
- 10.1007/s00362-009-0251-7 may be a valid DOI for title: Comparison of PLS algorithms when number of object...
- 10.1002/cem.1248 may be a valid DOI for title: A comparison of nine PLS1 algorithms
- 10.1109/iccvw60793.2023.00055 may be a valid DOI for title: Improving Deep Learning on Hyperspectral Images of...
- No DOI given, and none found for title: Analyzing Near-Infrared Hyperspectral Imaging for ...
- No DOI given, and none found for title: Array programming with NumPy
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Autograd: Effortless gradients in numpy
- 10.1177/09670335221078356 may be a valid DOI for title: Hyperspectral imaging for classification of bulk g...
- 10.1002/cem.3141 may be a valid DOI for title: Orders of magnitude speed increase in partial leas...
- 10.1002/cem.3201 may be a valid DOI for title: Much faster cross-validation in PLSR-modelling by ...
- 10.21105/joss.01190 may be a valid DOI for title: Multiblock PLS: Block dependent prediction modelin...
- No DOI given, and none found for title: Shortcutting Cross-Validation: Efficiently Derivin...

INVALID DOIs

- None

crvernon commented 2 months ago

:wave: @Sm00thix - I just need you to make the following changes before we can accept this for publication:

In your paper:

[x] LINE 18: "...algorithm by Engstrøm (O.-C. G. Engstrøm, 2024), significantly..." should use an in text citation resulting in "algorithm by Engstrøm (2024), significantly...". You can achieve this by removing the brackets from the in-text mention of the bib reference in your paper. For example, instead of by Engstrøm [@ref] you can simply use by @ref
[x] LINE 34-35: The references for S. Wold should appear together in a single set of parenthesis. This formatting issue occurs in several other places throughout the paper. I will not mention all of them, but please fix those as well. To fix this, just combine the references in a single set of brackets delimited by a semicolon (e.g., [@ref1; @ref2]
[x] LINE 34-36: I am also confused by the phrasing here "...or a classification model, PLS-DA (PLS discriminant analysis), (Barker & Rayens, 2003)..." should this be "...or a classification model, PLS-DA (PLS discriminant analysis) (Barker & Rayens, 2003)..." where the comma is removed before the reference? If so, please remove other similar occurrences of this in the text.
[x] LINE 47: Same comment here about in-line text citation for the Dayal and MacGregor citation.
[x] There are many missing DOI in your references. Please add them into your bib file. See the message generated before this for hints but you will need to confirm that these are correct.
[x] Ensure that items needing capitalization in the references are accounted for. You can maintain formatting in your references using curly brackets around parts of text in your bib file that you want keep the formatting of.

openjournals / joss-reviews

[REVIEW]: IKPLS: Improved Kernel Partial Least Squares and Fast Cross-Validation Algorithms for Python with CPU and GPU Implementations Using NumPy and JAX #6533

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