[REVIEW]: chemotools: A Python Package that Integrates Chemometrics and scikit-learn

[editorialbot]

Submitting author: @paucablop (Pau Cabaneros López)
Repository: https://github.com/paucablop/chemotools
Branch with paper.md (empty if default branch):
Version: v0.1.5
Editor: @bmcfee
Reviewers: @vinayak2019, @Kastakin
Archive: 10.5281/zenodo.13118393

Status

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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

@vinayak2019 & @Kastakin, 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 @bmcfee 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 @Kastakin

📝 Checklist for @vinayak2019

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.48 s (331.4 files/s, 33488.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              6              0             15           3882
CSV                             14              0              0           3609
Markdown                        45           1007              0           1916
Python                          44           1115           1864           1782
HTML                            39              0              0            539
YAML                             8             30             39            190
TeX                              1              7              0             59
JSON                             1              0              0              8
TOML                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                           159           2159           1918          11991
-------------------------------------------------------------------------------

Commit count by author:

   396	paucablop
    22	Pau Cabaneros
    13	dependabot[bot]

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1209

✅ 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 📄 👈

[Kastakin]

Review checklist for @Kastakin

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/paucablop/chemotools?
• 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 (@paucablop) 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?

[vinayak2019]

Review checklist for @vinayak2019

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/paucablop/chemotools?
• 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 (@paucablop) 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?

[Kastakin]

Hello, I am sorry for my late review!

I really appreciated the topic which is really close to my field of study. I think that the documentation for the project is really well written and clear.

The paper is clear in the exposition and succeeds in being a nice introduction to the package. While it does not give a full start to finish example of application I think that it clearly shows its capabilities for who it is targeted for.

I do not see any problem in publishing it in its current form, it is a 👍 from my part!

[bmcfee]

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 pull request)
• 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

[bmcfee]

@editorialbot generate pdf

[editorialbot]

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

[bmcfee]

Thanks @Kastakin and @vinayak2019 for your reviews!

@paucablop please refer to #6802 (comment) and complete the items listed for the author.

I'm now going down the editor post-review checklist. I have the following comments on the draft:

• Lines 15-16:

  "have excelled by developing advanced preprocessing methods designed to attenuate instrument and measuring artifacts from the spectra"

  seem grammatically strange. Should this be "attenuate instrument noise" or something to that effect?

• Line 32:

  model persistence to standardized files such as joblib or pickle

  joblib is not a file format, so it's not clear what this means. If you're referring to joblib.dump, is this not just an interface to pickle?

• Line 55:

  asymmetrically reweighed penalized least squares

  should this be reweighted?

• Several references (line 110, 113, 121) have slightly broken URLs, eg

  https://doi.org/https://doi.org/10.1002/bit.27586

  It's not clear if this is problem on the .bib end or in the rendering of the pdf, but it should be checked.

[bmcfee]

@paucablop 👋 just checking in to see how you're doing with this?

[paucablop]

Hi @bmcfee 👋 had a busy week at work, will try to work on it this weekend 😃

[paucablop]

Hi @bmcfee and reveiwers 👋

Thanks a lot for the help and the comments for the paper. I have updated the manuscript with the suggested improvements.

❗ @bmcfee After knowing if the references work, I will proceed with the Zenodo submission 😄

Reviewer and Editors Comments

1. Comment 1 [line 15-16]: I have updated the text to and substitute the term artifacts by noise. I agree it is a better term.
2. Comment 2 [line 32]: I have updated the text to: _using standardized libraries such as joblib or pickle, as you are right, after reading the documentation I can see that joblib.dump is an interface to pickle.
3. Comment 3 [line 55]: nicely spotted 🚀
4. Comment 4: [references]: I have reviewed all the links in the references, and it seems to be right, I have also tested the links from the generated PDF on two computers (Ubuntu and Windows 10) and opening the links in two different browsers (Edge and Firefox) and they worked fine. I am not so sure how to proceed with this 😕, could you provide some more info about the issue?

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.

[bmcfee]

@editorialbot generate pdf

[editorialbot]

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

[bmcfee]

Thanks @paucablop !

4. could you provide some more info about the issue?

The issue I was seeing was a redundant https://doi.org in the URL. DOI.org seems to be smart enough to parse this out, so it's not a huge deal, but really it should only be there once. I expect it could be fixed by replacing

https://github.com/paucablop/chemotools/blob/f0e78800a341281003c9da33dd8bc7860afd6c48/paper/paper.bib#L9C1-L9C47

by

    doi = {10.1002/bit.27586},

to remove the URL prefix, which will be added back in automatically at compile time. (Same goes for all other bib entries.)

• This is the version that will be used in the JOSS paper.

Can you post the version number here so we can update the bot?

[paucablop]

Hi @bmcfee!

Thanks for the feedback! 🚀

✔️ I have fixed the bibliography
✔️ The version number is v0.1.5
✔️ The DOI number is: 10.5281/zenodo.13118393
✔️ I have ensured that the author information, version number, ORCID and License match!

Many thanks for helping with this process 🥳

[bmcfee]

@editorialbot set v0.1.5 as version

[editorialbot]

Done! version is now v0.1.5

[bmcfee]

@editorialbot set 10.5281/zenodo.13118393 as archive

[bmcfee]

Thanks for confirming that @danielskatz ! Doubly annoying that they put "doi" in the URL for resolving the DOI-like-string 🤣

@paucablop we can skip DOI on that one, but the other ref should be updated.

[danielskatz]

For future knowledge, anything from ACM that starts with 10.5555 is using their placeholder for things that don't have DOIs...

[paucablop]

Thanks @bmcfee and @danielskatz for the feedback 😄

I have updated the aforementioned reference 🚀

[bmcfee]

@editorialbot generate pdf

[bmcfee]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1002/bit.27586 is OK
- 10.1039/c4an01061b is OK
- 10.1016/j.trac.2009.07.007 is OK
- 10.1016/j.trac.2020.116045 is OK

MISSING DOIs

- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python

INVALID DOIs

- None

[editorialbot]

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

[bmcfee]

Final read-through comments, mainly a few more minor typos/grammatical suggestions:

• line 49: "to generale" ⇒ "to generalize"
• line 57: "create a preprocessing pipelines" ⇒ "create a preprocessing pipeline"
• line 66: it looks like the last line of this code example is truncated. Perhaps you need to line-wrap it?
• line 70: "based on a given criteria" ⇒ "based on a given criterion" (singular) or "based on given criteria" (plural)
• line 84: "and/or" ⇒ "or" (implied by "either" earlier in sentence)
• line 91: "has being utilized" ⇒ "has been utilized"

Otherwise this looks good!

[paucablop]

Fantastic! 😄 Thanks for the thorough feedback! I have updated the text :)

[bmcfee]

@editorialbot generate pdf

[editorialbot]

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

[bmcfee]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1002/bit.27586 is OK
- 10.1039/c4an01061b is OK
- 10.1016/j.trac.2009.07.007 is OK
- 10.1016/j.trac.2020.116045 is OK

MISSING DOIs

- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python

INVALID DOIs

- None

[editorialbot]

👋 @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#5712, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@paucablop as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, however the below are some points that require your attention:

• Please edit the ZENODO listed version tag to include the v so it matches your GitHub version tag which is v0.1.5.

[paucablop]

@Kevin-Mattheus-Moerman Done 🚀

Many thanks 😄

[Kevin-Mattheus-Moerman]

@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: Lopez
  given-names: Pau Cabaneros
  orcid: "https://orcid.org/0000-0003-2372-5082"
doi: 10.5281/zenodo.13118393
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Lopez
    given-names: Pau Cabaneros
    orcid: "https://orcid.org/0000-0003-2372-5082"
  date-published: 2024-08-02
  doi: 10.21105/joss.06802
  issn: 2475-9066
  issue: 100
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6802
  title: "chemotools: A Python Package that Integrates Chemometrics and
    scikit-learn"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06802"
  volume: 9
title: "chemotools: A Python Package that Integrates Chemometrics and
  scikit-learn"

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.

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[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.06802 joss-papers#5713
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06802
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...

[Kevin-Mattheus-Moerman]

@paucablop congratulations on this JOSS publication!

@bmcfee thanks for editing!

And a special thank you to the reviewers: @vinayak2019, @Kastakin !

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.06802

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[paucablop]

@Kevin-Mattheus-Moerman, @bmcfee, @Kastakin @vinayak2019 a lot for helping editing and reviewing the paper!! 🥳

[bmcfee]

Congrats @paucablop and thanks @Kastakin and @vinayak2019 ! 🎉