[REVIEW]: THzTools: data analysis software for terahertz time-domain spectroscopy

[editorialbot]

Submitting author: @jsdodge (J. Steven Dodge)
Repository: https://github.com/dodge-research-group/thztools
Branch with paper.md (empty if default branch): main
Version: 0.5.5
Editor: @crvernon
Reviewers: @crvernon
Archive: 10.5281/zenodo.14188761

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/228f65ed74c96fbea91ebe80a5c3427c"><img src="https://joss.theoj.org/papers/228f65ed74c96fbea91ebe80a5c3427c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/228f65ed74c96fbea91ebe80a5c3427c/status.svg)](https://joss.theoj.org/papers/228f65ed74c96fbea91ebe80a5c3427c)

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

@crvernon, 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 @crvernon 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 @crvernon

[editorialbot]

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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]

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

✅ OK DOIs

- 10.1017/9780511734809 is OK
- 10.1109/IRMMW-THz50927.2022.9895812 is OK
- 10.5281/zenodo.4326594 is OK
- 10.1109/IRMMW-THz50926.2021.9567242 is OK
- 10.1007/s10762-023-00947-w is OK
- 10.1364/OE.417724 is OK
- 10.1109/IRMMW-THz50926.2021.9566941 is OK
- 10.1063/1.5047659 is OK
- 10.1109/TTHZ.2018.2889227 is OK
- 10.1109/IRMMW-THz57677.2023.10299169 is OK
- 10.48550/arXiv.2403.04332 is OK
- 10.1021/acs.analchem.1c02132 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (1504.9 files/s, 230144.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              2              0              2           6444
Python                           7            558           1483           3055
Markdown                         5            150              0            537
reStructuredText                54            286            221            310
YAML                            10             28              9            255
Jupyter Notebook                 6              0            837            191
TOML                             1             18              0            156
TeX                              1             11              0            113
XML                              8              0              0            104
DOS Batch                        1              8              1             26
JSON                             1              0              0             11
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            97           1063           2560          11211
-------------------------------------------------------------------------------

Commit count by author:

   514	jsdodge
    93	Steve Dodge
    59	jonathan Posada Loaiza
    36	jonathan.posada1
    28	Santiago Higuera Quintero
    20	Naod Yimam
    19	jonathanpl20
    18	Randon Hall
     9	Alireza
     5	“Roboboy2000”
     1	Leya
     1	unknown

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 443

✅ The paper includes a Statement of need section

[crvernon]

Review checklist for @crvernon

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/dodge-research-group/thztools?
• 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 (@jsdodge) 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?

[editorialbot]

License info:

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

[editorialbot]

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

[crvernon]

The above review conducted under as a PyOpenSci review:

pyOpenSci/software-submission#209

[crvernon]

@editorialbot set 0.5.5 as version

[editorialbot]

Done! version is now 0.5.5

[crvernon]

@editorialbot set 10.5281/zenodo.14188761 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.14188761

[crvernon]

@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

- 10.1017/9780511734809 is OK
- 10.1109/IRMMW-THz50927.2022.9895812 is OK
- 10.5281/zenodo.4326594 is OK
- 10.1109/IRMMW-THz50926.2021.9567242 is OK
- 10.1007/s10762-023-00947-w is OK
- 10.1364/OE.417724 is OK
- 10.1109/IRMMW-THz50926.2021.9566941 is OK
- 10.1063/1.5047659 is OK
- 10.1109/TTHZ.2018.2889227 is OK
- 10.1109/IRMMW-THz57677.2023.10299169 is OK
- 10.48550/arXiv.2403.04332 is OK
- 10.1021/acs.analchem.1c02132 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ 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#6202, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[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: Loaiza
  given-names: Jonathan Posada
  orcid: "https://orcid.org/0009-0004-4443-6161"
- family-names: Higuera-Quintero
  given-names: Santiago
  orcid: "https://orcid.org/0000-0001-6905-4662"
- family-names: Noori
  given-names: Alireza
  orcid: "https://orcid.org/0009-0009-1091-0802"
- family-names: Mohtashemi
  given-names: Laleh
  orcid: "https://orcid.org/0000-0002-2706-857X"
- family-names: Hall
  given-names: R. P.
  orcid: "https://orcid.org/0009-0004-1137-3651"
- family-names: Yimam
  given-names: Naod Ayalew
  orcid: "https://orcid.org/0009-0007-7522-5027"
- family-names: Dodge
  given-names: J. Steven
  orcid: "https://orcid.org/0000-0003-3219-7314"
contact:
- family-names: Dodge
  given-names: J. Steven
  orcid: "https://orcid.org/0000-0003-3219-7314"
doi: 10.5281/zenodo.14188761
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Loaiza
    given-names: Jonathan Posada
    orcid: "https://orcid.org/0009-0004-4443-6161"
  - family-names: Higuera-Quintero
    given-names: Santiago
    orcid: "https://orcid.org/0000-0001-6905-4662"
  - family-names: Noori
    given-names: Alireza
    orcid: "https://orcid.org/0009-0009-1091-0802"
  - family-names: Mohtashemi
    given-names: Laleh
    orcid: "https://orcid.org/0000-0002-2706-857X"
  - family-names: Hall
    given-names: R. P.
    orcid: "https://orcid.org/0009-0004-1137-3651"
  - family-names: Yimam
    given-names: Naod Ayalew
    orcid: "https://orcid.org/0009-0007-7522-5027"
  - family-names: Dodge
    given-names: J. Steven
    orcid: "https://orcid.org/0000-0003-3219-7314"
  date-published: 2024-12-02
  doi: 10.21105/joss.07542
  issn: 2475-9066
  issue: 104
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7542
  title: "THzTools: data analysis software for terahertz time-domain
    spectroscopy"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07542"
  volume: 9
title: "THzTools: data analysis software for terahertz time-domain
  spectroscopy"

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]

🦋🦋🦋 👉 Bluesky post 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.07542 joss-papers#6203
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07542
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 @jsdodge! This was published as a part of the pyOpenSci review listed in this thread.

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.07542/status.svg)](https://doi.org/10.21105/joss.07542)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.07542">
  <img src="https://joss.theoj.org/papers/10.21105/joss.07542/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07542/status.svg
   :target: https://doi.org/10.21105/joss.07542

This is how it will look in your documentation:

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[jsdodge]

Thanks! I just added myself to the reviewer list.