[REVIEW]: Fitspy: A Python package for spectral decomposition

[editorialbot]

Submitting author: @patquem (Patrick Quéméré)
Repository: https://github.com/CEA-MetroCarac/fitspy
Branch with paper.md (empty if default branch):
Version: 2024.4
Editor: @phibeck
Reviewers: @maurov, @FCMeng
Archive: 10.5281/zenodo.10812332

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Checklists

📝 Checklist for @maurov

📝 Checklist for @FCMeng

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (631.3 files/s, 105279.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          19            667            770           2284
Markdown                         3            133              0            256
JSON                             1              0              0            251
TeX                              1              3              0             80
YAML                             2              5              4             47
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            27            808            774           2921
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gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.11813 is OK
- 10.5281/zenodo.8092679 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 1201

[editorialbot]

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

[phibeck]

@maurov, @FCMeng, thanks again for reviewing! Please go ahead and create your checklist first using the command @editorialbot generate my checklist. Feel free to create issues in project repository directly or write them down as comments here, but please do link the issues in this review so it's easy to follow for everyone. Please let me know if you have any questions about the review process.

[maurov]

@phibeck thanks for the reminder. Sorry, I have been very busy these days. I hope to start the review by next week.

[patquem]

Hello @phibeck,
Many thanks for your follow-up and reminders.
As a potential reviewer, I forgot to mention @teuben, who had few words about my draft the day I posted it (see #5655). He was interested in the Fitspy tool and I just saw he is listed as a reviewer. Feel free to invite him to review the paper.

[phibeck]

Thanks for the suggestion @patquem. Since we're still at an early stage of the review, adding another reviewer probably won't delay the process significantly.

👋 @teuben, would you be willing to review this submission for JOSS?

[phibeck]

👋 @maurov & @FCMeng How are things going? Let me know if there are any questions.

[phibeck]

👋 Hi @maurov & @FCMeng it would be great to hear from you when you plan to start your reviews or if there's anything that's holding you up. Thanks!

[maurov]

@phibeck thanks for the reminder. I apologize for taking so long in reviewing this. From my side, there is nothing special holding me up, simply the fact that I am very busy with my official work. I will try doing this task as soon as possible.

[maurov]

Review checklist for @maurov

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/CEA-MetroCarac/fitspy?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@patquem) 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?

[maurov]

@patquem @phibeck

I have started reviewing fitspy by reading the paper and the (short) documentation. I will install and play with the examples (plus trying some of my own data) soon, but I would like to express my general comments first.

A graphical interface on top of lmfit may be of interest for those users who want to build a quick fitting model and apply it on multiple similar spectra, without prior knowledge of Python programming. I support this idea, but this software should be put in the right context and clearly stated in the paper/documentation. In fact, in addition to what here is called "spectral decomposition", "peak fitting" or "curve fitting" is performed in any field of science. This means that there already many (open source) softwares available and almost every researcher/community has a preferred tool. Clarifying the specific problems fitspy solves (a GUI for Lmfit?) and to which research community is targeted (X-ray fluorescence?) is mandatory. For example, why not comparing fitspy design to Fityk? Why two fancy astrophysics tools (specutils and pyspeckit) are cited (apart the obvious fact that they do peak fitting)?

In conclusion, the current "Statement of need" is too generic and unclear. I am asking myself if there is "substantial scholarly effort" behind this project. Is this a "yet another peak fitting tool"?

[FCMeng]

@phibeck Apologize for the late response. I have been really stacked this semester. I will start the review process as soon as possible.

[FCMeng]

Review checklist for @FCMeng

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/CEA-MetroCarac/fitspy?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@patquem) 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?

[patquem]

Hi,
Thank you @maurov for your reviewing and your comments.
You mentioned a lack of clarity regarding the objectives of the software and I will try to clarify them.
Which communauty is this tool aimed at ? I would tell anyone who needs to do peak fitting (and only peak fitting) in the easiest and the quickest (in term of accessibility) way possible.
While I agree with you (there are already many other softwares that do peak fitting and Fitspy may appear like "yet another peak fitting tool"), most of the softwares with a GUI don't manage 2D-maps and/or do not have multiprocessing capabilities (see the (non exhaustive) list of open-source softwares below).
Although Fitik that you mentioned is a tool with an advanced GUI and is undeniably more evoluated that Fitspy, it does not have 2D-map and parallel capabilities.
The only ones that I have identified and that combine these 2 features are XISMUS and HyperspyUI.
From what I have seen, XISMUS is strongly attached to X-Ray Fluorescence datasets.
On this point, Fitspy aims to be a generic and agnostic tool.
HyperspyUI seems to be the closest tool but (in my experience) is not as easy to use as Fitspy and this tool aims at the end to adress all Hyperspy options, far from the only need of peak fitting to cover.
After testing Fitspy, @maurov do you agree to consider Fitspy as satisfying some of the terms used in the "scholarly effort" section : faster and/or easier and/or simpler than most open source software already existing?
If so, I will rewrite the "Statement of need", with emphasis on consideration about the dedicated easy-to-use peak fitting tool and its 2D-map/parallel capabilities.

[maurov]

@patquem I apologize for not being very reactive on this review, but I am very busy these days. I hope to move forward in the next two weeks.

As said in my previous comment, you should clearly give in the "Statement of need" which scientific community this code is targeting and give a real application example. I understand that you want to provide a generic and efficient peak fitting tool, but it is impossible to get all features for all users communities, so the point here is not to demonstrate which software is the best, but just to provide a given tool to a given community. For example, when you refer to 2D maps, are you referring to X-ray fluorescence maps? For such application, one very good open source software that is not in your table is PyMca.

[phibeck]

Thanks @maurov for getting the review started! Have your issues in CEA-MetroCarac/fitspy#9 been addressed? It sounds like there are some clear steps for @patquem to improve the manuscript, too.

@FCMeng could you provide an update on the progress of your review? Thank you!

[patquem]

Hello @maurov,
Thank you again for your comments.
As previously said, Fitspy (like Fityk) is a generic and agnostic tool dedicated to do peak fitting and only peak fitting and is not intended for any specific community or specific applications.
To justify my point and answer to your questions, I would say I work in a multidisciplinary institute working on many fields like biology, batteries and semi-conductor with a wide range of characterization techniques. Over the last 5-6 months, Fitspy has been used to process spectra issued from Raman, PL, XPS, XRD and EELS to characterize materials from the range of several microns to the range of thousands of mm (wafers). The number of spectra processed by Fitspy during these studies varied from a few to several hundred thousand. The 2D map characterisation was used both for the characterisation of PL spectra (at the wafer scale) and to process EELS spectra at the micrometer scale.
Fitspy has been used by both experienced and interns who have appreciated the tool for its “easy-to-use” compared to the reference tools they currently use (as they said: “reference tools offer a large range of services but, as a consequence, are more complex and not so ergonomic to use for such basic and (often) repetitive tasks that peak fitting operations are”).
These are the reasons why it does not seem appropriate to me to focus the Fitspy “statement of need” on a particular community and specific applications.

[patquem]

@maurov @FCMeng and @phibeck :
With the revisited Statement of need below: Does the article have a chance of being published or do you consider it as definitively rejected ?
Indeed, I need an answer because articles issued from applicative studies with Fitspy are now about to be submitted and authors need to know if a Fistpy reference does exist (Initially, in July, when I submitted the present article to JOSS, I was thinking IT could be the reference paper).
Thank you.

[patquem]

Statement of need (revisited)

Numerous open-source tools for spectral fitting exist. However, most of them have been designed for specific application domains, offering a broad range of services beyond mere spectral fitting. Consequently, these tools can prove challenging to use, especially for less experienced individuals.

In the vein of generic tools like Fityk or PRISMA, Fitspy is a dedicated tool for spectral fitting—and only spectral fitting—with the following characteristics or functionalities:

Agnostic Nature: Fitspy is not tied to any specific physical quantity or database. It is designed to process spectra regardless of their x-support and y-intensity without requiring prior knowledge.

Python Implementation: Fitspy is coded in Python. As a result, spectra can be easily processed using Python scripts, catering to individuals with basic knowledge of the language.

2D Maps: Fitspy has been designed to handle spectra derived from 2D acquisitions. Note that beyond "2D", dimensions can encompass time or any other dimension. When dealing with 2D data, an interactive map in the Fitspy GUI allows users to locate and select spectra of interest easily.

Multiprocessing Capabilities: Fitspy enables spectral fit processing on multiple processors, enhancing efficiency.

Constrained Parameters: Leveraging the Lmfit library, Fitspy empowers users to impose constraints on parameter ranges or establish constraints between parameters using literal expressions.

Simple GUI: Fitspy has been designed to be as intuitive and simple to use as possible (subjective criterion).

To the author's knowledge, although many open-source software applications are more advanced in certain aspects mentioned, none of them appears to encompass all the functionalities described above.

[phibeck]

@editorialbot set 2024.4 as version

[editorialbot]

Done! version is now 2024.4

[matbryan52]

@patquem test mention (checking notifications)

[patquem]

@phibeck
I have taken into account all your remarks/suggestions.

(I noticed that I have not been receiving any notifications since your last two messages from this 'JOSS' page, even though my notification settings are correctly set up (?).)

[phibeck]

@editorialbot generate pdf

[editorialbot]

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

[phibeck]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1107/S0021889810030499 is OK
- 10.1002/cmtd.202100094 is OK
- 10.5281/zenodo.11813 is OK
- 10.5281/zenodo.8092679 is OK

MISSING DOIs

- No DOI given, and none found for title: Full wafer-scale characterization method for 2D ma...

INVALID DOIs

- None

[phibeck]

@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

- 10.1107/S0021889810030499 is OK
- 10.1002/cmtd.202100094 is OK
- 10.5281/zenodo.11813 is OK
- 10.5281/zenodo.8092679 is OK

MISSING DOIs

- No DOI given, and none found for title: Full wafer-scale characterization method for 2D ma...

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#5203, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@patquem 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 create a tagged release on your repository (i.e. one that will be listed here: https://github.com/CEA-MetroCarac/fitspy/tags), its version tag should match what we listed here and what is listed for the archive here which is currently 2024.4 (if you end up creating a new version/archive, let us know then we can update the version tag and archive link here to match).
• In the paper replace softwares by software e.g. one could phrase your sentence using ...although other open-source software packages are much more....
• Change visualization, characterize, customize (which is American English) to visualisation, characterise, and customise, to be consistent with the rest of the European English used throughout the paper.

[Kevin-Mattheus-Moerman]

@patquem 👋

[patquem]

Hi @Kevin-Mattheus-Moerman,
I have created the tag and put the corrections you mentioned in the article.
Let me know if something is wrong/missing.

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@patquem thanks for making those changes. All looks good now to proceed.

[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.

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CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Quéméré
  given-names: Patrick
  orcid: "https://orcid.org/0009-0008-6936-1249"
doi: 10.5281/zenodo.10812332
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Quéméré
    given-names: Patrick
    orcid: "https://orcid.org/0009-0008-6936-1249"
  date-published: 2024-04-15
  doi: 10.21105/joss.05868
  issn: 2475-9066
  issue: 96
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5868
  title: "Fitspy: A Python package for spectral decomposition"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05868"
  volume: 9
title: "Fitspy: A Python package for spectral decomposition"

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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.05868 joss-papers#5243
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3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

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[Kevin-Mattheus-Moerman]

@patquem congratulations on this JOSS publication! 🎉

At this point I would like to thank @phibeck for editing this submission.

A special thank you also to the reviewers: @maurov, @FCMeng !!!

[editorialbot]

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[patquem]

Thank you all (@maurov , @FCMeng , @phibeck and @Kevin-Mattheus-Moerman ) for reviewing, editing, and publishing the article.
The Citations and the Acknowlegments section of the Github FITSPY site have been updated :)