[REVIEW]: spectrapepper: A Python toolbox for advanced analysis of spectroscopic data for materials and devices #3781

whedon · 2021-09-29T16:56:04Z

Submitting author: @enricgrau (Enric Grau-Luque)
Repository: https://github.com/spectrapepper/spectrapepper
Version: 0.1.3
Editor: @rkurchin
Reviewer: @stuartcampbell, @ksunden
Archive: 10.5281/zenodo.5708435

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Markdown: [![status](https://joss.theoj.org/papers/d65c85c8917de62f951050c3deaa85f0/status.svg)](https://joss.theoj.org/papers/d65c85c8917de62f951050c3deaa85f0)

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Reviewer instructions & questions

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Review checklist for @stuartcampbell

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General checks

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Functionality

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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 and who the target audience is?
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?

Review checklist for @ksunden

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
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 (@enricgrau) made major contributions to the software? Does the full list of paper authors seem appropriate and complete? (See Joss Authorship spectrapepper/spectrapepper#3)
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 and who the target audience is?
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?

The text was updated successfully, but these errors were encountered:

whedon · 2021-09-29T16:56:07Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @stuartcampbell, @ksunden it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

whedon · 2021-09-29T16:56:14Z

Wordcount for paper.md is 884

whedon · 2021-09-29T16:56:16Z

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

OK DOIs

- 10.1016/j.solmat.2015.12.036 is OK
- 10.1038/s41598-017-01381-4 is OK
- 10.1039/c9ta03625c is OK
- 10.1063/1.5061809 is OK
- 10.1002/PIP.541 is OK
- 10.1039/d1ta01299a is OK
- 10.1002/aenm.201903242 is OK
- 10.1016/j.respol.2005.12.006 is OK
- 10.1002/9781119148739.ch4 is OK
- 10.1016/j.joule.2018.05.009 is OK
- 10.1039/d0ee02838j is OK
- 10.1039/c9ta02356a is OK
- 10.1038/s41586-018-0337-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/ZENODO.4681666 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/ZENODO.4743323 is OK
- 10.1177/0003702819839098 is OK
- 10.1016/j.chemolab.2018.06.009 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.5555/1593511 is INVALID

whedon · 2021-09-29T16:56:19Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.21 s (301.9 files/s, 203317.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      17           4513           4497          17139
HTML                            11           1976             33           5174
SVG                              1              0              0           2671
Python                          10            762            880           1786
XML                              1              0              2           1618
CSS                              4            191             35            757
TeX                              1             40              0            335
Markdown                         4             41              0            163
YAML                             7             18              9            163
reStructuredText                 7             89             55            147
JSON                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                            64           7630           5511          29959
-------------------------------------------------------------------------------


Statistical information for the repository '78a4a889db4b38b5652b2815' was
gathered on 2021/09/29.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Enric Tomas Grau Luq            60        111899          82323          100.00
unknown                          1             3              2            0.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Enric Tomas Grau Luq      29577           26.4          2.8               16.06

whedon · 2021-09-29T16:56:34Z

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

rkurchin · 2021-09-29T16:57:08Z

☝️ note to @enricgrau to fix that invalid DOI issue at some point (not urgent, but will need to be done eventually)

enricgrau · 2021-09-30T08:05:47Z

☝️ note to @enricgrau to fix that invalid DOI issue at some point (not urgent, but will need to be done eventually)

Thank you for the note @rkurchin. I've fixed the issue in the .bib file and push the changes into the repository. Any other actions I should take? Thank you again.

rkurchin · 2021-09-30T12:35:26Z

@whedon generate pdf

That's all! It should rerun the checks again and verify...

whedon · 2021-09-30T12:35:55Z

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

danielskatz · 2021-09-30T12:36:56Z

@whedon check references

@rkurchin - this is how to run the checks - doing that and generating the pdf are separate commands

whedon · 2021-09-30T12:37:06Z

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

OK DOIs

- 10.1016/j.solmat.2015.12.036 is OK
- 10.1038/s41598-017-01381-4 is OK
- 10.1039/c9ta03625c is OK
- 10.1063/1.5061809 is OK
- 10.1002/PIP.541 is OK
- 10.1039/d1ta01299a is OK
- 10.1002/aenm.201903242 is OK
- 10.1016/j.respol.2005.12.006 is OK
- 10.1002/9781119148739.ch4 is OK
- 10.1016/j.joule.2018.05.009 is OK
- 10.1039/d0ee02838j is OK
- 10.1039/c9ta02356a is OK
- 10.1038/s41586-018-0337-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/ZENODO.4681666 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/ZENODO.4743323 is OK
- 10.1177/0003702819839098 is OK
- 10.1016/j.chemolab.2018.06.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

rkurchin · 2021-09-30T12:44:52Z

Haha oops, thanks @danielskatz; I would've remembered that eventually but you beat me to it ;)

Anyway, @enricgrau, DOI's look good 👍

enricgrau · 2021-10-01T07:21:47Z

@rkurchin I just realize there is an author missing and reuploaded the .md file with the added author missing. Let me know if this is fine or I should roll it back and dot it later on. Thank you!

rkurchin · 2021-10-02T23:22:22Z

@whedon generate pdf

Nope, that's fine! I'll just regenerate it here and you can double-check that it all looks good...

whedon · 2021-10-02T23:22:49Z

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

enricgrau · 2021-10-03T11:05:40Z

Nope, that's fine! I'll just regenerate it here and you can double-check that it all looks good...

Thank you @rkurchin. The proof looks good!

rkurchin · 2021-10-05T12:52:24Z

👋 @stuartcampbell @ksunden reminder to get your reviews started!

rkurchin · 2021-10-11T15:07:27Z

(pinged reviewers via email)

stuartcampbell · 2021-10-12T19:13:06Z

(pinged reviewers via email)

Sorry - completely missed the notification. Will start it now.

whedon · 2021-10-13T16:56:23Z

👋 @stuartcampbell, please update us on how your review is going (this is an automated reminder).

whedon · 2021-10-13T16:56:23Z

👋 @ksunden, please update us on how your review is going (this is an automated reminder).

whedon · 2021-11-06T16:40:23Z

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

OK DOIs

- 10.1016/j.solmat.2015.12.036 is OK
- 10.1038/s41598-017-01381-4 is OK
- 10.1039/c9ta03625c is OK
- 10.1063/1.5061809 is OK
- 10.1002/PIP.541 is OK
- 10.1039/d1ta01299a is OK
- 10.1002/aenm.201903242 is OK
- 10.1016/j.respol.2005.12.006 is OK
- 10.1002/9781119148739.ch4 is OK
- 10.1016/j.joule.2018.05.009 is OK
- 10.1039/d0ee02838j is OK
- 10.1039/c9ta02356a is OK
- 10.1038/s41586-018-0337-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/ZENODO.4681666 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1177/0003702819839098 is OK
- 10.1016/j.chemolab.2018.06.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

rkurchin · 2021-11-06T20:21:23Z

I opened spectrapepper/spectrapepper#9 with a few editorial tweaks to the manuscript

rkurchin · 2021-11-09T16:32:06Z

@whedon generate pdf

whedon · 2021-11-09T16:32:37Z

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

enricgrau · 2021-11-09T16:33:07Z

I opened spectrapepper/spectrapepper#9 with a few editorial tweaks to the manuscript

@rkurchin Thank you for your suggested tweaks. We believe they do improve the way the manuscript reads and, with just a couple of exceptions, where approved and merged.

rkurchin · 2021-11-09T16:36:23Z

Great! The next steps are:

Create a new tagged release and comment here with the version number
Create an archive of the package (e.g. on Zenodo or figshare) with matching metadata (title, authors, etc.) to this submission and report the associated DOI here
And then we'll be ready to proceed with publication! 🎉

rkurchin · 2021-11-16T15:26:31Z

👆 @enricgrau, just checking in on this. We're nearly ready to publish!

enricgrau · 2021-11-17T17:07:48Z

@rkurchin Sorry for the delay. The archive of version 0.1.3 was created on Zenodo with DOI: 10.5281/zenodo.5708435 and matching metadata.

Also the paper.md file was updated with corrected ORCID numbers of the authors.

Thank you!

rkurchin · 2021-11-17T18:57:48Z

@whedon set 0.1.3 as version

whedon · 2021-11-17T18:57:52Z

OK. 0.1.3 is the version.

rkurchin · 2021-11-17T18:58:00Z

@whedon set 10.5281/zenodo.5708435 as archive

whedon · 2021-11-17T18:58:05Z

OK. 10.5281/zenodo.5708435 is the archive.

rkurchin · 2021-11-17T18:58:22Z

@whedon recommend-accept

whedon · 2021-11-17T18:58:25Z

Attempting dry run of processing paper acceptance...

whedon · 2021-11-17T18:58:35Z

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

OK DOIs

- 10.1016/j.solmat.2015.12.036 is OK
- 10.1038/s41598-017-01381-4 is OK
- 10.1039/c9ta03625c is OK
- 10.1063/1.5061809 is OK
- 10.1002/PIP.541 is OK
- 10.1039/d1ta01299a is OK
- 10.1002/aenm.201903242 is OK
- 10.1016/j.respol.2005.12.006 is OK
- 10.1002/9781119148739.ch4 is OK
- 10.1016/j.joule.2018.05.009 is OK
- 10.1039/d0ee02838j is OK
- 10.1039/c9ta02356a is OK
- 10.1038/s41586-018-0337-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/ZENODO.4681666 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1177/0003702819839098 is OK
- 10.1016/j.chemolab.2018.06.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-11-17T18:58:54Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2756

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2756, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

arfon · 2021-11-19T12:13:19Z

@whedon accept deposit=true

whedon · 2021-11-19T12:13:22Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2021-11-19T12:14:03Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-11-19T12:14:04Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03781 joss-papers#2757
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03781
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2021-11-19T12:19:42Z

@stuartcampbell, @ksunden – many thanks for your reviews here and to @rkurchin for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@enricgrau – your paper is now accepted and published in JOSS ⚡🚀💥

whedon · 2021-11-19T12:19:46Z

🎉🎉🎉 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.03781/status.svg)](https://doi.org/10.21105/joss.03781)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03781">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03781/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03781/status.svg
   :target: https://doi.org/10.21105/joss.03781

This is how it will look in your documentation:

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whedon added Python review TeX labels Sep 29, 2021

whedon assigned rkurchin Sep 29, 2021

whedon mentioned this issue Sep 29, 2021

[PRE REVIEW]: spectrapepper: A Python toolbox for advanced analysis of spectroscopic data for materials and devices #3759

Closed

whedon assigned ksunden and stuartcampbell Sep 30, 2021

ksunden mentioned this issue Oct 12, 2021

Quickstart contains method which does not exist logo spectrapepper/spectrapepper#1

Closed

ksunden mentioned this issue Oct 13, 2021

Joss Authorship spectrapepper/spectrapepper#3

Closed

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Nov 17, 2021

whedon added accepted published Papers published in JOSS labels Nov 19, 2021

arfon closed this as completed Nov 19, 2021

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[REVIEW]: spectrapepper: A Python toolbox for advanced analysis of spectroscopic data for materials and devices #3781

[REVIEW]: spectrapepper: A Python toolbox for advanced analysis of spectroscopic data for materials and devices #3781

Comments

whedon commented Sep 29, 2021 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @stuartcampbell

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @ksunden

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Sep 29, 2021

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enricgrau commented Oct 1, 2021

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arfon commented Nov 19, 2021

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