[PRE REVIEW]: Pinard: A Python package for Near Infrared Reflectance Spectroscopy

[editorialbot]

Submitting author: !--author-handle-->@gbeurier<!--end-author-handle-- (Grégory Beurier) Repository: https://github.com/GBeurier/pinard Branch with paper.md (empty if default branch): Version: 1.0.1 Editor: !--editor-->@lucydot<!--end-editor-- Reviewers: @ayoubft, @untzag Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/69a17f530e558cf0fe3b7049d977f839"><img src="https://joss.theoj.org/papers/69a17f530e558cf0fe3b7049d977f839/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/69a17f530e558cf0fe3b7049d977f839/status.svg)](https://joss.theoj.org/papers/69a17f530e558cf0fe3b7049d977f839)

Author instructions

Thanks for submitting your paper to JOSS @gbeurier. Currently, there isn't a JOSS editor assigned to your paper.

@gbeurier if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (1038.8 files/s, 193974.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          28            620           1201           1489
Jupyter Notebook                 3              0           4202            399
Markdown                         5             97              0            247
reStructuredText                 8            364            935            138
YAML                             6             29             47            126
TeX                              1             13              0            119
DOS Batch                        1              8              1             26
make                             1              4              7              9
INI                              1              0              0              2
-------------------------------------------------------------------------------
SUM:                            54           1135           6393           2555
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 477

[editorialbot]

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

OK DOIs

- 10.1016/j.aca.2018.04.004 is OK
- 10.1038/s41597-023-02189-w is OK
- 10.3389/fpls.2022.836488 is OK
- 10.1255/jnirs.716 is OK
- 10.3389/fchem.2018.00576 is OK
- 10.1007/BFb0062108 is OK
- 10.1016/j.isprsjprs.2008.01.001 is OK
- 10.3390/s22249764 is OK
- 10.1016/j.vibspec.2019.103009 is OK

MISSING DOIs

- 10.1111/pce.13718 may be a valid DOI for title: Estimating photosynthetic traits from reflectance spectra: A synthesis of spectral indices, numerical inversion, and partial least square regression

INVALID DOIs

- None

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@GBeurier thanks for this submission. I am the AEiC on this track and here to help with initial steps. For the moment, below are some points that require your attention:

• [ ] Please check that above potentially missing DOI, if the suggestion is correct please implement it. You can call @editorialbot check references, to check them again, and use @editorialbot generate pdf to update the paper draft.
• [ ] Please define the NIRS acronym in the text.
• [ ] Add space after full stop in .Although

[Kevin-Mattheus-Moerman]

@editorialbot invite @lucydot as editor

[editorialbot]

Invitation to edit this submission sent!

[lucydot]

@editorialbot assign me as editor

[editorialbot]

Assigned! @lucydot is now the editor

[lucydot]

Hi @Kevin-Mattheus-Moerman @GBeurier - happy to edit this submission. Though please note I am at a conference for the next week; I will resume editing duties w/c 10th July. In the meantime @GBeurier please see notes above from @Kevin-Mattheus-Moerman ☝️ , and please suggest potential reviewers (more details on this are also above, in the first post).

[GBeurier]

Hi @lucydot, thank you for reviewing pinard. I have done the requested modifications and I suggest the following reviewers:

• Ayoub Fatihi
• @ksunden

[GBeurier]

@editorialbot check references

@editorialbot generate pdf

[editorialbot]

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

OK DOIs

- 10.1016/j.aca.2018.04.004 is OK
- 10.1038/s41597-023-02189-w is OK
- 10.3389/fpls.2022.836488 is OK
- 10.1255/jnirs.716 is OK
- 10.3389/fchem.2018.00576 is OK
- 10.1007/BFb0062108 is OK
- 10.1016/j.isprsjprs.2008.01.001 is OK
- 10.3390/s22249764 is OK
- 10.1016/j.vibspec.2019.103009 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1111/pce.13718 is INVALID because of 'https://doi.org/' prefix

[GBeurier]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.aca.2018.04.004 is OK
- 10.1038/s41597-023-02189-w is OK
- 10.3389/fpls.2022.836488 is OK
- 10.1255/jnirs.716 is OK
- 10.3389/fchem.2018.00576 is OK
- 10.1007/BFb0062108 is OK
- 10.1016/j.isprsjprs.2008.01.001 is OK
- 10.3390/s22249764 is OK
- 10.1016/j.vibspec.2019.103009 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1111/pce.13718 is INVALID because of 'https://doi.org/' prefix

[GBeurier]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.aca.2018.04.004 is OK
- 10.1038/s41597-023-02189-w is OK
- 10.3389/fpls.2022.836488 is OK
- 10.1255/jnirs.716 is OK
- 10.3389/fchem.2018.00576 is OK
- 10.1111/pce.13718 is OK
- 10.1007/BFb0062108 is OK
- 10.1016/j.isprsjprs.2008.01.001 is OK
- 10.3390/s22249764 is OK
- 10.1016/j.vibspec.2019.103009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[lucydot]

Thanks @GBeurier,

@ayoubft, @ksunden - are you available to review this submission to JOSS?

@ayoubft I believe you are a new reviewers to JOSS, so welcome! Our process is a little different to more traditional journals, being Github-based and completely transparent. If you have any questions, please ask! There are some more details at the docs here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

[ayoubft]

Hey, Thanks @lucydot for the welcome; very excited to review for joss. I will start by reading the docs.

[ayoubft]

@editorialbot commands

[editorialbot]

Hello @ayoubft, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[GBeurier]

Hi, Thank you for accepting the reviews. I will be on vacation until August 6th.

[lucydot]

Thanks for letting us know @GBeurier, noted!

And excellent @ayoubft, pleased to have you on board 🚋

@jwuttke @untzag - are you available to review this submission to JOSS?

[lucydot]

Hello,

Just to let you know that I am on Annual Leave until the 8th of July. The invite still stands @jwuttke @untzag; if either (or both!) of you are able to accept the invite I will get the review going.

[untzag]

I will review, thanks @lucydot @GBeurier

[lucydot]

That is great - thank you @untzag

[lucydot]

@editorialbot add @ayoubft as reviewer

[editorialbot]

@ayoubft added to the reviewers list!

[lucydot]

@editorialbot add @untzag as reviewer

[editorialbot]

@untzag added to the reviewers list!

[lucydot]

Excellent @GBeurier @untzag @ayoubft we are onto the next stage!

I have added reviewers and will now ask editorial-bot to generate a new review thread - this is where the review will be conducted. You will receive a github notification for this, and there are instructions generated at the top. The first reviewer task will be to generate the review checklist. Any questions, please ask on the new thread.

[lucydot]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5747.