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[PRE REVIEW]: pySLM2: A full-stack python package for holographic beam shaping #6205

Closed editorialbot closed 8 months ago

editorialbot commented 9 months ago

Submitting author: !--author-handle-->@ldes89150<!--end-author-handle-- (Chung-You Shih) Repository: https://github.com/QITI/pySLM2 Branch with paper.md (empty if default branch): paper Version: v0.1.0 Editor: !--editor-->@HaoZeke<!--end-editor-- Reviewers: @brandondube, @sidihamady, @ktahar Managing EiC: Kyle Niemeyer

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Markdown: [![status](https://joss.theoj.org/papers/70246ad674d3806798e343f6ecffa686/status.svg)](https://joss.theoj.org/papers/70246ad674d3806798e343f6ecffa686)

Author instructions

Thanks for submitting your paper to JOSS @ldes89150. Currently, there isn't a JOSS editor assigned to your paper.

@ldes89150 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 commented 9 months ago

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 commented 9 months ago

Checking the BibTeX entries failed with the following error: 

No paper file path
editorialbot commented 9 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (695.6 files/s, 66611.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26            773            554           1888
YAML                             2              9              4             61
Markdown                         1             21              0             49
reStructuredText                 5             30             44             36
DOS Batch                        1              8              1             26
TOML                             1              2              0             17
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            37            847            610           2086
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 9 months ago

Failed to discover a Statement of need section in paper

editorialbot commented 9 months ago

:warning: An error happened when generating the pdf. Paper file not found.

kyleniemeyer commented 9 months ago

Hello @ldes89150, thanks for your submission to JOSS. We'll use this pre-review issue to assign an editor and find reviewers; unfortunately, we don't have any editors available to handle your submission right now, so I need to put this on our waitlist until someone can edit it.

In the meantime, any reviewer recommendations you can make would be welcome.

kyleniemeyer commented 9 months ago

@ldes89150 it looks like the JOSS paper is located on the paper.md branch, is that correct?

ldes89150 commented 9 months ago

Hi @kyleniemeyer ,

Yes, it is in the paper.md branch. Do you need me to make any changes?

kyleniemeyer commented 9 months ago

@editorialbot set paper.md as branch

editorialbot commented 9 months ago

Done! branch is now paper.md

kyleniemeyer commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

:warning: An error happened when generating the pdf.

kyleniemeyer commented 9 months ago

@ldes89150 we just needed to specify the branch, since our editorialbot looks for the paper in the main branch by default.

I'm not quite sure what is causing the error in building the PDF, though.

editorialbot commented 9 months ago

:warning: An error happened when generating the pdf.

kyleniemeyer commented 9 months ago

@openjournals/dev @arfon do you understand this error in the PDF build job?

Run bundle exec ruby /home/runner/work/_actions/xuanxu/paper-action/main/get_paper.rb
/home/runner/work/_actions/xuanxu/paper-action/main/vendor/bundle/ruby/3.2.0/gems/commonmarker-0.23.10/lib/commonmarker.rb:38:in `render_doc': text must be a String; got a NilClass! (TypeError)

      raise TypeError, "text must be a String; got a #{text.class}!" unless text.is_a?(String)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    from /home/runner/work/_actions/xuanxu/paper-action/main/vendor/bundle/ruby/3.2.0/gems/theoj-1.9.0/lib/theoj/submission.rb:189:in `plaintext'
    from /home/runner/work/_actions/xuanxu/paper-action/main/vendor/bundle/ruby/3.2.0/gems/theoj-1.9.0/lib/theoj/submission.rb:100:in `all_metadata'
    from /home/runner/work/_actions/xuanxu/paper-action/main/vendor/bundle/ruby/3.2.0/gems/theoj-1.9.0/lib/theoj/submission.rb:78:in `metadata_info'
    from /home/runner/work/_actions/xuanxu/paper-action/main/vendor/bundle/ruby/3.2.0/gems/theoj-1.9.0/lib/theoj/submission.rb:57:in `article_metadata'
    from /home/runner/work/_actions/xuanxu/paper-action/main/get_paper.rb:25:in `<main>'
Error: Process completed with exit code 1.
xuanxu commented 9 months ago

Probably the error comes from the branch being named paper.md. Git creates internal files with the names of every branch so there is a paper.md file that can confuse the bot if it finds it before the real paper file. Renaming the branch should fix the error.

marvelousmonicaaa commented 9 months ago

@editorialbot set paper as branch

editorialbot commented 9 months ago

Done! branch is now paper

marvelousmonicaaa commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

editorialbot commented 9 months ago

Five most similar historical JOSS papers:

PySDM v1: particle-based cloud modeling package for warm-rain microphysics and aqueous chemistry Submitting author: @piotrbartman Handling editor: @dhhagan (Active) Reviewers: @darothen, @josephhardinee Similarity score: 0.8052

SkyPy: A package for modelling the Universe Submitting author: @rrjbca Handling editor: @arfon (Active) Reviewers: @cescalara, @rmorgan10 Similarity score: 0.8029

prysm: A Python optics module Submitting author: @brandondube Handling editor: @xuanxu (Active) Reviewers: @aquilesC Similarity score: 0.8027

s(ound)lab: An easy to learn Python package for designing and running psychoacoustic experiments. Submitting author: @DrMarc Handling editor: @arfon (Active) Reviewers: @hadware, @sneakers-the-rat Similarity score: 0.7999

beamshapes: a Python package to generate directivity patterns for various sound source models Submitting author: @thejasvibr Handling editor: @faroit (Active) Reviewers: @nils-werner, @hagenw Similarity score: 0.7998

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

marvelousmonicaaa commented 9 months ago

@kyleniemeyer changing the paper.md branch name to paper made the pdf work

kyleniemeyer commented 9 months ago

Excellent! Thanks @xuanxu for pointing out the issue.

kyleniemeyer commented 9 months ago

@editorialbot invite @HaoZeke as editor

editorialbot commented 9 months ago

Invitation to edit this submission sent!

HaoZeke commented 9 months ago

Thanks for the invite @kyleniemeyer. I will be able and willing to edit the submission.

@editorialbot assign @HaoZeke as editor

kyleniemeyer commented 9 months ago

@editorialbot assign @HaoZeke as editor

Thanks @HaoZeke! FYI, any commands to @editorialbot have to be at the beginning of a comment.

editorialbot commented 9 months ago

Assigned! @HaoZeke is now the editor

HaoZeke commented 9 months ago

👋 @ldes89150 I will facilitate the review of your paper/software as the editor. The first step will be to find reviewers, so I will start contacting potential reviewers over the weekend.

@kyleniemeyer mentioned this already, but if you have any suggestions for potential reviewers, then please mention them here in this thread (without tagging them with an @). Feel free to use the list of volunteers here or the authors of the similar papers above.

HaoZeke commented 9 months ago

hi @brandondube @aquilesC @caldarolamartin 👋 would you be interested in and available to review this JOSS submission? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

If not, could you recommend any potential reviewers?

HaoZeke commented 8 months ago

hi @maurov 👋 would you be interested in and available to review this JOSS submission? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

If not, could you recommend any potential reviewers?

brandondube commented 8 months ago

@HaoZeke I can do a review from a general perspective on code quality, the paper, and so-on. But I do not have access to the hardware devices I believe the package is meant to control, and could not verify the functionality in a strict way

HaoZeke commented 8 months ago

@HaoZeke I can do a review from a general perspective on code quality, the paper, and so-on. But I do not have access to the hardware devices I believe the package is meant to control, and could not verify the functionality in a strict way

That makes sense to me, and thank you for clarifying. It seems like there is a software only component which would be better reviewed and the hardware control aspect would generally be very hard to verify.

HaoZeke commented 8 months ago

@editorialbot add @brandondube as reviewer

editorialbot commented 8 months ago

@brandondube added to the reviewers list!

maurov commented 8 months ago

hi @maurov 👋 would you be interested in and available to review this JOSS submission? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

If not, could you recommend any potential reviewers?

@HaoZeke thank you for the invitation. Unfortunately this contribution is out of my field of expertise and I do not know any addition potential reviewers for it.

HaoZeke commented 8 months ago

hi @maurov 👋 would you be interested in and available to review this JOSS submission? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html If not, could you recommend any potential reviewers?

@HaoZeke thank you for the invitation. Unfortunately this contribution is out of my field of expertise and I do not know any addition potential reviewers for it.

Thanks for the prompt response. Hope to see you around on another review later :)

caldarolamartin commented 8 months ago

Hi!

Unfortunately I do not have the time for reviewing this paper at the moment.

Best, Martin

Martin Caldarola

On Sat, 27 Jan 2024, 09:43 Rohit Goswami, @.***> wrote:

hi @brandondube https://github.com/brandondube @aquilesC https://github.com/aquilesC @caldarolamartin https://github.com/caldarolamartin 👋 would you be interested in and available to review this JOSS submission? If not, could you recommend any potential reviewers?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6205#issuecomment-1913079274, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAUGZKTDHXDILQUF66OEOG3YQS44BAVCNFSM6AAAAABBVOZQMCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJTGA3TSMRXGQ . You are receiving this because you were mentioned.Message ID: @.***>

aquilesC commented 8 months ago

Hello @HaoZeke ! Thanks for the invite but I am currently busy with another review and won't have enough bandwidth for this one as well. I did a previous review with @sidihamady on a paper by @ktahar

HaoZeke commented 8 months ago

hi @sidihamady and @ktahar 👋 would you be interested in and available to review this JOSS submission? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

If not, could you recommend any potential reviewers?

HaoZeke commented 8 months ago

Thanks for the prompt response @aquilesC (and for the reviewer suggestions) and @caldarolamartin, hope to see you around on other reviews.

ldes89150 commented 8 months ago

@HaoZeke I can do a review from a general perspective on code quality, the paper, and so-on. But I do not have access to the hardware devices I believe the package is meant to control, and could not verify the functionality in a strict way

Hey @HaoZeke @brandondube ,

Just want to clarify on the hardware part: Most part of the software and majority of the functionalities don't require the hardware. All the hardware related code is in pySLM2/utils.

And @brandondube Thank you for your interest in reviewing the paper/repo!

sidihamady commented 8 months ago

Hi @HaoZeke , I can review it. However, with the same remark as the colleague: I do not have access to the hardware part to test this functionality.

sidihamady commented 8 months ago

@editorialbot generate my checklist

editorialbot commented 8 months ago

Checklists can only be created once the review has started in the review issue

HaoZeke commented 8 months ago

@editorialbot add @sidihamady as reviewer

Hi @HaoZeke , I can review it. However, with the same remark as the colleague: I do not have access to the hardware part to test this functionality.

Excellent, thank you for the prompt response, testing only the software component will be fine.

editorialbot commented 8 months ago

@sidihamady added to the reviewers list!

HaoZeke commented 8 months ago

@HaoZeke I can do a review from a general perspective on code quality, the paper, and so-on. But I do not have access to the hardware devices I believe the package is meant to control, and could not verify the functionality in a strict way

Hey @HaoZeke @brandondube ,

Just want to clarify on the hardware part: Most part of the software and majority of the functionalities don't require the hardware. All the hardware related code is in pySLM2/utils.

And @brandondube Thank you for your interest in reviewing the paper/repo!

@ldes89150, since we haven't found any reviewers for testing the hardware integration, would you be willing to add [not-reviewed] to the section describing the integration? If so, we can immediately go ahead and start the review.

Any suggestions for other reviewers for the hardware section would also be very welcome.

sidihamady commented 8 months ago

@editorialbot generate my checklist

editorialbot commented 8 months ago

Checklists can only be created once the review has started in the review issue