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

editorialbot · 2024-01-10T21:30:23Z

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

Status

Status badge code:

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

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

editorialbot · 2024-01-10T21:30:25Z

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 · 2024-01-10T21:30:28Z

Checking the BibTeX entries failed with the following error:

No paper file path

editorialbot · 2024-01-10T21:30:29Z

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 · 2024-01-10T21:30:30Z

Failed to discover a Statement of need section in paper

editorialbot · 2024-01-10T21:30:51Z

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

kyleniemeyer · 2024-01-10T21:31:03Z

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 · 2024-01-10T21:32:28Z

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

ldes89150 · 2024-01-10T21:52:59Z

Hi @kyleniemeyer ,

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

kyleniemeyer · 2024-01-10T21:54:21Z

@editorialbot set paper.md as branch

editorialbot · 2024-01-10T21:54:23Z

Done! branch is now paper.md

kyleniemeyer · 2024-01-10T21:54:51Z

@editorialbot generate pdf

editorialbot · 2024-01-10T21:55:19Z

⚠️ An error happened when generating the pdf.

kyleniemeyer · 2024-01-10T21:59:44Z

@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 · 2024-01-10T22:00:31Z

⚠️ An error happened when generating the pdf.

kyleniemeyer · 2024-01-10T22:01:13Z

@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 · 2024-01-11T09:02:51Z

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 · 2024-01-11T19:28:11Z

@editorialbot set paper as branch

editorialbot · 2024-01-11T19:28:13Z

Done! branch is now paper

marvelousmonicaaa · 2024-01-11T19:28:27Z

@editorialbot generate pdf

editorialbot · 2024-01-11T19:29:35Z

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

editorialbot · 2024-01-11T19:30:13Z

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⚠️ 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 · 2024-01-11T19:31:41Z

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

sidihamady · 2024-01-31T08:15:15Z

@editorialbot generate my checklist

editorialbot · 2024-01-31T08:15:17Z

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

HaoZeke · 2024-01-31T11:41:52Z

@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 · 2024-01-31T11:41:55Z

@sidihamady added to the reviewers list!

HaoZeke · 2024-01-31T11:45:37Z

@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 · 2024-02-01T09:16:15Z

@editorialbot generate my checklist

editorialbot · 2024-02-01T09:16:16Z

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

HaoZeke · 2024-02-01T14:53:59Z

Sorry @sidihamady, I need to wait for @ldes89150 to confirm the [not-reviewed] label for the hardware section before I can start this one.

The checklist can be generated after that, in the [REVIEW] thread.

ldes89150 · 2024-02-02T04:33:28Z

@editorialbot commands

editorialbot · 2024-02-02T04:33:30Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

ldes89150 · 2024-02-02T04:33:36Z

@editorialbot commands

editorialbot · 2024-02-02T04:33:39Z

Hello @ldes89150, 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

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@editorialbot generate my checklist

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@editorialbot generate pdf

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@editorialbot generate preprint

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

ldes89150 · 2024-02-02T04:33:56Z

@editorialbot generate my checklist

editorialbot · 2024-02-02T04:33:57Z

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

ldes89150 · 2024-02-02T04:36:20Z

@HaoZeke What exactly do I need to do?
I confirm no review for the hardware section (pySLM2/utils).

ldes89150 · 2024-02-02T04:39:40Z

I added it to the paper. Let me know if there is still something I need to do.
https://github.com/QITI/pySLM2/blob/paper/paper.md#hardware-controls-not-reviewed

Thanks!

ldes89150 · 2024-02-02T04:40:35Z

@editorialbot generate pdf

editorialbot · 2024-02-02T04:41:18Z

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

editorialbot · 2024-02-02T04:41:38Z

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

editorialbot · 2024-02-02T04:42:00Z

Five most similar historical JOSS papers:

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editorialbot · 2024-02-02T04:42:15Z

Five most similar historical JOSS papers:

SkyPy: A package for modelling the Universe
Submitting author: @rrjbca
Handling editor: @arfon (Active)
Reviewers: @cescalara, @rmorgan10
Similarity score: 0.8171

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: 0.8155

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: 0.8144

prysm: A Python optics module
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Handling editor: @xuanxu (Active)
Reviewers: @aquilesC
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PiSCAT: A Python Package for Interferometric Scattering Microscopy
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Reviewers: @ziatdinovmax, @aquilesC
Similarity score: 0.8100

⚠️ 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.

ktahar · 2024-02-02T08:42:28Z

I could review this paper but the situation is the same as the other reviewers; I don't have the hardware.
(This reply might be too late, sorry.)

HaoZeke · 2024-02-02T11:35:43Z

@editorialbot add @ktahar as reviewer

I could review this paper but the situation is the same as the other reviewers; I don't have the hardware.

That's alright, thanks for accepting the request to review.

editorialbot · 2024-02-02T11:35:45Z

@ktahar added to the reviewers list!

HaoZeke · 2024-02-02T11:36:17Z

@editorialbot start review

@ldes89150 thanks for the quick turn-around. We can now proceed with the review.

editorialbot · 2024-02-02T11:36:21Z

OK, I've started the review over in #6315.

editorialbot added pre-review Track: 3 (PE) Physics and Engineering labels Jan 10, 2024

editorialbot added the Python label Jan 10, 2024

kyleniemeyer added waitlisted Submissions in the JOSS backlog due to reduced service mode. and removed Python labels Jan 10, 2024

kyleniemeyer added the Python label Jan 10, 2024

openjournals deleted a comment from editorialbot Jan 10, 2024

editorialbot assigned sidihamady Jan 31, 2024

editorialbot assigned ktahar Feb 2, 2024

editorialbot closed this as completed Feb 2, 2024

ktahar mentioned this issue Feb 22, 2024

[REVIEW]: Quantum Instrumentation Control Kit - Defect Arbitrary Waveform Generator (QICK-DAWG): A Quantum Sensing Control Framework for Quantum Defects #6380

Open

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

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

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