[REVIEW]: pySLM2: A full-stack python package for holographic beam shaping #6315

editorialbot · 2024-02-02T11:36:20Z

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, @wavefrontshaping
Archive: 10.5281/zenodo.14025566

Status

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

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@brandondube & @sidihamady & @ktahar & @wavefrontshaping, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @brandondube

📝 Checklist for @sidihamady

📝 Checklist for @wavefrontshaping

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

editorialbot · 2024-02-02T11:36:23Z

Hello humans, 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:

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

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editorialbot · 2024-02-02T11:36:25Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (342.9 files/s, 34522.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             16              0            159
Markdown                         1             39              0             65
YAML                             1              1              4             18
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SUM:                             3             56              4            242
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gitinspector failed to run statistical information for the repository

editorialbot · 2024-02-02T11:36:26Z

Wordcount for paper.md is 1738

editorialbot · 2024-02-02T11:36:26Z

Failed to discover a valid open source license

editorialbot · 2024-02-02T11:37:40Z

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

editorialbot · 2024-02-02T11:38:28Z

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

OK DOIs

- 10.5281/zenodo.6121191 is OK

MISSING DOIs

- 10.1038/s41534-021-00396-0 may be a valid DOI for title: Reprogrammable and high-precision holographic optical addressing of trapped ions for scalable quantum control
- 10.1364/oe.24.013881 may be a valid DOI for title: Ultra-precise holographic beam shaping for microscopic quantum control
- 10.1016/s0079-6638(08)70072-6 may be a valid DOI for title: III computer-generated holograms: Techniques and applications
- 10.1038/srep00721 may be a valid DOI for title: Robust digital holography for ultracold atom trapping
- 10.1103/physrevlett.127.263603 may be a valid DOI for title: Super-resolved imaging of a single cold atom on a nanosecond timescale
- 10.1103/physrevlett.127.143602 may be a valid DOI for title: Optical superresolution sensing of a trapped ion’s wave packet size
- 10.1103/physrevlett.97.170406 may be a valid DOI for title: Quantized rotation of atoms from photons with orbital angular momentum
- 10.1103/physrevlett.78.4713 may be a valid DOI for title: Novel optical trap of atoms with a doughnut beam
- 10.1364/oe.18.017193 may be a valid DOI for title: Multi-focus two-photon polymerization technique based on individually controlled phase modulation
- 10.1364/ol.44.003178 may be a valid DOI for title: Large-scale uniform optical focus array generation with a phase spatial light modulator
- 10.1038/nature15750 may be a valid DOI for title: Measuring entanglement entropy in a quantum many-body system
- 10.1038/nmeth.1241 may be a valid DOI for title: Holographic photolysis of caged neurotransmitters

INVALID DOIs

- None

HaoZeke · 2024-02-02T16:30:19Z

@ldes89150, sorry about this, but after deliberations with @kyleniemeyer (our Associate Editor-in-Chief) I believe it would be best to remove the section on Hardware Integration instead of leaving it in with [not-reviewed]. The rest of the review can proceed, just without that section.

The alternative (preferred) would be having a reviewer with the requisite hardware, but removing the section works as well.

kyleniemeyer · 2024-02-02T16:32:57Z

@ldes89150 yes - we can include that section in the paper, if you are able to help us find an editor with access to the hardware.

ldes89150 · 2024-02-03T03:46:21Z

@kyleniemeyer @HaoZeke
Based on the opensource works, a researcher I can think of that may have the right equipment is: https://github.com/wavefrontshaping

I can declare there is no conflict of interest.

HaoZeke · 2024-02-03T12:34:51Z

hi @wavefrontshaping 👋 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?

wavefrontshaping · 2024-02-08T14:03:43Z

Hi all,
Works for me. I can review this work!
Not sure how this works though, I read JOSS review guidelines, but where am I supposed to report my comments? Here?

HaoZeke · 2024-02-08T14:46:45Z

@editorialbot add @wavefrontshaping as reviewer

Thanks a ton for taking time to review this!

Not sure how this works though, I read JOSS review guidelines, but where am I supposed to report my comments? Here?

The review checklist is generated here by commenting @editorialbot generate my checklist, and the final discussion is here (along with responses to the review) but we also recommend directly opening issues in the repository (mentioning that they're part of a JOSS review.

editorialbot · 2024-02-08T14:46:48Z

@wavefrontshaping added to the reviewers list!

wavefrontshaping · 2024-02-08T16:29:03Z

Hi,

I installed the package in a new environment.
I tried to build the docs using make html.

First, the dependencies for the docs are not installed when I installed the package, did I do something wrong?
I did not find instructions for making the docs in the repo (maybe I missed something), so I add the packages one by one when the errors appeared.
It may be useful to a requirement file in the docs folder.

Then, after installing the necessary packages, I run into an error:

Theme error:
no theme named 'furo' found (missing theme.conf?)

How do I solve that?

brandondube · 2024-02-08T16:31:14Z

👋 @wavefrontshaping FYI, JOSS likes reviewers to use github issues on the being-reviewed repository for their reviews, not post questions, etc in the review issue on JOSS.

ldes89150 · 2024-02-08T17:12:50Z

Hey @wavefrontshaping ,

Thank you so much for helping the review. I opened an issue on github for the problem you encountered.
QITI/pySLM2#10

sidihamady · 2024-02-09T10:07:10Z

Review checklist for @sidihamady

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/QITI/pySLM2?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@ldes89150) 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?

sidihamady · 2024-02-09T10:37:58Z

Issue: Authors can add a header to each source file

QITI/pySLM2#12

sidihamady · 2024-02-14T09:44:50Z

Installation: The package is easy to install and the examples provided allow you to test it without problem. The only example that I can't test is obviously the one that uses the Luxbeam controller since I don't have access to the hardware.

sidihamady · 2024-02-16T09:32:04Z

The use of TensorFlow is a good choice. It can permit faster calculations and other possibilities. Unfortunately I test it only on CPU, without using GPU, then I have no quantitative comparison between calculations speed using GPU and CPU.
The code is well written, documented and modular. Then it is easy to understand and to adapt to a specific application.
The manuscript is well written, clear and the examples are presented coherently.
In the "statement of need" section, authors highlight the advantage of holographic beam shaping using SLM, and then the need of their package. But are there other packages (in Python or not) with the same functionality? And if so, what else does pySLM2 bring?
The relative contribution of the three authors is not mentioned. It is assumed that the first author is the main one, but it is necessary to clarify the contributions.

kyleniemeyer · 2024-02-16T13:50:54Z

Hello @HaoZeke, @ktahar has asked to step down from reviewing this article. Fortunately, it has more than enough reviewers already.

kyleniemeyer · 2024-02-16T13:51:01Z

@editorialbot remove @ktahar as reviewer

marvelousmonicaaa · 2024-11-09T15:20:16Z

@marvelousmonicaaa could you update the reference by merging QITI/pySLM2#30?

Hey @HaoZeke, I've merge it. Thanks! Hopefully there's no other issues with the reference!

May I ask what tools you use to check references as editor? Maybe next time we can do the checks ourselves.

HaoZeke · 2024-11-09T23:12:00Z

@editorialbot recommend-accept

@marvelousmonicaaa generally I was using editorialbot commands, although that particular issue (wrong labels) should show up if you tried to build the .tex file locally.

editorialbot · 2024-11-09T23:12:01Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-11-09T23:12:19Z

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

✅ OK DOIs

- 10.1038/s41534-021-00396-0 is OK
- 10.1364/OE.24.013881 is OK
- 10.1016/S0079-6638(08)70072-6 is OK
- 10.5281/zenodo.6121191 is OK
- 10.1038/srep00721 is OK
- 10.1103/PhysRevLett.127.263603 is OK
- 10.1103/PhysRevLett.127.143602 is OK
- 10.1103/PhysRevResearch.6.033038 is OK
- 10.1103/PhysRevLett.97.170406 is OK
- 10.1103/PhysRevLett.78.4713 is OK
- 10.1364/OE.18.017193 is OK
- 10.1364/OL.44.003178 is OK
- 10.1038/nature15750 is OK
- 10.1038/nmeth.1241 is OK
- 10.1364/JOSA.61.000648 is OK
- 10.61835/jcv is OK
- 10.1364/DH.2021.DTh7C.1 is OK
- 10.1364/OPTICA.6.000465 is OK
- 10.1364/OE.16.002176 is OK
- 10.1038/s41467-024-50864-2 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A practical algorithm for the determination of pha...
- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-11-09T23:13:41Z

👋 @openjournals/pe-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#6109, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kyleniemeyer · 2024-11-15T18:17:55Z

@ldes89150 can you please correct the author list in the Zenodo archive to match the paper?

kyleniemeyer · 2024-11-15T18:18:23Z

or @marvelousmonicaaa, if both of you are authors

kyleniemeyer · 2024-11-15T18:23:36Z

@ldes89150 @marvelousmonicaaa regarding the paper, a few things to fix:

figure mentions in the paper currently appear as "Fig. Figure 1" and "Fig. Figure 2". Please remove the unnecessary "Fig." occurences in the text.
The paper mentions depending on TensorFlow, but I don't see a citation for that. Please add a citation for that and any other dependencies.
When you have instances of author names in the text for a citation, please use the @author:2001 citation command format (without square brackets) to get the author name in the text like "Author et al. (2001)". (Such as in the sentence "For a detailed description of the latter method, one can refer to Shih et al. (Shih et al., 2021)." -> "For a detailed description of the latter method, one can refer to Shih et al. (2021).")

ldes89150 · 2024-11-26T02:55:16Z

@editorialbot check references

editorialbot · 2024-11-26T02:55:43Z

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

✅ OK DOIs

- 10.1038/s41534-021-00396-0 is OK
- 10.1364/OE.24.013881 is OK
- 10.1016/S0079-6638(08)70072-6 is OK
- 10.5281/zenodo.6121191 is OK
- 10.1038/srep00721 is OK
- 10.1103/PhysRevLett.127.263603 is OK
- 10.1103/PhysRevLett.127.143602 is OK
- 10.1103/PhysRevResearch.6.033038 is OK
- 10.1103/PhysRevLett.97.170406 is OK
- 10.1103/PhysRevLett.78.4713 is OK
- 10.1364/OE.18.017193 is OK
- 10.1364/OL.44.003178 is OK
- 10.1038/nature15750 is OK
- 10.1038/nmeth.1241 is OK
- 10.1364/JOSA.61.000648 is OK
- 10.61835/jcv is OK
- 10.1364/DH.2021.DTh7C.1 is OK
- 10.1364/OPTICA.6.000465 is OK
- 10.1364/OE.16.002176 is OK
- 10.1038/s41467-024-50864-2 is OK
- 10.5281/zenodo.13989084 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A practical algorithm for the determination of pha...
- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

ldes89150 · 2024-11-26T02:56:20Z

@editorialbot generate pdf

editorialbot · 2024-11-26T02:57:46Z

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

marvelousmonicaaa · 2024-12-03T15:14:22Z

Hi @kyleniemeyer, sorry about the delay. We have fixed most of the issues now. Just one thing to confirm, I noticed the DOI number in the pdf generated by editoialbot is a '10.xxxxx/draft". I wonder if that is autogenerated DOI for this paper and it will be an actual number after it is published?

kyleniemeyer · 2024-12-05T22:43:31Z

@marvelousmonicaaa that paper DOI is a placeholder, it will be updated after accepting.

I only see one minor remaining issue: the author field is incorrect for the new Tensorflow citation (appearing as "Developers, T."). Anything that isn't a person's name needs to be protected with extra { }, otherwise it gets interpreted (and abbreviated) like a name.

editorialbot · 2024-12-07T04:14:22Z

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

marvelousmonicaaa · 2024-12-09T18:35:46Z

@editorialbot generate pdf

editorialbot · 2024-12-09T18:37:10Z

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

marvelousmonicaaa · 2024-12-09T18:40:20Z

@kyleniemeyer The tensorflow reference should be good now! Let me know if you spot any new issues!

kyleniemeyer · 2024-12-11T16:19:29Z

@editorialbot accept

editorialbot · 2024-12-11T16:19:31Z

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

editorialbot · 2024-12-11T16:26:26Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Shih
  given-names: Chung-You
  orcid: "https://orcid.org/0000-0002-7561-6833"
- family-names: Zhu
  given-names: Jingwen
  orcid: "https://orcid.org/0009-0009-0699-8258"
- family-names: Islam
  given-names: Rajibul
  orcid: "https://orcid.org/0000-0002-6483-8932"
contact:
- family-names: Shih
  given-names: Chung-You
  orcid: "https://orcid.org/0000-0002-7561-6833"
doi: 10.5281/zenodo.14025566
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Shih
    given-names: Chung-You
    orcid: "https://orcid.org/0000-0002-7561-6833"
  - family-names: Zhu
    given-names: Jingwen
    orcid: "https://orcid.org/0009-0009-0699-8258"
  - family-names: Islam
    given-names: Rajibul
    orcid: "https://orcid.org/0000-0002-6483-8932"
  date-published: 2024-12-11
  doi: 10.21105/joss.06315
  issn: 2475-9066
  issue: 104
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6315
  title: "pySLM2: A full-stack python package for holographic beam
    shaping"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06315"
  volume: 9
title: "pySLM2: A full-stack python package for holographic beam
  shaping"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-12-11T16:26:31Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-12-11T16:26:32Z

🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

editorialbot · 2024-12-11T16:26:32Z

🚨🚨🚨 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.06315 joss-papers#6251
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06315
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2024-12-11T16:30:30Z

Congratulations @ldes89150 & @marvelousmonicaaa on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already.

Many thanks to @brandondube, @sidihamady, and @wavefrontshaping for reviewing this, and @HaoZeke for editing.

editorialbot · 2024-12-11T16:30:33Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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editorialbot added Python review Track: 3 (PE) Physics and Engineering labels Feb 2, 2024

editorialbot assigned HaoZeke Feb 2, 2024

editorialbot mentioned this issue Feb 2, 2024

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

Closed

editorialbot added the TeX label Feb 2, 2024

editorialbot assigned wavefrontshaping Feb 8, 2024

ktahar mentioned this issue Feb 16, 2024

[PRE REVIEW]: NOMAD CAMELS: Configurable Application for Measurements, Experiments and Laboratory Systems #6204

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Nov 9, 2024

editorialbot added accepted published Papers published in JOSS labels Dec 11, 2024

kyleniemeyer closed this as completed Dec 11, 2024

[REVIEW]: pySLM2: A full-stack python package for holographic beam shaping #6315

[REVIEW]: pySLM2: A full-stack python package for holographic beam shaping #6315

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