[PRE REVIEW]: Quantum Instrumentation Control Kit - Defect Arbitrary Waveform Generator (QICK-DAWG): A Quantum Sensing Control Framework for Quantum Defects #6102

editorialbot · 2023-11-30T16:48:58Z

Submitting author: @egriendeau (Emmeline Riendeau)
Repository: https://github.com/sandialabs/qick-dawg
Branch with paper.md (empty if default branch): paper
Version: 0.1.0
Editor: @phibeck
Reviewers: @14shreyasp, @ktahar, @sidihamady
Managing EiC: Kyle Niemeyer

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/95570a487ebbef23514eb099e5ffc656/status.svg)](https://joss.theoj.org/papers/95570a487ebbef23514eb099e5ffc656)

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

editorialbot · 2023-11-30T16:49:01Z

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:

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editorialbot · 2023-11-30T16:49:08Z

Software report:

github.com/AlDanial/cloc v 1.88  T=1.25 s (341.1 files/s, 308659.5 lines/s)
-----------------------------------------------------------------------------------
Language                         files          blank        comment           code
-----------------------------------------------------------------------------------
XML                                 84             44             32         279370
Verilog-SystemVerilog              112           4687           4890          16865
VHDL                                75           2045           5173          16365
Tcl/Tk                              28           1221           1136          14610
Python                              55           3016           5742          10114
JSON                                 2              0              0           3175
SVG                                  9              8              8           2328
Jupyter Notebook                    19              0           9969           2220
Markdown                            15            314              0            768
Perl                                 2            146            132            576
DOS Batch                            2             39              5            231
MATLAB                               5             64             73            198
make                                 2             36              6            171
TeX                                  4              9              0            119
reStructuredText                     4             67             74            104
YAML                                 4             13             35             89
Assembly                             2             11             19             33
CSS                                  1              3              3             15
Bourne Shell                         2              3              5             12
-----------------------------------------------------------------------------------
SUM:                               427          11726          27302         347363
-----------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-11-30T16:49:13Z

Wordcount for paper.md is 1820

editorialbot · 2023-11-30T16:49:33Z

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

OK DOIs

- 10.1063/5.0076249 is OK
- 10.1145/3529397 is OK
- 10.1109/QCE53715.2022.00123 is OK
- 10.1088/2633-4356/ace095 is OK
- 10.1109/TQE.2021.3116540 is OK

MISSING DOIs

- 10.1038/s41596-019-0201-3 may be a valid DOI for title: Quantum diamond spectrometer for nanoscale NMR and ESR spectroscopy
- 10.1038/natrevmats.2017.88 may be a valid DOI for title: Probing condensed matter physics with magnetometry based on nitrogen-vacancy centres in diamond
- 10.1063/5.0083774 may be a valid DOI for title: Nanoscale solid-state nuclear quadrupole resonance spectroscopy using depth-optimized nitrogen-vacancy ensembles in diamond
- 10.1126/sciadv.abg8562 may be a valid DOI for title: Noninvasive measurements of spin transport properties of an antiferromagnetic insulator

INVALID DOIs

- None

editorialbot · 2023-11-30T16:50:20Z

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

editorialbot · 2023-11-30T16:51:05Z

Five most similar historical JOSS papers:

A Framework to Quality Control Oceanographic Data
Submitting author: @castelao
Handling editor: @kthyng (Active)
Reviewers: @jessicaaustin, @evanleeturner
Similarity score: 0.8028

UQit: A Python package for uncertainty quantification (UQ) in computational fluid dynamics (CFD)
Submitting author: @salrm8
Handling editor: @drvinceknight (Active)
Reviewers: @jayten, @ctdegroot
Similarity score: 0.8011

MUQ: The MIT Uncertainty Quantification Library
Submitting author: @mparno
Handling editor: @pdebuyl (Active)
Reviewers: @martinmodrak, @georgiastuart
Similarity score: 0.7972

ShakeNBreak: Navigating the defect configurational landscape
Submitting author: @ireaml
Handling editor: @rkurchin (Active)
Reviewers: @obaica, @mkhorton
Similarity score: 0.7916

CheckQC: Quick quality control of Illumina sequencing runs
Submitting author: @johandahlberg
Handling editor: @pjotrp (Retired)
Reviewers: @brainstorm
Similarity score: 0.7913

⚠️ 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.

egriendeau · 2023-11-30T16:55:41Z

Potential reviewers who might be a good fit, JackTyson, mzszym, OHildreth

kyleniemeyer · 2023-11-30T16:56:07Z

Hello @egriendeau, we'll use this pre-review issue to sort out any initial problems with the paper, and find an editor and reviewers.

It looks like the citations in the paper are not building properly, because you have backticks (``) around all the citation commands—please remove those. The citation commands should just appear normally in the text source (e.g., "ARTIQ [@Bourdeauducq:2016]"), though make sure there is a space before the [@ or `@`.

In addition, can you check the missing DOI warnings above, and add any that are missing?

Also, I noticed in the submission notes that you mentioned publications related to the software. Do any of those describe the software package itself?

egriendeau · 2023-11-30T16:56:21Z

@editorialbot commands

editorialbot · 2023-11-30T16:56:25Z

Hello @egriendeau, 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

egriendeau · 2023-11-30T16:58:18Z

Hello @egriendeau, we'll use this pre-review issue to sort out any initial problems with the paper, and find an editor and reviewers.

It looks like the citations in the paper are not building properly, because you have backticks (``) around all the citation commands—please remove those. The citation commands should just appear normally in the text source (e.g., "ARTIQ [@Bourdeauducq:2016]"), though make sure there is a space before the [@ or `@`.

In addition, can you check the missing DOI warnings above, and add any that are missing?

Also, I noticed in the submission notes that you mentioned publications related to the software. Do any of those describe the software package itself?

I will fix the the citation back tick error and check on the DOIs. None of the publications descibe this software package itself.

egriendeau · 2023-11-30T17:12:52Z

I fixed the citation ticks and added the DOIs. It looks like the citations are generating correctly in the proof pdf now.

kyleniemeyer · 2023-11-30T17:29:58Z

@editorialbot generate pdf

editorialbot · 2023-11-30T17:31:23Z

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

editorialbot · 2023-11-30T17:32:05Z

Five most similar historical JOSS papers:

A Framework to Quality Control Oceanographic Data
Submitting author: @castelao
Handling editor: @kthyng (Active)
Reviewers: @jessicaaustin, @evanleeturner
Similarity score: 0.8045

UQit: A Python package for uncertainty quantification (UQ) in computational fluid dynamics (CFD)
Submitting author: @salrm8
Handling editor: @drvinceknight (Active)
Reviewers: @jayten, @ctdegroot
Similarity score: 0.8009

MUQ: The MIT Uncertainty Quantification Library
Submitting author: @mparno
Handling editor: @pdebuyl (Active)
Reviewers: @martinmodrak, @georgiastuart
Similarity score: 0.7984

ShakeNBreak: Navigating the defect configurational landscape
Submitting author: @ireaml
Handling editor: @rkurchin (Active)
Reviewers: @obaica, @mkhorton
Similarity score: 0.7928

CheckQC: Quick quality control of Illumina sequencing runs
Submitting author: @johandahlberg
Handling editor: @pjotrp (Retired)
Reviewers: @brainstorm
Similarity score: 0.7923

⚠️ 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.

phibeck · 2024-01-09T11:19:43Z

Hi @kyleniemeyer I could take this on.

kyleniemeyer · 2024-01-09T17:34:14Z

@editorialbot add @phibeck as editor

Thanks @phibeck!

editorialbot · 2024-01-09T17:34:17Z

Assigned! @phibeck is now the editor

phibeck · 2024-01-09T19:41:30Z

Hi @egriendeau, thanks for your submission and for the reviewer suggestions. I'll be looking for reviewers next. As a side note, with six pages your paper is on the longer side (we aim for <= 1000 words, but not strict), so you could think about moving parts, e.g. the example features, into the repository directly.

phibeck · 2024-01-09T19:42:52Z

👋 @JackTyson, @mzszym & @OHildreth, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

phibeck · 2024-01-09T19:43:16Z

@editorialbot check references

editorialbot · 2024-01-09T19:43:23Z

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

OK DOIs

- 10.1063/5.0076249 is OK
- 10.1145/3529397 is OK
- 10.1109/QCE53715.2022.00123 is OK
- 10.1088/2633-4356/ace095 is OK
- 10.1109/TQE.2021.3116540 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.5281/zenodo.1478113 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/natrevmats.2017.88 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1063/5.0083774 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1126/sciadv.abg8562 is INVALID because of 'https://doi.org/' prefix

phibeck · 2024-01-09T19:45:21Z

@egriendeau Could you also please fix the DOIs (remove the extra 'https://doi.org/' prefix) Thanks!

egriendeau · 2024-01-09T19:56:42Z

@editorialbot check references

phibeck · 2024-02-13T16:01:14Z

Hi @egriendeau a few more notes on the manuscript: In line 45 in the manuscript one reference isn't picked up. Could you please also check the formatting of the references in lines 134f. in the text, it looks like perhaps this isn't the intentional formatting. There are also still a couple of https://doi.org/ too many in some of the references in the manuscript.

In the meantime, I'm still trying to find reviewers. If you have more suggestions, let me know.

14shreyasp · 2024-02-14T06:41:38Z

Okay, thank you @jayich!

👋 @14shreyasp would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

Yes, I am happy to review it!

phibeck · 2024-02-14T16:05:37Z

Great, thank you very much!

phibeck · 2024-02-14T16:06:22Z

@editorialbot add @14shreyasp as reviewer

editorialbot · 2024-02-14T16:06:25Z

@14shreyasp added to the reviewers list!

egriendeau · 2024-02-14T17:01:32Z

@editorialbot generate pdf

egriendeau · 2024-02-14T17:02:09Z

@editorialbot check repository

editorialbot · 2024-02-14T17:02:17Z

Software report:

github.com/AlDanial/cloc v 1.88  T=1.32 s (322.6 files/s, 291901.2 lines/s)
-----------------------------------------------------------------------------------
Language                         files          blank        comment           code
-----------------------------------------------------------------------------------
XML                                 84             44             32         279370
Verilog-SystemVerilog              112           4687           4890          16865
VHDL                                75           2045           5173          16365
Tcl/Tk                              28           1221           1136          14610
Python                              55           3016           5742          10114
JSON                                 2              0              0           3175
SVG                                  9              8              8           2328
Jupyter Notebook                    19              0          10016           2220
Markdown                            15            305              0            746
Perl                                 2            146            132            576
DOS Batch                            2             39              5            231
MATLAB                               5             64             73            198
make                                 2             36              6            171
TeX                                  4              9              0            120
reStructuredText                     4             67             74            104
YAML                                 4             13             35             89
Assembly                             2             11             19             33
CSS                                  1              3              3             15
Bourne Shell                         2              3              5             12
-----------------------------------------------------------------------------------
SUM:                               427          11717          27349         347342
-----------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2024-02-14T17:02:21Z

Wordcount for paper.md is 1463

editorialbot · 2024-02-14T17:02:51Z

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

editorialbot · 2024-02-14T17:03:44Z

Five most similar historical JOSS papers:

A Framework to Quality Control Oceanographic Data
Submitting author: @castelao
Handling editor: @kthyng (Active)
Reviewers: @jessicaaustin, @evanleeturner
Similarity score: 0.8018

UQit: A Python package for uncertainty quantification (UQ) in computational fluid dynamics (CFD)
Submitting author: @salrm8
Handling editor: @drvinceknight (Active)
Reviewers: @jayten, @ctdegroot
Similarity score: 0.7963

ShakeNBreak: Navigating the defect configurational landscape
Submitting author: @ireaml
Handling editor: @rkurchin (Active)
Reviewers: @obaica, @mkhorton
Similarity score: 0.7923

MUQ: The MIT Uncertainty Quantification Library
Submitting author: @mparno
Handling editor: @pdebuyl (Active)
Reviewers: @martinmodrak, @georgiastuart
Similarity score: 0.7919

CheckQC: Quick quality control of Illumina sequencing runs
Submitting author: @johandahlberg
Handling editor: @pjotrp (Retired)
Reviewers: @brainstorm
Similarity score: 0.7906

⚠️ 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.

egriendeau · 2024-02-14T17:07:15Z

@editorialbot check references

editorialbot · 2024-02-14T17:07:23Z

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

OK DOIs

- 10.1063/5.0076249 is OK
- 10.1145/3529397 is OK
- 10.1109/QCE53715.2022.00123 is OK
- 10.48550/arXiv.2309.17233 is OK
- 10.5281/zenodo.1478113 is OK
- 10.1038/natrevmats.2017.88 is OK
- 10.1088/2633-4356/ace095 is OK
- 10.1063/5.0083774 is OK
- 10.1126/sciadv.abg8562 is OK
- 10.1109/TQE.2021.3116540 is OK

MISSING DOIs

- None

INVALID DOIs

- None

egriendeau · 2024-02-14T17:07:53Z

@editorialbot generate pdf

editorialbot · 2024-02-14T17:09:17Z

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

editorialbot · 2024-02-14T17:09:56Z

Five most similar historical JOSS papers:

A Framework to Quality Control Oceanographic Data
Submitting author: @castelao
Handling editor: @kthyng (Active)
Reviewers: @jessicaaustin, @evanleeturner
Similarity score: 0.8018

UQit: A Python package for uncertainty quantification (UQ) in computational fluid dynamics (CFD)
Submitting author: @salrm8
Handling editor: @drvinceknight (Active)
Reviewers: @jayten, @ctdegroot
Similarity score: 0.7963

ShakeNBreak: Navigating the defect configurational landscape
Submitting author: @ireaml
Handling editor: @rkurchin (Active)
Reviewers: @obaica, @mkhorton
Similarity score: 0.7923

MUQ: The MIT Uncertainty Quantification Library
Submitting author: @mparno
Handling editor: @pdebuyl (Active)
Reviewers: @martinmodrak, @georgiastuart
Similarity score: 0.7919

CheckQC: Quick quality control of Illumina sequencing runs
Submitting author: @johandahlberg
Handling editor: @pjotrp (Retired)
Reviewers: @brainstorm
Similarity score: 0.7906

⚠️ 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.

phibeck · 2024-02-16T16:20:10Z

👋 @sidihamady & @ktahar, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

In case this submission is not directly be in your area of expertise, we would still appreciate your review of the quality of the software.

ktahar · 2024-02-17T08:15:53Z

Hi @phibeck , I'm particulary interested in this paper and I would like to review.
But I've already been assigned for another paper #6204 and amount of my spare time is limited until several weeks from now.
So my review will take quite a while, like a month.

Please assign me if such lead time is acceptable.

sidihamady · 2024-02-17T14:16:30Z

Dear @phibeck, I'm in a similar situation to my colleague: I can't free up time until early March to mid-March. If it fits, I can review the article.

phibeck · 2024-02-19T20:01:27Z

Thank you for your responses. @ktahar I apologize I missed that you are already reviewing another submission, but would be very grateful for your help with this one when you find the time. Since it has been difficult finding reviewers for this submission, I will assign you and @sidihamady for this one, keeping your time constraints in mind. Thanks in advance!

phibeck · 2024-02-19T20:02:03Z

@editorialbot add @ktahar as reviewer

editorialbot · 2024-02-19T20:02:06Z

@ktahar added to the reviewers list!

phibeck · 2024-02-19T20:02:19Z

@editorialbot add @sidihamady as reviewer

editorialbot · 2024-02-19T20:02:22Z

@sidihamady added to the reviewers list!

phibeck · 2024-02-19T20:02:55Z

@editorialbot start review

editorialbot · 2024-02-19T20:02:58Z

OK, I've started the review over in #6380.

editorialbot added pre-review Track: 3 (PE) Physics and Engineering labels Nov 30, 2023

editorialbot added Jupyter Notebook Tcl labels Nov 30, 2023

editorialbot added the VHDL label Nov 30, 2023

editorialbot assigned phibeck Jan 9, 2024

editorialbot assigned 14shreyasp Feb 14, 2024

editorialbot assigned ktahar Feb 19, 2024

editorialbot assigned sidihamady Feb 19, 2024

editorialbot closed this as completed Feb 19, 2024

[PRE REVIEW]: Quantum Instrumentation Control Kit - Defect Arbitrary Waveform Generator (QICK-DAWG): A Quantum Sensing Control Framework for Quantum Defects #6102

[PRE REVIEW]: Quantum Instrumentation Control Kit - Defect Arbitrary Waveform Generator (QICK-DAWG): A Quantum Sensing Control Framework for Quantum Defects #6102

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