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

[editorialbot]

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

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

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[editorialbot]

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[editorialbot]

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]

Wordcount for paper.md is 1820

[editorialbot]

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]

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

[editorialbot]

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]

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

[kyleniemeyer]

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]

@editorialbot commands

[editorialbot]

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

# List all available commands
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# 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

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# 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]

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]

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

[kyleniemeyer]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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]

Hi @kyleniemeyer I could take this on.

[kyleniemeyer]

@editorialbot add @phibeck as editor

Thanks @phibeck!

[editorialbot]

Assigned! @phibeck is now the editor

[phibeck]

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]

:wave: @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]

@editorialbot check references

[editorialbot]

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]

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

[egriendeau]

@editorialbot check references

[editorialbot]

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
- 10.5281/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]

@phibeck The DOIs should be all set now

[phibeck]

:wave: @kavanase, @peter-janderks & @TejasAvinashShetty, 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

[kavanase]

Hi @phibeck, unfortunately this software is not in my area of expertise, as it is geared toward experimental measurements (of quantum defect phenomena).

[egriendeau]

@phibeck Can we suggest reviewers in the subject area but who have not reviewed a JOSS paper before? Also, I'm working on cutting the paper length down a bit. Thanks!

[egriendeau]

Andrew Jayich (jayich@physics.ucsb.edu) at UCSB would be good

[phibeck]

@egriendeau yes absolutely, that would be very helpful and it perfectly fine as long as there's no conflict of interest. If you have more suggestions, please mention their github handles (without the @ to avoid tagging them). Thank you.

[phibeck]

:wave: @jayich, 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

[egriendeau]

@phibeck I just uploaded a revised paper copy

[egriendeau]

@editorialbot commands

[editorialbot]

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]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=1.64 s (260.6 files/s, 235790.5 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          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            122
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         347344
-----------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1464

[jayich]

I am concerned about the possibility of perceived COI. I have found someone with more expertise in the field who may review: @14shreyasp

[phibeck]

Okay, thank you @jayich!

:wave: @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

[phibeck]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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: 0.8017

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: 0.7961

ShakeNBreak: Navigating the defect configurational landscape Submitting author: @ireaml Handling editor: @rkurchin (Active) Reviewers: @obaica, @mkhorton Similarity score: 0.7940

MUQ: The MIT Uncertainty Quantification Library Submitting author: @mparno Handling editor: @pdebuyl (Active) Reviewers: @martinmodrak, @georgiastuart Similarity score: 0.7918

CheckQC: Quick quality control of Illumina sequencing runs Submitting author: @johandahlberg Handling editor: @pjotrp (Retired) Reviewers: @brainstorm Similarity score: 0.7901

⚠️ 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]

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]

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]

Great, thank you very much!

[phibeck]

@editorialbot add @14shreyasp as reviewer

[editorialbot]

@14shreyasp added to the reviewers list!

[egriendeau]

@editorialbot generate pdf

[egriendeau]

@editorialbot check repository