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[PRE REVIEW]: Scanbot: An STM Automation Bot #5432

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editorialbot opened this issue May 3, 2023 · 60 comments
Closed

[PRE REVIEW]: Scanbot: An STM Automation Bot #5432

editorialbot opened this issue May 3, 2023 · 60 comments
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@jagar2 @zhubonan @ziatdinovmax
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pre-review Python TeX Track: 3 (PE) Physics and Engineering

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editorialbot commented May 3, 2023 •
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Submitting author: @ceds92 (Julian Ceddia)
Repository: https://github.com/New-Horizons-SPM/scanbot
Branch with paper.md (empty if default branch): joss
Version: v2.0.0
Editor: @zhubonan
Reviewers: @ziatdinovmax, @jagar2
Managing EiC: Kyle Niemeyer

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/dd610b087f2f82d4488515b21dfda185"><img src="https://joss.theoj.org/papers/dd610b087f2f82d4488515b21dfda185/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/dd610b087f2f82d4488515b21dfda185/status.svg)](https://joss.theoj.org/papers/dd610b087f2f82d4488515b21dfda185)

Author instructions

Thanks for submitting your paper to JOSS @ceds92. Currently, there isn't a JOSS editor assigned to your paper.

@ceds92 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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

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Wordcount for paper.md is 1074

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

OK DOIs

- 10.1088/2632-2153/ab42ec is OK
- 10.1021/acs.jpca.0c10731 is OK
- 10.1038/s42005-020-0317-3 is OK
- 10.5281/zenodo.7402665 is OK
- 10.1021/acsnano.8b02208 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

@kyleniemeyer
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@editorialbot set V2 as branch

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Done! branch is now V2

@kyleniemeyer
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@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (192.2 files/s, 98737.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           5            719            442           2343
Markdown                         1             19              0             50
TOML                             1              2              0             21
-------------------------------------------------------------------------------
SUM:                             7            740            442           2414
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

@kyleniemeyer
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@editorialbot set joss as branch

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Done! branch is now joss

@openjournals openjournals deleted a comment from editorialbot May 3, 2023
@openjournals openjournals deleted a comment from editorialbot May 3, 2023
@kyleniemeyer
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@editorialbot invite @zhubonan as editor

Hi @zhubonan, could you edit this submission?

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Invitation to edit this submission sent!

@zhubonan
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zhubonan commented May 5, 2023

Thanks for the invitation @kyleniemeyer, happy to handle this one

@zhubonan
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zhubonan commented May 5, 2023

@editorialbot assign @zhubonan as editor

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Assigned! @zhubonan is now the editor

@zhubonan
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Hi @ceds92, thanks for the submission 🚀. I am wondering if you have any suggestions for the potential reviewers. I can see that the package requires installation of specific (propitiatory) software. Please do not directly @ any potential reviewer directly in the reply.

@ceds92
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ceds92 commented May 17, 2023

Hey @zhubonan! Thanks for looking into this and apologies for my late reply - I've been away until now.
I will look at this today/tomorrow and get back to you ASAP.

@ceds92
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ceds92 commented May 22, 2023

Hi @zhubonan,

Testing this software requires Spec's Nanonis V5 which is a licensed product. Further, it may be challenging for reviewers to find time in their schedules to pause their research and test this software on a live system (STM). However, this Scanbot can be tested on the STM simulator V5 software provided by Specs here. All functionality except for Scanbot's control over the STM tip via the motors + camera feed can be tested using this simulator.
For tracking the motion of the tip through the camera feed, I can upload a video recording of the STM tip moving, which can be used to replace the camera feed by running Scanbot in a 'demo' mode.

Some potential reviewers could be members of the following groups:
Michael Crommie (UBC)
Sarah Burke (UBC)
Doug Bonn (UBC)
Robert Wolkow (Alberta)
Peter Liljeroth (Aalto)
David Ecija (IMDEA)
Willi Auwärter (TUM)

Let me know if there's anything else I can help with!

@zhubonan
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@ceds92 Great! Thanks for the suggestions.

@zhubonan
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zhubonan commented Jun 6, 2023

Just a status update - I am still working on finding the referees.

@ceds92
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ceds92 commented Jun 6, 2023

Thanks for the update, no worries!

@zhubonan
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zhubonan commented Jun 29, 2023 •
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@ceds92 Sorry for the delay. Unfortunately, I am still struggling to find reviewers. Could you please suggest more potential reviewers? Thanks
PS, If you know any peers that are already on GitHub, usually they are more likely to respond.

@zhubonan
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Pinging @ceds92 - Please suggest some potential reviewers to help the pre-review process. Thanks a lot.

@zhubonan
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Hi @emilikv, @ziatdinovmax would you be interested to review this JOSS submission? It is about automating scanning tunnelling microscope and help for things like tip preparation.

The manuscript can be viewed here 👉 View article proof on GitHub
Software repository 👉 https://github.com/New-Horizons-SPM/scanbot
The JOSS reviewer policy and reviewer guideline for your reference 👉 Reviewer Guideline

Thanks!

@ziatdinovmax
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ziatdinovmax commented Oct 27, 2023 via email

@zhubonan
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@editorialbot add @ziatdinovmax as reviewer

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@ziatdinovmax added to the reviewers list!

@zhubonan
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@ziatdinovmax Thanks for agreeing to review. We are still one reviewer short. Do you know anyone who may be able to help review this package?

@ziatdinovmax
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@zhubonan - I recommend @jagar2 as a reviewer

@zhubonan
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zhubonan commented Nov 1, 2023

Hi @jagar2 would you be interested to review this JOSS submission? It is about automating scanning tunnelling microscope and help for things like tip preparation.

The manuscript can be viewed here 👉 View article proof on GitHub
Software repository 👉 https://github.com/New-Horizons-SPM/scanbot
The JOSS reviewer policy and reviewer guideline for your reference 👉 Reviewer Guideline

Thanks!

@jagar2
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jagar2 commented Nov 1, 2023 via email

@zhubonan
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zhubonan commented Nov 1, 2023

@jagar2 Thanks that would be great! No problem if more time is needed. Would it be possible for you to give an ETA?

@ceds92
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ceds92 commented Nov 4, 2023

Hi all,

@zhubonan thanks for sticking with this and finding reviewers, it is much appreciated!
@jagar2 @ziatdinovmax, thanks for agreeing to review!!

Just a heads up... I have been doing some work on Scanbot over the few months since it was submitted.
It has a GUI now which should make things easier when testing - this is available on the V3 branch. All core functionality is basically the same.

Also, given that STM time is generally precious, I've created ways to test Scanbot's functionality, without needing an STM, through introducing a demo mode (along with nanonis V5 simulator).
For example, when tracking the motion of the STM tip in demo mode, the camera feed will be replaced by a recording of the tip moving. The other main example is when automated tip shaping is initiated, STM images of previously acquired tip imprints will be loaded from a pickled file instead of using images from the simulator.

The files for testing can be downloaded from this link. Just save and extract it in Scanbot's root directory.

If you have any questions, let me know!

Thanks!!

@zhubonan
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zhubonan commented Nov 6, 2023

@editorialbot add @jagar2 as reviewer

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@jagar2 added to the reviewers list!

@zhubonan
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zhubonan commented Nov 7, 2023

Hi all,

@zhubonan thanks for sticking with this and finding reviewers, it is much appreciated! @jagar2 @ziatdinovmax, thanks for agreeing to review!!

Just a heads up... I have been doing some work on Scanbot over the few months since it was submitted. It has a GUI now which should make things easier when testing - this is available on the V3 branch. All core functionality is basically the same.

Also, given that STM time is generally precious, I've created ways to test Scanbot's functionality, without needing an STM, through introducing a demo mode (along with nanonis V5 simulator). For example, when tracking the motion of the STM tip in demo mode, the camera feed will be replaced by a recording of the tip moving. The other main example is when automated tip shaping is initiated, STM images of previously acquired tip imprints will be loaded from a pickled file instead of using images from the simulator.

The files for testing can be downloaded from this link. Just save and extract it in Scanbot's root directory.

If you have any questions, let me know!

Thanks!!

@ceds92 Thanks for the update. I think we can start the review.

@zhubonan
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zhubonan commented Nov 7, 2023

@editorialbot start review

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OK, I've started the review over in #6028.

@zhubonan
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Hi @kasasxav @jonatanalvelid @ianhi, would you be able to review this submission to JOSS? We need at least one more reviewer for this submission. Based on the reviewer record, you have background in microcopy automation and python. Please let me know. Thanks in advance!

@ianhi
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ianhi commented Mar 12, 2024

Am I correct in interpreting the below as saying that the free mimea substitutes for the nanonis V5?

Testing this software requires Spec's Nanonis V5 which is a licensed product. Further, it may be challenging for reviewers to find time in their schedules to pause their research and test this software on a live system (STM). However, this Scanbot can be tested on the STM simulator V5 software provided by Specs here. All functionality except for Scanbot's control over the STM tip via the motors + camera feed can be tested using this simulator.

I unfortunately have no experience with STM. That said if no one with expertise is available and it is possible to test without access to the licensed software/STM then I would be wiling to review. However, I would not be able to start until next week.

@ceds92
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ceds92 commented Mar 13, 2024

Hi @ianhi, thanks so much for agreeing! Yes, the software can be tested with the freely available STM simulator. I hope I have included enough detail in the documentation such that a non-STM'r can still download and test the software. Otherwise please ask if you have any questions.

https://new-horizons-spm.github.io/scanbot/web-app-test/

Your time is very much appreciated!

@zhubonan
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zhubonan commented Mar 13, 2024 •
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@ianhi thanks for agreeing to review. I hope @ceds92 has addressed your concern. It is absolutely fine if you want to start the review next week.

@jonatanalvelid
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Hi @zhubonan, I unfortunately have no experience with STM, and very limited time currently, so I will have to pass this time. Thanks for asking, and hope I can be of help another time.

@xcasas
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xcasas commented Mar 18, 2024

Hi @zhubonan, same for me I'm sorry, I don't feel I have enough knowledge to review the paper.
Thank you for considering me though!

@zhubonan
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zhubonan commented Apr 9, 2024

@ianhi Are you happy to review the package? If so, I will add you to reviewers. Please let me know. Thanks a lot 😄

@ceds92
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ceds92 commented Apr 15, 2024

@zhubonan I think @ianhi has already been added as a reviewer. I can see he has run the command to generate the checklist, although I can't seem to see it?

@ceds92
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ceds92 commented Apr 17, 2024

@zhubonan someone else who has a background in STM and seems to have experience writing code to control STMs is Koen Lauwaet (GitHub, google scholar) . Maybe they will be willing to review?

@zhubonan
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Hi @KoenImdea would you be able to help review this JOSS submission? It is about automating scanning tunnelling microscope and help for things like tip preparation.

We are currently short for reviewers. There is already one reviewer who have completed the review and recommanded for publication. However, we do need to have two reviews in order to accept the work. Your contribution would be really appreciated.

The manuscript can be viewed here 👉 View article proof on GitHub
Software repository 👉 https://github.com/New-Horizons-SPM/scanbot
The JOSS reviewer policy and reviewer guideline for your reference 👉 Reviewer Guideline

Thanks in advance.

@KoenImdea
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Hi @zhubonan and @ceds92 ,
I am willing to give that a go. I probably will need a guide for dummies about how to submit the review though. I have not had the pleasure to work with the collaboration features of GitHub so far...
Cheers,
Koen

@zhubonan
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Thanks, @KoenImdea, glad to know you will be able to review the submission!

We have documentation about how to carry out the review. It basically involves: 1. generating a checklist. 2. going through the items in the checklist. You will need to download, install and test the code. If you have any comment or problem, you can directly raise an GitHub issue in the code's repository and mention the JOSS review issue's link. You can also leave comments and ask questions in the review issue directly.

Once you are satisfied with the submission and all the boxes are ticked, just leave a comment for recommending acceptance in the review issue and ping me.

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