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[PRE REVIEW]: cppTPSA/pyTPSA: a C++/Python package for truncated power series algebra #3665

Closed whedon closed 2 years ago

whedon commented 3 years ago

Submitting author: !--author-handle-->@zhanghe9704<!--end-author-handle-- (He Zhang) Repository: https://github.com/zhanghe9704/tpsa Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@pibion<!--end-editor-- Reviewers: @dtabell, @chrisrogers1234 Managing EiC: Daniel S. Katz

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/1fa756415c650531cdfd292233b4cc8d/status.svg)](https://joss.theoj.org/papers/1fa756415c650531cdfd292233b4cc8d)

Author instructions

Thanks for submitting your paper to JOSS @zhanghe9704. Currently, there isn't an JOSS editor assigned to your paper.

@zhanghe9704 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 @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands
whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf
whedon commented 3 years ago

Wordcount for paper.md is 1523

whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.29 s (1083.2 files/s, 241410.9 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
HTML                            151            761            395          25217
C/C++ Header                      4           3194           1160          14119
TeX                              28           1100            241           7933
C++                               7            728           1379           4056
JavaScript                      100            173            200           3195
XML                               4              0            129           1954
CSS                               4            361             51           1785
Markdown                          3            133              0            200
Bourne Again Shell                1             31              9            141
SVG                               3              1              1            129
make                              2             10              0             33
DOS Batch                         1              4              0             27
CMake                             1              4              6              9
--------------------------------------------------------------------------------
SUM:                            309           6500           3571          58798
--------------------------------------------------------------------------------

Statistical information for the repository 'a2f691db07025c0871d7d47b' was
gathered on 2021/08/27.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
He Zhang                        53         49545          21629           91.92
hezhang                          6          3316           2937            8.08

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
He Zhang                  28204           56.9         11.2                9.93
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1016/s1076-5670(08)x7018-1 may be a valid DOI for title: Modern Map Methods in Particle Beam Physics
- 10.2172/812598 may be a valid DOI for title: Lecture notes on topics in accelerator physics
- 10.1063/1.52348 may be a valid DOI for title: COSY INFINITY Version 9
- 10.2514/6.2018-0398 may be a valid DOI for title: Differential Algebra software library with automatic code generation for space embedded applications

INVALID DOIs

- None
whedon commented 3 years ago

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

danielskatz commented 3 years ago

👋 @meg-simula - Do you think you edit this submission for JOSS?

danielskatz commented 3 years ago

@whedon invite @meg-simula as editor

whedon commented 3 years ago

@meg-simula has been invited to edit this submission.

danielskatz commented 3 years ago

👋 @zhanghe9704 - while we find an editor, you could work on the possibly missing DOIs that whedon suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @whedon check references to check again, and the command @whedon generate pdf when the references are right to make a new PDF. Whedon commands need to be the first entry in a new comment.

zhanghe9704 commented 3 years ago

@whedon check references

He Zhang Computational Accelerator Physicist Center for Advanced Science of Accelerators Jefferson Lab (O) 757-269-6657 www.hezhang.us

On Fri, Aug 27, 2021 at 4:41 PM whedon @.***> wrote:

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

OK DOIs

  • None

MISSING DOIs

  • 10.1016/s1076-5670(08)x7018-1 may be a valid DOI for title: Modern Map Methods in Particle Beam Physics
  • 10.2172/812598 may be a valid DOI for title: Lecture notes on topics in accelerator physics
  • 10.1063/1.52348 may be a valid DOI for title: COSY INFINITY Version 9
  • 10.2514/6.2018-0398 may be a valid DOI for title: Differential Algebra software library with automatic code generation for space embedded applications

INVALID DOIs

  • None

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3665#issuecomment-907464568, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5QICWNWN7NFCG65NHSBBDT67Z65ANCNFSM5C6IDXXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1063/1.41975 is OK
- 10.1023/A:1024467732637 is OK
- 10.1016/j.nima.2011.01.053 is OK
- 10.1016/s1076-5670(08)x7018-1 is OK
- 10.2172/812598 is OK
- 10.1016/j.nima.2005.11.109 is OK
- 10.2514/6.2018-0398 is OK

MISSING DOIs

- None

INVALID DOIs

- None
zhanghe9704 commented 3 years ago

@whedon generate pdf

He Zhang Computational Accelerator Physicist Center for Advanced Science of Accelerators Jefferson Lab (O) 757-269-6657 www.hezhang.us

On Tue, Aug 31, 2021 at 11:02 AM whedon @.***> wrote:

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

OK DOIs

  • 10.1063/1.41975 is OK
  • 10.1023/A:1024467732637 is OK
  • 10.1016/j.nima.2011.01.053 is OK
  • 10.1016/s1076-5670(08)x7018-1 is OK
  • 10.2172/812598 is OK
  • 10.1016/j.nima.2005.11.109 is OK
  • 10.2514/6.2018-0398 is OK

MISSING DOIs

  • None

INVALID DOIs

  • None

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3665#issuecomment-909321003, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5QICQ6VUTHN6MHZSUVNL3T7TVJ7ANCNFSM5C6IDXXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

whedon commented 3 years ago

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

meg-simula commented 3 years ago

In light of the delay in response in just this editor request, I think I will have to pass on this one...

kyleniemeyer commented 3 years ago

@meg-simula if you are willing, I don't think checking in once a week or so is too slow of a response time, and fine with me!

arfon commented 3 years ago

Thanks to Dr. Lingyun Yang for providing his tpsa code.

@zhanghe9704 - I noticed this comment in your README and wondered if you had considered including them as an author of your submission?

arfon commented 3 years ago

@whedon invite @pibion as editor

:wave: @pibion – would you be willing to edit this submission for JOSS?

whedon commented 3 years ago

@pibion has been invited to edit this submission.

zhanghe9704 commented 3 years ago

Hello Dr. Smith,

Indeed I was hesitant about whether to include Lingyun as an author. The reason that I didn't are (1) Lingyun's code was included in the previous versions of MAD-X so it has been published somewhere else as part of the MAD-X; and (2) except for the two files used in the cppTPSA repository He has not been involved in the work of the two repositories of the paper, although I did contact him and get his permission before I put the codes on GitHub.

If you think it's better to include him as an author, I can contact him.

Thanks and best regards,

He Zhang Computational Accelerator Physicist Center for Advanced Science of Accelerators Jefferson Lab (O) 757-269-6657 www.hezhang.us

On Fri, Sep 10, 2021 at 4:00 AM Arfon Smith @.***> wrote:

Thanks to Dr. Lingyun Yang for providing his tpsa code.

@zhanghe9704 https://github.com/zhanghe9704 - I noticed this comment in your README and wondered if you had considered including them as an author of your submission?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3665#issuecomment-916711404, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5QICXXPOHW7CCYXTS7JB3UBG3KFANCNFSM5C6IDXXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

Kevin-Mattheus-Moerman commented 3 years ago

@whedon invite @meg-simula as editor

whedon commented 3 years ago

@meg-simula has been invited to edit this submission.

Kevin-Mattheus-Moerman commented 3 years ago

@meg-simula if you are able to it would be great if you could help with this submission. Let us know if you can or elaborate on your comment above :point_up:. No worries if you cannot. Thanks.

Kevin-Mattheus-Moerman commented 3 years ago

@arfon sorry I see you just invited @pibion also. For some reason I missed that, I think my window here had not been refreshed yet. Well hopefully either @pibion or @meg-simula can handle this submission. Apologies for the confusion.

meg-simula commented 3 years ago

Not available for this one, my apologies.

Kevin-Mattheus-Moerman commented 3 years ago

@whedon invite @pibion as editor

whedon commented 3 years ago

@pibion has been invited to edit this submission.

pibion commented 3 years ago

Hi all, I'm at limited bandwidth for the next week and a half. @zhanghe9704 do you have any recommended reviewers for this submission? If you do we can get started with invitations to them.

zhanghe9704 commented 3 years ago

Hello,

When I submitted the paper, I looked through the reviewer list. To speak frankly, I don't know who is familiar with this topic of TPSA/DA. Outside the list, I can think of a few persons.

Axel Huelb at Lawrence Berkeley National Laboratory, https://github.com/ax3l Stephen Coleman at Radiasoft, https://github.com/sjcrs

The above two are experts in computational particle beam dynamics and accelerator modeling.

Alex Wittig at the University of Southampton, https://github.com/abgandar

Dr. Wittig is an expert on TPSA/DA. He has contributed codes to COSY Infinity and DACE. We had worked in the same group for about five years as graduate students from 2006 to 2011.

Best,

He Zhang Computational Accelerator Physicist Center for Advanced Science of Accelerators Jefferson Lab (O) 757-269-6657 www.hezhang.us

On Thu, Sep 16, 2021 at 7:06 PM pibion @.***> wrote:

Hi all, I'm at limited bandwidth for the next week and a half. @zhanghe9704 https://github.com/zhanghe9704 do you have any recommended reviewers for this submission? If you do we can get started with invitations to them.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3665#issuecomment-921321522, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5QICTZYNVKAQMQVFTM6T3UCJ2AJANCNFSM5C6IDXXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

arfon commented 3 years ago

Hi all, I'm at limited bandwidth for the next week and a half. @zhanghe9704 do you have any recommended reviewers for this submission? If you do we can get started with invitations to them.

Sounds like you're OK to take this on, albeit with a short delay. As such, I'm going to go ahead and assign this one to you, thanks!

arfon commented 3 years ago

@whedon assign @pibion as editor

whedon commented 3 years ago

OK, the editor is @pibion

pibion commented 3 years ago

@zhanghe9704 thank you for the initial suggestions for reviewers, that's a very helpful place to start!

pibion commented 3 years ago

@ax3l, @sjcrs, @abgandar 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

sjcrs commented 3 years ago

I'd like to help, but I think I have a COI - my company works with He Zhang's JSPEC code, and have publications in progress that may involve him as an author (He, I'll be sending you an email about that soon).

pibion commented 3 years ago

@sjcrs thanks for letting me know. Do you have any suggestions on who else might be a good reviewer?

sjcrs commented 3 years ago

Rob Ryne at LBNL or David Sagan at Cornell. Sorry, I don't know their github handles.

pibion commented 3 years ago

@sjcrs no worries, that's very helpful, thank you!

zhanghe9704 commented 3 years ago

Hello Stephen,

Thanks for your reply. I didn't know you guys are writing the paper but I'll be glad to help if needed.

Best, He

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On Tue, Oct 12, 2021 at 7:15 PM Stephen Coleman @.***> wrote:

I'd like to help, but I think I have a COI - my company works with He Zhang's JSPEC code, and have publications in progress that may involve him as an author (He, I'll be sending you an email about that soon).

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3665#issuecomment-941732906, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5QICVHNOKERUVPUS5VVN3UGS6P7ANCNFSM5C6IDXXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

zhanghe9704 commented 3 years ago

David Sagan: https://github.com/DavidSagan Robert Ryne: https://github.com/RobertRyne

However, they are very senior accelerator physicists. I suppose they are very busy and not sure whether they will have time to review this submission.

Best regards,

He Zhang Computational Accelerator Physicist Center for Advanced Science of Accelerators Jefferson Lab (O) 757-269-6657 www.hezhang.us

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On Thu, Oct 14, 2021 at 1:06 PM pibion @.***> wrote:

@sjcrs https://github.com/sjcrs no worries, that's very helpful, thank you!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3665#issuecomment-943550416, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5QICVNXCK5QEDMX7RFDM3UG4EXRANCNFSM5C6IDXXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

zhanghe9704 commented 2 years ago

Happy new year to everyone! Just want to follow up on the review progress of this submission. Is there anything I could/should do to help? Thanks.

Best regards,

He Zhang Computational Accelerator Physicist Center for Advanced Science of Accelerators Jefferson Lab (O) 757-269-6657 www.hezhang.us

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On Thu, Oct 14, 2021 at 3:02 PM Zhang He @.***> wrote:

David Sagan: https://github.com/DavidSagan Robert Ryne: https://github.com/RobertRyne

However, they are very senior accelerator physicists. I suppose they are very busy and not sure whether they will have time to review this submission.

Best regards,

He Zhang Computational Accelerator Physicist Center for Advanced Science of Accelerators Jefferson Lab (O) 757-269-6657 www.hezhang.us

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On Thu, Oct 14, 2021 at 1:06 PM pibion @.***> wrote:

@sjcrs https://github.com/sjcrs no worries, that's very helpful, thank you!

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ax3l commented 2 years ago

Hi, I am sorry that I fully missed the ping earlier in the thread. I have a big backlog on GitHub notifications (about 400), I am sorry for that.

I pinged Robert Ryne and David Sagan on your request, but don't know their schedules. I also asked other people on our team if they can help out.

With the topic of the submission, I might be able to do the technical review but would have to read into the domain science part (I am a Laser-Plasma accelerator person by training).

pibion commented 2 years ago

@ax3l thank you for responding! If @zhanghe9704 could comment here - would it be useful to have someone do the technical review, somewhat separate from the domain science?

That could be nice, as that could potentially reduce the work someone would need to do.

pibion commented 2 years ago

@zhanghe9704 apologies for the long delay - I'm sending emails again to find reviewers now that people are coming back from the holidays somewhat.

zhanghe9704 commented 2 years ago

Hello,

Thanks for all your replies. I understand everyone is very busy especially at the end of the year. I'm not in a hurry but I'm glad to see it starts to move forward again.

I think a technical review will be very helpful. Actually, the current version of the lib includes only the mathematical implementation of TPSA and does not have any specific application in accelerator physics.

Best regards,

He Zhang Computational Accelerator Physicist Center for Advanced Science of Accelerators Jefferson Lab (O) 757-269-6657 www.hezhang.us

On Mon, Jan 3, 2022 at 8:05 PM pibion @.***> wrote:

@zhanghe9704 https://github.com/zhanghe9704 apologies for the long delay - I'm sending emails again to find reviewers now that people are coming back from the holidays somewhat.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3665#issuecomment-1004457560, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5QICTOA7TVHVKVV3L5MX3UUJBUXANCNFSM5C6IDXXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

pibion commented 2 years ago

@zhanghe9704 thanks for this input! @ax3l it sounds like you'd be valuable as a reviewer if you're available. Please let me know if you think this is something you would like to take on.

zhanghe9704 commented 2 years ago

Good morning, Just want to ask if there is any update in this review. Thanks.

He Zhang

On Tue, Jan 4, 2022 at 4:30 PM pibion @.***> wrote:

@zhanghe9704 https://github.com/zhanghe9704 thanks for this input! @ax3l https://github.com/ax3l it sounds like you'd be valuable as a reviewer if you're available. Please let me know if you think this is something you would like to take on.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3665#issuecomment-1005184741, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5QICUE7IM33FXZ7IOPT3TUUNRHLANCNFSM5C6IDXXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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zhanghe9704 commented 2 years ago

Hello,

Could anyone give me some update on this review? Thanks a lot! Have a good weekend!

He

On Thu, Feb 24, 2022 at 6:58 AM Zhang He @.***> wrote:

Good morning, Just want to ask if there is any update in this review. Thanks.

He Zhang

On Tue, Jan 4, 2022 at 4:30 PM pibion @.***> wrote:

@zhanghe9704 https://github.com/zhanghe9704 thanks for this input! @ax3l https://github.com/ax3l it sounds like you'd be valuable as a reviewer if you're available. Please let me know if you think this is something you would like to take on.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3665#issuecomment-1005184741, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5QICUE7IM33FXZ7IOPT3TUUNRHLANCNFSM5C6IDXXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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pibion commented 2 years ago

@zhanghe9704 apologies for the extremely slow start. I've been having a hard time finding reviewers and am increasing my emailing rate to 15 potential editors per week.

One of the ways I find people to email is through related papers - so if you could refer me to papers that are related to this work that would be helpful!

pibion commented 2 years ago

@ax3l would you be interested and able to be a reviewer for this paper? Your technical perspective would be a useful one!

zhanghe9704 commented 2 years ago

Here is a paper on the tpsa package used in MAD-X:

https://cds.cern.ch/record/2141771/files/mopje039.pdf

He

On Fri, Mar 4, 2022 at 1:18 PM pibion @.***> wrote:

@zhanghe9704 https://github.com/zhanghe9704 apologies for the extremely slow start. I've been having a hard time finding reviewers and am increasing my emailing rate to 15 potential editors per week.

One of the ways I find people to email is through related papers - so if you could refer me to papers that are related to this work that would be helpful!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3665#issuecomment-1059406331, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5QICWHH7MN4G3F4A4D3F3U6JHWZANCNFSM5C6IDXXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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