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[PRE REVIEW]: Micro Manager: a Python package for adaptive and flexible two-scale coupling #5785

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editorialbot opened this issue Aug 28, 2023 · 37 comments
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[PRE REVIEW]: Micro Manager: a Python package for adaptive and flexible two-scale coupling #5785

editorialbot opened this issue Aug 28, 2023 · 37 comments
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@mrogowski @mbkumar @mayrmt @philipcardiff
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pre-review Python Shell TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Aug 28, 2023 •
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Submitting author: @IshaanDesai (Ishaan Desai)
Repository: https://github.com/precice/micro-manager
Branch with paper.md (empty if default branch): joss-submission
Version: v0.3.0
Editor: @philipcardiff
Reviewers: @mayrmt, @mrogowski, @mbkumar
Managing EiC: Daniel S. Katz

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status

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HTML: <a href="https://joss.theoj.org/papers/f1487e848f10b3dd2360aa14d6993a57"><img src="https://joss.theoj.org/papers/f1487e848f10b3dd2360aa14d6993a57/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f1487e848f10b3dd2360aa14d6993a57/status.svg)](https://joss.theoj.org/papers/f1487e848f10b3dd2360aa14d6993a57)

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

@IshaanDesai if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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:

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@editorialbot editorialbot added pre-review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Aug 28, 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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Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (936.9 files/s, 140744.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              1              1              1           4696
Python                          20            502            763           1431
Markdown                        11            172              0            407
YAML                            10             36              4            350
JSON                            10              0              0            164
TeX                              1             16              0            163
XML                              3             27              0            148
C++                              1             16             23             48
C/C++ Header                     1              5              4             20
Bourne Shell                     2              0              0             16
-------------------------------------------------------------------------------
SUM:                            60            775            795           7443
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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

OK DOIs

- 10.23967/eccomas.2022.037 is OK
- 10.12688/openreseurope.14445.2 is OK
- 10.1007/978-3-319-40528-5_11 is OK
- 10.1016/j.amc.2020.125933 is OK
- 10.1016/j.jcp.2012.12.025 is OK
- 10.5281/zenodo.6006701 is OK
- 10.3389/fmats.2019.00075 is OK
- 10.1002/pamm.202000290 is OK
- 10.1109/MCSE.2021.3083216 is OK
- 10.1098/rsta.2018.0147 is OK
- 10.1007/978-3-030-50433-5_33 is OK
- 10.1016/j.jcp.2015.05.004 is OK
- 10.1051/0004-6361/201321252 is OK
- 10.1016/j.jocs.2017.07.004 is OK
- 10.1145/3295500.3356197 is OK
- 10.18419/opus-12291 is OK
- 10.1029/2020WR027585 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Wordcount for paper.md is 884

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

@danielskatz
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👋 @IshaanDesai - Thanks for your submission. I notice that in your submission note, you say "This is the first JOSS paper for this package." Have there been other papers on this package?

@danielskatz
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Also, can you explain the relationship between this code and preCICE in a short statement here? I'm not sure I fully understand this, even as stated in the paper.

And, is there any code overlap between this repository and preCICE?

@IshaanDesai
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👋 @danielskatz thanks for starting off this process. Last year we (I) wrote a short conference paper introducing the Micro Manager: Desai, Ishaan, & Bringedal, Carina & Uekermann, Benjamin. A flexible software approach to simulate two-scale coupled problems. ECCOMAS Congress 2022. 10.23967/eccomas.2022.037. The software has matured quite a bit since then, and the intention is to have a citeable journal paper of the software. There have not been any journal papers or other papers about the Micro Manager.

Also, can you explain the relationship between this code and preCICE in a short statement here?

preCICE is a library which facilitates black-box partitioned coupling between simulation solvers on the same physical scales, meaning the solvers solve physics on the same physical domain. The Micro Manager is run together with preCICE to allow for coupling between solvers on different scales, and more precisely, allow a user to couple a solver on a coarse scale to a solver on a fine scale.

And, is there any code overlap between this repository and preCICE?

No, there is no code overlap between the Micro Manager and the core preCICE library. The Micro Manager is a repository in the preCICE project on GitHub, but the code itself is independent.

@danielskatz
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👋 @IshaanDesai - thanks, this all sounds good. You might want to see if you think the paper would benefit from a clear statement like you make in the second answer above. Please feel free to make changes to your .md file, then use the command @editorialbot generate pdf to make a new PDF, if you want. editorialbot commands need to be the first entry in a new comment.

I'll now look for an editor.

@danielskatz
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👋 @philipcardiff - would you be able to edit this submission?

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@editorialbot invite @philipcardiff as editor

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Invitation to edit this submission sent!

@philipcardiff
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Sure; I am happy to act as editor for this submission. I am familiar with the preCICE project.

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@editorialbot assign me as editor

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Assigned! @philipcardiff is now the editor

@philipcardiff
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Hi @IshaanDesai , please let me know if you have any suggestions for appropriate reviewers.

@IshaanDesai
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IshaanDesai commented Aug 28, 2023 •
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Hi @philipcardiff, thanks for taking over the editors role! I am going through the list of reviewers and will shortly suggest names. Pinging @uekerman to be part of this discussion.

@IshaanDesai
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Suggestions for reviewers:

@philipcardiff
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Hi @ jamiebramwell, @mayrmt, @zbeekman, would you like to review this submission?

The submission under consideration is Micro Manager: a Python package for adaptive and flexible two-scale coupling (https://github.com/precice/micro-manager).

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria and review checklist to get an idea of what is expected.

Philip

@philipcardiff
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Hi @jamiebramwell, would you like to review this submission? See my comment above, where I accidentally added a space to your tag.

@mayrmt
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mayrmt commented Sep 4, 2023

@philipcardiff I am happy to review.

@philipcardiff
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@philipcardiff I am happy to review.

Thanks @mayrmt!

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@editorialbot add @mayrmt as reviewer

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@mayrmt added to the reviewers list!

@zbeekman
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zbeekman commented Sep 5, 2023

Hi @philipcardiff @IshaanDesai,

I would have loved to be a reviewer on this, but I do not have the bandwidth (until perhaps November) to be responsive enough to be a good reviewer. I must sadly decline. Thanks for considering me!

@philipcardiff
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Hi @philipcardiff @IshaanDesai,

I would have loved to be a reviewer on this, but I do not have the bandwidth (until perhaps November) to be responsive enough to be a good reviewer. I must sadly decline. Thanks for considering me!

No problem, thanks anyway @zbeekman.

@philipcardiff
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Hello @mbkumar, @mrogowski, would you like to review this submission?

The submission under consideration is Micro Manager: a Python package for adaptive and flexible two-scale coupling (https://github.com/precice/micro-manager).

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria and review checklist to get an idea of what is expected.

Philip

@mrogowski
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@philipcardiff I'm happy to review this submission!

@philipcardiff
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@philipcardiff I'm happy to review this submission!

Thanks @mrogowski

@philipcardiff
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@editorialbot add @mrogowski as reviewer

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@mrogowski added to the reviewers list!

@mbkumar
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mbkumar commented Sep 12, 2023 via email

@philipcardiff
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Bharat

Thanks Bharat

@philipcardiff
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@editorialbot add @mbkumar as reviewer

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@mbkumar added to the reviewers list!

@philipcardiff
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@editorialbot start review

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OK, I've started the review over in #5842.

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