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[REVIEW]: Micro Manager: a Python package for adaptive and flexible two-scale coupling #5842

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editorialbot opened this issue Sep 12, 2023 · 69 comments
Closed

[REVIEW]: Micro Manager: a Python package for adaptive and flexible two-scale coupling #5842

editorialbot opened this issue Sep 12, 2023 · 69 comments
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accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review Shell TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Sep 12, 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
Archive: 10.18419/darus-3764

Status

status

Status badge code:

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)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@mayrmt & @mrogowski & @mbkumar, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @philipcardiff know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @mayrmt

📝 Checklist for @mrogowski

📝 Checklist for @mbkumar
@editorialbot editorialbot added Python review Shell TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Sep 12, 2023
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Hello humans, 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

@editorialbot editorialbot mentioned this issue Sep 12, 2023
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Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (846.9 files/s, 127218.2 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 📄 👈

@mayrmt
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mayrmt commented Sep 12, 2023 •
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Review checklist for @mayrmt

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/precice/micro-manager?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@IshaanDesai) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@mrogowski
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mrogowski commented Sep 14, 2023 •
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Review checklist for @mrogowski

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/precice/micro-manager?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@IshaanDesai) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@mrogowski
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Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

@IshaanDesai: It seems that this is missing. Let me know if I missed it. Something like a simple CONTRIBUTING.md file is enough.

@IshaanDesai
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@mrogowski yes it is missing, thanks for spotting this! I will add a CONTRIBUTING.md file.

@IshaanDesai
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@editorialbot generate pdf

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

@IshaanDesai
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@mrogowski I added a CONTRIBUTING.md file.

@philipcardiff
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Hi @mbkumar, a reminder about this review. Thanks!

@mbkumar
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mbkumar commented Oct 10, 2023 •
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Review checklist for @mbkumar

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/precice/micro-manager?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@IshaanDesai) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@mbkumar
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mbkumar commented Oct 10, 2023

Sorry for the delay in starting the review.

Since this is an addon package, installation is difficult. I installed libprecice v2.5.0, however, the documentation is not helping me figure out how to install the latest version of pyprecice. Can the authors point to a dev container, which can aid in the installation and testing of micromanager?

@IshaanDesai
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Hi @mbkumar

We have associated the Micro Manager v0.3.0 with this paper. If you install the Micro Manager using pip, the corresponding pyprecice (v2.5.0.2) will be automatically.

We do not have a dev container to work with out of the box, but if things get too difficult, we can set something up.

@mbkumar
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mbkumar commented Oct 11, 2023

I have tested the software and found it to be rough around the edges. It could be improved in a few aspects. For example, instead of using a fixed name for the MicroManager class, it could be made an abstract class. Then users could subclass it and the macro-manager could be supplied the subclass name in its config file. But, the software is useful and useable in its present form. The manuscript is reasonably good. So, I recommend its publication.

@IshaanDesai
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Thank you @mbkumar for the testing the Micro Manager, opening issues for things that did not work, and reviewing the manuscript. We really appreciate it!

At some point we had a configurable class name for the MicroSimulation name that the Micro Manager demands right now. To keep things simple and avoid user-side mistakes, we fixed this name. I will open an issue to discuss this once again.

@IshaanDesai IshaanDesai mentioned this issue Oct 12, 2023
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@philipcardiff
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Hi @IshaanDesai, have you addressed all outstanding issues from @mrogowski and @mayrmt?

@IshaanDesai
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Hi @philipcardiff, yes, so far everything has been addressed.

@philipcardiff
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Thanks @IshaanDesai.

@mrogowski and @mayrmt: I see your checklists are not yet complete; do you have other comments, queries or suggestions?

@mayrmt
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mayrmt commented Oct 19, 2023

@philipcardiff I have update my checklist. No further comments from my side!

@philipcardiff
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Hi @kyleniemeyer, this paper is ready for processing.

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👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4760, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Nov 7, 2023
@IshaanDesai
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IshaanDesai commented Nov 7, 2023 •
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@philipcardiff the archive link is 10.18419/darus-3764 and not the Zenodo link that you pointed to. That one appears to be for another software. Could we please reset it?

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@editorialbot set 10.18419/darus-3764 as archive

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Done! archive is now 10.18419/darus-3764

@philipcardiff
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@philipcardiff the archive link is 10.18419/darus-3764 and not the Zenodo link that you pointed to. That one appears to be for another software. Could we please reset it?

Thanks. Sorry, this was a copy'n'paste error. It should be correct now.

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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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
- 10.18419/opus-13560 is OK
- 10.1029/2020WR027585 is OK
- 10.1016/j.camwa.2020.02.012 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@editorialbot
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👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4763, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@danielskatz
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👋 @IshaanDesai - I'm the track editor for this submission, and I'll process the remaining steps. I'll next proofread the paper, and let you know if you need to do anything else.

@danielskatz
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I've suggested a few small changes in precice/micro-manager#71 - please merge this, or let me know what you disagree with, then we can continue towards acceptance and publication

@danielskatz
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@editorialbot recommend-accept

@IshaanDesai
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@danielskatz thanks for proofreading and suggesting changes, I have merged them now.

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Attempting dry run of processing paper acceptance...

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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
- 10.18419/opus-13560 is OK
- 10.1029/2020WR027585 is OK
- 10.1016/j.camwa.2020.02.012 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4764, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@danielskatz
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@editorialbot accept

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Doing it live! Attempting automated processing of paper acceptance...

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff 

cff-version: "1.2.0"
authors:
- family-names: Desai
  given-names: Ishaan
  orcid: "https://orcid.org/0000-0002-2552-7509"
- family-names: Scheurer
  given-names: Erik
  orcid: "https://orcid.org/0009-0000-9396-2994"
- family-names: Bringedal
  given-names: Carina
  orcid: "https://orcid.org/0000-0003-0495-2634"
- family-names: Uekermann
  given-names: Benjamin
  orcid: "https://orcid.org/0000-0002-1314-9969"
doi: 10.18419/darus-3764
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Desai
    given-names: Ishaan
    orcid: "https://orcid.org/0000-0002-2552-7509"
  - family-names: Scheurer
    given-names: Erik
    orcid: "https://orcid.org/0009-0000-9396-2994"
  - family-names: Bringedal
    given-names: Carina
    orcid: "https://orcid.org/0000-0003-0495-2634"
  - family-names: Uekermann
    given-names: Benjamin
    orcid: "https://orcid.org/0000-0002-1314-9969"
  date-published: 2023-11-07
  doi: 10.21105/joss.05842
  issn: 2475-9066
  issue: 91
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5842
  title: "Micro Manager: a Python package for adaptive and flexible
    two-scale coupling"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05842"
  volume: 8
title: "Micro Manager: a Python package for adaptive and flexible
  two-scale coupling"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05842 joss-papers#4765
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05842
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Nov 7, 2023
@danielskatz
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Congratulations to @IshaanDesai (Ishaan Desai) and co-authors!!

And thanks to @mayrmt, @mrogowski, and @mbkumar for reviewing, and to @philipcardiff for editing!
JOSS depends on volunteers and couldn't be successful without you

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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05842/status.svg)](https://doi.org/10.21105/joss.05842)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05842">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05842/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05842/status.svg
   :target: https://doi.org/10.21105/joss.05842

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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@editorialbot editorialbot mentioned this issue Oct 11, 2024
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