Hi @kellyrowland I've completed my review. There are no changes that I have to suggest. The implementation, examples and documentation is quite thorough for this latest version of the library. 😄 One thing that I found is, this library will be very helpful for a lot of people in the field of Computational Science such as myself and my peers. So, kudos to the author @akashdhruv for coming up with this.🚀

Note: I have checked all the items in the checklist.

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@rvg296 @AnnikaStein Please use this version here for review: I have included reference to performance data repository.

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@kellyrowland @rvg296 @AnnikaStein

I transferred the repository to: https://github.com/Box-Tools/BoxKit to meet licensing requirements from Argonne National Laboratory. It should not change anything.

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@akashdhruv Tried installing this in a virtual environment created with Conda with Py310. I get this installation error. (py310) C:\Users\MENDR>pip install BoxKit --user

Collecting BoxKit
  Downloading BoxKit-2023.6.7.tar.gz (852 kB)
     ---------------------------------------- 852.5/852.5 kB 1.9 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [10 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-jv7ymwcp\boxkit_f17c2e8a1aef4428bab1ef1a7d2994e5\setup.py", line 14, in <module>
          import bin.cmd as bin_cmd  # pylint: disable=wrong-import-position
        File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-jv7ymwcp\boxkit_f17c2e8a1aef4428bab1ef1a7d2994e5\bin\cmd.py", line 13, in <module>
          from cbox import cbox_build  # pylint: disable=wrong-import-position
        File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-jv7ymwcp\boxkit_f17c2e8a1aef4428bab1ef1a7d2994e5\bin\cbox.py", line 21, in <module>
          if os.path.exists(os.getenv("PWD") + "/boxkit/depends/boost")
      TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

(py310) C:\Users\MENDR>pip install BoxKit
Collecting BoxKit
  Using cached BoxKit-2023.6.7.tar.gz (852 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [10 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-r2sw90yv\boxkit_decd8282603049f5bb2d36ea2947c869\setup.py", line 14, in <module>
          import bin.cmd as bin_cmd  # pylint: disable=wrong-import-position
        File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-r2sw90yv\boxkit_decd8282603049f5bb2d36ea2947c869\bin\cmd.py", line 13, in <module>
          from cbox import cbox_build  # pylint: disable=wrong-import-position
        File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-r2sw90yv\boxkit_decd8282603049f5bb2d36ea2947c869\bin\cbox.py", line 21, in <module>
          if os.path.exists(os.getenv("PWD") + "/boxkit/depends/boost")
      TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

I think this maybe originating from the command os.getenv("PWD") being executed on a Windows Operating System. $PWD only exists on Linux/Unix based Operating Systems. I will write a fix for this.

Thank you for reporting this bug.

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@rvg296 It has been fixed. See: https://github.com/Box-Tools/BoxKit/actions/runs/6344172628/job/17233705158?pr=144

Can you try, pip install boxkit==2023.9.1 --user

and also, git+ssh://[email protected]/akashdhruv/BoxKit.git@main --user

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I was referring to these, under contribution and usage.

Done.

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@akashdhruv , In the paper, you have mentioned the performance is improved ~5x for measuring the bubble shape and size for Flash-X boiling simulations. Could you please locate that in the box-kit performance repo. Is that in the Jupyter notebook?

All the raw data with performance measurements is in the archive/ The Jupyter notebook contains data picked from the archive.

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Hello everyone,

Just touching base to see if there are anymore edits/roadblocks to get the review finished in a timely manner? I am hoping to get a DOI for this so I can cite it in other publications.

Warmly,
Akash

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great, thanks!

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hi @marjanAlbouye thanks for your quick response - I think we're set with two reviewers on this submission now, so I'm not going to add you to the reviewers list unless we need a third person to step in.

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@kellyrowland @Abinashbunty
I believe I have completed most of the required checks. Anything else that you would want me go through before this gets accepted and published?

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@Abinashbunty thanks for getting started on your review! Dropping a note to check in on things; please let me know if you have any questions.

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Thank you!

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Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

I cannot make changes to the comment above so I am copying the checklist here:

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.18 s (903.6 files/s, 177908.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      13           2405           2470           9222
HTML                            31            605             93           4863
C/C++ Header                    18            478            257           2719
Python                          51            930            846           2699
SVG                              3              0              0           2673
CSS                              4            191             35            759
YAML                             7             22             29            227
reStructuredText                28            213            380            225
C++                              6             28             50            180
Markdown                         1             22              0            106
TeX                              1              5              0             68
DOS Batch                        1              8              1             26
make                             3             10             10             26
-------------------------------------------------------------------------------
SUM:                           167           4917           4171          23793
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 840

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

OK DOIs

- 10.1016/j.softx.2022.101168 is OK
- 10.5281/zenodo.8039787 is OK
- 10.1088/0067-0049/192/1/9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Review checklist for @AnnikaStein

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/akashdhruv/BoxKit?
• 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 (@akashdhruv) 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?

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@editorialbot check references

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

OK DOIs

- 10.1016/j.softx.2022.101168 is OK
- 10.5281/zenodo.8039787 is OK
- 10.1088/0067-0049/192/1/9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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@editorialbot generate pdf

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@rvg296 I believe the command is:

@editorialbot generate my checklist

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@rvg296 I believe the command is:

@editorialbot generate my checklist

Yes I have corrected it

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@editorialbot check references

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

OK DOIs

- 10.1016/j.softx.2022.101168 is OK
- 10.5281/zenodo.8039787 is OK
- 10.1088/0067-0049/192/1/9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Review checklist for @AnnikaStein

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/akashdhruv/BoxKit?
• 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 (@akashdhruv) 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?

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Review checklist for @rvg296

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/akashdhruv/BoxKit?
• 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 (@akashdhruv) 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?

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hi @AnnikaStein @rvg296 thanks for getting started here - please let me know if you have any questions or concerns.

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hi @AnnikaStein @rvg296 friendly reminder about this review 👋 please let me know if you have any questions or concerns, or if you need to set this down.

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Hi @kellyrowland dont have any questions at this moment. In the process of review currently stage by stage.

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Same for me, I also don‘t have any questions at the moment, but just recently came back from a vacation. Continuing reviewing this + next week.

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Great, thank you both!

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@akashdhruv May be a minor edit, but in line 54 of the paper should'nt the Scikit method be named as skimage.measure instead of skimage_measure for measuring the bubble shape and size??

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@akashdhruv May be a minor edit, but in line 54 of the paper should'nt the Scikit method be named as skimage.measure instead of skimage_measure for measuring the bubble shape and size??

I will address this.

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@akashdhruv May be a minor edit, but in line 54 of the paper should'nt the Scikit method be named as skimage.measure instead of skimage_measure for measuring the bubble shape and size??

I will address this.

Done!

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@akashdhruv Tried installing this in a virtual environment created with Conda with Py310. I get this installation error.
(py310) C:\Users\MENDR>pip install BoxKit --user

Collecting BoxKit
  Downloading BoxKit-2023.6.7.tar.gz (852 kB)
     ---------------------------------------- 852.5/852.5 kB 1.9 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [10 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-jv7ymwcp\boxkit_f17c2e8a1aef4428bab1ef1a7d2994e5\setup.py", line 14, in <module>
          import bin.cmd as bin_cmd  # pylint: disable=wrong-import-position
        File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-jv7ymwcp\boxkit_f17c2e8a1aef4428bab1ef1a7d2994e5\bin\cmd.py", line 13, in <module>
          from cbox import cbox_build  # pylint: disable=wrong-import-position
        File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-jv7ymwcp\boxkit_f17c2e8a1aef4428bab1ef1a7d2994e5\bin\cbox.py", line 21, in <module>
          if os.path.exists(os.getenv("PWD") + "/boxkit/depends/boost")
      TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

(py310) C:\Users\MENDR>pip install BoxKit
Collecting BoxKit
  Using cached BoxKit-2023.6.7.tar.gz (852 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [10 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-r2sw90yv\boxkit_decd8282603049f5bb2d36ea2947c869\setup.py", line 14, in <module>
          import bin.cmd as bin_cmd  # pylint: disable=wrong-import-position
        File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-r2sw90yv\boxkit_decd8282603049f5bb2d36ea2947c869\bin\cmd.py", line 13, in <module>
          from cbox import cbox_build  # pylint: disable=wrong-import-position
        File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-r2sw90yv\boxkit_decd8282603049f5bb2d36ea2947c869\bin\cbox.py", line 21, in <module>
          if os.path.exists(os.getenv("PWD") + "/boxkit/depends/boost")
      TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Are there any specific dependencies that needs to be installed prior to this?

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Can you try pip install boxkit==2023.9

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Yes, I have tried. Here's what I get and I believe its related to pathname

`Collecting boxkit==2023.9
  Downloading BoxKit-2023.9.0.tar.gz (1.4 MB)
     ---------------------------------------- 1.4/1.4 MB 3.2 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [10 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "C:\Users\MENDR\AppData\Local\Temp\1\pip-install-zydhqfqy\boxkit_9dbb73bbaeb0445ca87594bacf0d2c0f\setup.py", line 49, in <module>
          packages=find_packages(where="./"),
        File "C:\Users\MENDR\AppData\Local\ESRI\conda\envs\py310\lib\site-packages\setuptools\discovery.py", line 127, in find
          convert_path(str(where)),
        File "C:\Users\MENDR\AppData\Local\ESRI\conda\envs\py310\lib\site-packages\setuptools\_distutils\util.py", line 141, in convert_path
          raise ValueError("path '%s' cannot end with '/'" % pathname)
      ValueError: path './' cannot end with '/'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.`

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It looks like I will have to fix the source code to be able to work with either windows or linux machines. I originally intended BoxKit to be used on HPC clusters which are largely linux based.

I have setup a minimal test to replicate your windows test problem: https://github.com/Box-Tools/BoxKit/actions/runs/6343640315

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@akashdhruv That worked, thanks for fixing that.

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Perfect. Thank you for reporting the bug.

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Please update this link (https://akashdhruv.github.io/BoxKit/) in BoxKit docs wherever related.

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Please update this link (https://akashdhruv.github.io/BoxKit/) in BoxKit docs wherever related.

Its already up to date on the repository page: https://github.com/Box-Tools/BoxKit

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I was referring to these, under contribution and usage.

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@akashdhruv , In the paper, you have mentioned the performance is improved ~5x for measuring the bubble shape and size for Flash-X boiling simulations. Could you please locate that in the box-kit performance repo. Is that in the Jupyter notebook?

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Thank you. Please update the new links here as well.

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Done!

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Thanks everyone for the progress here!

@AnnikaStein are you able to continue with your review here as well? No problem if you need to set it down, just please let me know either way in case I should look for an additional reviewer.

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I don't think I have anymore major edits or revisions for the manuscript, but will keep you posted as I move forward

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As I mentioned earlier, I dont see any major edits/roadblocks as of now.

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@rvg296 if you are satisfied with the software status, please check off all of the items in your checkbox list accordingly

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@AnnikaStein please let me know if you are able to proceed with the review here or if I should find another reviewer

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@AnnikaStein please let me know if you are able to proceed with the review here or if I should find another reviewer

Sorry for the delay. Due to personal reasons, I am sadly not able to proceed after all.

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@AnnikaStein no worries, thanks for letting me know. Best wishes.

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@editorialbot remove @AnnikaStein from reviewers

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@AnnikaStein removed from the reviewers list!

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hi @marjanAlbouye @Abinashbunty 👋 would you be interested in and available to review this JOSS submission?

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Hi @kellyrowland Yeah sure. I'll be able to review it.

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@editorialbot add @Abinashbunty to reviewers

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@Abinashbunty added to the reviewers list!

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Hi @kellyrowland, yes I’d be happy to review this.

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Review checklist for @Abinashbunty

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/akashdhruv/BoxKit?
• 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 (@akashdhruv) 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?

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@rvg296 thanks for your review here - it looks like the "reproducibility" box is still unchecked in your list, so please check that off if you see fit based on the note there or feel free to add any other questions/comments.

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Hello everyone. Just touching base here. @Abinashbunty let me know if you have any comments

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@akashdhruv I'm almost done with the review. Apologies for taking up some time. I'll notify once done

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@akashdhruv As mentioned above, I am done with the review. Please keep me posted if there is anything else that needs to be done. Thanks.

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@akashdhruv As mentioned above, I am done with the review. Please keep me posted if there is anything else that needs to be done. Thanks.

Thank you

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@akashdhruv I'm almost done with the review. Apologies for taking up some time. I'll notify once done

Ok. Thank you :)

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@editorialbot generate post-review checklist

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I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

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Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• Read the text of the paper and offer comments/corrections (as either a list or a PR)
• Check the references in the paper for corrections (e.g. capitalization)
• Check that the archive title, author list, version tag, and the license are correct
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

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@akashdhruv can you please:

• make a release of the software with the latest changes from the review and post the version number here
• archive the release on Zenodo, figshare, etc. and post the DOI here

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Hi @kellyrowland I've completed my review. There are no changes that I have to suggest. The implementation, examples and documentation is quite thorough for this latest version of the library. 😄 One thing that I found is, this library will be very helpful for a lot of people in the field of Computational Science such as myself and my peers. So, kudos to the author @akashdhruv for coming up with this.🚀

Note: I have checked all the items in the checklist.

@Abinashbunty Thank you for finishing the reviews and the comments. I appreciate feedback from potential users like you. Hoping to continue evolving this tool for different uses cases.

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@akashdhruv can you please:

• make a release of the software with the latest changes from the review and post the version number here
• archive the release on Zenodo, figshare, etc. and post the DOI here

Yes. Will do.

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@editorialbot commands

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Hello @akashdhruv, 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

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@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.13 s (1287.3 files/s, 252346.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      13           2405           2470           9222
HTML                            31            605             93           4867
C/C++ Header                    18            478            257           2719
Python                          52            931            846           2710
SVG                              3              0              0           2673
CSS                              4            191             35            759
YAML                             7             23             29            248
reStructuredText                28            213            380            225
C++                              6             28             50            180
Markdown                         1             23              0            113
TeX                              1              6              0             72
DOS Batch                        1              8              1             26
make                             3             10             10             26
-------------------------------------------------------------------------------
SUM:                           168           4921           4171          23840
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 912

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@editorialbot generate pdf

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

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@kellyrowland

Release version number: 2023.12
Zenodo DOI: 10.5281/zenodo.10257565

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@akashdhruv I can't do that because you are not a reviewer

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@editorialbot set 2023.12 as version

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Done! version is now 2023.12

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@editorialbot set 10.5281/zenodo.10257565 as archive

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