editorialbot commented 11 months ago

Submitting author: !--author-handle-->@the-rccg@kyleniemeyer<!--end-editor-- Reviewers: @archermarx, @Uddiptaatwork Archive: 10.5281/zenodo.10365012

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/f5334c75275080b267d40b0429d711a2/status.svg)](https://joss.theoj.org/papers/f5334c75275080b267d40b0429d711a2)

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

@archermarx & @Uddiptaatwork, 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 @kyleniemeyer 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 @archermarx

📝 Checklist for @Uddiptaatwork

editorialbot commented 11 months ago

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

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editorialbot commented 11 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (1046.4 files/s, 93583.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          35            508            691           1900
Markdown                         2            106              0            251
YAML                             5             24             19            149
TOML                             1             16              0            147
TeX                              1              8              0            116
-------------------------------------------------------------------------------
SUM:                            44            662            710           2563
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 11 months ago

Wordcount for paper.md is 1095

editorialbot commented 11 months ago

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

OK DOIs

- 10.1063/1.871116 is OK
- 10.1006/jcph.1997.5697 is OK
- 10.1088/1361-6587/aaa373 is OK
- 10.1088/1361-6587/ace993 is OK
- 10.1063/1.5122865 is OK
- 10.1088/1361-6587/abad02 is OK
- 10.1063/1.871566 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 11 months ago

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

kyleniemeyer commented 11 months ago

👋 @the-rccg @archermarx @Uddiptaatwork the review will take place here

archermarx commented 11 months ago

Review checklist for @archermarx

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/the-rccg/hw2d?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@the-rccg) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

Uddiptaatwork commented 11 months ago

Review checklist for @Uddiptaatwork

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/the-rccg/hw2d?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@the-rccg) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

archermarx commented 10 months ago

I have completed most of my review, except for actually running the software. Overall, I think this is a very nice contribution. I have two main comments:

You do a good job of documenting the available methods, but you are missing an example or two to demonstrate how to use the code. I would include a small tutorial in the documentation showing how to use the code and showing off a few configurable options.
On a similar point, you mention in the installation instructions that you can use accelerators like numba. It would be good to have a list of which ones are supported by the code.

I will try and run the software tomorrow.

the-rccg commented 10 months ago

@archermarx I added an example for the CLI interface with an explanation for the kwargs used. There is also an additional paragraph on the accelerators that clearly labels available accelerators (currently only Numba). Others should be ready soon, and will be added to the readme and installation. For a full workflow example, a more thorough framework would be needed like a Google Colab Notebook, which is planned for the future.

archermarx commented 10 months ago

Great! I've now run the code and it mostly works. However, I encounter an error using the following input

python3 -m hw2d --step_size=0.025 --end_time=100 --grid_pts=128 --c1=1.0 --k0=0.15 --N=3 --nu=5.0e-08 --snaps=1 --buffer_size=100 --output_path="test.h5" --movie=1 --min_fps=10 --speed=5 --debug=0

The code runs to completion and generates a (very nice looking) movie. However, in the "Plotting properties" step, I get this error:

100%|███████████████████████████████████████████████████████████████████████████████████| 41/41 [00:16<00:00,  2.46it/s]
Plotting properties...███████████████████████████████████████████████████████████████▉  | 40/41 [00:16<00:00,  2.53it/s]
/home/marksta/.local/lib/python3.10/site-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice
  ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
/home/marksta/.local/lib/python3.10/site-packages/numpy/core/_methods.py:163: RuntimeWarning: invalid value encountered in divide
  arrmean = um.true_divide(arrmean, div, out=arrmean,
/home/marksta/.local/lib/python3.10/site-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in divide
  ret = ret.dtype.type(ret / rcount)
/home/marksta/.local/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/marksta/.local/lib/python3.10/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in divide
  ret = ret.dtype.type(ret / rcount)
test_enstrophy-energy-kinetic_energy-thermal_energy.jpg
202it [02:02,  1.65it/s]

And no image is produced.

the-rccg commented 10 months ago

@archermarx I updated the error handling to give graceful explanations and handling of this case. The issue was that end_time=100 is not inside of the saturated turbulent phase, so all statistical properties would be meaningless for the turbulent system. It now provides a warning and includes a picture of the non-converged data. The start of the different phases are given in the section subtitled "Dynamics of the different phases" in the readme.

archermarx commented 10 months ago

Excellent! In that case, I think I can mark my review as completed. Very cool work!

the-rccg commented 10 months ago

@archermarx Thank you very much for your time and effort in finding these issues and reviewing the submission! Really appreciate it.

Uddiptaatwork commented 10 months ago

I have now concluded my review. The code works great and the tests ran smoothly without any errors. Here is one point that the author might consider:

The documentation could use a home/introduction page very similar to the github-repo README. It would help new users accessing the code directly via the documentation page to get an overview of what it entails.

The documentation pertaining to the API is very well done and appears highly useful for any new user of the code. The article is succinct with analytical descriptions and citations where necessary.

Overall, I would like to congratulate the author for a very well written code and article. I can mark my review as completed.

kyleniemeyer commented 9 months ago

Thank you, @Uddiptaatwork.

@the-rccg, is that suggestion on a home page for the documentation something you could address?

the-rccg commented 9 months ago

@Uddiptaatwork Thank you very much for the review. I have added a dynamic link for the top-level that includes the README.md dynamically in documentation creation upon commit. pdoc3 currently has some issues with latex formulas in include and does no support for GitHub Flavored Markdown (GFM), therefore some things are not properly displayed at this time. I have opened an issue with pdoc3 and will try to get the support implemented myself to make sure it displays properly. For now, it's a crude approximation of the readme and should be fixed soon with progress on the pdoc3.

Preview of the ReadMe in the docs: https://the-rccg.github.io/hw2d/index.html

kyleniemeyer commented 9 months ago

@the-rccg in the past, I think I converted my Markdown README to ReST and then used that for the docs generation to avoid some issues like that, but may have been with Sphinx. This looks like a good solution, though

the-rccg commented 9 months ago

@kyleniemeyer After a lot of back and forth, I have now moved from pdoc3 to pdoc. Images and equations now work and all information is pulled dynamically from the readme.

kyleniemeyer commented 9 months ago

That looks great! At this point, I think the review is complete.

kyleniemeyer commented 9 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] 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.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

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

kyleniemeyer commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

kyleniemeyer commented 9 months ago

Hi @the-rccg, above you can see a checklist of items to complete as we wrap up the review. Can you work through your items?

the-rccg commented 9 months ago

Additional Author Tasks After Review is Complete:

[x] Double check authors and affiliations (including ORCIDs)
[x] 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.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Release: v1.0.0 (Official JOSS release)

Check GitHub: https://github.com/the-rccg/hw2d/releases/tag/release
Check PyPI: https://pypi.org/project/hw2d/1.0.0/

ORCID from Zenodo: https://zenodo.org/doi/10.5281/zenodo.10365012

kyleniemeyer commented 9 months ago

@the-rccg I made a few edits to the paper, can you merge those? https://github.com/the-rccg/hw2d/pull/4

kyleniemeyer commented 9 months ago

Also, can you add the DOI to the Goumiri et al. reference? 10.1063/1.4796190

kyleniemeyer commented 9 months ago

@editorialbot set 10.5281/zenodo.10365012 as archive

editorialbot commented 9 months ago

Done! archive is now 10.5281/zenodo.10365012

kyleniemeyer commented 9 months ago

@editorialbot 1.0.0 as version

editorialbot commented 9 months ago

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

@editorialbot commands

kyleniemeyer commented 9 months ago

@editorialbot set 1.0.0 as version

editorialbot commented 9 months ago

Done! version is now 1.0.0

the-rccg commented 9 months ago

@kyleniemeyer merged and added all missing DOIs

kyleniemeyer commented 9 months ago

@editorialbot generate pdf

kyleniemeyer commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

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

OK DOIs

- 10.1063/1.871116 is OK
- 10.1006/jcph.1997.5697 is OK
- 10.1088/1361-6587/aaa373 is OK
- 10.1088/1361-6587/ace993 is OK
- 10.1063/1.5122865 is OK
- 10.1103/PhysRevLett.50.682 is OK
- 10.1063/1.4796190 is OK
- 10.1088/1361-6587/abad02 is OK
- 10.1063/1.871566 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 9 months ago

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

kyleniemeyer commented 9 months ago

OK, all looks great @the-rccg!

kyleniemeyer commented 9 months ago

@editorialbot recommend-accept

editorialbot commented 9 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 9 months ago

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

OK DOIs

- 10.1063/1.871116 is OK
- 10.1006/jcph.1997.5697 is OK
- 10.1088/1361-6587/aaa373 is OK
- 10.1088/1361-6587/ace993 is OK
- 10.1063/1.5122865 is OK
- 10.1103/PhysRevLett.50.682 is OK
- 10.1063/1.4796190 is OK
- 10.1088/1361-6587/abad02 is OK
- 10.1063/1.871566 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 9 months ago

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

athrm{d}^2 x \space \left(n \partial_y \
                   ^
unexpected control sequence \space
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

athrm{d}^2 x \space \left(n - \phi\right
                   ^
unexpected control sequence \space
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

            = \small \frac{1}{2} \normal
                   ^
unexpected control sequence \small
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

            = \small \frac{1}{2} \normal
                   ^
unexpected control sequence \small
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

mathrm{d} k_y \space \Gamma^n \small (k_
                   ^
unexpected control sequence \space
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

  \delta \small (k_y)  \normalsize \spac
              ^
unexpected control sequence \small
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

  E^N  \small (k_y)  \normalsize \space 
            ^
unexpected control sequence \small
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

  E^V  \small (k_y)  \normalsize \space 
            ^
unexpected control sequence \small
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

 \mathrm{d}^2 x \space (n \mathfrak{D^n}
                   ^
unexpected control sequence \space
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

 \mathrm{d}^2 x \space (n - \Omega)(\mat
                   ^
unexpected control sequence \space
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

 \mathfrak{D}^n \small (x,y) \normalsize
                   ^
unexpected control sequence \small
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

editorialbot commented 9 months ago

:wave: @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4832, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

the-rccg commented 9 months ago

Can the Tex warnings be safely ignored or do I need to removethe \space and \small from it still?

kyleniemeyer commented 9 months ago

@the-rccg let's try removing \space and \small in the equations. If you need spacing in math mode, I believe you can use \,, \:, and \; instead.

As for \small, I'm not sure the output you were aiming for there. Is that needed?

the-rccg commented 9 months ago

@kyleniemeyer removed all \small, \normalsize, and \space and replaces some with more explicit spacings.

kyleniemeyer commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

kyleniemeyer commented 9 months ago

@editorialbot recommend-accept

openjournals / joss-reviews

[REVIEW]: HW2D: A reference implementation of the Hasegawa-Wakatani model for plasma turbulence in fusion reactors #5959

Status

Reviewer instructions & questions

Checklists

Review checklist for @archermarx

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @Uddiptaatwork

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance