editorialbot commented 6 months ago

Submitting author: !--author-handle-->@vidarsko@lucydot<!--end-editor-- Reviewers: @flokno, @sharanroongta, @sbacchio Archive: 10.5281/zenodo.11395524

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/7fa0aca16b8652afacb2548b87bf0132"><img src="https://joss.theoj.org/papers/7fa0aca16b8652afacb2548b87bf0132/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/7fa0aca16b8652afacb2548b87bf0132/status.svg)](https://joss.theoj.org/papers/7fa0aca16b8652afacb2548b87bf0132)

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

@flokno & @sharanroongta & @sbacchio, 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 @lucydot 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 @sharanroongta

📝 Checklist for @sbacchio

📝 Checklist for @flokno

editorialbot commented 6 months ago

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 commented 6 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.13 s (1523.6 files/s, 273924.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         161           3034           2466           6570
Markdown                        13           1011              0           2800
SVG                              3              2              2            896
Jupyter Notebook                15              0          17614            681
TeX                              1             32              0            240
YAML                             4             31              6            195
CSS                              1              2              1             16
-------------------------------------------------------------------------------
SUM:                           198           4112          20089          11398
-------------------------------------------------------------------------------

Commit count by author:

   480  Vidar Skogvoll
   278  jonasron
    77  Jonas Rønning
     2  MilosJoks
     1  Harish P Jain
     1  Milos Joksimovic

editorialbot commented 6 months ago

Paper file info:

📄 Wordcount for paper.md is 920

✅ The paper includes a Statement of need section

editorialbot commented 6 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 6 months ago

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

OK DOIs

- 10.1103/PhysRevLett.78.401 is OK
- 10.1103/PhysRevE.59.1574 is OK
- 10.1103/PhysRevE.85.011153 is OK
- 10.1006/jcph.2002.6995 is OK
- 10.1103/PhysRevE.95.052144 is OK
- 10.1103/PhysRevLett.121.255501 is OK
- 10.1103/PhysRevE.93.042137 is OK
- 10.1103/PhysRevE.93.032106 is OK
- 10.1103/PhysRevB.103.014107 is OK
- 10.1103/PhysRevB.103.224107 is OK
- 10.1016/j.jmps.2022.104932 is OK
- 10.1088/1361-651X/ac9493 is OK
- 10.1038/s41524-023-01077-6 is OK
- 10.1039/D3SM00316G is OK
- 10.1088/1367-2630/ab95de is OK
- 10.1103/PhysRevResearch.5.023108 is OK

MISSING DOIs

- No DOI given, and none found for title: A Unified Perspective on Two-Dimensional Quantum T...
- No DOI given, and none found for title: Symmetry, Topology, and Crystal Deformations: A Ph...
- No DOI given, and none found for title: Topological Defects and Flows in BECs and Active M...

INVALID DOIs

- None

editorialbot commented 6 months ago

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

sharanroongta commented 6 months ago

Review checklist for @sharanroongta

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/vidarsko/ComFiT?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@vidarsko) 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?

sbacchio commented 6 months ago

Review checklist for @sbacchio

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/vidarsko/ComFiT?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@vidarsko) 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?

vidarsko commented 6 months ago

Thanks for your review @sbacchio. I have added a second paragraph to the Statement of need to try and adress the state of the field. Let me know if you do not find it satisfactory and I will try to amend accordingly.

vidarsko commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

vidarsko commented 6 months ago

@lucydot I realize that I have not capitalized the p in "Python" for the submission on the JOSS website. Is it possible to amend that?

sharanroongta commented 6 months ago

@vidarsko Thanks for adding the state of the art. Is it also possible to add references for other open-source library for solving PDE?

vidarsko commented 6 months ago

@sharanroongta Yes, I have added the references to for mentionned packages.

vidarsko commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

sbacchio commented 6 months ago

@vidarsko, Thank you for promptly addressing the missing item. The added paragraphs are satisfactory to me. I warmly recommend the work for publication! It is a nice package with a very good documentation and examples.

I have only a marginal suggestion: you should add the example you provided in the manuscript to the tests and CI, such that you guarantee it will always be supported in the future :)

lucydot commented 6 months ago

I realize that I have not capitalized the p in "Python" for the submission on the JOSS website. Is it possible to amend that?

Do you mean in the issue thread title @vidarsko? I have just updated.

vidarsko commented 6 months ago

I realize that I have not capitalized the p in "Python" for the submission on the JOSS website. Is it possible to amend that?

Do you mean in the issue thread title @vidarsko? I have just updated.

Thanks for updating. I suppose the p in the issue thread is not capitalized because I forgot to do it in the submission on the JOSS website. This is how my pending submission looks like on the website.

lucydot commented 6 months ago

Thanks for your timely review @sbacchio ✨ - can you confirm that as part of the review you were able to install and run the package successfully? I ask as it is unusual for there to be no hiccups, so want to double check..

sharanroongta commented 5 months ago

@vidarsko Please have a look at https://github.com/vidarsko/ComFiT/issues/9

sbacchio commented 5 months ago

Thanks for your timely review @sbacchio ✨ - can you confirm that as part of the review you were able to install and run the package successfully? I ask as it is unusual for there to be no hiccups, so want to double check..

@lucydot, sure I've been able to install it on my machine and reproduce examples and tutorials. At least with my Python version, it worked out fine!

flokno commented 5 months ago

Review checklist for @flokno

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/vidarsko/ComFiT?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@vidarsko) 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?

flokno commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

vidarsko commented 5 months ago

@vidarsko Please have a look at vidarsko/ComFiT#9

We have addressed and closed the issue. Feel free to raise another issue if you find other problems and or are not satisfied with the resolution.

vidarsko commented 5 months ago

Note: I have added the custom domain https://comfitlib.com/ to the repository and changed the links in the paper and relevant sections of the code repository. Hope that is okay.

flokno commented 5 months ago

@vidarsko regarding the summary in the paper (Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?):

For my taste it is a bit too general for a non-expert in PDEs. Maybe you could name one or several widely-known PDEs and physical areas as examples right in the introduction (e.g. Navier-Stokes for fluid dynamcis?)

vidarsko commented 5 months ago

@vidarsko regarding the summary in the paper (Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?):

For my taste it is a bit too general for a non-expert in PDEs. Maybe you could name one or several widely-known PDEs and physical areas as examples right in the introduction (e.g. Navier-Stokes for fluid dynamcis?)

Thank you for your comment, @flokno. I have elaborated a little in the Statement of need to include some examples of famous PDEs.

vidarsko commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

sharanroongta commented 5 months ago

Hi @vidarsko, Here you have mentioned about two examples - one for scalar order parameter, and the other for a vector. I don't see any example for vector order parameter. Am I missing something?

vidarsko commented 5 months ago

Hi @vidarsko, Here you have mentioned about two examples - one for scalar order parameter, and the other for a vector. I don't see any example for vector order parameter. Am I missing something?

Thanks for pointing this out! I have extended the tutorial to include an example with a vector-valued order parameter.

sharanroongta commented 5 months ago

@vidarsko From my side, it is all fine now.

I just have a suggestion, the documentation is adequate but could be improved. I know it's an iterative process. The BaseSystem Class can be better explained in terms of how one could set up pde (like anisotropic heat conduction). I am happy with the clarification you have provided in the issue I had raised.

Thanks and all the best! :)

lucydot commented 5 months ago

Thanks @sharanroongta ✨

@flokno how is your review going?

flokno commented 5 months ago

@vidarsko regarding the summary in the paper (Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?): For my taste it is a bit too general for a non-expert in PDEs. Maybe you could name one or several widely-known PDEs and physical areas as examples right in the introduction (e.g. Navier-Stokes for fluid dynamcis?)

Thank you for your comment, @flokno. I have elaborated a little in the Statement of need to include some examples of famous PDEs.

Thank you @vidarsko . I find "Maxwell's equations which dictate how electromagnetic fields encode those well-crafted cat memes" a little bit too colloquial and confusing, but that's just a comment.

I have found some problems when running the tutorials locally and not in the cloud, please see https://github.com/vidarsko/ComFiT/issues/13

vidarsko commented 5 months ago

@vidarsko regarding the summary in the paper (Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?): For my taste it is a bit too general for a non-expert in PDEs. Maybe you could name one or several widely-known PDEs and physical areas as examples right in the introduction (e.g. Navier-Stokes for fluid dynamcis?)

Thank you for your comment, @flokno. I have elaborated a little in the Statement of need to include some examples of famous PDEs.

Thank you @vidarsko . I find "Maxwell's equations which dictate how electromagnetic fields encode those well-crafted cat memes" a little bit too colloquial and confusing, but that's just a comment.

I have found some problems when running the tutorials locally and not in the cloud, please see vidarsko/ComFiT#13

Thank you for your thorough review, @flokno. I suggested a solution to your raised issue. Have a look and see if it is to your satisfaction.

I have also revised the sentece which, I agree, was perhaps a bit too colloquial.

flokno commented 4 months ago

@vidarsko I tried the other tutorials and ran into a bunch of errors, see issues. I stopped for now -- please double-check all tutorials and let me know when they are ready. Once all tutorials works, I'm fine with the JOSS paper!

As an optional comment: there are tools to auto-format python files and jupyter notebooks. For example: https://github.com/drillan/jupyter-black

I strongly recommend consistent code formatting complying with PEP8 (and possibly tools like flake8 to check), though this is of course optional

jonasron commented 4 months ago

@vidarsko I tried the other tutorials and ran into a bunch of errors, see issues. I stopped for now -- please double-check all tutorials and let me know when they are ready. Once all tutorials works, I'm fine with the JOSS paper!

As an optional comment: there are tools to auto-format python files and jupyter notebooks. For example: https://github.com/drillan/jupyter-black

I strongly recommend consistent code formatting complying with PEP8 (and possibly tools like flake8 to check), though this is of course optional

@flokno Thank you for going over the tutorials. We have checked all tutorials and they are now working.

flokno commented 4 months ago

@jonasron @vidarsko good, thank you! I ticked the last box.

@lucydot I'm done with my review and I think the package is good to go!

vidarsko commented 4 months ago

Thank you! @lucydot, what is the next step?

lucydot commented 4 months ago

Excellent work @flokno @sharanroongta @sbacchio; on behalf of the JOSS team, thank you for your expertise and time.

lucydot commented 4 months ago

We are onto the final stages of the process now @vidarsko I'll ask editorialbot to generate the post-review to-do list; let me know when each item is done.

lucydot commented 4 months ago

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

[x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[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
[x] Recommend acceptance with @editorialbot recommend-accept

lucydot commented 4 months ago

@editorialbot generate pdf

lucydot commented 4 months ago

@editorialbot check references

editorialbot commented 4 months ago

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

editorialbot commented 4 months ago

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

OK DOIs

- 10.1103/PhysRevLett.78.401 is OK
- 10.1103/PhysRevE.59.1574 is OK
- 10.1103/PhysRevE.85.011153 is OK
- 10.1006/jcph.2002.6995 is OK
- 10.1103/PhysRevE.95.052144 is OK
- 10.1103/PhysRevLett.121.255501 is OK
- 10.1103/PhysRevE.93.042137 is OK
- 10.1103/PhysRevE.93.032106 is OK
- 10.1103/PhysRevB.103.014107 is OK
- 10.1103/PhysRevB.103.224107 is OK
- 10.1016/j.jmps.2022.104932 is OK
- 10.1088/1361-651X/ac9493 is OK
- 10.1038/s41524-023-01077-6 is OK
- 10.1039/D3SM00316G is OK
- 10.1088/1367-2630/ab95de is OK
- 10.1103/PhysRevResearch.5.023108 is OK
- 10.11588/ans.2015.100.20553 is OK
- 10.25561/104839 is OK
- 10.1103/PhysRevResearch.2.023068 is OK

MISSING DOIs

- Errored finding suggestions for "A Unified Perspective on Two-Dimensional Quantum T...", please try later
- Errored finding suggestions for "Symmetry, Topology, and Crystal Deformations: A Ph...", please try later
- Errored finding suggestions for "Topological Defects and Flows in BECs and Active M...", please try later
- Errored finding suggestions for "PyClaw: Accessible, Extensible, Scalable Tools for...", please try later

INVALID DOIs

- None

lucydot commented 4 months ago

@vidarsko, some comments on the paper:

The sentence spanning lines 58-62 is rather long (and "between" is used twice). I think this could be split into two sentences.
Acronym UiOis undefined.
I've made several other small corrections to improve readability. Please see PR here, and double check all changes before merging: https://github.com/vidarsko/ComFiT/pull/19

Once you have updated the paper, please run @editorialbot generate pdf to double check that the paper compiles and reads as expected.

Nearly there!

lucydot commented 4 months ago

@vidarsko for the cited doctoral theses, please can you double check if there are DOIs associated. Usually there is an institutional record with an assigned DOI. Thanks.

openjournals / joss-reviews

[REVIEW]: ComFiT: a Python library for computational field theory with topological defects #6599

Status

Reviewer instructions & questions

Checklists

Review checklist for @sharanroongta

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @sbacchio

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @flokno

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