[REVIEW]: PyFPT: A Python package for first-passage times

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@Jacks0nJ@drvinceknight<!--end-editor-- Reviewers: @CFGrote, @geraintpalmer Archive: 10.5281/zenodo.7436767

Status

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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

@CFGrote & @geraintpalmer, 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 @drvinceknight 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 @geraintpalmer

📝 Checklist for @CFGrote

editorialbot commented 2 years ago

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editorialbot commented 2 years ago

Software report:

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TOML                             1              0              0             10
make                             1              4              7              9
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gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

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

OK DOIs

- 10.1140/epjc/s10052-015-3643-y is OK
- 10.1088/1475-7516/2017/10/046 is OK
- 10.1142/9789814327183_0010 is OK
- 10.1088/1361-6471/abc534 is OK
- 10.1140/epjb/s10051-021-00246-0 is OK
- 10.1016/S0375-9474(98)00478-3 is OK
- 10.1088/1475-7516/2022/05/027 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

Wordcount for paper.md is 487

editorialbot commented 2 years ago

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

Jacks0nJ commented 2 years ago

@drvinceknight I've been updating the code to also have functionality for n-dimensions. Currently, the main branch is only for 1D. Apart from a few functions being renamed for clarity and some efficiency savings I've found, the old 1D code is untouched and relevant guides will be the same. There would also be a new, 4th guide to explain the nD code.

The nD code is almost ready to merge with the main branch (along with the updated guides). Should I hold off on doing this until after the review is completed? Or would it be possible to have the JOSS paper be for the nD code?

Jacks0nJ commented 2 years ago

@drvinceknight @CFGrote @geraintpalmer Any updates on the review? Is there anything I need to be doing?

arfon commented 2 years ago

@drvinceknight – it looks like neither of the reviewers have formally started their reviews here yet. Can you check in with them and see how they're getting on?

drvinceknight commented 2 years ago

Hi @Jacks0nJ, thanks for your patience.

I have spoken to @geraintpalmer and he is working on this.

I will attempt to get an update from @CFGrote.

No action needed from you @Jacks0nJ.

CFGrote commented 2 years ago

I'm on it

Jacks0nJ commented 2 years ago

Cheers both!

geraintpalmer commented 2 years ago

Review checklist for @geraintpalmer

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/Jacks0nJ/PyFPT?
[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 (@Jacks0nJ) 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?

CFGrote commented 2 years ago

Review checklist for @CFGrote

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/Jacks0nJ/PyFPT?
[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 (@Jacks0nJ) 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?

CFGrote commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

CFGrote commented 2 years ago

IMO you should wait with merging until the JOSS paper is out. This is a major change and warrants a major version increment. That's my point of view, but I'm happy to discuss.

On Thu, 2022-08-18 at 07:40 -0700, Joe Jackson wrote:

@drvinceknight I've been updating the code to also have functionality for n- dimensions. Currently, the main branch is only for 1D. Apart from a few functions being renamed for clarity and some efficiency savings I've found, the old 1D code is untouched and relevant guides will be the same. There would also be a new, 4th guide to explain the nD code. The nD code is almost ready to merge with the main branch (along with the updated guides). Should I hold off on doing this until after the review is completed? Or would it be possible to have the JOSS paper be for the nD code? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

Jacks0nJ commented 2 years ago

That makes good sense, I'll wait then.

Jacks0nJ commented 2 years ago

Any ETA on when the review will be finished? As I've already had interest in the 2D version of the code, which I would like to be available in the main branch and through PyPI (rather than TestPyPI as is currently the case). Additionally I will be presenting a tutorial on the code next month, so ideally I would have the merged the multi-dimensional version of the code before then.

danielskatz commented 2 years ago

👋 @drvinceknight - can you help this submission move along? It looks almost done, all review criteria are checked except one (reproducibility) from @CFGrote

CFGrote commented 2 years ago

Sorry, my bad. I checked the last box. All good from my side.

drvinceknight commented 2 years ago

I'll finish this up tomorrow @danielskatz :+1:

drvinceknight commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

drvinceknight commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1140/epjc/s10052-015-3643-y is OK
- 10.1088/1475-7516/2017/10/046 is OK
- 10.1142/9789814327183_0010 is OK
- 10.1088/1361-6471/abc534 is OK
- 10.1140/epjb/s10051-021-00246-0 is OK
- 10.1016/S0375-9474(98)00478-3 is OK
- 10.1088/1475-7516/2022/05/027 is OK

MISSING DOIs

- 10.1088/1475-7516/2022/09/045 may be a valid DOI for title: Smooth coarse-graining and colored noise dynamics in stochastic inflation

INVALID DOIs

- None

drvinceknight commented 2 years ago

Everything looks good to me @Jacks0nJ. The suggestion made by editorial bot does seem correct to me, would you be able to add the doi 10.1088/1475-7516/2022/09/045 which points at https://iopscience.iop.org/article/10.1088/1475-7516/2022/09/045 (unless I'm wrong and it differs from the arXiv preprint).

Let me know once that's done and there will be a couple of other steps to take but it won't take us long.

Jacks0nJ commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1140/epjc/s10052-015-3643-y is OK
- 10.1088/1475-7516/2017/10/046 is OK
- 10.1142/9789814327183_0010 is OK
- 10.1088/1361-6471/abc534 is OK
- 10.1140/epjb/s10051-021-00246-0 is OK
- 10.1016/S0375-9474(98)00478-3 is OK
- 10.1088/1475-7516/2022/09/045 is OK
- 10.1088/1475-7516/2022/05/027 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Jacks0nJ commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

Jacks0nJ commented 2 years ago

@drvinceknight I've added the doi to the reference. The pre-print version does in fact differ from the published version in content, but the key point of their code not being open source is till valid.

I've also made some very minor changes: I've changed my name to "Joseph H. P. Jackson", swapped the second and third sentence around, added "in general" and added an additional grant number to the acknowledgments. Feel free to check the changes are ok and are indeed minor.

Do let me know if there is anything else I need to do.

drvinceknight commented 2 years ago

That looks good to me @Jacks0nJ!

drvinceknight commented 2 years ago

Could you make a tagged release and archive, and report the version number and archive DOI here please.

Please make sure the archive deposit has the correct metadata (title and author list that match here).

Jacks0nJ commented 2 years ago

Mind linking to a guide on how to do this? Apologies but I'm slightly unsure what tagged release is.

Do I just need to follow the steps outlined in the link below?

https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository

drvinceknight commented 2 years ago

No problem @Jacks0nJ (no need to apologise), the steps here are indeed what you need to do: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository#creating-a-release

Jacks0nJ commented 2 years ago

@drvinceknight I've made a release. How do archive and report the DOI?

drvinceknight commented 1 year ago

You can make an archive using Zenodo: https://zenodo.org

You can do this manually (although a lot of people set up something automatic between their repos). Once you create the archive (you'll need to upload a version of the release) you'll have a DOI which you can just put here. Let me know.

Jacks0nJ commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

Jacks0nJ commented 1 year ago

@drvinceknight The tagged release is v1.0.2.1 and the DOI is 10.5281/zenodo.7436767. The link is https://zenodo.org/record/7436767#.Y5mm2HbP1PY

Zenodo did not have much info how it archives a repository. But GitHub did at https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content

To make it easier for future publications, would it be possible that these steps could by added to the JOSS documentation?

And thanks again for all your work and help!

Jacks0nJ commented 1 year ago

And do let me know if there are any other steps I need to take.

drvinceknight commented 1 year ago

Sorry! But I'm afraid the archive needs to be modified a bit: the title needs to be PyFPT: A Python package for first-passage times the same as the article. I believe you can edit the archive directly on Zenodo without the need for a new release.

Jacks0nJ commented 1 year ago

Apologies, I forgot to make that final step. This should (hopefully) be fixed. I've also added the other authors and their Orchid numbers.

Jacks0nJ commented 1 year ago

@drvinceknight Do let me know if there is anything else I need to do!

drvinceknight commented 1 year ago

@editorialbot set 10.5281/zenodo.7436767 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7436767

drvinceknight commented 1 year ago

@editorialbot set 1.00 as version

editorialbot commented 1 year ago

Done! version is now 1.00

drvinceknight commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

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