[REVIEW]: PyFPT: A Python package for first-passage times #4607

editorialbot · 2022-07-26T10:06:03Z

Submitting author: @Jacks0nJ (Joseph Jackson)
Repository: https://github.com/Jacks0nJ/PyFPT
Branch with paper.md (empty if default branch):
Version: v1.0.2.1
Editor: @drvinceknight
Reviewers: @CFGrote, @geraintpalmer
Archive: 10.5281/zenodo.7436767

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/771dacf123576f6d5e3fbde659ca6e21"><img src="https://joss.theoj.org/papers/771dacf123576f6d5e3fbde659ca6e21/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/771dacf123576f6d5e3fbde659ca6e21/status.svg)](https://joss.theoj.org/papers/771dacf123576f6d5e3fbde659ca6e21)

Reviewers and authors:

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Reviewer instructions & questions

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✨ 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

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-07-26T10:06:04Z

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editorialbot · 2022-07-26T10:06:07Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (890.2 files/s, 79137.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          65            621           1231           1649
Jupyter Notebook                 5              0           2646            456
Markdown                         2            102              0            165
Cython                           1             26             25            147
TeX                              1             11              0            104
YAML                             4              9              6             69
reStructuredText                 4             92             80             52
DOS Batch                        1              8              1             26
TOML                             1              0              0             10
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            85            873           3996           2687
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-07-26T10:06:09Z

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 · 2022-07-26T10:06:09Z

Wordcount for paper.md is 487

editorialbot · 2022-07-26T10:07:33Z

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

Jacks0nJ · 2022-08-18T14:40:21Z

@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 · 2022-09-09T09:53:54Z

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

arfon · 2022-09-10T08:52:33Z

@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 · 2022-09-19T08:10:47Z

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 · 2022-09-19T09:02:16Z

I'm on it

Jacks0nJ · 2022-09-19T19:19:43Z

Cheers both!

geraintpalmer · 2022-09-26T12:19:19Z

Review checklist for @geraintpalmer

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/Jacks0nJ/PyFPT?
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 (@Jacks0nJ) 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?

CFGrote · 2022-09-27T05:09:43Z

Review checklist for @CFGrote

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/Jacks0nJ/PyFPT?
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 (@Jacks0nJ) 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?

CFGrote · 2022-09-27T06:16:36Z

@editorialbot generate pdf

editorialbot · 2022-09-27T06:18:37Z

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

CFGrote · 2022-10-11T08:12:22Z

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 · 2022-10-11T08:14:48Z

That makes good sense, I'll wait then.

Jacks0nJ · 2022-10-24T09:55:22Z

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 · 2022-11-10T09:37:33Z

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

CFGrote · 2022-11-15T07:30:45Z

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

Jacks0nJ · 2022-12-14T11:56:23Z

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 · 2022-12-15T15:06:02Z

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

drvinceknight · 2023-01-13T11:44:40Z

@editorialbot set 10.5281/zenodo.7436767 as archive

editorialbot · 2023-01-13T11:44:42Z

Done! Archive is now 10.5281/zenodo.7436767

drvinceknight · 2023-01-13T11:45:49Z

@editorialbot set 1.00 as version

editorialbot · 2023-01-13T11:45:50Z

Done! version is now 1.00

drvinceknight · 2023-01-13T11:46:02Z

@editorialbot recommend-accept

editorialbot · 2023-01-13T11:46:03Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-01-13T11:46:29Z

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

editorialbot · 2023-01-13T11:48:06Z

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3871, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2023-01-13T14:50:12Z

@editorialbot set v1.0.2.1 as version

editorialbot · 2023-01-13T14:50:14Z

Done! version is now v1.0.2.1

danielskatz · 2023-01-13T14:59:04Z

@Jacks0nJ - I'm the track editor, handling the final processing. I've suggested some small changes in Jacks0nJ/PyFPT#47 - please merge this, or let me know what you disagree with, then we can proceed.

Jacks0nJ · 2023-01-14T13:43:34Z

@danielskatz Hi Daniel. I've merged the your suggestions. Do let me know if I need to make any other changes.

danielskatz · 2023-01-14T14:05:08Z

@editorialbot recommend-accept

editorialbot · 2023-01-14T14:05:09Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-01-14T14:05:15Z

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

editorialbot · 2023-01-14T14:06:57Z

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3879, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2023-01-14T14:09:26Z

@editorialbot accept

editorialbot · 2023-01-14T14:09:28Z

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

editorialbot · 2023-01-14T14:11:39Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-01-14T14:11:40Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-01-14T14:11:41Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04607 joss-papers#3880
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04607
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2023-01-14T14:29:30Z

Congratulations to @Jacks0nJ (Joseph Jackson) and coauthors!!

And thanks to @CFGrote and @geraintpalmer for your reviews, and to @drvinceknight for editing!
We couldn't do this without you

editorialbot · 2023-01-14T14:29:32Z

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

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

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  <img src="https://joss.theoj.org/papers/10.21105/joss.04607/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.04607

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Jacks0nJ · 2023-01-17T14:01:52Z

Cheers @danielskatz @drvinceknight @geraintpalmer @CFGrote for all your hard work! It is very much appreciated!

editorialbot added Cython Python review TeX labels Jul 26, 2022

editorialbot assigned drvinceknight Jul 26, 2022

editorialbot mentioned this issue Jul 26, 2022

[PRE REVIEW]: PyFPT: A Python package for first-passage times #4509

Closed

editorialbot added the Track: 7 (CSISM) Computer science, Information Science, and Mathematics label Sep 10, 2022

arfon added Track: 7 (CSISM) Computer science, Information Science, and Mathematics and removed Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Sep 12, 2022

CFGrote mentioned this issue Sep 27, 2022

[JOSS Review] Comments on User Guide 3 notebook Jacks0nJ/PyFPT#45

Open

16 tasks

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jan 13, 2023

editorialbot added accepted published Papers published in JOSS labels Jan 14, 2023

danielskatz closed this as completed Jan 14, 2023

[REVIEW]: PyFPT: A Python package for first-passage times #4607

[REVIEW]: PyFPT: A Python package for first-passage times #4607

Comments

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Reviewer instructions & questions

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Review checklist for @geraintpalmer

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

CFGrote commented Sep 27, 2022 • edited Loading

Review checklist for @CFGrote

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

CFGrote commented Sep 27, 2022

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