[PRE REVIEW]: STReNGTHS, a python package to model and simulate reaction-diffusion systems #6153

editorialbot · 2023-12-15T18:42:52Z

Submitting author: @ThibaultFillion (Thibault Fillion)
Repository: https://github.com/ThibaultFillion/strengths
Branch with paper.md (empty if default branch): paper
Version: v0.0.8
Editor: @Nikoleta-v3
Reviewers: @parikshitbajpai, @jakryd
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/6ab8888e81d77b4c8b30be118c67d484/status.svg)](https://joss.theoj.org/papers/6ab8888e81d77b4c8b30be118c67d484)

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editorialbot · 2023-12-15T18:42:55Z

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editorialbot · 2023-12-15T18:42:56Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (807.8 files/s, 138242.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          35           1889           2207           5036
C/C++ Header                     8            212            216           1155
JSON                             8              0              0           1100
reStructuredText                29            691            765            925
C++                              1             92             36            464
Markdown                         1             33              0            258
TeX                              1             19              0            135
CSS                              1             11              1             56
DOS Batch                        1              8              1             26
YAML                             2              1              4             25
make                             1              4              7              9
JavaScript                       1              1              0              8
TOML                             1              0              0              8
-------------------------------------------------------------------------------
SUM:                            90           2961           3237           9205
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-12-15T18:42:58Z

Wordcount for paper.md is 2346

editorialbot · 2023-12-15T18:42:58Z

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

OK DOIs

- 10.1021/j100540a008 is OK
- 10.1103/PhysRevE.71.041103 is OK
- 10.1063/1.1378322 is OK
- 10.1093/bioinformatics/bti431 is OK
- 10.1049/sb:20045021 is OK
- 10.1093/bioinformatics/btw469 is OK
- 10.3389/neuro.11.015.2009 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- 10.1371/journal.pcbi.1006830 may be a valid DOI for title: ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics

INVALID DOIs

- None

editorialbot · 2023-12-15T18:44:22Z

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

editorialbot · 2023-12-15T18:45:03Z

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Kevin-Mattheus-Moerman · 2024-01-11T22:58:27Z

@ThibaultFillion thanks for this submission. While I look for a handling editor please can you work on the following:

Please check the above potentially missing/invalid DOIs ☝️ and amend your .bib file where needed. You can call @editorialbot check references to check them again.
Please expand your README to include more information as is customary e.g. links to documentation/testing, an installation/ getting started section, contributing guidelines (or a link to them), and a link to the license.

Kevin-Mattheus-Moerman · 2024-01-11T22:59:57Z

@editorialbot invite @Nikoleta-v3 as editor

editorialbot · 2024-01-11T22:59:59Z

Invitation to edit this submission sent!

Nikoleta-v3 · 2024-01-12T10:55:51Z

@editorialbot assign me as editor

editorialbot · 2024-01-12T10:55:54Z

Assigned! @Nikoleta-v3 is now the editor

ThibaultFillion · 2024-01-13T04:34:04Z

@Kevin-Mattheus-Moerman thank you for having assigned an editor.
@Nikoleta-v3 thank you for accepting to be the editor for this review process.
I take care of the changes you requested as soon as i can.

ThibaultFillion · 2024-01-13T04:35:13Z

@editorialbot check references

editorialbot · 2024-01-13T04:35:15Z

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

OK DOIs

- 10.1021/j100540a008 is OK
- 10.1103/PhysRevE.71.041103 is OK
- 10.1063/1.1378322 is OK
- 10.1371/journal.pcbi.1006830 is OK
- 10.1093/bioinformatics/bti431 is OK
- 10.1049/sb:20045021 is OK
- 10.1093/bioinformatics/btw469 is OK
- 10.3389/neuro.11.015.2009 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Nikoleta-v3 · 2024-01-13T10:26:12Z

Great, thank you for fixing the DOI @ThibaultFillion. When you address the comments regarding the README, please ping me here 😄 Also, could you include the commit hash when you do?

ThibaultFillion · 2024-01-16T05:44:24Z

@Nikoleta-v3 Sorry for the delay. I tried to expand the README file as requested.
The corresponding commit hash is 6a4ae34 (i think).

Nikoleta-v3 · 2024-01-22T10:58:08Z

Thank you @ThibaultFillion for your work on the Readme! I just have two questions:

Regarding the contribution guidelines, is there a particular reason why you are referring to this copy of the file instead of this one?
Regarding your test setup, it's great that you have implemented tests. As you point out, one has to run the command

python run_all_tests.py

Are you familiar with the package pytest? I recommend pytest because it works similarly to your run file. It runs all files that have "test" in the name and each function that also has "test" in its name, providing more informative output.

This is what it looks like when I run pytest in the tests folder.

You can also run pytest tests from the root of the directory.

I'm not saying you should use pytest; it's just a recommendation. If not, could you state something like, "If the command runs and you receive no output, then the tests have passed." after the python run_all_tests.py.

At this point, could you also please check out this page: https://reviewers.joss.theoj.org/lookup and suggest at least three reviewers? 😄

ThibaultFillion · 2024-02-10T11:40:07Z

@Nikoleta-v3 Sorry again for the delay. To answer your questions :

I have made a mistake here, linking the github page would be better.
I will edit the links, thank you for telling me.
Thank you for recommending pytest,
it would indeed work great with the current implementation.
For now, i will just go for the second option,
but i might definitly switch for pytest in the future.
Thank you again for the advice.

For the reviewers, we recommend :

ggmirandac
lorenzo-rovigatti
ASinanSaglam (not on the list)

Nikoleta-v3 · 2024-02-28T18:11:37Z

Hello @ThibaultFillion ! I am really sorry for the delay with your submission. The past month has been overwhelming. I am going to start looking for reviewers right away.

Nikoleta-v3 · 2024-02-28T18:16:01Z

👋🏻 @ggmirandac @ASinanSaglam would any of you be willing to review this submission for JOSS?

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

The submission I'd like you to review is titled: "STReNGTHS, a python package to model and simulate reaction-diffusion systems". You can find more information at the top of this Github issue 🆙

Please let me know if you're available 😄 Thank you!

ThibaultFillion · 2024-03-01T15:59:14Z

@Nikoleta-v3 No problem, thank you for looking for reviewers !

Nikoleta-v3 · 2024-03-03T12:35:42Z

👋🏻 @Wrzlprmft @parikshitbajpai would any of you be willing to review this submission for JOSS?

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

The submission I'd like you to review is titled: "STReNGTHS, a python package to model and simulate reaction-diffusion systems". You can find more information at the top of this Github issue 🆙

Please let me know if you're available 😄 Thank you!

Wrzlprmft · 2024-03-03T17:38:55Z

👋🏻 @Wrzlprmft […] would any of you be willing to review this submission for JOSS?

Generally yes, but I am very busy until the mid of April, so I won’t be able to even start the review before then.

At a very first glance, the paper seems rather long (for JOSS’s standards) and contains things like installation instructions that do not need to be there.

parikshitbajpai · 2024-03-03T18:10:22Z

👋🏻 @Wrzlprmft @parikshitbajpai would any of you be willing to review this submission for JOSS?

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

The submission I'd like you to review is titled: "STReNGTHS, a python package to model and simulate reaction-diffusion systems". You can find more information at the top of this Github issue 🆙

Please let me know if you're available 😄 Thank you!

Yes, I can review this paper.

Nikoleta-v3 · 2024-03-07T16:08:28Z

Generally yes, but I am very busy until the mid of April, so I won’t be able to even start the review before then.

At a very first glance, the paper seems rather long (for JOSS’s standards) and contains things like installation instructions that do not need to be there.

@Wrzlprmft, thanks for getting back to me! 🙏🏻 🚀 No problem at all; I will try to find another reviewer. If I can't find one by mid-April, I might ping you again.

Appreciate your feedback! You're right about the length of the paper. Once we get into the review process, I'll make sure to give the author some pointers on that.

Nikoleta-v3 · 2024-03-07T16:09:37Z

@editorialbot add @parikshitbajpai as reviewer

editorialbot · 2024-03-07T16:09:40Z

@parikshitbajpai added to the reviewers list!

Nikoleta-v3 · 2024-03-07T16:16:52Z

@corettialessandro @shivupa would any of you be willing to review this submission for JOSS?

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

The submission I'd like you to review is titled: "STReNGTHS, a python package to model and simulate reaction-diffusion systems". You can find more information at the top of this Github issue 🆙

Please let me know if you're available 😄 Thank you!

shivupa · 2024-03-07T16:34:54Z

Hi I'm actually in the same situation of having low bandwidth until April, and this also feels a bit too far outside of my area of expertise. I apologize for the difficulty, but I wouldn't feel confident reviewing this work.

Nikoleta-v3 · 2024-03-07T16:53:06Z

No problem at all @shivupa! Thank you very much for your reply 🚀

corettialessandro · 2024-03-12T11:05:04Z

Sorry for the late answer, I was trying to find a replacement, but I did not succeed. At the moment my schedule is really tight, so I would not be able to provide a good quality review. I am sorry.

ThibaultFillion · 2024-03-12T12:58:10Z

@Wrzlprmft Thank you for your feedback, I'll remove the installation instructions from the summary.
@parikshitbajpai Thank you for accepting to review the paper.
@shivupa @corettialessandro No problem, thank you for taking the time to answer, and thank you @corettialessandro for having searched for a replacement.

Nikoleta-v3 · 2024-03-14T19:23:28Z

Thank you both for your replies! No problem at all 😄 I really hope things become a bit less hectic for you in the next month!

Hi I'm actually in the same situation of having low bandwidth until April, and this also feels a bit too far outside of my area of expertise. I apologize for the difficulty, but I wouldn't feel confident reviewing this work.

Sorry for the late answer, I was trying to find a replacement, but I did not succeed. At the moment my schedule is really tight, so I would not be able to provide a good quality review. I am sorry.

Nikoleta-v3 · 2024-03-14T19:27:04Z

👋🏻 @jakryd @maxscheurer would any of you be willing to review this submission for JOSS?

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

The submission I'd like you to review is titled: "STReNGTHS, a python package to model and simulate reaction-diffusion systems". You can find more information at the top of this Github issue 🆙

Please let me know if you're available 😄 Thank you!

jakryd · 2024-03-15T08:50:18Z

Sure! I would be happy to review this.

Nikoleta-v3 · 2024-03-16T10:25:57Z

@editorialbot add @jakryd as reviewer

editorialbot · 2024-03-16T10:25:59Z

@jakryd added to the reviewers list!

Nikoleta-v3 · 2024-03-16T10:27:06Z

@editorialbot start review

editorialbot · 2024-03-16T10:27:09Z

OK, I've started the review over in #6495.

ThibaultFillion · 2024-03-16T13:19:39Z

@jakryd Thank you for accepting !

editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Dec 15, 2023

editorialbot added C++ Python TeX labels Dec 15, 2023

editorialbot assigned Nikoleta-v3 Jan 12, 2024

editorialbot assigned parikshitbajpai Mar 7, 2024

editorialbot assigned jakryd Mar 16, 2024

editorialbot closed this as completed Mar 16, 2024

[PRE REVIEW]: STReNGTHS, a python package to model and simulate reaction-diffusion systems #6153

[PRE REVIEW]: STReNGTHS, a python package to model and simulate reaction-diffusion systems #6153

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