[REVIEW]: ProbNumDiffEq.jl: Probabilistic Numerical Solvers for Ordinary Differential Equations in Julia

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@nathanaelbosch@jbytecode<!--end-editor-- Reviewers: @PieterjanRobbe, @ranocha Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/d9a7797fbd0b950105f1d8e77d00359d/status.svg)](https://joss.theoj.org/papers/d9a7797fbd0b950105f1d8e77d00359d)

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

@PieterjanRobbe & @ranocha, 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 @jbytecode 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 @PieterjanRobbe

📝 Checklist for @ranocha

editorialbot commented 1 month ago

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.20 s (906.0 files/s, 168948.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                             56              0              0          16901
Julia                           85           1158           1341           6903
Markdown                        24            833              0           6205
TeX                              2             34              0            484
YAML                            10             10             11            226
TOML                             5              9              1            161
CSS                              1              0              0             17
INI                              1              3              0             14
-------------------------------------------------------------------------------
SUM:                           184           2047           1353          30911
-------------------------------------------------------------------------------

Commit count by author:

   830  Nathanael Bosch
    93  github-actions[bot]
     4  dependabot[bot]
     2  Pietro Monticone
     1  Christopher Rackauckas
     1  CompatHelper Julia
     1  Cornelius Roemer
     1  Daniel González Arribas
     1  David Widmann
     1  Jose Storopoli
     1  Qingyu Qu
     1  Tim Holy
     1  Vedant Puri

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 898

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

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

OK DOIs

- 10.48550/arXiv.2112.02100 is OK
- 10.5334/jors.151 is OK
- 10.1007/s11222-017-9798-7 is OK
- 10.1007/s11222-019-09900-1 is OK
- 10.1007/s11222-020-09972-4 is OK
- 10.1007/s11222-021-09993-7 is OK
- 10.48550/arXiv.2310.01145 is OK
- 10.1137/141000671 is OK

MISSING DOIs

- No DOI given, and none found for title: Probabilistic ODE Solutions in Millions of Dimensi...
- No DOI given, and none found for title: Fenrir: Physics-Enhanced Regression for Initial Va...
- No DOI given, and none found for title: Probabilistic Exponential Integrators
- No DOI given, and none found for title: Diffusion Tempering Improves Parameter Estimation ...
- No DOI given, and none found for title: Data-Adaptive Probabilistic Likelihood Approximati...
- No DOI given, and none found for title: probdiffeq: Probabilistic solvers for differential...
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Differentiable Likelihoods for Fast Inversion of ’...
- No DOI given, and none found for title: A Probabilistic State Space Model for Joint Infere...
- No DOI given, and none found for title: Linear-Time Probabilistic Solution of Boundary Val...
- No DOI given, and none found for title:  Probabilistic Numerical Method of Lines for Time-...
- No DOI given, and none found for title:  Pick-and-Mix Information Operators for Probabilis...
- No DOI given, and none found for title:  Calibrated Adaptive Probabilistic ODE Solvers 
- No DOI given, and none found for title: Stable Implementation of Probabilistic ODE Solvers

INVALID DOIs

- None

editorialbot commented 1 month ago

License info:

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

editorialbot commented 1 month ago

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

jbytecode commented 1 month ago

@PieterjanRobbe, @ranocha - Dear reviewers, you can start with creating your task lists. In that list, there are several tasks.

Whenever you perform a task, you can check on the corresponding checkbox. Since the review process of JOSS is interactive, you can always interact with the author, the other reviewers, and the editor during the process. You can open issues and pull requests in the target repo. Please mention the url of this page in there so we can keep tracking what is going on around.

Please create your tasklist by typing

@editorialbot generate my checklist

Thank you in advance.

PieterjanRobbe commented 1 month ago

Review checklist for @PieterjanRobbe

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/nathanaelbosch/ProbNumDiffEq.jl?
[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 (@nathanaelbosch) 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?

jbytecode commented 3 weeks ago

@PieterjanRobbe, @ranocha - Could you please update your status and inform us how is your review going?

@ranocha - It seems you haven't created your checklist yet. May I kindly ask you to start your review, please?

Thank you in advance.

PieterjanRobbe commented 3 weeks ago

Hi @jbytecode, I'm a little caught up with another JOSS review right now, but I should be able to continue working on this next week.

jbytecode commented 3 weeks ago

@PieterjanRobbe - thank you for the response.

ranocha commented 3 weeks ago

@PieterjanRobbe, @ranocha - Could you please update your status and inform us how is your review going?

@ranocha - It seems you haven't created your checklist yet. May I kindly ask you to start your review, please?

Thank you in advance.

As I said in https://github.com/openjournals/joss-reviews/issues/7015#issuecomment-2254372560, it will take a few weeks. I didn't see any reason to generate the review checklist before having the time to look at the contribution but I will generate it right now since you seem to prefer this approach.

ranocha commented 3 weeks ago

Review checklist for @ranocha

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/nathanaelbosch/ProbNumDiffEq.jl?
[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 (@nathanaelbosch) 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

[ ] 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

[x] 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

[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?

jbytecode commented 3 weeks ago

@ranocha - I totally forgot your deadline, I am so sorry, btw, thank you for creating your checklist, we usually ask our reviewers to create their checklists as a proof of the awareness of the review issue. Feel free to start your review when you are available. Thank you!

ranocha commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

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