[REVIEW]: SOUPy: Stochastic PDE-constrained optimization under high-dimensional uncertainty in Python

editorialbot commented 7 months ago

Submitting author: !--author-handle-->@dc-luo@jedbrown<!--end-editor-- Reviewers: @Himscipy, @IgorBaratta Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/6812f29c90f8081df9888553911ac771/status.svg)](https://joss.theoj.org/papers/6812f29c90f8081df9888553911ac771)

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

@Himscipy & @IgorBaratta, 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 @jedbrown 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 @Himscipy

📝 Checklist for @IgorBaratta

editorialbot commented 7 months ago

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editorialbot commented 7 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (895.7 files/s, 143403.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          71           2635           3144           6908
Jupyter Notebook                 4              0           1661            429
Markdown                         5            132              0            375
TeX                              2             36              0            217
reStructuredText                11             82            152             84
YAML                             3              9             10             55
DOS Batch                        1              8              1             26
Bourne Shell                     2              9              2             16
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           100           2915           4977           8119
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 7 months ago

Wordcount for paper.md is 1222

editorialbot commented 7 months ago

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

OK DOIs

- 10.1016/j.jcp.2019.01.047 is OK
- 10.1016/j.jcp.2021.110114 is OK
- 10.1145/3428447 is OK
- 10.21105/joss.00940 is OK
- 10.48550/arXiv.2305.20053 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1007/BF01589116 is OK
- 10.1007/BF02591944 is OK
- 10.1137/0917003 is OK
- 10.1137/20M1381381 is OK
- 10.21105/joss.01292 is OK
- 10.1145/2566630 is OK
- 10.48550/arXiv.2209.02454 is OK
- 10.1007/978-1-4939-8636-1_2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 7 months ago

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

jedbrown commented 7 months ago

Hi, @Himscipy @IgorBaratta 👋 Welcome to JOSS and thanks for agreeing to review! The comments from @editorialbot above outline the review process, which takes place in this thread (possibly with issues filed in the SOUPy repository). I'll be watching this thread if you have any questions.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention this issue so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within a month or two. Please let me know if you require some more time. We can also use editorialbot to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@jedbrown) if you have any questions/concerns.

jedbrown commented 5 months ago

@Himscipy @IgorBaratta 👋 Could you please let us know when you'll be able to do this review?

Himscipy commented 5 months ago

Review checklist for @Himscipy

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/hippylib/soupy?
[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 (@dc-luo) 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?

Himscipy commented 5 months ago

Hi @jedbrown, I have started the checklist and will complete it in a couple of weeks.

dc-luo commented 4 months ago

Hello @jedbrown 👋 are there any updates on the review? Thanks!

jedbrown commented 4 months ago

@Himscipy @IgorBaratta :wave: Could you let us know how your reviews are going?

tomoleary commented 3 months ago

@jedbrown 👋 are there any updates on this review?

jedbrown commented 3 months ago

@Himscipy @IgorBaratta 👋 It's been months since we last heard from you. Could you please let us know when you'll be able to make progress on your review?

Himscipy commented 2 months ago

Hi @tomoleary, Thank you for submitting the paper+ software to JOSS. The developed package will be a great additions to the scientific computing research community. Following are my comments and feedback on the submission.

The submitted write-up clearly states the need and highlights relevant literature.
I would recommend simplifying the installation of the package through containerization (docker). Currently, there are multiple dependencies for the package. Having the containerization will also ease the installation process and ensure that the library can be quickly used on HPC/large systems. For example during the installation process listed on the documentation I encountered following error
```
conda create -n soupy -c conda-forge python=3.11 fenics==2019.1.0 petsc4py==3.19 matplotlib scipy jupyter
Retrieving notices: ...working... done
Channels:
- conda-forge
- defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed
```

PackagesNotFoundError: The following packages are not available from current channels:

fenics==2019.1.0

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.


4. Below is how the repository compares to the community standards. If you can improve this, you could allow potential users to be major contributors to the project.
![Screenshot 2024-05-11 at 3 54 08 PM](https://github.com/openjournals/joss-reviews/assets/7496964/993fe82e-09f2-4ae7-9964-c62d42d08ad8)

Please assist in resolving the installation issue, I have also created a issue on the repo.

dc-luo commented 2 months ago

Hello @Himscipy, thank you for your initial feedback on the package!

We'll add installation instructions with docker. In the meantime, to make sure you can continue with the review, I believe the installation issue can be resolved by adding the flag --platform osx-64 to the conda call, i.e. conda create -n soupy --platform osx-64 -c conda-forge python=3.11 fenics==2019.1.0 petsc4py==3.19 matplotlib scipy jupyter Please me know if it works for you. If so, I'll also update the current installation instruction for arm mac users.

IgorBaratta commented 1 month ago

Review checklist for @IgorBaratta

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/hippylib/soupy?
[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 (@dc-luo) 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?

dc-luo commented 1 month ago

Hello everyone @Himscipy @IgorBaratta @jedbrown

Thank you all for your feedback on the submission! I appreciate your time in helping to improve the project.

So far, I have gone and dealt with the initial comments:

Installation: This was on both reviewers' checklists. I have updated the installation instructions to highlight the case of macos on arm machines. Also, based on suggestions from @Himscipy, I have also included a section on running through docker. Please see the latest INSTALL.md or the readthedocs for the updated installation instructions.
I have added an issue template and code of conduct to the repo for improvements based on community standards, as suggested by @Himscipy. Basic instructions for pull requests are available under the CONTRIBUTING.md.

I notice there are still some unchecked boxes under functionality/documentation. Please let me know if you have any comments with respect to these or any issues you would like addressed.

tomoleary commented 1 month ago

Hi all @Himscipy @IgorBaratta @jedbrown.

Please let us know if there are any further comments in light of the modifications delineated above by @dc-luo.

Thanks!

Himscipy commented 1 month ago

Hi @tomoleary, Thank you for addressing the comments and revising the repository. I tried the installation fixes and it works. I have completed my review checklist and I have no additional comments. Thank you for your contributions to the scientific computing research community with Soupy.

@jedbrown I have finished my review for the repo.

Best, Himanshu

tomoleary commented 3 weeks ago

Hi @Himscipy,

Thank you very much for finishing your review in light of the changes that @dc-luo made.

Best, Tom

dc-luo commented 3 weeks ago

Hello @Himscipy, thank you for completing the review. We appreciate your feedback for the project.

I notice @IgorBaratta has also completed their checklist. Please let me know if you have any further comments.

@jedbrown if everything looks good, can you please let me know of the next steps for me?

danielskatz commented 1 week ago

👋 @jedbrown - it seems like this is ready to be completed. Can you help the authors work on the final steps?

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