[PRE REVIEW]: DiffOpt: Parallel optimization of Jax models

[editorialbot]

Submitting author: @AlanPearl (Alan Pearl)
Repository: https://github.com/AlanPearl/diffopt
Branch with paper.md (empty if default branch): paper
Version: v1.0.0
Editor: @jbytecode
Reviewers: @landreman, @ewu63
Managing EiC: Chris Vernon

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/211b25a3f9df01ca85be7100ad149e87"><img src="https://joss.theoj.org/papers/211b25a3f9df01ca85be7100ad149e87/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/211b25a3f9df01ca85be7100ad149e87/status.svg)](https://joss.theoj.org/papers/211b25a3f9df01ca85be7100ad149e87)

Author instructions

Thanks for submitting your paper to JOSS @AlanPearl. Currently, there isn't a JOSS editor assigned to your paper.

@AlanPearl if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

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

✅ OK DOIs

- 10.21105/astro.2105.05859 is OK
- 10.1093/mnras/stac3118 is OK
- 10.1093/mnras/stad456 is OK
- 10.1109/ICNN.1995.488968 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Multivariate Density Estimation
- No DOI given, and none found for title: Mathematical methods of statistics

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1073.5 files/s, 171591.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          23            532            805           1893
Jupyter Notebook                 5              0           1789            782
Markdown                         2             34              0            157
TeX                              1              6              0             86
YAML                             3              6              4             59
reStructuredText                 3             48             54             50
TOML                             1              5              0             29
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            40            643           2660           3091
-------------------------------------------------------------------------------

Commit count by author:

    16	Alan Pearl

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1259

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

ParMOO: A Python library for parallel multiobjective simulation optimization
Submitting author: @thchang
Handling editor: @kellyrowland (Active)
Reviewers: @Viech, @JianqiaoMao
Similarity score: 0.7167

SIMSOPT: A flexible framework for stellarator optimization
Submitting author: @landreman
Handling editor: @dfm (Active)
Reviewers: @ZedThree, @StanczakDominik
Similarity score: 0.7135

libEnsemble: A complete Python toolkit for dynamic ensembles of calculations
Submitting author: @jmlarson1
Handling editor: @jbytecode (Active)
Reviewers: @jsoishi, @SergeyYakubov
Similarity score: 0.7126

PyAutoFit: A Classy Probabilistic Programming Language for Model Composition and Fitting
Submitting author: @Jammy2211
Handling editor: @dfm (Active)
Reviewers: @arm61, @karllark
Similarity score: 0.7118

EnsembleKalmanProcesses.jl: Derivative-free ensemble-based model calibration
Submitting author: @odunbar
Handling editor: @jbytecode (Active)
Reviewers: @odow, @ziyiyin97
Similarity score: 0.7004

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[crvernon]

@editorialbot invite @ymzayek as editor

👋 @ymzayek - can you take this one on as editor?

[crvernon]

@editorialbot invite @ymzayek as editor

[crvernon]

@openjournals/dev - the invite call does not seem to be working.

[xuanxu]

@crvernon it should be fixed now, please retry

[crvernon]

@editorialbot invite @ymzayek as editor

👋 @ymzayek - can you take this one on as editor?

[editorialbot]

Invitation to edit this submission sent!

[crvernon]

Thanks @xuanxu!

[ymzayek]

@crvernon sorry for the delay. I have to decline this one.

[crvernon]

@editorialbot invite @fabian-s as editor

👋 @fabian-s - can you take this one on as editor? Thanks!

[editorialbot]

Invitation to edit this submission sent!

[fabian-s]

Sorry, have to decline. Don't know JAX and don't know much optimization.

[AlanPearl]

If Dan Foreman-Mackey (dfm) is still serving as an editor, he would certainly be an expert in the subject.

[crvernon]

@editorialbot invite @dfm as editor

👋 @dfm - I know your schedule is busy right now. Do you have time to take this on as editor? I'll find another if not. Thanks.

[editorialbot]

Invitation to edit this submission sent!

[dfm]

@crvernon — I'm so sorry for the slow response! I was offline for a bit and only catching up now. Unfortunately I'm not available to edit this submission.

[crvernon]

No problem @dfm! Thanks!

[crvernon]

@editorialbot invite @jbytecode as editor

👋 @jbytecode can you take this one on as editor?

[editorialbot]

Invitation to edit this submission sent!

[jbytecode]

@crvernon - sure, gladly. But I have a bunch of issues about the submission.

Do you think a scope check voting needs to be conducted for this study?

Because,

• The commit history goes back to Oct 3rd, 2024. I think it's a young project.
• The README.md has not enough information, so the documentation may be improved before considering any further review tasks.

These issues might also likely require subsequently scholar effort voting.

What do you think?

[AlanPearl]

@jbytecode

• The young age is due to it being a resubmission. Initially, the subpackages were their own repositories, which are still hosted on my GitHub with their own histories that date back roughly a year (at least for multigrad which is the oldest of the three subpackages).
• Sorry that the README is not sufficient. My typical philosophy is having a very short one containing an easy-to-find link to the readthedocs page, which contains the extensive documentation. Let me know if there is anything specific that needs to go in the README.

[jbytecode]

@AlanPearl - Thank you for the quick response. It seems the umbrella package wraps other packages. Are they yours? If so it's a better approach to attach the package names in the README.md file as dependencies and let our reviewers to consider them.

And it's time to hear from our track editor. Thank you in advance.

[crvernon]

@jbytecode FYI...here is the previous submission that was withdrawn so that the current submission could be reviewed as a complete product:

#7218

[jbytecode]

@crvernon - Now, that makes sense.

@AlanPearl - Could you please provide a list of the dependencies of the submitted package in README.md file so our reviewers can take them into consideration in the review process.

[jbytecode]

@editorialbot assign me as editor

[editorialbot]

Assigned! @jbytecode is now the editor

[jbytecode]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

SIMSOPT: A flexible framework for stellarator optimization
Submitting author: @landreman
Handling editor: @dfm (Active)
Reviewers: @ZedThree, @StanczakDominik
Similarity score: 0.7146

pyOptSparse: A Python framework for large-scale constrained nonlinear optimization of sparse systems
Submitting author: @nwu63
Handling editor: @poulson (Retired)
Reviewers: @jgoldfar, @vissarion, @matbesancon
Similarity score: 0.7140

PyAutoFit: A Classy Probabilistic Programming Language for Model Composition and Fitting
Submitting author: @Jammy2211
Handling editor: @dfm (Active)
Reviewers: @arm61, @karllark
Similarity score: 0.7119

libEnsemble: A complete Python toolkit for dynamic ensembles of calculations
Submitting author: @jmlarson1
Handling editor: @jbytecode (Active)
Reviewers: @jsoishi, @SergeyYakubov
Similarity score: 0.7106

EnsembleKalmanProcesses.jl: Derivative-free ensemble-based model calibration
Submitting author: @odunbar
Handling editor: @jbytecode (Active)
Reviewers: @odow, @ziyiyin97
Similarity score: 0.7013

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[AlanPearl]

@jbytecode I updated the README.md with the dependency info on the paper branch. Does that look good?

[jbytecode]

@AlanPearl - Looks beautiful, thank you.

[jbytecode]

@AlanPearl - Do you have any suggestions for the potential reviewers? Editorial bot shows us many similar submissions and I think the author of the submission

#3525

can be invited as a reviewer. Would you provide a list of potential reviewers for your submission? You can also use the list of people to search over people who volunteer to review. Please mention their GitHub handles without using the @ character (because we don't want to bother them by being too much verbose).

Thank you in advance.

[jbytecode]

👋👋👋 Dear @landreman👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

DiffOpt: Parallel optimization of Jax models

You can find more information at the top of this Github issue (#7356).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be around 20 check items for each single reviewer.

Thank you in advance!

[AlanPearl]

@jbytecode I just scanned through editorialbot suggestions, and I agree that @(landreman)'s submission is the closest. Next would probably be @(ewu63), submitting author of #2564. Their method doesn't use jax/autodiff, but it could still be useful to have someone working on parallel gradient-based optimization problems from another angle take a look.

Other possible suggestions of people with similar interests in optimization + astrophysics I found on the JOSS list of people:

• @(htjb)
• @(astrogilda)
• @(athulpg007)
• @(DingXuefeng)

[jbytecode]

👋👋👋 Dear @htjb 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

DiffOpt: Parallel optimization of Jax models

You can find more information at the top of this Github issue (#7356).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be around 20 check items for each single reviewer.

Thank you in advance!

[jbytecode]

👋👋👋 Dear @ewu63 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

DiffOpt: Parallel optimization of Jax models

You can find more information at the top of this Github issue (#7356).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be around 20 check items for each single reviewer.

Thank you in advance!

[landreman]

👋👋👋 Dear @landreman👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

Hi, I'm available to be a reviewer.

[jbytecode]

@editorialbot add @landreman as reviewer

[editorialbot]

@landreman added to the reviewers list!

[ewu63]

👋👋👋 Dear @ewu63 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

DiffOpt: Parallel optimization of Jax models

You can find more information at the top of this Github issue (#7356).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be around 20 check items for each single reviewer.

Thank you in advance!

I am also happy to be a reviewer.

[jbytecode]

@editorialbot add @ewu63 as reviewer

@ewu63 - Thank you for accepting our invitation.

@landreman , @ewu63 - Now we have two suitable reviewers. I'm starting the review in a separate thread. I'll introduce the review instructions there. See you soon!

[editorialbot]

@ewu63 added to the reviewers list!

[jbytecode]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7522.

[htjb]

@jbytecode sorry I was a bit slow to get to this! I am quite busy at the moment, but it looks like you have found some reviewers. Sorry!