[REVIEW]: flowMC: Normalizing-flow enhanced sampling package for probabilistic inference in Jax

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@kazewong@rkurchin<!--end-editor-- Reviewers: @matt-graham, @Daniel-Dodd Archive: 10.5281/zenodo.7706605

Status

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Markdown: [![status](https://joss.theoj.org/papers/5b60695b2a844550730dd104150d11f1/status.svg)](https://joss.theoj.org/papers/5b60695b2a844550730dd104150d11f1)

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

@matt-graham & @daniel-dodd, 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 @rkurchin 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 @Daniel-Dodd

📝 Checklist for @matt-graham

editorialbot commented 1 year ago

Hello humans, 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 commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (416.5 files/s, 58964.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          21            473            451           1625
Jupyter Notebook                 6              0           2277            681
reStructuredText                10            182            159            244
Markdown                         3             64              0            192
TeX                              1              0              0            179
YAML                             3              6              8             55
DOS Batch                        1              8              1             26
make                             1              4              7              9
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            47            737           2903           3014
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1268

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

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

OK DOIs

- 10.1073/pnas.2109420119 is OK
- 10.1103/PhysRevD.100.034515 is OK
- 10.1109/TPAMI.2020.2992934 is OK
- 10.1103/PhysRevE.101.023304 is OK
- 10.1103/PhysRevE.101.053312 is OK
- 10.1007/s11222-008-9110-y is OK
- 10.1137/17M1134640 is OK

MISSING DOIs

- 10.1093/mnras/stac2272 may be a valid DOI for title: Accelerating astronomical and cosmological inference with Preconditioned Monte Carlo

INVALID DOIs

- None

rkurchin commented 1 year ago

@kazewong do fix that one missing DOI when you have a moment

Reviewers @matt-graham and @Daniel-Dodd, let me know if you have any questions about getting your reviews started!

daniel-dodd commented 1 year ago

@editorialbot generate my checklist

editorialbot commented 1 year ago

@Daniel-Dodd I can't do that because you are not a reviewer

daniel-dodd commented 1 year ago

@Daniel-Dodd I can't do that because you are not a reviewer

Hi @rkurchin, is there something I should have done before running @editorialbot generate my checklist? Thanks. :)

danielskatz commented 1 year ago

Something seems broken here - let me try a couple of things....

danielskatz commented 1 year ago

@editorialbot remove @Daniel-Dodd as reviewer

editorialbot commented 1 year ago

@Daniel-Dodd is not in the reviewers list

danielskatz commented 1 year ago

@editorialbot add @Daniel-Dodd as reviewer

editorialbot commented 1 year ago

@Daniel-Dodd added to the reviewers list!

danielskatz commented 1 year ago

@xuanxu - can you see what's going on here with the reviewer list?

danielskatz commented 1 year ago

@Daniel-Dodd - can you try to generate your checklist again?

xuanxu commented 1 year ago

The problem was that the reviewer added initially in the pre-review issue was @daniel-dodd instead of @Daniel-Dodd, and for the bot those are two different usernames (GitHub shows both cases as the canonical form so it's difficult to see the difference unless you edit the comment)

daniel-dodd commented 1 year ago

Review checklist for @Daniel-Dodd

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/kazewong/flowMC?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@kazewong) 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)?
- Opened PR (first-pass) edits https://github.com/kazewong/flowMC/pull/80
[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?

daniel-dodd commented 1 year ago

Thank you, @danielskatz and @xuanxu. :)

matt-graham commented 1 year ago

Review checklist for @matt-graham

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/kazewong/flowMC?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@kazewong) 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?

rkurchin commented 1 year ago

Happy New Year, everyone! Hope you had a great holiday. Just a friendly reminder to reviewers @Daniel-Dodd and @matt-graham to keep working on these reviews and let me know if you have any questions about the process or anything. :)

daniel-dodd commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

rkurchin commented 1 year ago

👋 hi there, checking in on this! I see a few of the review-related issues have been resolved, but several remain open. @kazewong, any updates on that?

kazewong commented 1 year ago

@rkurchin I have been in a couple paper crunch so my bandwidth on this is somewhat limited for the past couple of weeks. The only remaining substantial issue now is the unit test, which I think I should have sometime in the coming 2-3 weeks in resolving.

rkurchin commented 1 year ago

Hi @kazewong, just checking in on this again!

kazewong commented 1 year ago

@rkurchin We are almost done with most of the issues, which should finish by next week

daniel-dodd commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

kazewong commented 1 year ago

@rkurchin We have implemented changes for the issues in the code repo suggested by @matt-graham and @danielskatz . Please let us know if there is anything we need to iterate on and we will be happy to get on them quickly. Thanks so much for all the very constructive suggestions!

matt-graham commented 1 year ago

@kazewong thanks for all your and @marylou-gabrie's works on the issues we raised. Nearly everything looks good to me other than a small issue (https://github.com/kazewong/flowMC/issues/100) I found with the pinned version of an upstream dependency causing the tests to fail on some Python versions and there were a couple of very minor suggested changes to the paper text I've made in https://github.com/kazewong/flowMC/pull/101.

kazewong commented 1 year ago

@matt-graham We have fixed the version problems and merged the changes in the text. Thanks for your time and effort again!

@rkurchin It seems the two review checklists are completed. Please let us know if there is anything we need to do on our side.

rkurchin commented 1 year ago

Thanks everyone! Authors, I'll do an editorial pass over the manuscript and send any comments shortly. In the meantime, the next steps for you are:

Merge any and all changes from this review into your main branch and issue a new version tag. (If you want to merge in the paper, you may, but it is not required that the actual manuscript live into the repo in perpetuity since JOSS will host it and you can simply add a badge link or whatever you like. But the actual changes to software and docs do need to be merged!)
Create a DOI for the contents of the repo at the same commit corresponding to that version tag, e.g. using figshare or Zenodo. Please make sure that the metadata (version number, title, author list, etc.) match those of your manuscript.
Post a comment here with the version number and DOI.

rkurchin commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1073/pnas.2109420119 is OK
- 10.1103/PhysRevD.100.034515 is OK
- 10.1109/TPAMI.2020.2992934 is OK
- 10.1103/PhysRevE.101.023304 is OK
- 10.1103/PhysRevE.101.053312 is OK
- 10.1007/s11222-008-9110-y is OK
- 10.1137/17M1134640 is OK

MISSING DOIs

- 10.1093/mnras/stac2272 may be a valid DOI for title: Accelerating astronomical and cosmological inference with Preconditioned Monte Carlo

INVALID DOIs

- None

rkurchin commented 1 year ago

@kazewong, make sure to fix that missing DOI, too.

rkurchin commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

rkurchin commented 1 year ago

Minor editorial comments:

line 37: hyphenate "black-box" (compound adjective modifying "interface") and replace "by" with "with"
38: I would rephrase to "...default parameters, as well as an extensive guide..."
48: add a comma after "kernel"
69-70: rephrase to "until chains of the desired length are obtained"
83-85: sentence is a bit long and hard to parse, maybe just put in numbers, as in "The only inputs we require from the users are (1) [...], and (2) [...]"

Otherwise, it all looks good! (apart from missing DOI above)

marylou-gabrie commented 1 year ago

@rkurchin Thank you very much for the corrections, they are implemented. I also added the missing DOI.

rkurchin commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1073/pnas.2109420119 is OK
- 10.1103/PhysRevD.100.034515 is OK
- 10.1109/TPAMI.2020.2992934 is OK
- 10.1103/PhysRevE.101.023304 is OK
- 10.1103/PhysRevE.101.053312 is OK
- 10.1007/s11222-008-9110-y is OK
- 10.1093/mnras/stac2272 is OK
- 10.1137/17M1134640 is OK

MISSING DOIs

- None

INVALID DOIs

- None

rkurchin commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

rkurchin commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Paper is not ready for acceptance yet, the archive is missing

rkurchin commented 1 year ago

Thanks everyone! Authors, I'll do an editorial pass over the manuscript and send any comments shortly. In the meantime, the next steps for you are:

Merge any and all changes from this review into your main branch and issue a new version tag. (If you want to merge in the paper, you may, but it is not required that the actual manuscript live into the repo in perpetuity since JOSS will host it and you can simply add a badge link or whatever you like. But the actual changes to software and docs do need to be merged!)

Create a DOI for the contents of the repo at the same commit corresponding to that version tag, e.g. using figshare or Zenodo. Please make sure that the metadata (version number, title, author list, etc.) match those of your manuscript.

Post a comment here with the version number and DOI.

@kazewong, make sure to follow these steps so that I can finalize acceptance of this paper!

kazewong commented 1 year ago

@rkurchin The version number is v0.1 https://github.com/kazewong/flowMC/releases/tag/latest and the DOI on zenodo is https://doi.org/10.5281/zenodo.7706605

rkurchin commented 1 year ago

@editorialbot set 0.1 as version

editorialbot commented 1 year ago

Done! version is now 0.1

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