[REVIEW]: BESMARTS: A toolkit for data-driven force field design using binary-encoded SMARTS

editorialbot commented 2 months ago

Submitting author: !--author-handle-->@trevorgokey@lucydot<!--end-editor-- Reviewers: @AntObi, @Sulstice, @Ruibin-Liu Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/32f6091cd797f5041578cd35f4676087/status.svg)](https://joss.theoj.org/papers/32f6091cd797f5041578cd35f4676087)

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

@AntObi & @Sulstice & @Ruibin-Liu, 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 @lucydot 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 @AntObi

📝 Checklist for @Ruibin-Liu

editorialbot commented 2 months ago

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editorialbot commented 2 months ago

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

OK DOIs

- 10.26434/chemrxiv-2023-v969f-v3 is OK
- 10.1021/acs.jctc.8b00640 is OK
- 10.26434/chemrxiv.8304578.v1 is OK

MISSING DOIs

- No DOI given, and none found for title: Sage-2.1.0

INVALID DOIs

- None

editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.15 s (1043.7 files/s, 178972.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          60           4771           4534          15410
reStructuredText                89            426            880            503
Markdown                         5             67              0            270
TeX                              1              3              0             36
make                             1              4              7              9
Bourne Shell                     1              0              0              3
-------------------------------------------------------------------------------
SUM:                           157           5271           5421          16231
-------------------------------------------------------------------------------

Commit count by author:

    95  Trevor Gokey
     1  trevorgokey

editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 1242

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

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

lucydot commented 2 months ago

I assumed JOSS reviewers would install the branch considered for submission, in this case joss-manuscript. In this case, the clone command should be followed by git checkout joss-manuscript before the install command.

@trevorgokey The JOSS review is usually based on the main / master branch, with any additional joss-manuscript branch usually containing the JOSS paper. If you want joss-manuscript to be reviewed that is fine also, and then we'd typically expect it to be merged into main once review is complete.

(Re-pasting from the pre-review thread so not lost as we move across to the review thread)

editorialbot commented 2 months ago

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

AntObi commented 2 months ago

Review checklist for @AntObi

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/trevorgokey/besmarts?
[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 (@trevorgokey) 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?
[ ] 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.
[ ] 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?
[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] (https://pandoc.org/MANUAL.html#extension-citations)?

Ruibin-Liu commented 2 months ago

Review checklist for @Ruibin-Liu

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/trevorgokey/besmarts?
[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 (@trevorgokey) 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?
[ ] 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?

trevorgokey commented 2 months ago

The JOSS review is usually based on the main / master branch, with any additional joss-manuscript branch usually containing the JOSS paper. If you want joss-manuscript to be reviewed that is fine also, and then we'd typically expect it to be merged into main once review is complete.

@lucydot thanks for the explanation. I am fine with merging the paper into main after review. I am still actively contributing to the codebase and pushing to main, so I intended the joss-manuscript branch to be a frozen, versioned codebase to review. I've already made some commits to main since submitting this, but while this is under review I'll develop on a different branch to avoid unintentionally breaking something.

Ruibin-Liu commented 2 months ago

@trevorgokey I can install through the method in the README.md page but cannot run the examples in the RTD. Also, the RTD installation page says the packages can be directly installed through pip. Please make them consistent and ensure the examples can run.

lucydot commented 2 months ago

Hi @trevorgokey - a nudge in case you missed the notification from message above ☝️ . This appears important to address for review process.

@Ruibin-Liu - can you point towards what the problem was with the examples in RTD. Is there a particular error message you are getting? This may help @trevorgokey address the issue.

Ruibin-Liu commented 2 months ago

The error is: ...besmarts-git/besmarts-core/python/setup.py", line 5, in with open("README.md", "r") as fh: ^^^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: 'README.md' [end of output]

trevorgokey commented 2 months ago

Hi, thanks for indicating the issue. I fixed that error in the pre-review stage when @Ruibin-Liu first reported issues with installing. I just installed the code using a fresh environment and I did not have any issue.

I can install through the method in the README.md page but cannot run the examples in the RTD

I am noticing that some of the RTD is out of date and I will need to go over it and make it consisent with the package. I worked on the examples in besmarts/besmarts-core/python/examples but did not update the docs examples. Thank you @Ruibin-Liu for pointing this out.

lucydot commented 2 months ago

I just installed the code using a fresh environment and I did not have any issue.

Could this confusion result from using different branches? @Ruibin-Liu - I believe the branch to review is joss-manuscript - can you confirm that is correct @trevorgokey ?

Ruibin-Liu commented 1 month ago

I don't have issue to install manually now but I don't think the RTD claim for pip installation method is correct. Specifically, this line pip install besmarts-hierarchy besmarts-splitter besmarts-resolve is incorrect in that none of them is in PyPI.

Other issues in the RTD examples I have checked.

from besmarts.codecs import native doesn't work in the Graphs section.

The following doesn't work in the Graphs section:

for indices in graphs.graph_dihedrals(g):
    print(indices)
for indices in graphs.graph_impropers(g):
    print(indices)

print(geometry.bond(idx[::-1])) incorrect because idx is int

There are more in the RTD doc. I stopped checking. Please make sure those examples can run without any issue.

lucydot commented 1 month ago

Thanks for update @Ruibin-Liu - @trevorgokey it sounds like there is some more updates to make to the documentation so examples can be ran locally. If you could update here with expected timescales for fixing that would be useful -

trevorgokey commented 1 month ago

I'm out for a conference right now and will work on the documentation immediately after it ends. I should have it done in the next few days.

On Wed, May 15, 2024, 10:17 AM Lucy Whalley @.***> wrote:

Thanks for update @Ruibin-Liu https://github.com/Ruibin-Liu - @trevorgokey https://github.com/trevorgokey it sounds like there is some more updates to make to the documentation so examples can be ran locally. If you could update here with expected timescales for fixing that would be useful -

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6653#issuecomment-2111866271, or unsubscribe https://github.com/notifications/unsubscribe-auth/AL7KZRVA7LZGWH2ITQ7YPJLZCMKZ7AVCNFSM6AAAAABGSVONAGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJRHA3DMMRXGE . You are receiving this because you were mentioned.Message ID: @.***>

AntObi commented 1 month ago

Hi @trevorgokey , I've opened up an issue trevorgokey/besmarts#1 which contains my detailed breakdown of my current problems that I have found in this repository. A few may overlap @Ruibin-Liu 's comments.

Here is a checklist summary of what needs to be done before I can complete the review on my end, but also look at the issue for full details:

[x] Installation instructions in Readthedocs (RTD) should be consistent with README in the main repo
[ ] Examples/Usage
- [ ] Make sure all the examples in the repo are functional
- [ ] Fill out the README in besmarts/besmarts-core/python/examples to ensure that a new user can fully understand how each example works.
- [ ] Make sure all the usage examples in the RTD are functional
[ ] Testing
- [x] Apply my suggestion in the linked issue to ensure that pytest runs with no issues.
- [ ] Make sure that the codebase is sufficiently covered with tests
- [ ] I would recommend that you set up some form of continuous integration (Github Actions, Circle Ci etc) in your repository in order to automatically test your code. This will help when you have new contributors to the package in terms of making sure new commits don't break your package
- [ ] Documentation
- [ ] A lot of the code is undocumented (many classes and functions lack docstrings). This makes using many functions inaccessible to a someone unfamiliar with the codebase.

trevorgokey commented 1 month ago

Thanks for going through the documentation @Ruibin-Liu and @AntObi. I've since given the RTD documentation an overhaul and should be all working as far as I can tell, including installation, tests, and examples. Also, I've made the main and joss-manuscript branches the same just to reduce any confusion.

I'll continue to work on code quality such as docstrings; lots of the newer stuff is in flux and so I haven't quite fixed their behavior. Unfortunately, a lof of the newer stuff is also the most complicated so I apologize if the interesting bits of the code have been opaque. I'll continue working on the second checklist provided by @AntObi.

lucydot commented 1 month ago

Thanks for the update @trevorgokey ; what do you think a reasonable estimate for timescale until points are addressed? Note that we do not require full test or documentation coverage (although of course this is a good point to aim for), rather we require the core functionality is sufficiently tested and documented.

trevorgokey commented 1 month ago

In a week's time I should be able to give everything a first pass. My plan is to go through all of the examples and tests and make sure that all forward-facing code (examples and everything in RTD) are all documented. I'll check back in once this is complete.

lucydot commented 3 weeks ago

A quick note here to say I will be on Annual Leave for the next week, will be back on the 24th June.

lucydot commented 1 week ago

@trevorgokey; an update on how the amendments are going and timeframe would be great.

openjournals / joss-reviews