editorialbot commented 1 year ago

Submitting author: !--author-handle-->@NicoRenaud@jarvist<!--end-editor-- Reviewers: @tonnylou44853, @scemama, @AbdAmmar Archive: 10.5281/zenodo.10122190

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/f045eb5310a1c8be51d340e23b43c153/status.svg)](https://joss.theoj.org/papers/f045eb5310a1c8be51d340e23b43c153)

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

@tonnylou44853 & @scemama & @AbdAmmar, 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 @jarvist 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 @tonnylou44853

📝 Checklist for @scemama

📝 Checklist for @AbdAmmar

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:

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.20 s (1313.0 files/s, 140140.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         153           5719           5360          11789
reStructuredText                86            338            506            528
Jupyter Notebook                10              0           2743            211
TeX                              1             19              0            141
Markdown                         5             46              0            102
YAML                             3             19              9             93
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                           259           6145           8624          12874
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1796

editorialbot commented 1 year ago

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

OK DOIs

- 10.1103/physrevb.99.085121 is OK
- 10.1088/1361-648X/aab9c3 is OK
- 10.1007/978-3-642-38718-0_14 is OK
- 10.1063/5.0139024 is OK
- 10.1103/PhysRevResearch.2.033429 is OK
- 10.1038/s41557-020-0544-y is OK
- 10.1002/jcc.1056 is OK
- 10.1063/1.4948778 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

scemama commented 1 year ago

Review checklist for @scemama

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/NLESC-JCER/QMCTorch?
[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 (@NicoRenaud) 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?

scemama commented 1 year ago

I created an issue for my review in the repo of the code: https://github.com/NLESC-JCER/QMCTorch/issues/145

tonnylou44853 commented 1 year ago

Review checklist for @tonnylou44853

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/NLESC-JCER/QMCTorch?
[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 (@NicoRenaud) 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?

AbdAmmar commented 1 year ago

Review checklist for @AbdAmmar

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/NLESC-JCER/QMCTorch?
[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 (@NicoRenaud) 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?

jarvist commented 1 year ago

@NicoRenaud - are there any outstanding issues that the reviewers have brought up? It looks like the code has been tested, but either the reviewers are still to read the documentation + paper, or it is in some way lacking.

NicoRenaud commented 1 year ago

Hey @jarvist ! I am not aware of any issues the reviewers would have brought up. The paper + doc are of course linked here for the reviewers to assess. Let me know if I can do anything to help the process ! thanks

scemama commented 1 year ago

Hi @NicoRenaud ! I have posted issues in the main repository to request changes: https://github.com/NLESC-JCER/QMCTorch/issues/145 https://github.com/NLESC-JCER/QMCTorch/issues/146 I thought you would have received a notification... Next time, I will add a message here. Sorry for the misunderstanding!

arfon commented 11 months ago

@jarvist – looks like we're waiting on the author to make changes at this point? It might be worth giving them a friendly nudge, either here, or even better over email :-)

scemama commented 11 months ago

@arfon @jarvist -https://github.com/NLESC-JCER/QMCTorch/issues/145 and https://github.com/NLESC-JCER/QMCTorch/issues/146 were addressed, but there are still some other bugs to fix, in https://github.com/NLESC-JCER/QMCTorch/issues/149 and https://github.com/NLESC-JCER/QMCTorch/issues/150

arfon commented 11 months ago

Thanks @scemama. Do you have an estimate for when you might get to these?

scemama commented 11 months ago

I am not the developer, I am the reviewer who posted the bug reports. :-)

Kevin-Mattheus-Moerman commented 10 months ago

@NicoRenaud :wave: please can you work to address the issues raised?

NicoRenaud commented 10 months ago

Hi @scemama and @Kevin-Mattheus-Moerman Thanks a lot for your patience ! I haven't found so much time to work on the issue but I have a bit more free time now that I will devote to fixing all of that. I've already started on https://github.com/NLESC-JCER/QMCTorch/issues/150 but I need a bit more time. For the other issue I have to update the doc since ReadTheDoc changed its setup. That shouldn't be too difficult Thanks again for all your input !

scemama commented 10 months ago

Looks good to me now :-)

NicoRenaud commented 10 months ago

Thanks @scemama ! @Kevin-Mattheus-Moerman I ve made all the changes requested by the reviewers and made a new GH and pypi release. I'm happy to do anything else ! Thanks

jarvist commented 10 months ago

My apologies for the late reply, I did not notice this update.

jarvist commented 10 months ago

@tonnylou44853 and @AbdAmmar , could you please check that the edits are sufficient, and if so - complete your checklists.

jarvist commented 10 months ago

@scemama - you just have one last check box re: performance; may I assume that this is satisfied?

scemama commented 10 months ago

@scemama - you just have one last check box re: performance; may I assume that this is satisfied?

yes, all good!

tonnylou44853 commented 10 months ago

Hi! Sorry for the late response. The paper looks good to me after the corrections suggested by the other reviewers. However, I did find a few more typos in the docs and a small bug in the code.

Here is the list of issues that I opened/commented: https://github.com/NLESC-JCER/QMCTorch/issues/149 https://github.com/NLESC-JCER/QMCTorch/issues/145#issuecomment-1805958710 https://github.com/NLESC-JCER/QMCTorch/issues/154

jarvist commented 10 months ago

Great! Thanks Tonny. @AbdAmmar , unless you particularly want to weigh-in here, we should be able to finish this with Tonny and Scemama's input.

NicoRenaud commented 10 months ago

Thanks for the comments @tonnylou44853. I've made all the changes you suggested and merged everything. @jarvist let me know if I can do anything else. Thanks

jarvist commented 10 months ago

@editorialbot generate pdf

jarvist commented 10 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[ ] Double check authors and affiliations (including ORCIDs)
[ ] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[ ] Archive the release on Zenodo/figshare/etc and post the DOI here.
[ ] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[ ] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

jarvist commented 10 months ago

Thank you reviews & contributions @tonnylou44853 , @scemama and @AbdAmmar !

editorialbot commented 10 months ago

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

jarvist commented 10 months ago

@NicoRenaud - a couple of the DOIs in your references are a bit garbled (I think maybe they already contain some https://doi.org/ part of the URL?). Han2019 and Kessler2021

NicoRenaud commented 10 months ago

Thanks @jarvist I've fixed them now

jarvist commented 10 months ago

Great! There's a further list of tasks post-review a few messages above ^^^.

The key one is to make a release of the software; and then archive this (usually with Zenodo since you are on GitHub with the software) to get a DOI.

NicoRenaud commented 10 months ago

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper. Current version is 0.3.2
[x] Archive the release on Zenodo/figshare/etc and post the DOI here. Current DOI is 10.5281/zenodo.10122190
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

NicoRenaud commented 10 months ago

@jarvist I've checked everything and I think it's all done now. I've also made a new pypi release to facilitate install. Let me know if I've missed something. Thanks !

jarvist commented 10 months ago

@editorialbot set v0.3.2 as version

editorialbot commented 10 months ago

Done! version is now v0.3.2

jarvist commented 10 months ago

@editorialbot set 10.5281/zenodo.10122190 as archive

editorialbot commented 10 months ago

Done! archive is now 10.5281/zenodo.10122190

jarvist commented 10 months ago

@editorialbot generate pdf

jarvist commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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

OK DOIs

- 10.1103/physrevb.99.085121 is OK
- 10.1088/1361-648X/aab9c3 is OK
- 10.1007/978-3-642-38718-0_14 is OK
- 10.1063/5.0139024 is OK
- 10.1103/PhysRevResearch.2.033429 is OK
- 10.1038/s41557-020-0544-y is OK
- 10.1002/jcc.1056 is OK
- 10.1021/acs.jctc.9b01132 is OK
- 10.1016/j.jcp.2022.111765 is OK
- 10.1063/5.0032836 is OK
- 10.1103/PhysRevResearch.3.043126 is OK
- 10.1002/adts.202000269 is OK
- 10.1016/j.jcp.2019.108929 is OK
- 10.1038/s41467-020-15724-9 is OK
- 10.1103/PhysRevLett.47.807 is OK
- 10.1063/1.4948778 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 10 months ago

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

jarvist commented 10 months ago

@NicoRenaud - I have quite a full calendar for today (London time), but will try to fit in a final proof read and cross-check today.

jarvist commented 10 months ago

@editorialbot recommend-accept

🎉

editorialbot commented 10 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 10 months ago

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

OK DOIs

- 10.1103/physrevb.99.085121 is OK
- 10.1088/1361-648X/aab9c3 is OK
- 10.1007/978-3-642-38718-0_14 is OK
- 10.1063/5.0139024 is OK
- 10.1103/PhysRevResearch.2.033429 is OK
- 10.1038/s41557-020-0544-y is OK
- 10.1002/jcc.1056 is OK
- 10.1021/acs.jctc.9b01132 is OK
- 10.1016/j.jcp.2022.111765 is OK
- 10.1063/5.0032836 is OK
- 10.1103/PhysRevResearch.3.043126 is OK
- 10.1002/adts.202000269 is OK
- 10.1016/j.jcp.2019.108929 is OK
- 10.1038/s41467-020-15724-9 is OK
- 10.1103/PhysRevLett.47.807 is OK
- 10.1063/1.4948778 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 10 months ago

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

\textnormal{MO} = \textnormal{AO} \cdot 
           ^
unexpected control sequence \textnormal
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

editorialbot commented 10 months ago

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4777, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

openjournals / joss-reviews

[REVIEW]: QMCTorch: a PyTorch Implementation of Real-Space Quantum Monte Carlo Simulations of Molecular Systems #5472

Status

Reviewer instructions & questions

Checklists

Review checklist for @scemama

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @tonnylou44853

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @AbdAmmar

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

Additional Author Tasks After Review is Complete