[REVIEW]: PyCS3: A Python toolbox for time-delay measurements in lensed quasars

whedon commented 4 years ago

Submitting author: @martin-millon (Martin Millon) Repository: https://gitlab.com/cosmograil/PyCS3 Version: v3.0.2 Editor: @arfon Reviewer: @danhey, @coljac Archive: 10.5281/zenodo.4046260

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Reviewer instructions & questions

@danhey & @coljac, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 ✨

Review checklist for @danhey

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 repository url?
[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 (@martin-millon) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @coljac

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 repository url?
[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 (@martin-millon) 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

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)?
[ ] 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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @danhey, @coljac it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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whedon commented 4 years ago

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

OK DOIs

- 10.1051/0004-6361/202037740 is OK
- 10.1051/0004-6361/201220123 is OK
- 10.1051/0004-6361/201526704 is OK
- 10.1093/mnras/stw3006 is OK
- 10.1051/0004-6361/201935921 is OK
- 10.1093/mnras/stz3094 is OK
- 10.1051/0004-6361/201220352 is OK
- 10.1051/0004-6361/201833287 is OK
- 10.1088/0004-637X/800/1/11 is OK
- 10.1093/mnras/stx483 is OK
- 10.1038/s42254-019-0137-0 is OK
- 10.1086/170951 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

arfon commented 4 years ago

@danhey, @coljac - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

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 https://github.com/openjournals/joss-reviews/issues/2654 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 about 2-4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

arfon commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

danhey commented 4 years ago

Hi all,

I find the code to be well written and nicely documented. Great work! I have installed it without issue, and ran most of the example code.

My only issue appears to be running the the code in Sec. 1.2. I am getting an attribute error which seems to be caused by misconfigured imports. I can get around this by replacing import pycs3 with import pycs3.gen.lc_func.

Otherwise, this is an excellent package and I recommend it for publication.

martin-millon commented 4 years ago

Thanks @danhey for checking our code and thanks for spotting this problem in the documentation. I have pushed a fix on the master branch.

coljac commented 4 years ago

Hi authors,

I have a question about the multiprocessing. There are several methods that take a number of cores as an argument, for example pycs3.sim.run.multirun. The docs say:

ncpu – integer. Number of CPU tu use, if None I will use all available CPUs. Turn this to one if you use higher level of parallelisation

However, when I pass in a number > 1, I see this:

Multi-processing is not supported on this verison ! You can still use a higher level of parallelisation. I will run on a single core for the moment.
Starting the curve shifting on a single CPU, no multiprocessing...

However, the documentation doesn't seem to mention this. Should the docs reflect that this feature isn't implemented, or did I miss something?

coljac commented 4 years ago

Hi authors,

Here's the rest of my review.

Firstly, this is an excellent software package, and it serves a genuine scientific need, as time delay cosmology is only going to increase in the future and will be key in confirming or resolving the H0 tension. Congratulations on a great piece of work! It was also a pleasure to review, as everything is in great shape.

Regarding the paper: I am satisfied with the paper and don't need to see any revisions. I would suggest fixing the citations so that the nested parentheses are removed - "(for instance, Wang 2010.)" This is a minor issue, as is the phrase "Since almost three decades" should probably be "for almost three decades".

Regarding the software: I was able to successfully run the pytest tests in /tests. I'm familiar with using pytest; this process should probably be documented. On my system. the plots generated by the tests popped up in windows (many, many windows); perhaps setting the default backend to Agg would be more convenient here? (On the other hand, the documentation of the workflow in tdc_test seems adequate to get everything working.)

The notebooks were very good, all the examples ran for me (I had to install a latex package and dvipng; I don't think this was a deficiency on your end though).

Otherwise, the package is well documented and rich in features, meeting a genuine scientific need. Subject to a note on pytest, I am satisfied with this submission.

martin-millon commented 4 years ago

Thanks, @coljac and @danhey for your reviews and for helping us to improve this package.

I have made the following changes :

I have completely removed the multiprocessing computing at the level of the function pycs3.sim.applyopt(). This can be done at a higher level, i.e., at the level of the function pycs3.sim.multirun(). This is now better documented in the tutorial. I think this is the best solution as this improves (a bit) the performance and prevents some errors if the user is trying to parallelize the code at both levels at the same time.
- As you suggested, I have changed the backend to Agg in the \tests.
- I have added some documentation on how to run the tests.
- I have made the changes that you suggested in the paper

arfon commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

arfon commented 4 years ago

Thanks for the update @martin-millon. I found one small typo in your paper which I corrected in https://gitlab.com/cosmograil/PyCS3/-/merge_requests/5

@coljac - assuming that @martin-millon's response addresses your concerns about testing, could you please check off the final item in your checklist?

@martin-millon - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

The title of the archive is the same as the JOSS paper title
That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

martin-millon commented 4 years ago

@arfon - I have put an archive on Zenodo. Here is the DOI: http://doi.org/10.5281/zenodo.4046260

arfon commented 4 years ago

@whedon set 10.5281/zenodo.4046260 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.4046260 is the archive.

arfon commented 4 years ago

@whedon check references

whedon commented 4 years ago

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

OK DOIs

- 10.1051/0004-6361/202037740 is OK
- 10.1051/0004-6361/201220123 is OK
- 10.1051/0004-6361/201526704 is OK
- 10.1093/mnras/stw3006 is OK
- 10.1051/0004-6361/201935921 is OK
- 10.1093/mnras/stz3094 is OK
- 10.1051/0004-6361/201220352 is OK
- 10.1051/0004-6361/201833287 is OK
- 10.1088/0004-637X/800/1/11 is OK
- 10.1093/mnras/stx483 is OK
- 10.1038/s42254-019-0137-0 is OK
- 10.1086/170951 is OK

MISSING DOIs

- None

INVALID DOIs

- None

arfon commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

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

OK DOIs

- 10.1051/0004-6361/202037740 is OK
- 10.1051/0004-6361/201220123 is OK
- 10.1051/0004-6361/201526704 is OK
- 10.1093/mnras/stw3006 is OK
- 10.1051/0004-6361/201935921 is OK
- 10.1093/mnras/stz3094 is OK
- 10.1051/0004-6361/201220352 is OK
- 10.1051/0004-6361/201833287 is OK
- 10.1088/0004-637X/800/1/11 is OK
- 10.1093/mnras/stx483 is OK
- 10.1038/s42254-019-0137-0 is OK
- 10.1086/170951 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1746

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1746, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

arfon commented 4 years ago

@martin-millon - please make a last check of the PDF proof in https://github.com/openjournals/joss-papers/pull/1746 (I'll do the same).

I plan to loop back on this in the morning my time to process/accept this.

martin-millon commented 4 years ago

@arfon - I've been through the paper one more time and I don't have anything to change.

arfon commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1753
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02654
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 4 years ago

@danhey, @coljac - many thanks for your reviews here ✨

@martin-millon - your paper is now accepted into JOSS :zap::rocket::boom:

whedon commented 4 years ago

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reStructuredText:
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martin-millon commented 4 years ago

@arfon Is there a way with Whedon to get the Latex file from which the paper is generated? I would like to post it on the arXiv.

arfon commented 4 years ago

@martin-millon - not directly but you can hack it using this script from this issue: https://github.com/openjournals/joss/issues/132

martin-millon commented 4 years ago

Thanks !

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