[REVIEW]: PyFstat: a Python package for continuous gravitational-wave data analysis

whedon commented 3 years ago

Submitting author: @dbkeitel (David Keitel) Repository: https://github.com/PyFstat/PyFstat/ Version: v1.11.5 Editor: @danielskatz Reviewer: @khanx169, @RobertRosca Archive: 10.5281/zenodo.4660591

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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

@khanx169 & @RobertRosca, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @danielskatz 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 ✨

Review checklist for @khanx169

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 (@dbkeitel) 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 @RobertRosca

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 (@dbkeitel) 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?

danielskatz commented 3 years ago

@whedon set 10.5281/zenodo.4660591 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4660591 is the archive.

danielskatz commented 3 years ago

@whedon set v1.11.5 as version

whedon commented 3 years ago

OK. v1.11.5 is the version.

danielskatz commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

PDF failed to compile for issue #3000 with the following error:

Can't find any papers to compile :-(

danielskatz commented 3 years ago

@whedon accept from branch joss

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.7935/GT1W-FZ16 is OK
- 10.1103/PhysRevD.58.063001 is OK
- 10.1007/978-3-540-76965-1_24 is OK
- 10.1016/j.parco.2011.09.001 is OK
- 10.1103/PhysRevD.89.064023 is OK
- 10.1088/0264-9381/32/2/024001 is OK
- 10.1088/0264-9381/32/7/074001 is OK
- 10.1093/mnras/stv2422 is OK
- 10.1142/S021773231730035X is OK
- 10.1103/PhysRevD.97.103020 is OK
- 10.1103/PhysRevD.98.063011 is OK
- 10.1088/1361-6382/aade34 is OK
- 10.3390/universe5110217 is OK
- 10.1103/PhysRevLett.124.191102 is OK
- 10.1093/mnras/staa3624 is OK
- 10.1016/j.softx.2020.100634 is OK
- 10.1103/PhysRevD.103.064017 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 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/2181

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2181, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss

danielskatz commented 3 years ago

@dbkeitel - can you confirm this is ready to go from your point of view? I will also be doing a final proof read...

danielskatz commented 3 years ago

My proof read has found some minor changes that are needed - see https://github.com/PyFstat/PyFstat/pull/304. Please merge this, or let me know what you disagree with.

danielskatz commented 3 years ago

@whedon accept from branch joss

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.7935/GT1W-FZ16 is OK
- 10.1103/PhysRevD.58.063001 is OK
- 10.1007/978-3-540-76965-1_24 is OK
- 10.1016/j.parco.2011.09.001 is OK
- 10.1103/PhysRevD.89.064023 is OK
- 10.1088/0264-9381/32/2/024001 is OK
- 10.1088/0264-9381/32/7/074001 is OK
- 10.1093/mnras/stv2422 is OK
- 10.1142/S021773231730035X is OK
- 10.1103/PhysRevD.97.103020 is OK
- 10.1103/PhysRevD.98.063011 is OK
- 10.1088/1361-6382/aade34 is OK
- 10.3390/universe5110217 is OK
- 10.1103/PhysRevLett.124.191102 is OK
- 10.1093/mnras/staa3624 is OK
- 10.1016/j.softx.2020.100634 is OK
- 10.1103/PhysRevD.103.064017 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 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/2198

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2198, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss

danielskatz commented 3 years ago

@whedon accept deposit=true from branch joss

whedon commented 3 years ago

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

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 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/2199
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.03000
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

dbkeitel commented 3 years ago

@danielskatz Thanks for your proofread! I've merged it, then found one more missing comma in the acknowledgments, fixed on our branch just now. But if it's too late for that one now, it's also ok.

danielskatz commented 3 years ago

unless it's essential, let's ignore it at this point

dbkeitel commented 3 years ago

Ok, thanks for the support throughout!

danielskatz commented 3 years ago

Congratulations to @dbkeitel (David Keitel) and co-authors!!

and thanks to @khanx169 and @RobertRosca for reviewing!

whedon commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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