[REVIEW]: PySensors: A Python Package for Sparse Sensor Placement

whedon commented 3 years ago

Submitting author: @briandesilva (Brian de Silva) Repository: https://github.com/dynamicslab/pysensors/ Version: v0.3.3 Editor: @pdebuyl Reviewer: @jordanperr, @tuelwer Archive: 10.5281/zenodo.4542530

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Status

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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

@jordanperr & @tuelwer, 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 @pdebuyl 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 @jordanperr

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 (@briandesilva) 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 @tuelwer

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 (@briandesilva) 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?

briandesilva commented 3 years ago

Sorry about that @pdebuyl. The correct DOI is 10.5281/zenodo.4542530 and the version is v0.3.3.

pdebuyl commented 3 years ago

Thanks @briandesilva . Can you edit the metadata of the zenodo archive to match the paper please? Title should be "PySensors: A Python Package for Sparse Sensor Placement" and authors should be as here, with ORCID properly set.

pdebuyl commented 3 years ago

@whedon set 10.5281/zenodo.4542530 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4542530 is the archive.

pdebuyl commented 3 years ago

@whedon set v0.3.3 as version

whedon commented 3 years ago

OK. v0.3.3 is the version.

briandesilva commented 3 years ago

Thanks @briandesilva . Can you edit the metadata of the zenodo archive to match the paper please? Title should be "PySensors: A Python Package for Sparse Sensor Placement" and authors should be as here, with ORCID properly set.

@pdebuyl, I've updated the archive as you asked.

pdebuyl commented 3 years ago

Thanks @briandesilva

pdebuyl commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

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/2089

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2089, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon commented 3 years ago

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

OK DOIs

- 10.1287/opre.43.4.684 is OK
- 10.1145/3384419.3430407 is OK
- 10.1137/17M1162366 is OK
- 10.1109/JSEN.2018.2887044 is OK
- 10.1109/mcs.2018.2810460 is OK
- 10.1137/15M1036713 is OK
- 10.1017/jfm.2011.195 is OK
- 10.2514/6.2004-2415 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1109/access.2018.2886528 is OK
- 10.1109/access.2020.3023625 is OK
- 10.1126/science.1165893 is OK
- 10.1103/physrevmaterials.2.083802 is OK
- 10.1111/j.2517-6161.1996.tb02080.x is OK
- 10.5281/zenodo.1173754 is OK
- 10.1364/oe.24.030433 is OK
- 10.1063/1.5066099 is OK
- 10.1063/1.4977057 is OK
- 10.1016/j.ymssp.2018.08.033 is OK
- 10.1126/sciadv.1602614 is OK
- 10.1098/rspa.2016.0446 is OK
- 10.1137/16m1086637 is OK
- 10.1137/18m116798x is OK
- 10.1017/jfm.2017.823 is OK
- 10.1063/1.5018409 is OK
- 10.1016/j.ifacol.2016.10.249 is OK
- 10.1103/physreve.96.023302 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1098/rspa.2018.0335 is OK
- 10.1016/j.jcp.2019.07.049 is OK
- 10.1007/s00162-020-00536-w is OK
- 10.1103/physreve.101.010203 is OK
- 10.1115/1.4043148 is OK
- 10.1016/j.ocemod.2009.01.001 is OK
- 10.1109/cdc.2014.7040017 is OK
- 10.1017/jfm.2017.137 is OK
- 10.1073/pnas.1808909115 is OK
- 10.1016/j.jmsy.2018.01.011 is OK
- 10.1017/jfm.2018.147 is OK
- 10.1017/9781108380690 is OK
- 10.1007/s00162-020-00520-4 is OK
- 10.1002/cpa.20124 is OK
- 10.1016/0167-7152(84)90020-8 is OK
- 10.1016/j.crma.2004.08.006 is OK
- 10.1162/0899766053723032 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1109/tit.2006.885507 is OK
- 10.1109/tit.2005.862083 is OK
- 10.1109/MSP.2007.4286571 is OK
- 10.1109/tit.2009.2034811 is OK
- 10.1016/j.acha.2010.10.002 is OK
- 10.1145/1879141.1879192 is OK
- 10.1137/090766498 is OK
- 10.1111/j.1467-9868.2011.00783.x is OK
- 10.1137/110822724 is OK
- 10.1137/15M1019271 is OK
- 10.1109/tsipn.2016.2614903 is OK
- 10.1109/sam.2016.7569707 is OK
- 10.1137/16m1081270 is OK
- 10.2172/1405271 is OK

MISSING DOIs

- None

INVALID DOIs

- None

pdebuyl commented 3 years ago

For the eic: only orcid ids for authors seem missing from metadata.

briandesilva commented 3 years ago

I just added Orcid IDs for the authors to the paper. Sorry, I hadn't thought to add them when I added them to the DOI archive.

pdebuyl commented 3 years ago

Thanks @briandesilva . I don't think that we require them, I mentioned it as I believe that it brings value to the authors, to the readers, and to the journal :-)

The submission is in the hands of the Editors-in-chief in rotation.

arfon commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

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/2097

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2097, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon commented 3 years ago

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

OK DOIs

- 10.1287/opre.43.4.684 is OK
- 10.1145/3384419.3430407 is OK
- 10.1137/17M1162366 is OK
- 10.1109/JSEN.2018.2887044 is OK
- 10.1109/mcs.2018.2810460 is OK
- 10.1137/15M1036713 is OK
- 10.1017/jfm.2011.195 is OK
- 10.2514/6.2004-2415 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1109/access.2018.2886528 is OK
- 10.1109/access.2020.3023625 is OK
- 10.1126/science.1165893 is OK
- 10.1103/physrevmaterials.2.083802 is OK
- 10.1111/j.2517-6161.1996.tb02080.x is OK
- 10.5281/zenodo.1173754 is OK
- 10.1364/oe.24.030433 is OK
- 10.1063/1.5066099 is OK
- 10.1063/1.4977057 is OK
- 10.1016/j.ymssp.2018.08.033 is OK
- 10.1126/sciadv.1602614 is OK
- 10.1098/rspa.2016.0446 is OK
- 10.1137/16m1086637 is OK
- 10.1137/18m116798x is OK
- 10.1017/jfm.2017.823 is OK
- 10.1063/1.5018409 is OK
- 10.1016/j.ifacol.2016.10.249 is OK
- 10.1103/physreve.96.023302 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1098/rspa.2018.0335 is OK
- 10.1016/j.jcp.2019.07.049 is OK
- 10.1007/s00162-020-00536-w is OK
- 10.1103/physreve.101.010203 is OK
- 10.1115/1.4043148 is OK
- 10.1016/j.ocemod.2009.01.001 is OK
- 10.1109/cdc.2014.7040017 is OK
- 10.1017/jfm.2017.137 is OK
- 10.1073/pnas.1808909115 is OK
- 10.1016/j.jmsy.2018.01.011 is OK
- 10.1017/jfm.2018.147 is OK
- 10.1017/9781108380690 is OK
- 10.1007/s00162-020-00520-4 is OK
- 10.1002/cpa.20124 is OK
- 10.1016/0167-7152(84)90020-8 is OK
- 10.1016/j.crma.2004.08.006 is OK
- 10.1162/0899766053723032 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1109/tit.2006.885507 is OK
- 10.1109/tit.2005.862083 is OK
- 10.1109/MSP.2007.4286571 is OK
- 10.1109/tit.2009.2034811 is OK
- 10.1016/j.acha.2010.10.002 is OK
- 10.1145/1879141.1879192 is OK
- 10.1137/090766498 is OK
- 10.1111/j.1467-9868.2011.00783.x is OK
- 10.1137/110822724 is OK
- 10.1137/15M1019271 is OK
- 10.1109/tsipn.2016.2614903 is OK
- 10.1109/sam.2016.7569707 is OK
- 10.1137/16m1081270 is OK
- 10.2172/1405271 is OK

MISSING DOIs

- None

INVALID DOIs

- None

arfon commented 3 years ago

@whedon accept deposit=true

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/2098
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02828
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 3 years ago

@jordanperr, @tuelwer - many thanks for your reviews here and to @pdebuyl for editing this submission. JOSS relies upon the volunteer efforts of folks likes yourselves and we simply wouldn't be able to do this without you! ✨

@briandesilva - your paper is now accepted and published in JOSS :zap::rocket::boom:

whedon commented 3 years ago

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02828/status.svg)](https://doi.org/10.21105/joss.02828)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02828">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02828/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02828/status.svg
   :target: https://doi.org/10.21105/joss.02828

This is how it will look in your documentation:

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briandesilva commented 3 years ago

@arfon, I'm really sorry, but it was just pointed out to me that two of the author names were written in the wrong order in the paper. Is there any way to re-generate the pdf with the corrected order? I have corrected and pushed paper.md.

arfon commented 3 years ago

Sure thing. Updated in https://github.com/openjournals/joss-papers/commit/8f2fc952f6c9bb5f9d32b1acd0a1f9ec2d96ad0a

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