editorialbot commented 1 year ago

Submitting author: !--author-handle-->@MJWester@jgostick<!--end-editor-- Reviewers: @bencardoen, @ajinkyakadu Archive: 10.5281/zenodo.8327409

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/bb7451e778d9a92cf9370903a6712ea0/status.svg)](https://joss.theoj.org/papers/bb7451e778d9a92cf9370903a6712ea0)

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

@bencardoen, 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 @jgostick 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 @bencardoen

📝 Checklist for @ajinkyakadu

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:

@editorialbot generate pdf

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.57 s (1055.7 files/s, 126688.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                         512           6742          20580          35129
Markdown                        62            610              0           4200
CUDA                             6            388            470           1489
C++                              5            255            148            860
TeX                              2             34              0            404
C/C++ Header                     5             40             52             96
YAML                             2              2              9             36
make                             3             27             33             36
-------------------------------------------------------------------------------
SUM:                           597           8098          21292          42250
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

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

OK DOIs

- 10.1364/OPEX.13.007052 is OK
- 10.1126/science.1127344 is OK
- 10.1038/nmeth929 is OK
- 10.1126/science.1137395 is OK
- 10.1038/nprot.2011.336 is OK
- 10.1063/5.0069349 is OK
- 10.1021/acs.chemrev.6b00815 is OK
- 10.1016/j.bpj.2017.11.2912 is OK
- 10.1101/752287 is OK
- 10.1038/s41467-022-34894-2 is OK
- 10.1016/j.bpj.2018.11.1510 is OK
- 10.1016/j.bpj.2019.11.926 is OK
- 10.1101/2021.03.26.437196 is OK
- 10.1038/s41598-021-02850-7 is OK
- 10.3389/fbinf.2021.724325 is OK
- 10.7554/eLife.63678 is OK
- 10.1371/journal.pone.0246138 is OK
- 10.3791/63665 is OK
- 10.25827/CS2A-DH13 is OK
- 10.1016/j.bpj.2017.11.2912 is OK
- 10.1038/s41592-020-0938-1 is OK
- 10.14440/jbm.2014.36 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

Wordcount for paper.md is 813

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

MJWester commented 1 year ago

I am not sure why there is an error. Is this our paper? The most recent artifact produced under issues in the main repository seems to be correct, so I am not sure where to begin.

bencardoen commented 1 year ago

Review checklist for @bencardoen

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/LidkeLab/smite?
[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 (@MJWester) 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?

bencardoen commented 1 year ago

@MJWester when you check the output of the error, it seems it crashed on a missing affiliation

failure': Author (Eric A. Burns) is missing affiliation (Theoj::Error)

https://github.com/openjournals/joss-papers/actions/runs/5274452956/jobs/9538928136#step:3:93

MJWester commented 1 year ago

Thanks. I fixed the problem and pushed a corrected version of the repository. How do I (or do you) transfer this updated repo to the review chain?

bencardoen commented 1 year ago

@MJWester I think by

@editorialbot generate pdf

jgostick commented 1 year ago

@editorialbot add @ajinkyakadu as reviewer

editorialbot commented 1 year ago

@ajinkyakadu added to the reviewers list!

jgostick commented 1 year ago

Hi @ajinkyakadu. Thanks for agreeing to review. To get started, you should generate your checklist using @editorialbot generate my checklist (while logged in as yourself, obvs). You'll then get a list of speific things to look for, and your job as reviewer is then straightforward.

ajinkyakadu commented 1 year ago

Review checklist for @ajinkyakadu

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/LidkeLab/smite?
[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 (@MJWester) 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?

jgostick commented 1 year ago

Hi @ajinkyakadu I'm glad to see that you've made some good progress on your review. Hopefully you can finalize it in the week or so?

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:

ajinkyakadu commented 1 year ago

Hi @jgostick , I have finally managed to run and test the code. I shall finish the review by tonight. Sorry for the delay.

jgostick commented 1 year ago

Hi @ajinkyakadu, any progress here?

ajinkyakadu commented 1 year ago

Hi @jgostick I'm finished with the review.

jgostick commented 1 year ago

@ajinkyakadu, thank you very much for your time. This review has been going on for a while, so it's nice to have it almost wrapped up!

jgostick commented 1 year ago

@MJWester, good news. You and the reviewers have worked through the all the issues and tightened up this package considerably. It now seems like it's ready to accept. There are a few administrative steps still, like minting DOI's and whatnot. I will generate a checklist for this in a subsequent comment. The hard part is over now, yea!

jgostick commented 1 year ago

@editorialbot generate post-review checklist

editorialbot commented 1 year ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

jgostick commented 1 year ago

Post-Review Checklist for Editor and Authors

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.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[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.

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
[ ] Recommend acceptance with @editorialbot recommend-accept

jgostick commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1364/OPEX.13.007052 is OK
- 10.1126/science.1127344 is OK
- 10.1038/nmeth929 is OK
- 10.1126/science.1137395 is OK
- 10.1038/nprot.2011.336 is OK
- 10.1063/5.0069349 is OK
- 10.1021/acs.chemrev.6b00815 is OK
- 10.1016/j.bpj.2017.11.2912 is OK
- 10.1038/nmeth.1449 is OK
- 10.1101/752287 is OK
- 10.1038/s41467-022-34894-2 is OK
- 10.1016/j.bpj.2018.11.1510 is OK
- 10.1016/j.bpj.2019.11.926 is OK
- 10.1101/2021.03.26.437196 is OK
- 10.1038/s41598-021-02850-7 is OK
- 10.3389/fbinf.2021.724325 is OK
- 10.1103/PhysRevE.93.042401 is OK
- 10.7554/eLife.63678 is OK
- 10.1371/journal.pone.0246138 is OK
- 10.3791/63665 is OK
- 10.25827/CS2A-DH13 is OK
- 10.1016/j.bpj.2017.11.2912 is OK
- 10.1038/s41592-020-0938-1 is OK
- 10.14440/jbm.2014.36 is OK

MISSING DOIs

- None

INVALID DOIs

- None

MJWester commented 1 year ago

@jgostick Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper. This is in the top-level README? I think we made a mistake and am attempting to fix it. The software is currently version v1.0.0 and the DOI, which has a weird citation, is 10.5281/zenodo.8327410 . We tried to follow the instructions https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content , but the corresponding author and I did things separately producing the 1.0.0 release and allowing zenodo to produce the DOI, resulting in some confusion. Any advice? I see in another repository a CITATION.cff file, so I am guessing I need to make one of these???

jgostick commented 1 year ago

The thing that needs to match is the paper.md authors and the zenodo archive.

As for the mix-up, the best bet is probably just to do a new release and new doi? JOSS doesn't really mind which version you ultimately mint as the "joss" version. I actually think something like this happened when we did our joss paper a few years ago. I don't think the citation file is necessary for joss.

MJWester commented 1 year ago

@jgostick , OK. I am still confused about how I set the archive authors. This is done in zenodo or GitHub or ? (As you can see, I have never done this before.). Is there a tutorial I should look at?

MJWester commented 1 year ago

I am beginning to figure things out with some local help, who suggested a .zenodo.json file in the github top-level directory.

jgostick commented 1 year ago

A zenodo file in the repo does not sound right. I have also only done this once myself, but I think it's as simple as going to zenodo and entering the author info.. Maybe you're over thinking it and trying to get zenodo to do it automatically?

MJWester commented 1 year ago

@jgostick: No. The .zenodo.json file automatically provides correct metatdata for all releases of the repository to zenodo. Entering author info manually to zenodo is the usual way, but with a large number of co-authors in my case, it is very error prone. This method was recommended by our electronic information specialist. For an example, see the .zenodo.json file in my repository (DOI to follow) and for further details, see https://developers.zenodo.org/#add-metadata-to-your-github-repository-release

Anyway, the author list and license are now consistent. The correct DOI is 10.5281/zenodo.8336392 The version is v1.0.0 of September 11 (there is a version from September 7 from my first incorrect try with a different DOI).

MJWester commented 1 year ago

One more thing. In the paper, the 1st listed author and I are co-1st authors of the paper, but I didn't know how to do this in Zenodo, so I let us be listed in the same order in the DOI without this identification. Also, the last author is corresponding author. Again, not sure how to do this in Zenodo. I'll investigate, but hopefully the current DOI will do.

There might be a way to indicate authorship comments via a note description (I've left it blank). If you want exact match up of authorship information, I can try that. I'll look at it tonight.

MJWester commented 1 year ago

@jgostick Alright, I decided to just add the note and make one final release.

Same version v1.0.0 as just editing meta-data. DOI is 10.5281/zenodo.8336799 [Copied from zenodo: Cite all versions? You can cite all versions by using the DOI 10.5281/zenodo.8327409. This DOI represents all versions, and will always resolve to the latest one.]

Sorry for the extra DOIs---but now this is stable unless you find a problem.

MJWester commented 1 year ago

@jgostick I may have to add some more grant acknowledgments, so please wait a little longer. Getting these group papers requires careful navigation.

MJWester commented 1 year ago

@jgostick Acknowledgements updated. The all version DOI is 10.5281/zenodo.8327409 (for version v1.0.0). Hopefully, no further edits (unless you request some) will be needed.

jgostick commented 1 year ago

@editorialbot set 10.5281/zenodo.8327409 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8327409

jgostick commented 1 year ago

@editorialbot set 1.0.0 as version

editorialbot commented 1 year ago

Done! version is now 1.0.0

jgostick commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1364/OPEX.13.007052 is OK
- 10.1126/science.1127344 is OK
- 10.1038/nmeth929 is OK
- 10.1126/science.1137395 is OK
- 10.1038/nprot.2011.336 is OK
- 10.1063/5.0069349 is OK
- 10.1021/acs.chemrev.6b00815 is OK
- 10.1016/j.bpj.2017.11.2912 is OK
- 10.1038/nmeth.1449 is OK
- 10.1101/752287 is OK
- 10.1038/s41467-022-34894-2 is OK
- 10.1016/j.bpj.2018.11.1510 is OK
- 10.1016/j.bpj.2019.11.926 is OK
- 10.1101/2021.03.26.437196 is OK
- 10.1038/s41598-021-02850-7 is OK
- 10.3389/fbinf.2021.724325 is OK
- 10.1103/PhysRevE.93.042401 is OK
- 10.7554/eLife.63678 is OK
- 10.1371/journal.pone.0246138 is OK
- 10.3791/63665 is OK
- 10.1364/BOE.477501 is OK
- 10.25827/CS2A-DH13 is OK
- 10.1016/j.bpj.2017.11.2912 is OK
- 10.1038/s41592-020-0938-1 is OK
- 10.14440/jbm.2014.36 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:warning: Error preparing paper acceptance.

jgostick commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

bencardoen commented 1 year ago

@jgostick I think there's an issue with the ORCID for 1 author

 Problem with ORCID ( 0000-0002-9939-1923) for Farzin Farzam. ORCID looks to be the wrong length (Theoj::Error)

jgostick commented 1 year ago

@MJWester, I'm really sorry to do this to you but there is an extra 'space' at the beginning of Farzin Farzam's ORCID that is breaking our pdf builder. I will let our devs[^1] know about this so they can update the builder, but to get the process moving, can you update this paper.md file?

[^1]: edit, changed 'your devs' to 'our devs'

MJWester commented 1 year ago

@jgostick Sorry, I was off-grid for a couple of days. I just made the fix you requested. Hopefully, there are no other errors!

jgostick commented 1 year ago

@editorialbot recommend-accept

openjournals / joss-reviews

[REVIEW]: SMITE: Single Molecule Imaging Toolbox Extraordinaire (MATLAB) #5563

Status

Reviewer instructions & questions

Checklists

Review checklist for @bencardoen

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @ajinkyakadu

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