[REVIEW]: timeseriesflattener: A Python package for summarising features from (medical) time series

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@MartinBernstorff@mstimberg<!--end-editor-- Reviewers: @yarikoptic, @Ebedthan Archive: 10.5281/zenodo.7778588

Status

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Markdown: [![status](https://joss.theoj.org/papers/3bbea8745668d1aa40ff796c6fd3db87/status.svg)](https://joss.theoj.org/papers/3bbea8745668d1aa40ff796c6fd3db87)

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

@yarikoptic & @Ebedthan, 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 @mstimberg 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 @Ebedthan

📝 Checklist for @yarikoptic

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:

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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=0.29 s (205.3 files/s, 39338.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          33           1051           1379           3201
Markdown                         6            174              0            697
YAML                             9             43             37            262
Jupyter Notebook                 3              0           3936            234
TeX                              1             13              0            125
TOML                             1             12              0             84
reStructuredText                 6             87             68             76
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            60           1384           5427           4688
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1278

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:

editorialbot commented 1 year ago

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

OK DOIs

- 10.1038/s41746-018-0029-1 is OK
- 10.1017/neu.2021.22 is OK
- 10.1038/s41746-021-00529-x is OK

MISSING DOIs

- 10.1038/sdata.2016.35 may be a valid DOI for title: MIMIC-III, a freely accessible critical care database
- 10.1093/jamia/ocaa139 may be a valid DOI for title: Democratizing EHR analyses with FIDDLE: a flexible data-driven preprocessing pipeline for structured clinical data

INVALID DOIs

- None

mstimberg commented 1 year ago

👋🏼 @MartinBernstorff @yarikoptic @Ebedthan this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

There are additional guidelines in the message at the start of this issue.

Please feel free to ping me (@mstimberg) if you have any questions/concerns.

Ebedthan commented 1 year ago

Review checklist for @Ebedthan

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/Aarhus-Psychiatry-Research/timeseriesflattener?
[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 (@MartinBernstorff) 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?

mstimberg commented 1 year ago

:wave: @yarikoptic Just checking in to see whether you have any questions regarding the procedure/checklist (not meant to put any pressure on you, just to see whether everything is clear)?

yarikoptic commented 1 year ago

Review checklist for @yarikoptic

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/Aarhus-Psychiatry-Research/timeseriesflattener?
[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 (@MartinBernstorff) 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?

MartinBernstorff commented 1 year ago

@yarikoptic Thanks a lot for the issues and PRs! We've fixed/merged as appropriate, please let us know if there's anything else we can help with :-)

yarikoptic commented 1 year ago

@MartinBernstorff confusion with python 3.11 support remains. Filed issue(s).

MartinBernstorff commented 1 year ago

@MartinBernstorff confusion with python 3.11 support remains. Filed issue(s).

Thanks a lot for the nudge, @yarikoptic! Did some work on dependencies, support now covers 3.8, 3.9, 3.10 and 3.11.

yarikoptic commented 1 year ago

@mstimberg my checklist is complete now.

mstimberg commented 1 year ago

@yarikoptic Great, thanks a lot! I assume that means that from your side, software and paper are in a state that you'd recommend their publication?

@Ebedthan How are things coming along for you?

yarikoptic commented 1 year ago

@yarikoptic Great, thanks a lot! I assume that means that from your side, software and paper are in a state that you'd recommend their publication?

yes

mstimberg commented 1 year ago

Hi @Ebedthan, I saw that you checked the last box of your checklist. Could I ask you for a quick comment whether you consider your review done (and recommend the software/paper for publication), or whether there are still issues that you'd like to see addressed? Thanks :pray: !

Ebedthan commented 1 year ago

Hi @mstimberg , Yes, everything is good from my side and I recommend the software and paper for publication. Best

mstimberg 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

- 10.1038/s41746-018-0029-1 is OK
- 10.1017/neu.2021.22 is OK
- 10.1038/s41746-021-00529-x is OK
- 10.1038/sdata.2016.35 is OK
- 10.1093/jamia/ocaa139 is OK

MISSING DOIs

- None

INVALID DOIs

- None

mstimberg commented 1 year ago

@editorialbot generate pdf

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:

mstimberg commented 1 year ago

:wave: @MartinBernstorff As you've probably seen, the two reviewers have finished their reviews and recommend accepting the software/paper, congratulations :tada:

I've filed three minor issues regarding the paper (Aarhus-Psychiatry-Research/timeseriesflattener#154, Aarhus-Psychiatry-Research/timeseriesflattener#155, Aarhus-Psychiatry-Research/timeseriesflattener#156). As soon as they are fixed (assuming no errors/misunderstandings on my side, of course), we can proceed with finalizing the acceptance and publishing process.

MartinBernstorff commented 1 year ago

👋 @MartinBernstorff As you've probably seen, the two reviewers have finished their reviews and recommend accepting the software/paper, congratulations 🎉

I've filed three minor issues regarding the paper (Aarhus-Psychiatry-Research/timeseriesflattener#154, Aarhus-Psychiatry-Research/timeseriesflattener#155, Aarhus-Psychiatry-Research/timeseriesflattener#156). As soon as they are fixed (assuming no errors/misunderstandings on my side, of course), we can proceed with finalizing the acceptance and publishing process.

Thansk @mstimberg! I've fixed the issues, thanks for the attention to detail 👍

mstimberg commented 1 year ago

@MartinBernstorff great, thanks for the changes. There's still a minor issue with one reference, see my comment at https://github.com/Aarhus-Psychiatry-Research/timeseriesflattener/issues/155.

MartinBernstorff commented 1 year ago

Sorry about that! Commented in the issue.

mstimberg 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

- 10.1038/s41746-018-0029-1 is OK
- 10.1017/neu.2021.22 is OK
- 10.1145/2939672.2939785 is OK
- 10.1038/s41746-021-00529-x is OK
- 10.1109/RBME.2020.3007816 is OK
- 10.1038/sdata.2016.35 is OK
- 10.1093/jamia/ocaa139 is OK

MISSING DOIs

- None

INVALID DOIs

- None

mstimberg commented 1 year ago

@editorialbot generate pdf

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:

mstimberg commented 1 year ago

Thanks for the changes. I just realized that arxiv preprints also have DOIs nowadays, so you might also consider adding the https://doi.org/10.48550/arXiv.2210.12090 doi to the AutoPrognosis reference for completeness.

Apart from that, could you please:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

We can then move forward with a last check of the proof, and then I'll recommend acceptance of the submission.

HLasse commented 1 year ago

Hi @mstimberg, the last items should have been taken care of now.

I have added the DOI to AutoPrognosis.
The tagged release is v0.23.9
The package has been archived on Zenodo. The metadata has been updated to match.
The Zenodo DOI is 10.5281/zenodo.7778018

Please let me know if there's more that should be done!

mstimberg commented 1 year ago

@editorialbot check references

mstimberg commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

OK DOIs

- 10.1038/s41746-018-0029-1 is OK
- 10.1017/neu.2021.22 is OK
- 10.1145/2939672.2939785 is OK
- 10.1038/s41746-021-00529-x is OK
- 10.48550/arXiv.2210.12090 is OK
- 10.1038/sdata.2016.35 is OK
- 10.1093/jamia/ocaa139 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:

HLasse commented 1 year ago

I see that are writing the title as a headline right above the summary. I'll remove that line now. EDIT: fixed. Regenerating article proof

mstimberg commented 1 year ago

I see that are writing the title as a headline right above the summary. I'll remove that line now.

Indeed, good catch!

HLasse commented 1 year ago

@editorialbot generate pdf

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:

mstimberg commented 1 year ago

Could you (and/or your coauthors) have a final look at the proof to make sure everything is correct (in particular things I cannot easily verify, e.g. author names, affiliations, funding acknowledgements…)?

Since the paper is part of the repository/archive, it would be the cleanest to also release a new version/Zenodo archive with the change if not too much hassle.

HLasse commented 1 year ago

It looks good to me now! All author names, affiliations, funding, and orcids are correct.

No problem at all - I've bumped the version number which will start a new release to both GitHub and Zenodo. It will be out in ~15 mins (v.0.23.10)

mstimberg commented 1 year ago

Oh, I just noticed one more issue that editorialbot did not catch, unfortunately: the Shamouth et al. reference currently has two DOI entries, the second needs to go into the AutoPrognosis2.0 paper instead.

HLasse commented 1 year ago

Argh, nice catch! Has been amended and setup new release (v.0.23.11)

mstimberg commented 1 year ago

@editorialbot generate pdf

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:

mstimberg commented 1 year ago

@editorialbot set v0.23.11 as version

editorialbot commented 1 year ago

Done! version is now v0.23.11

mstimberg commented 1 year ago

@editorialbot set 10.5281/zenodo.7778588 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7778588

mstimberg commented 1 year ago

@editorialbot recommend-accept

openjournals / joss-reviews