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[REVIEW]: ewstools: A Python package for early warning signals of bifurcations in time series data #5038

Closed editorialbot closed 1 year ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@ThomasMBury<!--end-author-handle-- (Thomas M Bury) Repository: https://github.com/ThomasMBury/ewstools Branch with paper.md (empty if default branch): Version: v2.1.1 Editor: !--editor-->@osorensen<!--end-editor-- Reviewers: @mhu48, @mikesha2, @ranzhengcode Archive: 10.5281/zenodo.7630022

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/72d1a4bf216c2a4b22edab3b8f1feae0"><img src="https://joss.theoj.org/papers/72d1a4bf216c2a4b22edab3b8f1feae0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/72d1a4bf216c2a4b22edab3b8f1feae0/status.svg)](https://joss.theoj.org/papers/72d1a4bf216c2a4b22edab3b8f1feae0)

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

@mhu48 & @mikesha2 & @ranzhengcode, 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 @osorensen 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

πŸ“ Checklist for @mikesha2

πŸ“ Checklist for @ranzhengcode

πŸ“ Checklist for @mhu48

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=0.16 s (197.1 files/s, 139470.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           9            862           1251           1230
XML                              6              0              0            605
Markdown                         3             92              0            234
Jupyter Notebook                 4              0          17125            162
TeX                              1             22              4            148
YAML                             4             10              5             45
reStructuredText                 2             34             20             36
DOS Batch                        1              8              1             26
make                             1              4              6              9
-------------------------------------------------------------------------------
SUM:                            31           1032          18412           2495
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago

Wordcount for paper.md is 845

editorialbot commented 1 year ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/nature08227 is OK
- 10.1111/ele.12948 is OK
- 10.1098/rsif.2020.0482 is OK
- 10.1073/pnas.2106140118 is OK
- 10.1371/journal.pone.0041010 is OK
- 10.1111/2041-210X.13058 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.15681 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.1038/s41592-020-0772-5 is OK
- 10.48550/arXiv.1605.08695 is OK

MISSING DOIs

- 10.1163/1574-9347_bnp_e612900 may be a valid DOI for title: Keras

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:

mikesha2 commented 1 year ago

Review checklist for @mikesha2

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

ranzhengcode commented 1 year ago

@editorialbot generate my checklist

θŽ·ε–Outlook for Androidhttps://aka.ms/AAb9ysg


From: mikesha2 @.> Sent: Thursday, January 5, 2023 2:32:23 PM To: openjournals/joss-reviews @.> Cc: Zheng Ran @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: ewstools: A Python package for early warning signals of bifurcations in time series data (Issue #5038)

Review checklist for @mikesha2https://github.com/mikesha2 Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

― Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/5038#issuecomment-1371834247, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARMXINWK7ELN7Y5CEV66VG3WQZTHPANCNFSM6AAAAAATRSLPC4. You are receiving this because you were mentioned.Message ID: @.***>

ranzhengcode commented 1 year ago

Review checklist for @ranzhengcode

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

mhu48 commented 1 year ago

Review checklist for @mhu48

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

osorensen commented 1 year ago

πŸ‘‹ @mhu48

I notice there are a number of unchecked boxes in your review checklists. Are these related to issues which the authors should fix? If so, could you please elaborate here or by opening issues in the source repository?

mhu48 commented 1 year ago

@osorensen Thanks for the reminder! Apparently I made a mistake when I did the checklist. It should be updated correctly now? Please let me know if there is any further actions needed at this step.

osorensen commented 1 year ago

Thanks @mhu48, everything looks good now

osorensen commented 1 year ago

@editorialbot check references

osorensen 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/nature08227 is OK
- 10.1111/ele.12948 is OK
- 10.1098/rsif.2020.0482 is OK
- 10.1073/pnas.2106140118 is OK
- 10.1371/journal.pone.0041010 is OK
- 10.1111/2041-210X.13058 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.15681 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.1038/s41592-020-0772-5 is OK
- 10.48550/arXiv.1605.08695 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:

osorensen commented 1 year ago

@ThomasMBury, could you please replace the current pandas citation with those suggested here (preferably include both): https://pandas.pydata.org/about/citing.html

osorensen commented 1 year ago

@ThomasMBury, once you have fixed the pandas reference issue above, could you please

I can then move forward with recommending acceptance of the submission.

ThomasMBury 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:

ThomasMBury 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/nature08227 is OK
- 10.1111/ele.12948 is OK
- 10.1098/rsif.2020.0482 is OK
- 10.1073/pnas.2106140118 is OK
- 10.1371/journal.pone.0041010 is OK
- 10.1111/2041-210X.13058 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.15681 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.1038/s41592-020-0772-5 is OK
- 10.48550/arXiv.1605.08695 is OK

MISSING DOIs

- 10.1163/1574-9347_bnp_e612900 may be a valid DOI for title: Keras

INVALID DOIs

- None
ThomasMBury commented 1 year ago

@editorialbot commands

editorialbot commented 1 year ago

Hello @ThomasMBury, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
ThomasMBury commented 1 year ago

Hi @osorensen, thank you for serving as the editor for this paper. I've completed the tasks above.

The new version of the software is v2.1.1.

The DOI on Zenodo is 10.5281/zenodo.7630022.

Thanks.

osorensen commented 1 year ago

Thanks @ThomasMBury

osorensen commented 1 year ago

@editorialbot set 10.5281/zenodo.7630022 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7630022

osorensen commented 1 year ago

@editorialbot set v2.1.1 as version

editorialbot commented 1 year ago

Done! version is now v2.1.1

osorensen 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/nature08227 is OK
- 10.1111/ele.12948 is OK
- 10.1098/rsif.2020.0482 is OK
- 10.1073/pnas.2106140118 is OK
- 10.1371/journal.pone.0041010 is OK
- 10.1111/2041-210X.13058 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.15681 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.1038/s41592-020-0772-5 is OK
- 10.48550/arXiv.1605.08695 is OK

MISSING DOIs

- 10.1163/1574-9347_bnp_e612900 may be a valid DOI for title: Keras

INVALID DOIs

- None
osorensen 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:

ThomasMBury commented 1 year ago

I'm afraid I couldn't find a DOI for the Keras API - I hope this is ok. The bot didn't seem to mind the first time I submitted.

osorensen commented 1 year ago

Ok, then I think it's fine.

osorensen 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

- 10.1038/nature08227 is OK
- 10.1111/ele.12948 is OK
- 10.1098/rsif.2020.0482 is OK
- 10.1073/pnas.2106140118 is OK
- 10.1371/journal.pone.0041010 is OK
- 10.1111/2041-210X.13058 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.15681 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.1038/s41592-020-0772-5 is OK
- 10.48550/arXiv.1605.08695 is OK

MISSING DOIs

- 10.1163/1574-9347_dnp_e612900 may be a valid DOI for title: Keras

INVALID DOIs

- None
editorialbot commented 1 year ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3958, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 1 year ago

πŸ‘‹ @ThomasMBury - I'm working on the next steps for this submission, and after proofreading it, I have some suggested changes, in https://github.com/ThomasMBury/ewstools/pull/433 Please merge this, or let me know what you disagree with, then we can continue the process.

ThomasMBury commented 1 year ago

Thanks for proofreading @danielskatz. I approve of the changes and have merged the pull request.

danielskatz 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

- 10.1038/nature08227 is OK
- 10.1111/ele.12948 is OK
- 10.1098/rsif.2020.0482 is OK
- 10.1073/pnas.2106140118 is OK
- 10.1371/journal.pone.0041010 is OK
- 10.1111/2041-210X.13058 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.15681 is OK
- 10.25080/Majora-92bf1922-011 is OK
- 10.1038/s41592-020-0772-5 is OK
- 10.48550/arXiv.1605.08695 is OK

MISSING DOIs

- 10.1163/1574-9347_dnp_e612900 may be a valid DOI for title: Keras

INVALID DOIs

- None
editorialbot commented 1 year ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3959, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 1 year ago

🐦🐦🐦 πŸ‘‰ Tweet for this paper πŸ‘ˆ 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 πŸ‘‰ Toot for this paper πŸ‘ˆ 🐘🐘🐘