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[REVIEW]: DTW-C++: Fast dynamic time warping and clustering of time series data #6881

Closed editorialbot closed 1 day ago

editorialbot commented 2 months ago

Submitting author: !--author-handle-->@ElektrikAkar<!--end-author-handle-- (Volkan Kumtepeli) Repository: https://github.com/Battery-Intelligence-Lab/dtw-cpp Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@logological<!--end-editor-- Reviewers: @ZhenchenHong, @i64 Archive: 10.5281/zenodo.13551469

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e977a41cc895869aaf1f468a1b4946a3"><img src="https://joss.theoj.org/papers/e977a41cc895869aaf1f468a1b4946a3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e977a41cc895869aaf1f468a1b4946a3/status.svg)](https://joss.theoj.org/papers/e977a41cc895869aaf1f468a1b4946a3)

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

@dyigitpolat & @ZhenchenHong & @i64, 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 @logological 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 @dyigitpolat

📝 Checklist for @ZhenchenHong

📝 Checklist for @i64

editorialbot commented 2 months 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 2 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.is.2015.04.007 is OK
- 10.1109/TASSP.1978.1163055 is OK
- 10.1016/j.patcog.2010.09.013 is OK
- 10.1109/DSAA49011.2020.00096 is OK
- 10.1109/TASSP.1978.1163055 is OK
- 10.1016/j.rser.2019.109628 is OK
- 10.1007/s12532-017-0130-5 is OK

MISSING DOIs

- No DOI given, and none found for title: wannesm/dtaidistance v2. 0.0
- No DOI given, and none found for title: The UCR Time Series Classification Archive
- No DOI given, and none found for title: Tslearn, A Machine Learning Toolkit for Time Serie...
- No DOI given, and none found for title: The UCR Time Series Classification Archive
- No DOI given, and none found for title: Gurobi Optimizer Reference Manual
- No DOI given, and none found for title: Fast dynamic time warping and clustering in C++

INVALID DOIs

- https://doi.org/10.1016/0377-0427(87)90125-7 is INVALID because of 'https://doi.org/' prefix
editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.29 s (508.3 files/s, 662975.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                             27              0              0         176993
CSS                              3            788            255           3626
C++                             22            503            468           1459
CMake                           24            196            180           1187
Markdown                        28            261              0            756
C/C++ Header                    22            279            419            754
YAML                             9             41             20            368
Python                           6             62             63            172
TeX                              1             13              0            153
HTML                             1              7             20             61
TOML                             1              0              0              3
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                           145           2150           1425         185533
-------------------------------------------------------------------------------

Commit count by author:

   349  Volkan Kumtepeli
   174  beckyperriment
    31  David Howey
     5  dependabot[bot]
editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 2926

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

dyigitpolat commented 2 months ago

Review checklist for @dyigitpolat

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

logological commented 2 months ago

@ElektrikAkar You might start by fixing the invalid DOI identified by editorialbot upthread.

ZhenchenHong commented 2 months ago

Review checklist for @ZhenchenHong

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

i64 commented 2 months ago

Review checklist for @i64

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

logological commented 2 months ago

@i64 and @ZhenchenHong, thanks for starting your reviews. It's been a few weeks with no further updates from you -- any chance you could finish the reviews in the next week? We normally aim to get reviews back in two or three weeks. @dyigitpolat, same goes for you!

ZhenchenHong commented 2 months ago

@i64 and @ZhenchenHong, thanks for starting your reviews. It's been a few weeks with no further updates from you -- any chance you could finish the reviews in the next week? We normally aim to get reviews back in two or three weeks. @dyigitpolat, same goes for you!

Hi @logological, sure and I am almost done. One quick question, if I noticed some misunderstanding in code usage, shall I raise it in their repo issues session or here?Thanks!

logological commented 2 months ago

@ZhenchenHong Probably best if you raise it as an issue in the original repository and link it to this issue (either by referencing this issue in that one, or that one in this one).

ZhenchenHong commented 2 months ago

@ZhenchenHong Probably best if you raise it as an issue in the original repository and link it to this issue (either by referencing this issue in that one, or that one in this one).

Sure, added and will sign-off when the authors resolve the issues. Thanks!

logological commented 1 month ago

@i64 and @dyigitpolat Could you please confirm that you will be completing your reviews for this submission and let me know approximately when we can expect them to be done? Thanks!

i64 commented 1 month ago

@logological I'm currently working on it. I plan to finish it during the day.

i64 commented 1 month ago

@logological There are two "Statement of need" items in the checklist. In the paper, they have it as a section; however, in the documentation what should be our expectation? Can introduction/about sections of the documentation considered to be enough?

i64 commented 1 month ago

@logological I have raised all my issues. When the authors resolve them, I will check the remaining items in the checklist. Thanks!

logological commented 1 month ago

@ElektrikAkar From examining the project repository, I see that you're making progress on addressing the issues raised by i64. Please let us know once the software and paper are ready for further review. (No hurry!)

logological commented 1 month ago

It seems one of the reviewers has gone AWOL, so I will remove him. The review can proceed on the basis of the other two reviewers' comments.

logological commented 1 month ago

@editorialbot remove @dyigitpolat as reviewer

editorialbot commented 1 month ago

@dyigitpolat removed from the reviewers list!

i64 commented 3 weeks ago

All of my issues look resolved now @logological. Thank you for your collaboration @ElektrikAkar

ElektrikAkar commented 3 weeks ago

Thank you very much for the comments from both reviewers! Thanks to your efforts, we have significantly improved our software, particularly the installation process and documentation. We would greatly appreciate any further comments; otherwise, we have completed addressing the reviewers' feedback. @logological many thanks for facilitating a smooth review process.

logological commented 3 weeks ago

@ZhenchenHong Are you happy to sign off on your review now?

ZhenchenHong commented 3 weeks ago

Sure, it looks good to me. Thanks!

On Fri, Aug 16, 2024 at 6:05 PM Tristan Miller @.***> wrote:

@ZhenchenHong https://github.com/ZhenchenHong Are you happy to sign off on your review now?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6881#issuecomment-2294371387, or unsubscribe https://github.com/notifications/unsubscribe-auth/AI3PXRJBE6ALCLJXCVIQJ23ZRZZUFAVCNFSM6AAAAABJGXIYP6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJUGM3TCMZYG4 . You are receiving this because you were mentioned.Message ID: @.***>

logological commented 3 weeks ago

@ZhenchenHong @i64 Thanks for reviews! Since you're both satisfied with the state of the paper, I'll do some final checks to complete the review process.

logological commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

logological commented 3 weeks ago

@ElektrikAkar There appears to be a typo in your BibTeX file that breaks the hyperlink to tslearn. In the file paper.bib, could you please change the line url = {https://github.com/tslearn-team/tslearn.}, to url = {https://github.com/tslearn-team/tslearn},? (That is, delete the period character at the end of the URL.)

logological commented 3 weeks ago

@editorialbot check references

editorialbot commented 3 weeks ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.is.2015.04.007 is OK
- 10.1109/TASSP.1978.1163055 is OK
- 10.1016/j.patcog.2010.09.013 is OK
- 10.5281/zenodo.1202378 is OK
- 10.1109/DSAA49011.2020.00096 is OK
- 10.1109/JAS.2019.1911747 is OK
- 10.1109/TASSP.1978.1163055 is OK
- 10.1016/j.rser.2019.109628 is OK
- 10.1007/s12532-017-0130-5 is OK
- 10.48550/arXiv.2307.04904 is OK
- 10.1016/0377-0427(87)90125-7 is OK

MISSING DOIs

- No DOI given, and none found for title: The UCR Time Series Classification Archive
- No DOI given, and none found for title: Tslearn, A Machine Learning Toolkit for Time Serie...
- No DOI given, and none found for title: Gurobi Optimizer Reference Manual

INVALID DOIs

- None
logological commented 3 weeks ago

@ElektrikAkar I've spotted a few further issues with your references:

  1. Sakoe & Chiba is missing the issue number (1). You can add this to the BibTeX record with number = 1,.
  2. Tavenard et al. (2020) is missing the issue number (118). You can add this to the BibTeX record with number = 118,.
  3. You might consider having the url field for Tavenard et al. (2020) set to the location of the paper (http://jmlr.org/papers/v21/20-091.html) rather than the GitHub repository (https://github.com/tslearn-team/tslearn).
  4. The URL supplied for the Gurobi Optimizer Reference Manual goes to the company's home page rather than the manual itself. Consider using the exact URL for the manual: https://www.gurobi.com/documentation/11.0/refman/ (substitute 10.0, 9.5, etc. for 11.0 if you meant to cite an earlier version of the manual).
ElektrikAkar commented 3 weeks ago

Hi @logological,

Thank you very much for your comments! I updated references accordingly.

logological commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

logological commented 3 weeks ago

@ElektrikAkar Thanks, but it seems your edits have inadvertently introduced or revealed some further errors:

  1. Huangfu & Hall (2018) now has both an issue and a number field, but only one of these should be specified. (The way you have it now, LaTeX is typesetting the issue number as "(1, 1)".) You can delete the issue field.
  2. Sakoe & Chiba (1978) has the same problem as Huangfu & Hall (2018). Please delete the issue field.
  3. I hadn't noticed before that you had the wrong entry type for Tavenard et al. (2020), and as a result the formatting of the volume, issue, and page numbers differs from the other articles. Please change its type from @misc to @article.

Could you please fix these?

ElektrikAkar commented 3 weeks ago

Hi @logological,

I apologise for the inconvenience caused by the newly introduced errors. I have now corrected them exactly as per your comments.

logological commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

logological commented 3 weeks ago

@ElektrikAkar Thanks; the references look good now! Could you please now handle the author tasks in the checklist below?

logological commented 3 weeks ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

ElektrikAkar commented 3 weeks ago

Hi @logological ,

Thank you very much for your help. I believe this will require all authors to do a final check on the manuscript. For example, one of the ORCID IDs will probably need to be changed. I will wait for their input, so it might take a bit of time to complete these tasks, but we will do our best. Have a nice week ahead.

logological commented 3 weeks ago

@ElektrikAkar No problem. Let me know once you've completed all the steps. I'll then review the Zenodo archive and if everything looks OK, we can proceed with a publication recommendation. Take as much time as you need.

ElektrikAkar commented 1 week ago

Hi @logological,

Thank you very much for your patience. We have corrected ORCIDs, and released software on Github and Zenodo.

https://github.com/Battery-Intelligence-Lab/dtw-cpp/releases/tag/v1.0.0

DOI

Hopefully everything is alright. Looking forward to your further instructions. Have a nice Friday and weekend.

logological commented 1 week ago

@editorialbot set 10.5281/zenodo.13551469 as archive

editorialbot commented 1 week ago

Done! archive is now 10.5281/zenodo.13551469

logological commented 1 week ago

@editorialbot set v1.0.0 as version

editorialbot commented 1 week ago

Done! version is now v1.0.0

logological commented 1 week ago

@editorialbot generate pdf