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[REVIEW]: PyLithics: A Python package for stone tool analysis #3738

Closed whedon closed 2 years ago

whedon commented 3 years ago

Submitting author: @JasonGellis (Jason Gellis) Repository: https://github.com/alan-turing-institute/Palaeoanalytics Version: v1.0.0 Editor: @Nikoleta-v3 Reviewer: @MichaelHoltonPrice , @steko Archive: 10.5281/zenodo.5898149

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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

@MichaelHoltonPrice & @steko , please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @MichaelHoltonPrice

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @steko

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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Software paper

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @MichaelHoltonPrice , @steko it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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whedon commented 3 years ago

Wordcount for paper.md is 1151

whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (179.3 files/s, 166854.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              1              0              1          13109
Python                           8            496            561            861
Markdown                         4            156              0            501
TeX                              1              5              0             91
YAML                             3              4              0             36
-------------------------------------------------------------------------------
SUM:                            17            661            562          14598
-------------------------------------------------------------------------------

Statistical information for the repository '8456365535258f8c256f4453' was
gathered on 2021/09/19.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Camila Rangel Smith              3           301            301            6.68
Jason Gellis                     1           140              0            1.55
JasonGellis                      6           175              8            2.03
crangelsmith                   167          4042           2628           74.03
jasongellis                      5           708            707           15.70

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Camila Rangel Smith           5            1.7          0.7                0.00
crangelsmith               1676           41.5          3.4               11.16
jasongellis                 237           33.5          1.6               12.24
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

-  10.25080/Majora-92bf1922-00a  is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 3 years ago

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

Nikoleta-v3 commented 3 years ago

👋🏼 @JasonGellis @MichaelHoltonPrice @steko this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements 🔝 As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#3738 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@Nikoleta-v3 ) if you have any questions/concerns 👍🏻 😄

steko commented 3 years ago

@Nikoleta-v3 are the steps we have taken so far (specific issues that were addressed by the authors) the good way to move forward with the review?

Nikoleta-v3 commented 3 years ago

Yup @steko 👍🏻

Working your way through the checklist and opening issues if you think that the paper hasn't filled the requirements is exactly what we want.

If you feel that some points require more discussion feel free to share your thoughts and comments here, and also feel free to share your overall thoughts about the paper.

I hope I have answered your question 😄

whedon commented 3 years ago

:wave: @MichaelHoltonPrice , please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @steko , please update us on how your review is going (this is an automated reminder).

Nikoleta-v3 commented 3 years ago

@whedon re-invite @MichaelHoltonPrice as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

@michaelholtonprice please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

Nikoleta-v3 commented 3 years ago

👋🏻 @MichaelHoltonPrice and @steko! please update us on how your review is going 😄

MichaelHoltonPrice commented 3 years ago

@steko and I have raised some issues that, speaking for myself at least, need to be addressed before finishing the review. None are major, but they do prevent me from marking some items in the checklist.

Nikoleta-v3 commented 3 years ago

Thank you for the reply @MichaelHoltonPrice! My bad, sorry, I didn’t see the issues 👍🏻 😄

JasonGellis commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #3738 with the following error: 

 Error reading bibliography file paper.bib:
(line 12, column 17):
unexpected "e"
expecting space or ","
Looks like we failed to compile the PDF
Nikoleta-v3 commented 2 years ago

👋🏻 @JasonGellis whedon failed to compile the pdf because of an error in the bib file. Can you please tweak the file?

JasonGellis commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

JasonGellis commented 2 years ago

@Nikoleta-v3 The bib file has been fixed and the PDF can be generated. I have also addressed all issues raised by @steko and @MichaelHoltonPrice and merged them into the main branch of the repo.

JasonGellis commented 2 years ago

@Nikoleta-v3 Hello, what is the next step please?

Nikoleta-v3 commented 2 years ago

@JasonGellis 👋🏻 We are going to give the reviewers some time to go over your corrections. Once they are happy with how you addressed their comments and they recommend the paper for publication I will also have a final look. Then we should be good to go 👍🏻 😄

steko commented 2 years ago

Hi, and apologies for the delay. I still have two comments about the paper that aren't specific to any of the checks but I think would help improve the quality and clarity of the final version.

  1. be more explicit not only about the input images that work well, but also about the drawing styles that don't work - in my experience a lot of lithics drawings have more details than just the outline of scars and your tool does a good job but not optimal, e.g.

sanremo1

sanremo1_lithium_scars

  1. the JSON output is incredibly rich but not documented in the paper, you should at least inlcude what is now in output_example.md file already in the repository - and maybe give some example of how to process the JSON data for further analysis?
JasonGellis commented 2 years ago

@steko @MichaelHoltonPrice @Nikoleta-v3 Thank you for your feedback. While differences in drawing styles are addressed in greater detail on the README.md of the repo, we agree that it belongs in the paper too, and this has been added.

We agree that that an example output of the JSON file should be included, and a new figure has been added (Figure 5). However, we feel that further discussion of how the data should be processed and analysed should be left to the user and does not belong in this paper. Metric output data and surface identification data are included in (current) figures 2 and 3. We feel that the addition of the JSON file to these two figures will adequately inform users/readers of the type of data PyLithics will produce.

All requests have been updated and merged to the main branch

steko commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

steko commented 2 years ago

Looks good to me!

JasonGellis commented 2 years ago

@steko @Nikoleta-v3 Great! What are the next steps on my end?

Nikoleta-v3 commented 2 years ago

👋🏻 @JasonGellis. Nothing to do on your end. We are currently waiting on @MichaelHoltonPrice to also review your changes :)

JasonGellis commented 2 years ago

@Nikoleta-v3 thanks Nikoleta!

Nikoleta-v3 commented 2 years ago

Hey @JasonGellis thank you for your patience. I have reached out to the reviewer via email. I have seen that you have addressed their comments but I would like to wait a little bit more from them to confirm the changes.

Some minor comments from me:

JasonGellis commented 2 years ago

@Nikoleta-v3 I will get right on this.

JasonGellis commented 2 years ago

Happy New Year @Nikoleta-v3 I have addressed the above issues and merged into main. Can I request a new editor as @MichaelHoltonPrice has not been in contact since October.

MichaelHoltonPrice commented 2 years ago

Apologies, the notifications are not always informative (e.g., I don't think you realized I was waiting for updates from your team on such things as the test script for some time). Nikoleta let me know that the manuscript was ready for me again Dec 19th but I have been on vacation since then (and still am). I can complete my review by the end of next week.

On Tue, Jan 4, 2022 at 8:43 AM Jason Gellis @.***> wrote:

Happy New Year @Nikoleta-v3 https://github.com/Nikoleta-v3 I have addressed the above issues and merged into main. Can I request a new editor as @MichaelHoltonPrice https://github.com/MichaelHoltonPrice has not been in contact since October.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3738#issuecomment-1004918572, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEGORL4GTQBX4EDGIGD5AD3UUMIR5ANCNFSM5EKP7ILA . You are receiving this because you were mentioned.Message ID: @.***>

Nikoleta-v3 commented 2 years ago

Thank you for the update @MichaelHoltonPrice and enjoy the rest of your holiday.

Nikoleta-v3 commented 2 years ago

Hey @JasonGellis 👋🏻 MichaelHoltonPrice opened three last issues. They made it clear that they recommend the article for publication and that these issues are not sufficient to hold up publication of the article.

Nevertheless, I would you like you to address issue #167 and issue #169. Issue 169 is similar to my comment which I can see you addressed by including information regarding Travis in the README file. Could you also include guidelines on how one can run the tests locally on their machines before pushing on GitHub?

Nikoleta-v3 commented 2 years ago

@whedon generate pdf

Nikoleta-v3 commented 2 years ago

@whedon check references

whedon commented 2 years ago

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

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

OK DOIs

- 10.25080/Majora-92bf1922-00a is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.7717/peerj.453 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- 10.1093/bib/5.3.305 may be a valid DOI for title: Digital code of life : how bioinformatics is revolutionizing science, medicine, and business

INVALID DOIs

- None
Nikoleta-v3 commented 2 years ago

👋🏻 @JasonGellis. The missing DOI that whedon is recommending is the DOI to a review of the book. So please ignore the message (feel free to also check).

Anyway, everything looks good to me!

At this point could you:

I can then move forward with accepting the submission.

JasonGellis commented 2 years ago

Hi @Nikoleta-v3 I'm a bit unclear. 1) The version is still v1.0 so we'll keep that. 2) What am I supposed to archive on Zenodo - a copy of the repo? A pdf of the paper? 3) I understand this. 4) Will the zenodo DOI be different from the one provided by JOSS?

Nikoleta-v3 commented 2 years ago
  1. 👍🏻
  2. Please archive the repository! In case you are not familiar, Zenodo and Github work quite nicely together (Referencing and citing content). You can create an archive by selecting the repo and a tagged release. I can see that you haven't made a tagged release of the software on GitHub: your releases. Please make one and name it v1.0.0 then use that one to archive the software.
  3. 👍🏻
  4. The Zenodo DOI will be different from the JOSS one. The Zenodo archive will appear with your paper under the Software Archive tab. An example paper: https://joss.theoj.org/papers/10.21105/joss.03937.

This is to ensure that an archived version of the software at the time that it was published exists 😄 Please let me know if you have any further questions, and I would be more than happy to assist you with Zenodo etc if you come across any issues!

p.s. regarding Referencing and citing content. I am sure that even if you have a Zenodo account already you can link it with your GitHub account.

JasonGellis commented 2 years ago

Hi @Nikoleta-v3 1) The software has been tagged v1.0.0 2) The repo/software are now archived on Zenodo 3) The metadata on Zenodo is correct 4) https://zenodo.org/badge/latestdoi/303727518

Nikoleta-v3 commented 2 years ago

@whedon set 10.5281/zenodo.5897149 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5897149 is the archive.

Nikoleta-v3 commented 2 years ago

@whedon set v1.0.0 as version

whedon commented 2 years ago

OK. v1.0.0 is the version.

Nikoleta-v3 commented 2 years ago

@whedon recommend-accept