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[REVIEW]: Distant Viewing Toolkit: A Python Package for the Analysis of Visual Culture #1800

Closed whedon closed 4 years ago

whedon commented 5 years ago

Submitting author: @statsmaths (Taylor Arnold) Repository: https://github.com/distant-viewing/dvt Version: v0.3.0 Editor: @arfon Reviewer: @jgonggrijp, @elektrobohemian Archive: 10.5281/zenodo.3614034

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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

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

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arfon know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @jgonggrijp

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @elektrobohemian

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 5 years ago

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

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whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

arfon commented 5 years ago

@jgonggrijp, @elektrobohemian - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Any questions/concerns please let me know.

arfon commented 5 years ago

@whedon remind @elektrobohemian in three weeks

whedon commented 5 years ago

Reminder set for @elektrobohemian in three weeks

whedon commented 4 years ago

:wave: @elektrobohemian, please update us on how your review is going.

arfon commented 4 years ago

@jgonggrijp, @elektrobohemian - it doesn't look like you've made any progress on your reviews here. Do you think you could complete them in the next two weeks?

jgonggrijp commented 4 years ago

@arfon In my case, that was to be expected. As I mentioned in the pre-review, I wouldn't be able to start before yesterday in any case.

I'll try to do the review within the next two weeks.

arfon commented 4 years ago

@arfon In my case, that was to be expected. As I mentioned in the pre-review, I wouldn't be able to start before yesterday in any case.

Apologies @jgonggrijp - I failed to read back up the issue to see this.

I'll try to do the review within the next two weeks.

Perfect, thanks!

arfon commented 4 years ago

@elektrobohemian - could you give us an ETA on your review?

jgonggrijp commented 4 years ago

@arfon I'm a bit delayed. I'm trying to finish upcoming Friday, 29. November.

arfon commented 4 years ago

@elektrobohemian - could you give us an ETA on your review?

I just emailed @elektrobohemian to ask them to give us an update on their review.

statsmaths commented 4 years ago

Hi everyone. I know things get slowed down around the winter holidays, but wanted to check in now that things are starting to pick up again. I answered some issues that @jgonggrijp opened in the dvt repository, but had not seen anything since then.

If there are any issues people are running into, please let us know. If additional reviewers are needed I can try to recommend someone. Thanks again for everyone's help!

arfon commented 4 years ago

Thanks for the update @statsmaths. I've also heard back over email from @elektrobohemian that they should be starting their review imminently.

jgonggrijp commented 4 years ago

@statsmaths @arfon Just letting you know that this is still on my agenda. I hope to continue (and preferably finish) this Friday.

jgonggrijp commented 4 years ago

@statsmaths @arfon I completed my review. I just opened three new issues (referenced right above this post), one of which is acceptance-blocking in my opinion (https://github.com/distant-viewing/dvt/issues/17) and one of which I'm not sure whether it should be acceptance-blocking or not (https://github.com/distant-viewing/dvt/issues/16). The latter might or might not be due to “limited options” being an euphemism for “no options”.

The third issue (https://github.com/distant-viewing/dvt/issues/15) is definitely non-blocking as far as I'm concerned. The package can be accepted with this issue still open.

statsmaths commented 4 years ago

@jgonggrijp Thanks for all of the really helpful comments. I pushed three commits that should resolve the three issues that you opened.

statsmaths commented 4 years ago 
@whedon generate pdf
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

jgonggrijp commented 4 years ago

@statsmaths Welcome. dvt is a very interesting and well-documented package. @arfon I see no blockers after the above fixes by @statsmaths.

elektrobohemian commented 4 years ago

I really like the software and the documented installation process as it is very mature. This is why I tried to install the software without relying on my background language. Hence, all opened issues are non-blocking as far as I am concerned. I took a basic Ubuntu 18.04.3 LTS installation and tried to solve all issues by copy-and-pasting all occuring issues. Under Mac OS, I tried to run everything in a zsh environment.

Besides the issues discussed in the dvt project, I would suggest to extend the paper a little. As the paper als addresses layperson users, you would like to be a little more informative regarding the local web server section. I guess that not all DH researches might be familiar with the Java script-related security policies of all browsers.

I strongly recommend the dvt package for publication. My minor issues could be resolved after publication.

elektrobohemian commented 4 years ago

for the sake of completeness, the Mac OS values:

data data_left data_right 0 -1108 -1113 -1103 1 -1546 -1552 -1539 2 -1123 -1121 -1125 3 -1007 -1008 -1006 4 -1258 -1262 -1253 And frame_start frame_end rms 0 0 50 917.916747 1 50 200 1208.046528 2 200 220 997.259411

arfon commented 4 years ago

@elektrobohemian - many thanks for your feedback here! As you work through the checklist could you please be sure to tick the checkboxes at the top of the issue?

elektrobohemian commented 4 years ago

done.

arfon commented 4 years ago

@statsmaths - looks like this is getting pretty close to being accepted here 😄. Can you confirm that you've made all of the changes you planned to based on the feedback from @jgonggrijp & @elektrobohemian?

statsmaths commented 4 years ago

Thanks @elektrobohemian for all of the helpful feedback. I just pushed responses that resolve three of the four issues you opened. The only one still open is the issue with the web application on macOS, as I cannot replicate it on my mac (it currently runs on Firefox, Safari and Chrome for me). Not sure if that's blocking for the publication or not.

@arfon, other than a potential fix to the web server issue all of the changes have been made at this point.

elektrobohemian commented 4 years ago

regarding the web server: no, it's not as @jgonggrijp couldn't replicate it neither. at least in my opinion.

regarding the Ubuntu/virtualenv issue I wouldn't consider this blocking either as it would only happen to layperson users which might also not rely on a Ubuntu LTS. a layperson would prefer Anaconda IMHO. As said above, I was only checking these scenarios as everything else worked so fine.

arfon commented 4 years ago

@whedon accept

whedon commented 4 years ago

No archive DOI set. Exiting...

arfon commented 4 years ago

@statsmaths - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

I can then move forward with accepting the submission.

statsmaths commented 4 years ago

@arfon Great. Here is the DOI of the updated package. Thanks again to everyone!

DOI

arfon commented 4 years ago

@whedon set 10.5281/zenodo.3614034 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3614034 is the archive.

arfon commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1093/digitalsh/fqz013 is OK
- 10.22148/16.043 is OK

MISSING DOIs

- https://doi.org/10.1007/978-3-319-54226-3_5 may be missing for title: Task-driven programming pedagogy in the digital humanities
- https://doi.org/10.1109/fg.2018.00020 may be missing for title: Vggface2: A dataset for recognising faces across pose and age
- https://doi.org/10.1007/3-540-45103-x_50 may be missing for title: Two-frame motion estimation based on polynomial expansion
- https://doi.org/10.5749/movingimage.18.1.0080 may be missing for title: Building a Crowdsourcing Platform for the Analysis of Film Colors
- https://doi.org/10.1109/fg.2017.82 may be missing for title: Face detection with the faster R-CNN
- https://doi.org/10.1109/tsp.2015.7296366 may be missing for title: Color image (dis) similarity assessment and grouping based on dominant colors
- https://doi.org/10.1007/978-3-030-04212-7_44 may be missing for title: Recurrent RetinaNet: A Video Object Detection Model Based on Focal Loss
- https://doi.org/10.1109/cvpr.2015.7298682 may be missing for title: Facenet: A unified embedding for face recognition and clustering
- https://doi.org/10.1109/saner.2017.7884606 may be missing for title: Code of conduct in open source projects
- https://doi.org/10.1093/llc/fqy085 may be missing for title: The visual digital turn: Using neural networks to study historical images

INVALID DOIs

- None
whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1238

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1238, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
arfon commented 4 years ago

@statsmaths - could you check if any of the DOIs that Whedon has found are correct? If they are, please go ahead and add them to your bibtex file (without the https://doi.org/ preamble).

arfon commented 4 years ago

@statsmaths - I think this PR is correct too: https://github.com/distant-viewing/dvt/pull/22

statsmaths commented 4 years ago

Okay, merged PR and put all the DOIs into the bibles file.

arfon commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago

PDF failed to compile for issue #1800 with the following error:

W, [2020-01-20 21:37:53#804] WARN -- : Lexer: unbalanced braces at 403; brace level 0; mode :literal. /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/bibtex_parser.rb:45:in block in generate_citations': undefined methodkey' for # (NoMethodError) from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.0.1/lib/bibtex/bibliography.rb:149:in each' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.0.1/lib/bibtex/bibliography.rb:149:ineach' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/bibtex_parser.rb:41:in generate_citations' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/compilers.rb:245:incrossref_from_markdown' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/compilers.rb:21:in generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:95:incompile' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:79:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

arfon commented 4 years ago

@statsmaths - think this unmatched } is causing things to blow up: https://github.com/distant-viewing/dvt/blob/master/paper/paper.bib#L4

statsmaths commented 4 years ago

Yes, you are right (for some reason my pandoc compiled anyway). Fixed in 5f880da.

arfon commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1093/digitalsh/fqz013 is OK
- 10.22148/16.043 is OK
- 10.1007/978-3-319-54226-3_5 is OK
- 10.1109/fg.2018.00020 is OK
- 10.1007/3-540-45103-x_50 is OK
- 10.5749/movingimage.18.1.0080 is OK
- 10.1109/fg.2017.82 is OK
- 10.1109/tsp.2015.7296366 is OK
- 10.1007/978-3-030-04212-7_44 is OK
- 10.1109/cvpr.2015.7298682 is OK
- 10.1109/saner.2017.7884606 is OK
- 10.1093/llc/fqy085 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1239

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1239, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true