Joss-reviews: [PRE REVIEW]: PINE: An open source collaborative text annotation tool

[whedon]

Submitting author: @brantapl (Brant Chee)
Repository: https://github.com/jhuapl/PINE
Version: v1.0
Editor: @majensen
Reviewers: @bill-baumgartner, @bensonml
Managing EiC: Kevin M. Moerman

: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.

Author instructions

Thanks for submitting your paper to JOSS @brantapl. Currently, there isn't an JOSS editor assigned to your paper.

The author's suggestion for the handling editor is @kakiac.

@brantapl if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

: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.

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2587 with the following error:

Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=1.08 s (505.9 files/s, 103171.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           112           2739            263          30508
JSON                            20              0              0          15380
TeX                             10           3580            792          11272
JavaScript                      21           2452           2464          10236
Python                          70           1632           2247           6872
TypeScript                     133           1393            295           6520
CSS                             34            402             86           1656
YAML                            22             59             80           1320
Bourne Shell                    35            179             45            610
reStructuredText                66           3451           2814            394
Markdown                         8            139              0            330
Dockerfile                       7             99             43            250
Jupyter Notebook                 1              0            404             82
SVG                              1              0              0             59
make                             2             22             12             50
Mustache                         2             13              0             45
DOS Batch                        1              9              1             21
Sass                             1              6              0             13
-------------------------------------------------------------------------------
SUM:                           546          16175           9546          85618
-------------------------------------------------------------------------------


Statistical information for the repository '2587' was gathered on 2020/08/20.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Brant Chee                       1           862              0           21.27
Laura Glendenning                1          3099             78           78.39
brantapl                         5             9              5            0.35

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
Brant Chee                 7925          919.4          0.0               13.15
Laura Glendenning         32170         1038.1          0.0               16.36
brantapl                      9          100.0          1.1              100.00

[Kevin-Mattheus-Moerman]

@whedon generate pdf from branch JOSS

[whedon]

Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...

[whedon]

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

[Kevin-Mattheus-Moerman]

@whedon query scope

[whedon]

Submission flagged for editorial review.

[kthyng]

Hi @kakiac! Are you up for editing another submission? You look like a good fit for this one!

[kthyng]

@whedon invite @kakiac as editor

[whedon]

@kakiac has been invited to edit this submission.

[majensen]

@kthyng I would be happy to edit if @kakiac is unable-

[danielskatz]

@majensen - done, thanks!

[danielskatz]

@whedon assign @majensen as editor

[whedon]

OK, the editor is @majensen

[majensen]

@wdduncan - would you have time and interest to review this work for JOSS? Consideration is much appreciated!

[majensen]

@yongqunh - this is @majensen, we have worked in the KPMP consortium together.
As a Topic Editor for JOSS, I am wondering - would you be willing to perform a software review on this work for the journal?
An overview of the review process is here. Please let me know here in this thread, or feel free to reach out to me at maj -dot- fortinbras -at- gmail -dot- com.
Thanks for considering!

[wdduncan]

@wdduncan - would you have time and interest to review this work for JOSS? Consideration is much appreciated!

@majensen Sorry, I'm going to have to pass on this one. I have too many other reviews in the queue :(

[majensen]

No prob @wdduncan - thanks for reaponding

[majensen]

Hey @tvalerius - I'm a topic editor for the online Journal of Open Source Software, and I was thinking that this work would be right up your alley. Would you be willing to contribute your expertise on a review?
All reviews are open and performed online here in GitHub. Here is an overview of the process. Please respond in this thread, or feel free to reach out to me at _maj -dot- fortinbras -at- gmail -dot- com_, or my NIH address.

Really appreciate your consideration -- @majensen

[majensen]

@rvosa -- long time! I'm an editor now for the online journal JOSS. Would you be willing to review this work? All reviews are open and performed online here in GitHub. Here is an overview of the process. Please respond in this thread, or feel free to reach out to me at maj -dot- fortinbras -at- gmail -dot- com. I really appreciate your consideration --@majensen

[majensen]

@balhoff - can I trouble you again to consider a JOSS review of this work? All my other ontology experts seem to be working hard on their ontologies and I haven't got a bite.... Appreciate your consideration! @majensen

[rvosa]

@rvosa -- long time! I'm an editor now for the online journal JOSS. Would you be willing to review this work? All reviews are open and performed online here in GitHub. Here is an overview of the process. Please respond in this thread, or feel free to reach out to me at maj -dot- fortinbras -at- gmail -dot- com. I really appreciate your consideration --@majensen

Hi @majensen! Nice to hear from you. I'm sorry but I'll have to decline. Things are a bit hectic right now and this project also seems a bit outside of my expertise. Best, Rutger

[majensen]

Thanks for your consideration and quick response @rvosa - nice to hear a ping from you in any case!

[majensen]

Hey @sap218 -- would you have time and inclination to review this work for JOSS? Would love to have your expertise on this.
Thanks! --@majensen

[sap218]

@majensen Hi! Thank you for the invitation :-) I've had a look and I don't understand docker/sys admin enough to do a thorough review - really sorry. Best, Samantha.

[majensen]

@brantapl can you please provide me some suggestions for possible reviewers? Thanks.

[brantapl]

@majensen Thanks for all the help. Do you mean JOSS reviewers or outside of the community? Are their any requirements for reviewers?

[majensen]

@brantapl can be anyone who has some expertise in the field and is willing to do the software testing. Outside the JOSS community is fine, then we can being them in! You can have a look at https://joss.readthedocs.io/en/latest/reviewer_guidelines.html for an overview.

[balhoff]

@majensen sorry, I have to echo Rutger and Bill. :-( But I will email you some suggestions.

[majensen]

@balhoff that would be superb, thanks!

[majensen]

@callahantiff, @balhoff suggested that you would be a good reviewer for JOSS on this work. Would you be willing to provide your expertise? Here is an overview of the reviewing process.
Thanks for your consideration --@majensen

[callahantiff]

@callahantiff, @balhoff suggested that you would be a good reviewer for JOSS on this work. Would you be willing to provide your expertise? Here is an overview of the reviewing process.
Thanks for your consideration --@majensen

Hi @majensen - Thanks for the invitation to review (thanks for recommending me @balhoff). I feel horrible to decline given that it looks like it's been hard to find reviewers, but I am also currently slammed (have 5 reviews due this week) ☹️

I do have a few other people in mind that I think would be very qualified to review this work: @bill-baumgartner, @jmbanda, @mboguslav, @KevinBretonnelCohen, or @jdkim.

Thank you again for the invitation, please keep me in mind for future papers!

[majensen]

Thanks @callahantiff for your response and suggestions! Any of those mentioned, can you ping back on this thread if you are willing to review?

[bill-baumgartner]

Hi @majensen - I'm willing to review this work. Please let me know next steps at your convenience. Thanks - Bill

[majensen]

@bill-baumgartner thanks very much! I will add you as a reviewer now (via our @whedon bot). Once I get a second vic...volunteer, then we will be able to start the review. That will come up as a new GitHub issue. I will shepherd everyone duly.

[majensen]

@whedon assign @bill-baumgartner as reviewer

[whedon]

OK, @bill-baumgartner is now a reviewer

[majensen]

Thanks to my colleague @bensonml who happens to be a NLP expert and a great programmer, we can do this thing!

[majensen]

@whedon add @bensonml as reviewer

[whedon]

OK, @bensonml is now a reviewer

[majensen]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2726.

[majensen]

All, the review has begun in #2726 - please join the conversation there. Thanks