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[REVIEW]: daiR: an R package for OCR with Google Document AI #3538

Closed whedon closed 2 years ago

whedon commented 3 years ago

Submitting author: @Hegghammer (Thomas Hegghammer) Repository: https://github.com/Hegghammer/daiR Version: v0.9.2 Editor: @Nikoleta-v3 Reviewers: @cjbarrie , @geraintpalmer Archive: 10.5281/zenodo.5792037

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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.

Status

status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/b627ff1a4da50b1103c6eb5e0042cefd/status.svg)](https://joss.theoj.org/papers/b627ff1a4da50b1103c6eb5e0042cefd)

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

@cjbarrie & @shivam11, 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 @Nikoleta-v3 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 ✨

Review checklist for @cjbarrie

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @geraintpalmer

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @cjbarrie , @shivam11 it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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whedon commented 3 years ago

Wordcount for paper.md is 832

whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.42 s (95.7 files/s, 12700.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               15            685            824           2077
Markdown                         5             88              0            269
YAML                             5             34              2            247
Rmd                              6            287            483            216
TeX                              1              9              0             72
JSON                             7              0              0              7
CSS                              1              0              0              6
-------------------------------------------------------------------------------
SUM:                            40           1103           1309           2894
-------------------------------------------------------------------------------

Statistical information for the repository 'a672765447dcfee3eff150cd' was
gathered on 2021/07/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
hegghammer                       2           484            484          100.00

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

OK DOIs

- 10.31235/osf.io/6zfvs is OK
- 10.33011/computel.v1i.345 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

👋🏼 @Hegghammer @cjbarrie @shivam11 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#3538 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 👍🏻 😄

whedon commented 3 years ago

:wave: @shivam11, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

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

cjbarrie commented 3 years ago

Apologies for the delay--I am currently on leave and will return to complete this review in a week's time

Nikoleta-v3 commented 3 years ago

Thank you for letting me know @cjbarrie 😃 enjoy your leave!

cjbarrie commented 3 years ago

I am almost finished with my review. A few comments follow. The only check box remaining is the community guidelines, which I don't see on the Github Repo. The remainder of my comments pertain to the software paper. This is a great package and it deserves its place in JOSS.

Nikoleta-v3 commented 3 years ago

👋 @Hegghammer. This is just a little nudge 📳 Did you get a chance to look over the reviewer's comments?

Hegghammer commented 3 years ago

Thanks for the message and thanks to Chris Barrie for great comments. I've been swamped, unfortunately, but I will make the changes in the next few days. Best Thomas

On Wed, 25 Aug 2021 at 11:17, Nikoleta Glynatsi @.***> wrote:

👋 @Hegghammer https://github.com/Hegghammer. This is just a little nudge 📳 Did you get a chance to look over the reviewer's comments?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3538#issuecomment-905328366, or unsubscribe https://github.com/notifications/unsubscribe-auth/APNW4GXZZK4VTXZ6V7JN6E3T6SYJPANCNFSM5A7SRXHA .

Nikoleta-v3 commented 3 years ago

Not a problem @Hegghammer! Thank you for the update 😄

Hegghammer commented 3 years ago

Thanks for your understanding. I have now addressed all of @cjbarrie https://github.com/cjbarrie's comments, pushed the changes to the repository, and checked that the paper compiles. Best, Thomas

On Sat, 28 Aug 2021 at 10:06, Nikoleta Glynatsi @.***> wrote:

Not a problem @Hegghammer https://github.com/Hegghammer! Thank you for the update 😄

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3538#issuecomment-907591239, or unsubscribe https://github.com/notifications/unsubscribe-auth/APNW4GXXNMSCN6HIZVLZSELT7CKJXANCNFSM5A7SRXHA .

Nikoleta-v3 commented 3 years ago

commit: https://github.com/Hegghammer/daiR/commit/8061e439cd5eace1664cc72b40f844c05e5df2f3

Nikoleta-v3 commented 3 years ago

@whedon generate pdf

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

👋 @shivam11 & @cjbarrie, could you please update me on how your reviews are going 😄

cjbarrie commented 3 years ago

👋 @shivam11 & @cjbarrie, could you please update me on how your reviews are going 😄

Apologies for the delay on this! I am happy with how everything now looks and recommend acceptance.

Nikoleta-v3 commented 3 years ago

Fantastic. Thank you for your review and your time @cjbarrie!

Nikoleta-v3 commented 3 years ago

👋🏻 @shivam11 📳 Any updates on your review?

Nikoleta-v3 commented 3 years ago

Hey @shivam11 👋🏻 sorry for the repeated pings, I'll wait one more week and then start to seek out another reviewer. Hope all is ok :)

Nikoleta-v3 commented 3 years ago

@whedon remove @shivam11 as reviewer

whedon commented 3 years ago

OK, @shivam11 is no longer a reviewer

Nikoleta-v3 commented 3 years ago

@whedon add @geraintpalmer as reviewer

whedon commented 3 years ago

OK, @geraintpalmer is now a reviewer

Nikoleta-v3 commented 3 years ago

👋🏼 @geraintpalmer this is the review thread for the paper. Thank you for agreeing to review this submission!

You have a 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#3538 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 👍🏻 😄

Nikoleta-v3 commented 2 years ago

👋🏻 @geraintpalmer 📳 Any updates on your review?

cjbarrie commented 2 years ago

@Nikoleta-v3 may I suggest as an alternative reviewer Will Hanley (@whanley) who I know has experience of using dair and will be able to review speedily. He has told me in principle he's open to reviewing. I only suggest this as I'm conscious that this has review process has been stalling a while now since I reviewed and I wanted to help it along.

Nikoleta-v3 commented 2 years ago

Hey @cjbarrie 😄 Thank you so much for your suggestion and for taking the time to suggest a second reviewer!

I have spoken with @geraintpalmer and I know that he is currently reviewing the paper. So the submission should be moving forward very soon.

I am a new editor and I hadn’t thought of asking you (or someone who has completed their review) for suggestions in case the other reviewer dropped out. That’s something I will be doing in the future so sure. Thank you again! 🙏🏻

cjbarrie commented 2 years ago

Thanks @Nikoleta-v3! And good to hear this is progressing :)

geraintpalmer commented 2 years ago

Nearly done with the review, sorry for the delay.

@Hegghammer which License do you use? It looks a little bare, is it one listed here: https://opensource.org/licenses/alphabetical ?

Hegghammer commented 2 years ago

Thanks for reviewing! The license is MIT as per the description file, with the license file serving as a supplement. I'm not a specialist on licenses, so I don't know if it's ideal, but I've seen several other packages do it this way. Best Thomas

On Thu, 16 Dec 2021 at 21:50, Geraint Palmer @.***> wrote:

Nearly done with the review, sorry for the delay.

@Hegghammer https://github.com/Hegghammer which License do you use? It looks a little bare, is it one listed here: https://opensource.org/licenses/alphabetical ?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3538#issuecomment-996184099, or unsubscribe https://github.com/notifications/unsubscribe-auth/APNW4GSW2KEFWZ3H57UH6WDURJGJDANCNFSM5A7SRXHA . You are receiving this because you were mentioned.Message ID: @.***>

geraintpalmer commented 2 years ago

Thanks @Hegghammer, I'm not a license expert either, but I usually see the text of the licence copy and pasted into the LICENSE file which makes things much clearer. E.g https://github.com/jquery/jquery/blob/main/LICENSE.txt

Thanks, happy to accept the review then.

Hegghammer commented 2 years ago

That is a good suggestion which I will gladly incorporate. I will edit the LICENCE file accordingly. Many thanks for everyone's time and best wishes for the holidays. Best, Thomas

On Fri, 17 Dec 2021 at 00:14, Geraint Palmer @.***> wrote:

Thanks @Hegghammer https://github.com/Hegghammer, I'm not a license expert either, but I usually see the text of the licence copy and pasted into the LICENSE file which makes things much clearer. E.g https://github.com/jquery/jquery/blob/main/LICENSE.txt

Thanks, happy to accept the review then.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3538#issuecomment-996266332, or unsubscribe https://github.com/notifications/unsubscribe-auth/APNW4GWWDJPRNTH4UXT55O3URJXHDANCNFSM5A7SRXHA . You are receiving this because you were mentioned.Message ID: @.***>

Nikoleta-v3 commented 2 years ago

@whedon check references

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

OK DOIs

- 10.31235/osf.io/6zfvs is OK
- 10.33011/computel.v1i.345 is OK

MISSING DOIs

- None

INVALID DOIs

- None
Nikoleta-v3 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:

Nikoleta-v3 commented 2 years ago

Thank you very much for your patience @Hegghammer! Everything looks good 👍🏻

One minor comment regarding the point:

Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Could you please add a Contributing file to the project's repository?

Here is an example from the last submission I was handling: https://github.com/mscroggs/symfem/blob/main/CONTRIBUTING.md.

After you added the file could you:

I can then move forward with accepting the submission

Hegghammer commented 2 years ago

Dear Nikoleta,

Many thanks for your message. The sample Contributing file was very useful.

I have now:

I checked the Zenodo metadata to the best of my ability, but wasn't entirely sure how you like the title etc to be formatted, so just let me know if I should change anything.

Thanks again for considering my submission. I remain at your disposal for any further requests or questions.

Best, Thomas

On Sun, 19 Dec 2021 at 13:08, Nikoleta Glynatsi @.***> wrote:

Thank you very much for your patience @Hegghammer https://github.com/Hegghammer! Everything looks good 👍🏻

One minor comment regarding the point:

Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Could you please add a Contributing file to the project's repository?

Here is an example from the last submission I was handling: https://github.com/mscroggs/symfem/blob/main/CONTRIBUTING.md.

After you added the file could you:

  • Make a new tagged release of your software (only if necessary, the current tag is v.0.9.1 ), and list the version tag of the archived version here.
  • Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
  • Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
  • Please list the DOI of the archived version here.

I can then move forward with accepting the submission

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3538#issuecomment-997381040, or unsubscribe https://github.com/notifications/unsubscribe-auth/APNW4GRMHF5TUYS3NHINLJTURXDK3ANCNFSM5A7SRXHA . You are receiving this because you were mentioned.Message ID: @.***>

Nikoleta-v3 commented 2 years ago

Thank you @Hegghammer ! The CONTRIBUTING.md & CODE_OF_CONDUCT.md look great 😄

Nikoleta-v3 commented 2 years ago

@whedon set 10.5281/zenodo.5792037 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5792037 is the archive.

Nikoleta-v3 commented 2 years ago

@whedon set v0.9.2 as version

whedon commented 2 years ago

OK. v0.9.2 is the version.

Nikoleta-v3 commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2837

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2837, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true