[REVIEW]: corporaexplorer: an R package for dynamic exploration of text collections

whedon commented 5 years ago

Submitting author: @kgjerde (Kristian Lundby Gjerde) Repository: https://github.com/kgjerde/corporaexplorer Version: 0.5.1 Editor: @leouieda Reviewer: @kbenoit, @trinker Archive: 10.5281/zenodo.3239136

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/63b0c40585cd7bdf601f9ac9138642ae"><img src="http://joss.theoj.org/papers/63b0c40585cd7bdf601f9ac9138642ae/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/63b0c40585cd7bdf601f9ac9138642ae/status.svg)](http://joss.theoj.org/papers/63b0c40585cd7bdf601f9ac9138642ae)

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) 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

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

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

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @leouieda know.

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

Review checklist for @kbenoit

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: 0.5.1
[x] Authorship: Has the submitting author (@kgjerde) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] 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

Software paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @trinker

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: 0.5.1
[x] Authorship: Has the submitting author (@kgjerde) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] 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

Software paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

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:

kgjerde commented 5 years ago

Last change in pdf:

Manually added one case of hyphenation of package name
replaced 'highlighted text' with 'pattern matches highlighted'.

kgjerde commented 5 years ago

@leouieda Is there any action required on my part at the moment?

leouieda commented 5 years ago

@kgjerde I apologize for letting this hang for so long. Both reviewers have ticked all review boxes. I'll have a final look at the paper first and then we can move on to acceptance.

leouieda commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.1080/19312458.2017.1387238 is OK
- 10.1126/science.1167742 is OK

MISSING DOIs

- None

INVALID DOIs

- None

leouieda commented 5 years ago

@kgjerde the paper looks good to me so we're ready to move this forward. Before accepting, you'll need to:

Release a new version with the changes made after the review (please post the version number here)
Archive a copy of source code for this new version on Zenodo and post the DOI for the archive here.

Please don't hesitate to contact me if you have questions or need any help with this.

kgjerde commented 5 years ago

@whedon generate pdf

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:

kgjerde commented 5 years ago

@leouieda Great!

Please note that I now corrected some very few title capitalisation/formatting issues in https://github.com/kgjerde/corporaexplorer/commit/78d40ef and https://github.com/kgjerde/corporaexplorer/commit/284d6d1.
I have updated the version number. The version is now 0.5.1.
The Zenodo DOI is http://doi.org/10.5281/zenodo.3239136 (see https://zenodo.org/record/3239136).

~~2. I have updated the version number. The version is now 0.5.0.~~

~~3. The Zenodo DOI is http://doi.org/10.5281/zenodo.3239097 (see https://zenodo.org/record/3239097).~~

leouieda commented 5 years ago

@whedon set 0.5.1 as version

whedon commented 5 years ago

OK. 0.5.1 is the version.

leouieda commented 5 years ago

@whedon set 10.5281/zenodo.3239136 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.3239136 is the archive.

leouieda commented 5 years ago

@whedon generate pdf

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:

leouieda commented 5 years ago

@kgjerde thanks for the updates. I've done a last pass of the paper and we're ready to accept :fireworks:

leouieda commented 5 years ago

:wave: @openjournals/joss-eics this submission is ready for acceptance

arfon commented 5 years ago

@whedon accept

whedon commented 5 years ago

Attempting dry run of processing paper acceptance...

whedon commented 5 years ago


OK DOIs

- 10.1080/19312458.2017.1387238 is OK
- 10.1126/science.1167742 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/752

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/752, 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 5 years ago

@whedon accept deposit=true

whedon commented 5 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 5 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 5 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/753
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01342
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

arfon commented 5 years ago

@kbenoit, @trinker - many thanks for your reviews here and to @leouieda for editing this submission ✨

@kgjerde - your paper is now accepted into JOSS :zap::rocket::boom:

whedon commented 5 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01342/status.svg)](https://doi.org/10.21105/joss.01342)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01342">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01342/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01342/status.svg
   :target: https://doi.org/10.21105/joss.01342

This is how it will look in your documentation:

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kgjerde commented 5 years ago

Great news!

@leouieda, thank you for following up my submission so attentively. @trinker and @kbenoit, thank you for your highly useful reviews. @arfon, thank you for stepping in and swiftly addressing my paper layout issues. In sum, thanks to all of you for such a friendly and inspiring review process!

arfon commented 5 years ago

@whedon accept

whedon commented 5 years ago

Attempting dry run of processing paper acceptance...

whedon commented 5 years ago


OK DOIs

- 10.1080/19312458.2017.1387238 is OK
- 10.1126/science.1167742 is OK

MISSING DOIs

- None

INVALID DOIs

- None

leouieda commented 5 years ago

@kgjerde congratulations on the publication! Many thanks to @kbenoit and @trinker for the reviews and @arfon for handling the PDF troubles.

openjournals / joss-reviews