Closed editorialbot closed 9 months ago
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
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Software report:
github.com/AlDanial/cloc v 1.88 T=0.12 s (1540.0 files/s, 220803.4 lines/s)
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Language files blank comment code
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PHP 137 1923 2111 12447
PO File 3 1080 1562 2413
JavaScript 11 54 187 1147
CSS 2 220 14 1022
TypeScript 30 81 642 917
Markdown 3 419 0 644
JSON 1 0 0 183
YAML 1 1 4 18
INI 1 0 0 10
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SUM: 189 3778 4520 18801
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 574
@luxaritas, @koenedaele – This is the review thread for the paper. All of our communications will happen here from now on.
Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing (in a new comment on this thread):
@editorialbot generate my checklist
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 https://github.com/openjournals/joss-reviews/issues/5661
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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Hi @jmotis, I'm one of the reviewers having a look at your software. I'll conduct the review by creating issues in your repository to keep this thread clean as requested by JOSS.
I have reviewed the Software Paper and started on some of the documentation. I will be away for a bit. When I get back I'll have a further look at the documentation and the software itself.
Hi all, sorry for the delay on my end! Starting to work my way through this, and Koen has already filed some good issues.
@jmotis Since you do not appear to be a frequent committer to the codebase, can you describe your role as a contributor to the project? Additionally, I note Kim Nguyen as one of the larger committers to the project but is not a listed author, and I want to verify whether lack of authorship there is appropriate.
This was a grant-funded project. I was the PI (along with Lincoln Mullen as co-PI) and did a lot of different things: project management and reporting, developing the required feature set, consulting and testing throughout the development of the module, documentation, and outreach. Kim was invited to be on the paper but didn't join us.
Just finished my first pass, and this looks really solid! Kudos on the thorough documentation especially. Only one additional thing came up in what I saw beyond what Koen already called out.
Thanks both of you for your time and feedback. I've put a link in the readme.md to the external project website where we collected the concrete case studies and tutorials (vs. the abstracted documentation in the GitHub repository) and we'll tidy up the bibliography and add the CONTRIBUTING.md file.
Thanks for the update @jmotis.
@luxaritas, @koenedaele – could you take a look and see how much of your checklist can now be updated based on the recent changes from the authors?
Currently unable to continue review due to chnm/Datascribe-module#136. Could you handle this one first?
I have concluded my review. I have found the software to function as indicated. Being new to Omeka S, I had to learn about both Omeka S and Datascribe. I am especially pleased with the detailed documentation of the module. Congratulations on the authors, writing documentation is never an easy task.
I have created some minor issues that could be solved. I am aware the module only functions for the previous version of Omeka S, but I assume that's not an issue for JOSS (I have no information indicating it is). I do hope the module is updated to the newer version sooner or later.
Currently I'm awaiting a newer version of the paper with proper references, before I sign off on that last aspect. Once the citations are properly formatted, I'm ok with this paper.
Just did one more pass and agree, references is the only remaining thing to be resolved
Great, thanks for the updates @luxaritas & @koenedaele. @jmotis – please let us know when you've had a change to address the last outstanding items here.
Friendly reminder to check back in here @jmotis and update us on your progress making changes.
I'd hoped to have a coauthor pitch in here, but it looks like that's not going to be possible. I'm moving the last action item onto my to-do list and will try to finish it up soon.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@arfon @luxaritas @koenedaele I've addressed and closed the two outstanding issues (a documentation tweak and reformatting the paper's bibliography properly) and regenerated the PDF (please look at the second article proof not the one I did an hour ago). I think that's everything.
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- None
MISSING DOIs
- None
INVALID DOIs
- None
I'm noticing that a number of the references are showing up with just a date or even multiple non-disambiguated instances of n.d.
. Looking at prior JOSS papers, it is very rare that no author is listed on a reference, even for websites (in which case you'd typically use some variation on the copyright holder, site owner, responsible organization, etc). I don't know what JOSS preferences/standards on this are
Also for Tesseract, it may be preferable to use one of the citations listed in https://github.com/tesseract-ocr/tesseract/blob/main/CITATIONS.bib? Also not sure here what typical convention is since you're not referring to one of the papers specifically and they don't appear to list a specific preference
@luxaritas The multiple (n.d.)s are because the citation is referenced in line and you're just getting the date parenthetically after it. E.g. a "Smith (2018) talks about" style reference. I agree, though, it looks a little odd all coming in a row in the same sentence.
The goal of the software citations was to point readers to existing software websites/downloads, so people reading the article can go look at other software options we comped against. I didn't want to clutter up the text with non-hyperlinked URLs in parentheses. If there's some other way JOSS would like those displayed, I'm happy to add additional information/formatting. I could also remove those references if people think that's better, as they're not quite references in the traditional sense.
Right - what Im wondering is if you can add reasonable authors to those citations. Other JOSS papers appear to do this, even when there aren't specific named authors like there are for papers or articles
I can try to add some corporate authorships in and see if that works better.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@jmotis – looks like we're very close to being done here. I will circle back here next week, but in the meantime, please give your own paper a final read to check for any potential typos etc.
After that, 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:
Looks good to me. Haven't found any typos in the final paper.
Looks good to me as well
DOI: 10.5281/zenodo.10379756
The PDF looks good to me and I don't see any typos either. Thank you @koenedaele & @luxaritas for reviewing this for us!
@editorialbot set 10.5281/zenodo.10379756 as archive
Done! archive is now 10.5281/zenodo.10379756
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- None
MISSING DOIs
- 10.1093/jahist/jaad098 may be a valid DOI for title: American Religious Ecologies
INVALID DOIs
- None
:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.
Element cYear: This element is not expected.
Element cYear: This element is not expected.
Element cYear: This element is not expected.
@jmotis – I don't think the BibTeX entries with multiple year values are valid (e.g., https://github.com/chnm/Datascribe-module/blob/JOSS/paper.bib#L82). Please could you correct those three entries to only have a single year value?
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- None
MISSING DOIs
- 10.1093/jahist/jaad098 may be a valid DOI for title: American Religious Ecologies
INVALID DOIs
- None
:wave: @openjournals/dsais-eics, this paper is ready to be accepted and published.
Check final proof :point_right::page_facing_up: Download article
If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4883, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
Submitting author: !--author-handle-->@jmotis<!--end-author-handle-- (Jessica Otis) Repository: https://github.com/chnm/Datascribe-module Branch with paper.md (empty if default branch): JOSS Version: v1.1.0 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @luxaritas, @koenedaele Archive: 10.5281/zenodo.10379756
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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
@luxaritas & @koenedaele, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arfon 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 ✨
Checklists
📝 Checklist for @luxaritas
📝 Checklist for @koenedaele