Closed editorialbot closed 1 year ago
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Software report:
github.com/AlDanial/cloc v 1.88 T=0.05 s (363.7 files/s, 45068.6 lines/s)
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Markdown 2 46 0 183
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 807
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.21105/joss.01181 is OK
- 10.21105/joss.01943 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
I have left the following two issues on the main repository:
https://github.com/mzabrams/fars-cleaner/issues/1 https://github.com/mzabrams/fars-cleaner/issues/2
Hi @ethanwhite - how is your review coming along? Thanks.
@svburke I've addressed one of those two issues, and I am examining the other (mzabrams/fars-cleaner#1) -- I'm not sure why this is the behavior on windows and not on macOS, but I am trying to assess ways of importing the full dataset without running into the out-of-memory error on a 16GB setup. Further thoughts/progress will be addressed in the issue on the project repository as I work through it.
Overall things look good. I've opened 4 issues in the fars-cleaner repo related to installation, documentation, functionality, and community guidelines, all of which are linked above.
Hi @mzabrams - how is the work progressing on the reviewer comments?
@majensen I've made some progress on these -- two issues remain open, one may need to be closed with a note made to system requirements to run the package (there seems to be a Windows-based issue that I've been unable to resolve to this point, potentially based on the way Windows handles memory usage compared to macOS and Linux systems), and I'm working on fixing the packaging for download from conda/conda-forge. Hopefully by the end of the week I'll have all this sorted!
@majensen All but one of the relevant issues have been closed -- regarding issue mzabrams/fars-cleaner#3, the package is available for download via conda and pip, but is awaiting review by the conda-forge team to be accessed through that channel. Not sure what the timeline is for that team to move things on, but I think I've addressed everything else raised by @svburke and @ethanwhite
Thanks @mzabrams - I'll do my editorial review of the paper itself (usu. pretty minor comments)- hope I can do it this weekend. Then the final steps to prep for the recommendation to the EIC are pretty rapid.
@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 check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.21105/joss.01181 is OK
- 10.21105/joss.01943 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@mzabrams - I like this software a lot, it is the kind of work that increases the usability of siloed data; I hope it goes viral and energizes your field. 2 very minor items: 1) Can you put the Statement of Need section just after the Summary; 2) can you add links to your proceedings in the refs. I see, for example, this link is available: http://www.ircobi.org/wordpress/downloads/irc22/pdf-files/2212.pdf.
After doing the above, can you create an open archive of your code repo, using Zenodo, FigShare or similiar? A short tutorial using Zenodo is here. When this is done, please post the DOI you receive back in this thread. Thanks!
@majensen Thanks! I think I'd already set it up with Zenodo -- DOI for the most recent release version (1.3.3) is 10.5281/zenodo.7221282. I've made those additions to the references (there isn't a publicly available repository of World Congress of Biomechanics Proceedings, unfortunately), and moved the statement of need as well. Let me know if there's anything else! I appreciate the kind words about this project!!
@editorialbot check references
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.21105/joss.01181 is OK
- 10.21105/joss.01943 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Thanks @mzabrams - on the archive, JOSS prefers the archive name to be the name of the paper verbatim, and the archive authors to include all the paper authors. Would you be willing to change the title and author metadata on your current archive? Or alternatively, create a one-off archive that meets those desirables?
@majensen I'll get the archive renamed with the underscore'd name this afternoon (may take a bit, as it will require a rename on PyPi as well, which is for the best as the conda and pip package names apparently differ -- I seem to have made a mistake there somewhere as pip is fars-cleaner
and conda is fars_cleaner
). Re: author metadata, currently Dr. Bass is an author on the paper (he is my PhD advisor), but not in the code metadata as he will not be a maintainer or responsible for correspondence/support/maintenance of the package in the future. Happy to make that change if it is the preference of the JOSS team, though
Thanks @mzabrams - yeah, I've seen several pip packages where the dash is used in the name, but the package comes in with an underscore in code. Not sure that's a big problem, might be automatically translated even. If you're ok putting your supervisor's name in the archive, then let's go ahead - might save a little editor-in-chief overhead.
Sounds good -- I'll go ahead and do that! You're right it's not the biggest deal, just personally I think I'd like the pip/conda packages to have the same name to avoid future confusion with installation (although I'll look into whether that gets automatically translated).
Just need to add the name to pyproject.toml
? Or any other locations?
Dr. Bass is an author on the paper (he is my PhD advisor), but not in the code metadata as he will not be a maintainer or responsible for correspondence/support/maintenance of the package in the future. Happy to make that change if it is the preference of the JOSS team, though
@mzabrams - in cases like this we have included them as authors in the Zenodo archive (via a .zenodo.json
file; which is what JOSS wants) but not listed them in setup.py, pypi, etc. I think this both allows the software paper and repo to match the author line while not implying direct code contributions (or ability to serve as a maintainer).
I'll look into whether that gets automatically translated
For the record, it appears pip automatically gets the same package whether I run pip install fars_cleaner
or pip install fars-cleaner
Should be solved now -- the Zenodo DOI for the most recent version is 10.5281/zenodo.7249980
The DOI for all versions is 10.5281/zenodo.3735486
@editorialbot set 10.5281/zenodo.7249980 as archive
Done! Archive is now 10.5281/zenodo.7249980
@editorialbot set v1.3.5 as version
Done! version is now v1.3.5
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.21105/joss.01181 is OK
- 10.21105/joss.01943 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:wave: @openjournals/sbcs-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/3649, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
@mzabrams - fyi, we're waiting for the @openjournals/sbcs-eics (the editors-in-chief for this JOSS track, whom I just there cleverly pinged again) to do their final review.
@majensen Thanks for that update -- let me know if theres anything else you all need from me at this point!
:wave: @openjournals/sbcs-eics and maybe @arfon ...
@editorialbot accept
Doing it live! Attempting automated processing of paper acceptance...
🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨
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Apologies it took a little while to get this one wrapped up.
@ethanwhite, @svburke – many thanks for your reviews here and to @majensen for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨
@mzabrams – your paper is now accepted and published in JOSS :zap::rocket::boom:
:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:
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We need your help!
The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
Submitting author: !--author-handle-->@mzabrams<!--end-author-handle-- (Mitchell Abrams) Repository: https://github.com/mzabrams/fars-cleaner Branch with paper.md (empty if default branch): Version: v1.3.5 Editor: !--editor-->@majensen<!--end-editor-- Reviewers: @ethanwhite, @svburke Archive: 10.5281/zenodo.7249980
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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
@ethanwhite & @svburke, 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 @majensen 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
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