Closed editorialbot closed 1 year 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:
@editorialbot generate pdf
Software report:
github.com/AlDanial/cloc v 1.88 T=0.19 s (673.5 files/s, 76798.1 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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Python 66 2064 3281 4749
Markdown 7 130 0 419
reStructuredText 29 345 345 325
TeX 1 23 0 209
Bourne Shell 10 84 146 208
Jupyter Notebook 2 0 1638 158
YAML 6 15 15 107
DOS Batch 1 8 1 26
Dockerfile 1 7 7 18
make 1 4 7 9
HCL 1 4 4 6
TOML 1 0 0 6
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SUM: 126 2684 5444 6240
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1255
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.48550/arxiv.2206.11927 is OK
- 10.1093/mnras/stab2093 is OK
- 10.48550/arXiv.1110.3193 is OK
- 10.1093/mnras/stz2816 is OK
- 10.48550/ARXIV.1603.04467 is OK
- 10.1017/S1743921319008615 is OK
- 10.1017/pasa.2022.55 is OK
- 10.1038/nature14539 is OK
- 10.48550/ARXIV.2302.05442 is OK
- 10.48550/ARXIV.2104.10972 is OK
- 10.5281/zenodo.4414861 is OK
- 10.5281/zenodo.3828935 is OK
- 10.48550/ARXIV.1711.10604 is OK
- 10.48550/ARXIV.2303.00366 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:
@crhea93 thanks again for agreeing to review this submission! When you get a chance, please generate your reviewer checklist by replying to this thread with the comment
@editorialbot generate my checklist
Then, please read through the submission and update your checklist as you feel is appropriate. Let me know if you have any questions!
The authors is missing references in the software paper.
The requirements file is incorrectly formatted. There is also no reference to the requirements.txt file in the installation.
@crhea93 thanks for reviewing the software! For issues that should be addressed as part of the review, please open issues on the upstream repository. Thanks!
@editorialbot commands
Hello @crhea93, here are the things you can ask me to do:
# List all available commands
@editorialbot commands
# Get a list of all editors's GitHub handles
@editorialbot list editors
# Check the references of the paper for missing DOIs
@editorialbot check references
# Perform checks on the repository
@editorialbot check repository
# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist
# Set a value for branch
@editorialbot set joss-paper as branch
# Generates the pdf paper
@editorialbot generate pdf
# Generates a LaTeX preprint file
@editorialbot generate preprint
# Get a link to the complete list of reviewers
@editorialbot list reviewers
@plaplant Should the issues have a specific template? I can't find one in the JOSS documentation.
Hi @crhea93. Thanks for taking the time to review our JOSS submission!
The requirements file is incorrectly formatted. There is also no reference to the requirements.txt file in the installation.
The requirements.txt
file is deprecated (the first line is """Deprecated - see setup.py""" and the entire file is commented out). I will remove it now for clarity. Installation dependencies are instead included via setup.py
, which allows for more configuration (e.g. zoobot[pytorch]
, zoobot[tensorflow]
).
The authors is missing references in the software paper.
Which references are missing? Do you mean missing as in 'should be cited' or 'not linked correctly to bibliography'?
I'm happy to chat directly on here about issues not related to the software itself, or you're welcome to open issues (I don't think a specific structure is required, it's only me reading them ;) )
@crhea93 we do not have an official template, but thanks for checking! Sometimes reviewers make individual issues for each point they'd like addressed, and others make a single large "laundry list" issue. Either is fine, but my take is that having a separate issue for each point to be addressed can help keep the discussion more focused within the thread (and can potentially be addressed/fixed with multiple PRs).
In either case, you can link to the upstream issue(s) in this thread so everyone here can see the outstanding hurdles to acceptance. Thanks again for taking time to review!
Hi reviewers @devanshkv @crhea93. Thank you for your feedback thus far.
I just wanted to highlight a few pieces of code that may be relevant to your remaining checklist items:
@plaplant I've completed my review. I am very impressed with this work and @mwalmsley has cleared up any issues that I had. I recommend this code for publication.
@crhea93 thanks very much for your review!
@devanshkv are there any outstanding issues that you feel need to be addressed prior to publication? If so, please make an issue on the upstream repository and reply to this thread so we're aware. Otherwise, if you feel this is ready for publication, please update your reviewer checklist accordingly. Thanks again for reviewing!
@crhea93, all good from my side.
Great work @mwalmsley! Looking forward to seeing how the community utilizes this. My only suggestion would be to have a more comprehensive test suite. Nevertheless, I recommend this code for publication.
@devanshkv I see that there is still an unchecked item on your checklist about verifying the functional claims of the software. Please update your checklist accordingly if you have done this, or first verify the functionality before checking this box. (Per the JOSS reviewer docs, a review isn't complete until all items of the checklist have been ticked off.) Thanks!
@plaplant apologies, that was left unticked by mistake. All good from my side now.
@devanshkv thanks for the quick response!
@mwalmsley both reviewers have recommended acceptance of the submission, so we can move forward with the final acceptance checks. If the software has changed in the course of the review, please make a new tagged release of the repository. After that, please archive it (on Zenodo, figshare, or some other long-term hosting platform). Once those are done, please post the version number and DOI of the archive in this thread. Let me know if you have any questions!
@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
- 10.48550/arxiv.2206.11927 is OK
- 10.1093/mnras/stab2093 is OK
- 10.48550/arXiv.1110.3193 is OK
- 10.1093/mnras/stz2816 is OK
- 10.48550/ARXIV.1603.04467 is OK
- 10.1017/S1743921319008615 is OK
- 10.1017/pasa.2022.55 is OK
- 10.1038/nature14539 is OK
- 10.48550/ARXIV.2302.05442 is OK
- 10.48550/ARXIV.2104.10972 is OK
- 10.5281/zenodo.4414861 is OK
- 10.5281/zenodo.3828935 is OK
- 10.48550/ARXIV.1711.10604 is OK
- 10.48550/ARXIV.2303.00366 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@mwalmsley looking at the references in the paper, it seems like the reference for Phan et al. does not have a DOI associated with it. For this paper, you can find it here, so please update the reference in paper.bib
accordingly.
Also, it looks like the recommended reference for Pyro is this:
@article{bingham2019pyro,
author = {Eli Bingham and
Jonathan P. Chen and
Martin Jankowiak and
Fritz Obermeyer and
Neeraj Pradhan and
Theofanis Karaletsos and
Rohit Singh and
Paul A. Szerlip and
Paul Horsfall and
Noah D. Goodman},
title = {Pyro: Deep Universal Probabilistic Programming},
journal = {J. Mach. Learn. Res.},
volume = {20},
pages = {28:1--28:6},
year = {2019},
url = {http://jmlr.org/papers/v20/18-403.html}
}
It does not seem like the journal version has a DOI associated with it, but I think this is still the better version to cite (as opposed to the arXiv version). Thanks!
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Thanks for the references note @plaplant. I've added the DOI to Phan et al and updated the Pyro reference to the suggested reference.
I've created a new Zoobot tagged release, 1.0.3, which is versioned on Zenodo here. The all-versions DOI is 10.5281/zenodo.6483175
@mwalmsley thanks for the info!
One last question: I notice that not all of the authors have an ORCID associated with them. Does everyone in the author list who has an ORCID have one listed in the paper metadata? (Note that not all authors need an ORCID, just wanted to make sure they were linked if they had one.) Also, please add author ORCIDs to the Zenodo metadata as well. Thanks very much!
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.48550/arxiv.2206.11927 is OK
- 10.1093/mnras/stab2093 is OK
- 10.48550/arXiv.1110.3193 is OK
- 10.1093/mnras/stz2816 is OK
- 10.48550/ARXIV.1603.04467 is OK
- 10.1017/S1743921319008615 is OK
- 10.1017/pasa.2022.55 is OK
- 10.1038/nature14539 is OK
- 10.48550/ARXIV.2302.05442 is OK
- 10.48550/ARXIV.2104.10972 is OK
- 10.5281/zenodo.4414861 is OK
- 10.48550/arXiv.1912.11554 is OK
- 10.5281/zenodo.3828935 is OK
- 10.48550/ARXIV.1711.10604 is OK
- 10.48550/ARXIV.2303.00366 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@mwalmsley sorry, one last change to the paper references: please include the DOI link for Bommasani et al. (2021). Note that a new version + Zenodo release is not necessary for this, as these archives are for the code rather than the paper. Thanks!
@editorialbot set 10.5281/zenodo.7896025 as archive
Done! archive is now 10.5281/zenodo.7896025
@editorialbot set v1.0.3 as version
Done! version is now v1.0.3
Added DOI for Bommasani, thanks for noting.
On Thu, May 4, 2023 at 8:00 PM The Open Journals editorial robot < @.***> wrote:
Done! version is now v1.0.3
— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5312#issuecomment-1535258805, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB3BY3X37XEUBS2J2C4F5MDXEP4DJANCNFSM6AAAAAAWMUBWTM . You are receiving this because you were mentioned.Message ID: @.***>
Thanks! I think there are just a few outstanding issues:
At that point I think the paper is ready for acceptance. Let me know if you have any questions!
Brilliant, thank you!
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@mwalmsley fantastic! Thanks so much. I think this is ready to go.
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.48550/arxiv.2206.11927 is OK
- 10.1093/mnras/stab2093 is OK
- 10.48550/arXiv.1110.3193 is OK
- 10.1093/mnras/stz2816 is OK
- 10.48550/ARXIV.1603.04467 is OK
- 10.1017/S1743921319008615 is OK
- 10.1017/pasa.2022.55 is OK
- 10.1038/nature14539 is OK
- 10.48550/ARXIV.2302.05442 is OK
- 10.48550/arXiv.2108.07258 is OK
- 10.48550/ARXIV.2104.10972 is OK
- 10.5281/zenodo.4414861 is OK
- 10.48550/arXiv.1912.11554 is OK
- 10.5281/zenodo.3828935 is OK
- 10.48550/ARXIV.1711.10604 is OK
- 10.48550/ARXIV.2303.00366 is OK
MISSING DOIs
- None
INVALID DOIs
- None
The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.
citation bingham2018pyro not found
:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.
IDREFS attribute rid references an unknown ID "ref-bingham2018pyro"
Submitting author: !--author-handle-->@mwalmsley<!--end-author-handle-- (Mike Walmsley) Repository: https://github.com/mwalmsley/zoobot Branch with paper.md (empty if default branch): docs Version: v1.0.3 Editor: !--editor-->@plaplant<!--end-editor-- Reviewers: @crhea93, @devanshkv Archive: 10.5281/zenodo.7896025
Status
Status badge code:
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
@crhea93 & @devanshkv, 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 @plaplant 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 @devanshkv
📝 Checklist for @crhea93