Open editorialbot opened 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
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.5281/zenodo.50550 is OK
MISSING DOIs
- None
INVALID DOIs
- https://doi.org/10.1016/j.cageo.2016.11.008 is INVALID because of 'https://doi.org/' prefix
Software report:
github.com/AlDanial/cloc v 1.88 T=0.08 s (563.6 files/s, 114036.2 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 27 1621 2512 3549
Fortran 77 1 164 98 608
YAML 5 27 4 130
reStructuredText 6 81 21 123
Markdown 2 21 0 45
DOS Batch 1 8 1 26
TOML 1 3 0 25
TeX 1 2 0 16
make 1 4 7 9
-------------------------------------------------------------------------------
SUM: 45 1931 2643 4531
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 539
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Dear @alizma and @KParas, please read the first couple of comments in this thread and create your review checklist if not done already. You can read the reviewer guidelines here. Also, you can browse the closed "REVIEW" issues on the "joss-reviews" repository to get some ideas on how to complete the reviews. Good luck!
@prashjha How do we verify this checkpoint in case there seem to be no commits from an author but?
"Does the full list of paper authors seem appropriate and complete?"
Does JOSS also require/recommend an author contribution section like some other journals?
@KParas, good point. You can ask the author, @tmfrln, for clarification. While the "Contributions" section is not mandatory, as a reviewer, you can request authors to have one in the draft.
Hi @alizma, Could you please update how the review is progressing? I see that you have not yet created a checklist. I would appreciate it if you could get started soon. 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:
Hi everyone, we added a contributions section to the paper to address the question @KParas asked. If you need any additional information please let me know. We also fixed an invalid doi for one of the references.
Hi @tmfrln, could you add a CONTRIBUTING.md file that discusses "guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support"?
Also I know the dependencies are minimal, but nevertheless, these should be listed somewhere in the Installation section of your documentation, and ideally also provided as a requirements.txt
or equivalent for completeness sake.
Also @prashjha, could you suggest how I should confirm end-to-end functionality of the provided examples if I do not have access to Abaqus?
Hi @alizma,
I added the file that you requested to the repository.
The dependencies are indeed minimal, only numpy is required to run Paraqus. This dependency is specified in the file pyproject.toml (without a version number, since we are not aware of a specific requirement). The python interpreter shipped with Abaqus has numpy preinstalled, and if Paraqus is installed standalone via pip, numpy should be automatically installed also. I updated the documentation with this information as well, but think that a requirements.txt would conflict with the pyproject.toml.
Hi @tmfrln, could you add a CONTRIBUTING.md file that discusses "guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support"?
Also I know the dependencies are minimal, but nevertheless, these should be listed somewhere in the Installation section of your documentation, and ideally also provided as a
requirements.txt
or equivalent for completeness sake.Also @prashjha, could you suggest how I should confirm end-to-end functionality of the provided examples if I do not have access to Abaqus?
@alizma, it looks like the library comes with the Abaqus-produced files to test the scripts. You do not need to run Abaqus to test this library. The authors do provide instructions to reproduce the Abaqus output file in case anyone is interested. But for the review, you can assume that the Abaqus output file is given and the scripts work as intended. @tmfrln, does it sound right?
@prashjha The library is split up in two parts: The vtk writers and a general data model are independent of Abaqus and can be used/tested in any python environment. The second part is supposed to be run in Abaqus and implements the interface of the Abaqus database to the data model. So for some of the examples, Abaqus in indeed required to test them. One of the main ideas of this package is to export results from Abaqus once, and have them in a format that can be shared with people who do not use Abaqus afterwards. If this would be helpful, i could offer to showcase the Abaqus-related examples on a zoom call or similar. I am however not sure if that is ok with JOSS's requirements for peer review. If the group of @KParas has access to Abaqus, maybe it would be an option for him to share if the examples worked for him?
@KParas, could you please provide an update on your review? Thanks!
Hi @KParas, please provide an update on your review. It has been too long, and we need to speed up the review, please. There are a lot of items remaining in your checklist.
@alizma, could you please provide an update on your review? Thanks!
@prashjha Due to some unforeseen helath issues and othe commitments, it did not go as planned. To be realistic, I will be able to finish the review until January end, in case it still suits you. My sincere appologies for the delay and inconvenience caused.
Hi @KParas, thank you for letting me know. I sincerely hope everything gets sorted out. Yes, January end will work but it has to be a hard deadline. Please let me know if this is acceptable.
Dear @alizma and @KParas, we are running significantly behind, and I would greatly appreciate it if you could finish the review soon. Please share the update and realistic timeline by which you could finish the reviews. Again, I appreciate your help in reviewing this submission.
Hi, @alizma and @KParas. We are now significantly behind schedule. I have not heard from both of you, and you have ignored my pings. Please let me know if you can complete the reviews. It is unfair to the authors that the review has been stuck for so long.
Hi @prashjha, could you give us a small update since the review process got stuck for some time now?
Dear @prashjha, the last update on the review was already one year ago in September 2023. This seems quite a long time to me. When can we expect the review process to be finished?
Submitting author: !--author-handle-->@tmfrlm<!--end-author-handle-- (Tim Furlan) Repository: https://github.com/tmfrln/paraqus Branch with paper.md (empty if default branch): joss-submission Version: v1.0.0 Editor: !--editor-->@prashjha<!--end-editor-- Reviewers: @alizma, @KParas Archive: Pending
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
@alizma & @KParas, 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 @prashjha 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 @KParas
📝 Checklist for @alizma