Closed whedon closed 2 years ago
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Software report (experimental):
github.com/AlDanial/cloc v 1.88 T=0.11 s (767.7 files/s, 176938.5 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 16 957 1426 2095
Jupyter Notebook 21 0 10037 1772
reStructuredText 33 917 1000 637
TeX 2 28 0 231
HTML 6 15 0 193
Markdown 1 26 0 88
YAML 2 15 16 43
DOS Batch 1 8 1 27
CSS 1 4 4 13
INI 1 5 0 13
make 1 4 6 10
-------------------------------------------------------------------------------
SUM: 85 1979 12490 5122
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Statistical information for the repository '05048cb517afec299ab5068e' was
gathered on 2021/06/23.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
Domen Ocepek 4 517 8 0.71
Francesco Trainotti 2 48 260 0.42
Locke-D-A 3 1340 706 2.78
Miha 3 1 63 0.09
Tomaž BRegar 3 86 8 0.13
Tomaž Bregar 112 33908 32986 90.79
d.ocepek 1 23 6 0.04
mihakodric 17 807 457 1.72
mihapogacar 3 255 149 0.55
tb93 3 2018 31 2.78
Below are the number of rows from each author that have survived and are still
intact in the current revision:
Author Rows Stability Age % in comments
Domen Ocepek 511 98.8 2.7 15.07
Francesco Trainotti 24 50.0 2.6 0.00
Locke-D-A 2 0.1 12.0 0.00
Miha 1 100.0 0.2 0.00
Miha Kodrič 366 100.0 4.7 3.01
Tomaž Bregar 3365 9.9 12.4 14.56
mihapogacar 209 82.0 0.2 11.96
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- None
MISSING DOIs
- 10.1016/j.ymssp.2017.12.003 may be a valid DOI for title: System equivalent model mixing
- 10.21105/joss.01450 may be a valid DOI for title: PyVista: 3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK)
- 10.2514/1.33274 may be a valid DOI for title: General Framework for Dynamic Substructuring: History, Review and Classification of Techniques
- 10.1016/j.ymssp.2015.08.004 may be a valid DOI for title: General framework for transfer path analysis: History, theory and classification of techniques
- 10.1016/j.ymssp.2019.106440 may be a valid DOI for title: Including directly measured rotations in the virtual point transformation
- 10.4271/720093 may be a valid DOI for title: A combined experimental and analytical procedure for improving automotive system dynamics
- 10.2514/6.1984-941 may be a valid DOI for title: Combined Experimental/Analytical Modelling using component modes synthesis
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
:wave: @ngoiz @LolloCappo @Gunnstein @tb93 The actual review will take place in this issue.
Each reviewer has a separate checklist at the top, which they can work through; our reviewer guidelines may also be helpful. General comments and feedback can be given as comments in this issue, and if appropriate reviewers can open issues on the software repository.
Thanks again!
@tb93 while the reviewers begin their work, it looks like your article is missing DOIs for some/all references. Please add those when you get a chance.
Thank you @kyleniemeyer for your remark regarding the missing DOIs, we updated the references.
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
:wave: @ngoiz, please update us on how your review is going (this is an automated reminder).
:wave: @Gunnstein, please update us on how your review is going (this is an automated reminder).
Hello,
I have now gone through the review process for pyFBS
.
First, let me congratulate you for the tool, it is simple to use, provides great functionality and is technically very complete. In particular, let me praise the quality of the example jupyter notebooks and the effort that has gone into creating those. For a new user to the code, they are immensely helpful.
As part of my review, I only have minor comments related to the following items:
autoref{fig:3D}
which is not rendering properly.Other than that, I enjoyed going through your tool and again, well done on the examples.
Thanks, Norberto
👋 @kyleniemeyer - How is this review going?
@ngoiz thank you for your comments!
@tb93 As you can see above, @ngoiz left a few comments/suggestions for you. Can you please address these?
@Gunnstein have you been able to review this submission?
Dear Kyle
@ngoiz thank you for your comments!
@tb93 As you can see above, @ngoiz left a few comments/suggestions for you. Can you please address these?
@Gunnstein have you been able to review this submission?
Dear @kyleniemeyer,
I am working on the review now. I am not able to edit the review list, the link for review invitation is not valid, can you send a new one?
Best regards, Gunnstein
@whedon re-invite @Gunnstein as reviewer
OK, the reviewer has been re-invited.
@gunnstein please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations
@Gunnstein thanks for the update. If you click that link your invitation should be reactivated.
Dear all,
The package is a unique open source project in dynamic substructuring and is an important contribution to engineers and researchers in dynamics and the open source community. The overall design of the package is intuitive and it follows well established coding practice which makes it easy to understand and contribute to the project. The package also has concise documentation with useful examples that help new users evaluate and to start applying the software.
Comments associated with review:
Automated tests and Community guidelines:
References:
A comment on security:
Several examples (and provided example data?), tests and the MCK module use pickle for data storage/caching. Pickling represents a security issue where arbitrary code can be executed at load time. Practically it makes it challenging to maintain the package as any contribution on these elements are potential security risks. It will also stop certain users adopting the package entirely.
Since many of the users of this package may not be familiar with the security issue, a notification is appropriate in the docstring of methods/functions and at the top of example notebooks. It also seems like pickling can be avoided entirely in case of the MCK module since the data objects are essentially arrays and vectors which can readily be stored without pickling.
Best regards, Gunnstein
Thank you for this review @Gunnstein!
Hello @tb93, we now have a complete set of reviews, and a few items for you to address before accepting your submission. Are you able to address / work on these things?
Hey @kyleniemeyer, we are working on it. We will try to finalise all the outlined points as fast as possible.
Dear all,
sorry for the late response from our side. We have overhauled our documentation site, where we also added new examples and use-cases of the whole package.
Paper The mishandled reference was corrected.
Contributing We have added a detailed Contribute section within documentation.
Testing Instructions about testing were added in the Contribute section.
Installation With the current version, Python 3.8 should be used and the PyPi installation works without any problem. Nevertheless, we should be able to support Python 3.9 in the upcoming release.
Pickle issue A warning was added to the documentation - . However, in long term we already have a plan to implement hdf file format instead of pickle for file saving.
Best regards, Tomaž
Dear @kyleniemeyer, what is the next step in the revision of the joss submission? We updated the documentation of the package.
Sincerely, Tomaž
@tomazbregar sorry about that, I missed your update due to the end of our fall term and the holidays. I will review your updates.
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Hi @tomazbregar, I have reviewed your changes and I believe you have addressed the outstanding concerns.
I just submitted a PR for your paper that fixes some reference formatting and a few minor typos, can you please merge this? https://gitlab.com/pyFBS/pyFBS/-/merge_requests/15
Once you have merged this, please archive your repository (using Zenodo or Figshare) and provide the DOI here.
Hey @kyleniemeyer, thank you for finalizing the review. I merged your PR, thank you for this.
I have archived the current version of the repository - https://zenodo.org/record/5863174.
@whedon generate pdf
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@tomazbregar it looks like the authors associated with the Zenodo archive do not match those in the paper. Normally, these two author lists should be the same. Can you check this?
Hey @kyleniemeyer, you are correct. When we started to write the paper, we only had a limited team developing the package (3 PhDs studends), and now the team expanded, but we did not change the paper. How do you commonly handle those things?
@tomazbregar totally understandable, especially since this review has taken so long.
If the new team members have contributed to work that is reflected in the work considered here, in the version of the software that was reviewed and will be published, then they should be added to the author list of the paper. Since the Zenodo archive should only contain the latest version of the software that has been reviewed, usually these lists should match, and the paper author list be updated to reflect the newer work.
If your software has newer work that was not reviewed, then I would ask that you instead upload a snapshot of the repository that reflects the reviewed version, and have the Zenodo author list match.
It also looks like the last three authors on the paper are missing from the Zenodo archive—they should be added either way.
Thanks!
Hey @kyleniemeyer, thank you for the explanation. We made quite a lot of changes to the software, since we first started to write the paper. Therefore, we also included the new members in the Joss paper. The updated version is already on master branch and I also uploaded the new archive to zenodo (doi number down bellow). Now the authors match on the repository and on the joss paper.
@tomazbregar great, thanks
@whedon generate pdf
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@whedon set 10.5281/zenodo.5876734 as archive
OK. 10.5281/zenodo.5876734 is the archive.
@whedon accept
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@whedon recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1016/j.ymssp.2017.12.003 is OK
- 10.21105/joss.01450 is OK
- 10.2514/1.33274 is OK
- 10.1016/j.ymssp.2015.08.004 is OK
- 10.1016/j.ymssp.2019.106440 is OK
- 10.4271/720093 is OK
- 10.2514/6.1984-941 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.
Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2896
If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2896, then you can now move forward with accepting the submission by compiling again with the flag deposit=true
e.g.
@whedon accept deposit=true
@whedon accept deposit=true
Doing it live! Attempting automated processing of paper acceptance...
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Congratulations @tb93 on your article's publication in JOSS, and thank you for your patience for such a long journey!
Many thanks to @ngoiz, @LolloCappo, and @Gunnstein for reviewing this submission.
Submitting author: @tb93 (Tomaž Bregar) Repository: https://gitlab.com/pyFBS/pyFBS Version: 0.1.1 Editor: @kyleniemeyer Reviewer: @ngoiz, @LolloCappo, @Gunnstein Archive: 10.5281/zenodo.5876734
:warning: JOSS reduced service mode :warning:
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Review checklist for @ngoiz
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Review checklist for @Gunnstein
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