Closed whedon closed 5 years ago
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Attempting PDF compilation. Reticulating splines etc...
seems all right to me. Thanks at @sgrieve and @ixjlyons for being willing to review this package. Looking forward to your feedbacks!
Ok, my review is complete. Nice work @Chilipp!
Overall, straditize appears to be in excellent shape. Aside from a couple installation issues (filed against the target repository), all of the review criteria appear to me to be met. Beyond those, the code looks clean and well-written. I'm not all that familiar with digitization, but adding to the kinds of plots that can be "reverse-engineered" definitely seems worthwhile. The paper conveys that sentiment well and summarizes the package adequately. The documentation looks good standalone, but it shines inside the actual GUI and the integration with the tutorials is excellent.
Once the two installation issues I ran into are addressed, I recommend this submission be accepted.
Dear @ixjlyons, thank you very much for your time and your helpful feedback! I already implemented the suggested changes will merge them soon.
Hi @Chilipp, @yochannah Below is my review, as noted below I have also opened an issue in the straditize repo regarding the tests.
Firstly I would like to thank the author for this contribution. I have been very impressed by the quality of the software presented here, as well as it's potential utility to a wide range of users across disciplines. I am happy to recommend publication, pending the resolution of the issues outlined below.
I am performing this review on MacOS Sierra 10.12.6, and found no problems with the conda install as outlined in the documentation. However, one thing I did note is that the quick install instructions on the GitHub readme does not recommend installing in a separate virtual environment. I feel that installing into a virtual environment as the default quickstart install option is probably better than potentially causing problems in someones base environment.
I had the same problem as @ixjlyons when trying to install via pip and from source, that I needed to manually install PyQt
. It seems that you have already addressed this, but I just wanted to highlight that it was an issue on my environment as well.
Having worked through the tutorials I am happy to confirm that straditize works as described. More generally, I believe that this will be a significant tool for scientists in a range of disciplines, and the way that the software has been designed suggests to me that it will be straightforward to add more diagram types to straditize in future based on community need.
I am very impressed by the level and quality of the documentation, in particular the integration of the documentation and tutorials into the GUI. Aside from the broken links mentioned elsewhere in this review, I noted a typo on the first line of this section: https://straditize.readthedocs.io/en/latest/installing.html#running-the-tests
We us
should be We use
.
I just wanted to put a note here that your contribution/community guidelines are excellent. I will return to these the next time I have to write some for one of my projects. As above, I noted some broken links, but these have all been addressed in PR 7.
I have not been able to get the tests to pass on my machine. I have opened an issue to outline this further: https://github.com/Chilipp/straditize/issues/8
It may be useful to add some detail of what a user can expect when running these tests, for example the number of tests that will be run, what does a successful test run look like, are any tests skipped, the approximate duration of the tests.
The paper is very well written and clearly outlines the scientific problem the author is trying to address, as well as how straditize specifically addresses these issues. The format of the paper follows the general JOSS style, and I believe that all of the relevant literature and materials have been correctly cited.
In conclusion, I have thoroughly enjoyed the experience of reviewing this paper and would like to commend the author for their diligent work to address a pressing concern in our field. I am hoping to introduce this tool to some of my students in the future and look forward to using it in my own research. :rocket:
Wow, thanks @ixjlyons and @sgrieve for your thorough reviews, and @Chilipp for acting on the feedback so swiftly!
@sgrieve @Chilipp let me know when you two have managed to resolve the testing issue and are ready to go ahead! π
Dear @yochannah, @sgrieve and @ixjlyons,
thank you very much for your nice words, helpful feedbacks and the reported issues. I apologize for the inconveniences with pip and also with the tests @sgrieve. Unfortunately I have no good methodology to test such a GUI-based application. The unittest framework requires creating and closing lot's of widgets which produces quite some overhead (this especially causes problems on the CI services with very limited RAM, such as OSX on Travis). I would like to address these problems first before merging the suggested changes. But this should be done by Monday.
Dear @yochannah, @sgrieve and @ixjlyons,
thanks again for all the input and your fast responses! All reported issues (https://github.com/Chilipp/straditize/issues/1, https://github.com/Chilipp/straditize/issues/2, https://github.com/Chilipp/straditize/issues/3, https://github.com/Chilipp/straditize/issues/4 and https://github.com/Chilipp/straditize/issues/8) are closed and from my side, I am ready to make a new release with a fresh DOI. Is this okay for you?
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@whedon check references
Attempting to check references...
OK DOIs
- http://doi.org/10.1109/MCSE.2007.55 is OK
- http://doi.org/10.21105/joss.00363 is OK
- http://doi.org/10.7717/peerj.453 is OK
- http://doi.org/10.1016/j.quascirev.2007.04.007 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Okay, I've given it a finalish proofread and the text looks great π― . One strange thing I noted is that the figure appears in the middle of the reference section though - @arfon any idea what is up?
@sgrieve and @ixjlyons, y'all each have one checkbox left unticked. If you're happy to accept, can you check those boxes and make a comment once you're done?
@Chilipp Once those last two checkboxes are complete, please do make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive! It's probably worth giving the manuscript a final proofread if you feel you need to, as well. π
Thanks all, it's been really positive watching this all come together! π₯
@arfon any idea what is up?
@yochannah - this is standard LaTeX image layout issues. If the authors make this change the image placement is better: https://github.com/Chilipp/straditize/pull/9
Thanks @arfon! The PR has been merged.
@whedon generate pdf
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@yochannah I checked the last box assuming @Chilipp will make a release on PyPI soon based on the recent fixes so pip install straditize
Just Works™ per the installation instructions. Should a new release be made before getting a DOI?
@yochannah I've checked the final box, after the issue in the straditize repo was closed I forgot to do it...
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@Chilipp okay, looking good - one last thing before we accept - can you make sure the Zenodo archive title is the same as the paper title? Thanks!
@whedon set v0.1.1 as version
OK. v0.1.1 is the version.
@Chilipp okay, looking good - one last thing before we accept - can you make sure the Zenodo archive title is the same as the paper title? Thanks!
All right, done
@whedon set 10.5281/zenodo.2565036 as archive
OK. 10.5281/zenodo.2565036 is the archive.
@openjournals/joss-eics - we're ready to accept this one!! π π
@Chilipp Thanks for your great work on this package and fantastic collaboration with the reviewers.
@sgrieve @ixjlyons Thank you for your fantastic and in-depth reviews.
Thank you very much @yochannah and especially @sgrieve and @ixjlyons for your helpful inputs! I am very glad that everything worked out so well π
@whedon accept
Attempting dry run of processing paper acceptance...
OK DOIs
- http://doi.org/10.1109/MCSE.2007.55 is OK
- http://doi.org/10.21105/joss.00363 is OK
- http://doi.org/10.7717/peerj.453 is OK
- http://doi.org/10.1016/j.quascirev.2007.04.007 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/501
If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/501, then you can now move forward with accepting the submission by compiling again with the flag deposit=true
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@whedon accept deposit=true
@whedon accept deposit=true
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@ixjlyons, @sgrieve - many thanks for your reviews and to @yochannah for editing this submission β¨
@Chilipp - your paper is now accepted into JOSS :zap::rocket::boom:
:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:
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Submitting author: @Chilipp (Philipp S. Sommer) Repository: https://github.com/Chilipp/straditize Version: v0.1.1 Editor: @yochannah Reviewer: @ixjlyons, @sgrieve Archive: 10.5281/zenodo.2565036
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