Closed whedon closed 5 years ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @myousefi2016, it looks like you're currently assigned as the reviewer for this paper :tada:.
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Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #1072 with the following error:
% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 15 0 15 0 0 329 0 --:--:-- --:--:-- --:--:-- 333 pandoc-citeproc: reference pfannmoeller2013ees not found pandoc-citeproc: reference vanbavel2009nl not found pandoc-citeproc: reference pfannmoeller2013ees not found pandoc-citeproc: reference proudian2018arXiv not found pandoc-citeproc: reference heiber2018ising4 not found Error producing PDF. ! Missing $ inserted.
@whedon generate pdf from branch joss-edits
Attempting PDF compilation from custom branch joss-edits. Reticulating splines etc...
PDF failed to compile for issue #1072 with the following error:
% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 15 0 15 0 0 320 0 --:--:-- --:--:-- --:--:-- 326 Error producing PDF. ! Missing $ inserted.
@arfon Could you compile the again locally for me from the joss-edits branch? Still not sure why the compilation is failing.
@arfon Could you compile the again locally for me from the joss-edits branch? Still not sure why the compilation is failing.
Sure thing: 10.21105.joss.01072.pdf
@MikeHeiber I'm trying to run the MPI test but I'm getting this error:
[==========] Running 5 tests from 1 test case.
[----------] Global test environment set-up.
[----------] 5 tests from MPI_Test
[ RUN ] MPI_Test.CalculateProbHistAvgTests
test/test_mpi.cpp:46: Failure
Expected equality of these values:
6
(int)prob.size()
Which is: 3
[ FAILED ] MPI_Test.CalculateProbHistAvgTests (0 ms)
[ RUN ] MPI_Test.CalculateVectorAvgTests
test/test_mpi.cpp:68: Failure
Expected equality of these values:
4.5
data_avg[0]
Which is: 0
test/test_mpi.cpp:69: Failure
Expected equality of these values:
5.5
data_avg[1]
Which is: 1
test/test_mpi.cpp:70: Failure
Expected equality of these values:
6.5
data_avg[2]
Which is: 2
[ FAILED ] MPI_Test.CalculateVectorAvgTests (1 ms)
[ RUN ] MPI_Test.CalculateVectorSumTests
test/test_mpi.cpp:83: Failure
Expected equality of these values:
18.0
Which is: 18
data_sum[0]
Which is: 0
test/test_mpi.cpp:84: Failure
Expected equality of these values:
22.0
Which is: 22
data_sum[1]
Which is: 1
test/test_mpi.cpp:85: Failure
Expected equality of these values:
26.0
Which is: 26
data_sum[2]
Which is: 2
test/test_mpi.cpp:94: Failure
Expected equality of these values:
18
data_sum2[0]
Which is: 0
test/test_mpi.cpp:95: Failure
Expected equality of these values:
22
data_sum2[1]
Which is: 1
test/test_mpi.cpp:96: Failure
Expected equality of these values:
26
data_sum2[2]
Which is: 2
[ FAILED ] MPI_Test.CalculateVectorSumTests (0 ms)
[ RUN ] MPI_Test.GatherValuesTests
[ OK ] MPI_Test.GatherValuesTests (0 ms)
[ RUN ] MPI_Test.GatherVectorsTests
test/test_mpi.cpp:151: Failure
Expected equality of these values:
12
(int)data_all.size()
Which is: 3
test/test_mpi.cpp:162: Failure
Expected equality of these values:
12
(int)data_all2.size()
Which is: 3
[ FAILED ] MPI_Test.GatherVectorsTests (0 ms)
[----------] 5 tests from MPI_Test (1 ms total)
[----------] Global test environment tear-down
[==========] 5 tests from 1 test case ran. (1 ms total)
[ PASSED ] 1 test.
[ FAILED ] 4 tests, listed below:
[ FAILED ] MPI_Test.CalculateProbHistAvgTests
5 FAILED TESTS
By the way I baked your code by using OpenMPI/1.10.3 and gcc/6.3.0 and I'm using InfiniBand in our cluster. Any idea or suggestion?
@myousefi2016 Can you file an issue on the Ising_OPV repo with this info and also include the command that you used when running the test. I will take a look and see what the problem is.
(for provenance, that issue is https://github.com/MikeHeiber/Ising_OPV/issues/10)
@katyhuff I'm pretty much done with reviewing this software. @MikeHeiber Really interesting application to generate 3D microstructures. Good job Mike!
I've completed my review. Looks good!
@myousefi2016 and @mdoucet Thanks both for your prompt and thorough reviews! @MikeHeiber thank you for engaging promptly with reviewer comments.
We'll give @stuartcampbell a chance to complete functionality and documentation checks, and then we'll soon have a full slate of reviews.
Should be finished later today
@myousefi2016 The issue you filed due to incorrect testing instructions in the README has been fixed in the latest version on the joss-edits branch. Once all of the reviews are done I'll merge this branch into master and make a final release v4.0.0 for the paper.
Sorry for the delay.
All looks good to me - my review is completed.
One minor suggestion is to consider adding a simple CONTRIBUTING.md
, which could just link to the sections in your README.md
and CODE_OF_CONDUCT.md
- so just to provide a place with a standard name for folks to look. Not essential for this review - just a personal comment.
Thanks @stuartcampbell , @myousefi2016 , @mdoucet for your reviews !
@MikeHeiber thank you for a strong submission and for engaging actively in the review process! It looks like there are just a couple of minor suggestions from @stuartcampbell you might consider as you make your 4.0.0 release. Once you have your code and paper all ready in the release, it'll be good to double check the paper, review any lingering details in your code/readme/etc., and then make an archive of the reviewed software in Zenodo/figshare/other service. When you update this thread with the DOI of the archive, I'll move forward with accepting the submission! Until then, now is your moment for final touchups!
@stuartcampbell Thank you for the suggestion about the contributor instructions file. I had been meaning to add more detailed instructions for how new people could contribute, and your reminder helped give me the activation energy that I needed. There is now both a CONTRIBUTING.md and a CODE_OF_CONDUCT.md file. In addition, I have also added a CHANGELOG.md file as part of my final improvements.
@myousefi2016 and @mdoucet Thank you for taking the time to review my submission.
@katyhuff All of the changes are now merged into the master branch and are contained in the tagged release v4.0.0 that is archived on Zenodo with the following DOI:
10.5281/zenodo.1710685
This DOI needs to be added to the References section of the final paper.
The Changelog lists all changes made between the submitted v4.0.0-rc.2 and the final v4.0.0.
Please let me know if you need any more information from me to move things forward.
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@whedon set 10.5281/zenodo.1710685 as archive
OK. 10.5281/zenodo.1710685 is the archive.
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@myousefi2016 @mdoucet @stuartcampbell Thank you so much, once again, for your reviews of this work. JOSS relies on reviewers like you!
@MikeHeiber Thanks again for a strong submission, and congratulations, we're ready to accept your paper!
@arfon over to you!
@whedon accept
Attempting dry run of processing paper acceptance...
Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/90
If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/90, 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...
π¨π¨π¨ THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! π¨π¨π¨
Here's what you must now do:
Party like you just published a paper! πππ¦ππ»π€
Any issues? notify your editorial technical team...
@myousefi2016, @stuartcampbell, @mdoucet - many thanks for your reviews and to @katyhuff for editing this submission β¨
@MikeHeiber - your paper is now accepted into JOSS :zap::rocket::boom:
:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:
If you would like to include a link to your paper from your README use the following code snippets:
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<img src="http://joss.theoj.org/papers/10.21105/joss.01072/status.svg" alt="DOI badge" >
</a>
reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01072/status.svg
:target: https://doi.org/10.21105/joss.01072
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Submitting author: @MikeHeiber (Michael Heiber) Repository: https://github.com/MikeHeiber/Ising_OPV Version: v4.0.0 Editor: @katyhuff Reviewer: @myousefi2016, @stuartcampbell, @mdoucet Archive: 10.5281/zenodo.1710685
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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) 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.)
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@myousefi2016 & @stuartcampbell & @mdoucet, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
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Review checklist for @myousefi2016
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?Review checklist for @stuartcampbell
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?Review checklist for @mdoucet
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?