Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @djmitche, it looks like you're currently assigned as the reviewer for this paper 🎉.

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@whedon commands

Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

👋 @djmitche, @tanaken-basis - thanks for agreeing to review this submission. Please see the instructions above and feel free to ask me if you have any questions. Otherwise, I will assume that you will work through the checklist items above, and will bring up any issues with the submission with the author (via very short discussion here or via new issues in the source repo), who will resolve them.

It's worth noting that the most recent version is 2.5.2 now. That is the same in the repo and the package repository.

Any updates to the package to improve based on review comments will go to the dev branch. On a regular basis I will merge dev to master and update the PyPi packages.

@whedon generate pdf from branch feat/updates_paper_alan

Attempting PDF compilation from custom branch feat/updates_paper_alan. Reticulating splines etc...

👉 Check article proof 📄 👈

@whedon generate pdf from branch feat/updates_paper_alan

Just a heads up @eendebakpt - compiling from a branch doesn't seem to work very well. You might have to merge to master to see new changes with @whedon.

All - @tanaken-basis has informed me by email that he needs to be taken off this review because of a personal matter. So I need to find another reviewer - @djmitche, do you have any suggestion for someone else?

@gsagnol has been added as the second reviewer - thanks!

👋 @gsagnol - thanks for agreeing to review this submission. Please see the instructions above and feel free to ask me if you have any questions. Otherwise, I will assume that you will work through the checklist items above, and will bring up any issues with the submission with the author (via very short discussion here or via new issues in the source repo), who will resolve them.

This is my first JOSS review so no, I don't have ideas :/

@whedon list reviewers

Here's the current list of reviewers: https://bit.ly/joss-reviewers

👋 @gsagnol - how are things going? When will you be able to start on the review (at least the first 2 checkboxes regarding COIs and the JOSS CoC?)

Hi @danielskatz , I wanted to start with the review this week.

I tried to check some of the boxes, but this will not work, although I'm logged in to github. Is google-chrome under linux not supported ? I tried under firefox, but this did not work neither.

As in the first comment in this thread, can you:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

That's it... I probably did not accept the invitation, but I guess the invitation link expired:
"Sorry, we couldn't find that repository invitation. It is possible that the invitation was revoked or that you are not logged into the invited account."

👋 @arfon - can you help with this? Or tell me what I can do?

@gsagnol - I've re-made the invitation here: https://github.com/openjournals/joss-reviews/invitations

I installed the latest release from github, and oapackage.__version__ returns 2.5.2, while the check list above asks for 2.5.1. Should the checklist be updated, or should I review a former version ?

@gsagnol I don't know about JOSS policy on this matter. I submitted version 2.5.1 to JOSS, but since that moment (also based on reviewers comments) I updated the code and the paper and made a new release. I will continue to push updates based on the review to dev and once in a while merge dev to master (with an increase in version number)

@peendebak : I would like to have a look at your unit tests. I tried to run
coverage run --source='./oapackage' -m pytest,
but numpy raises some error:
ImportError: /homes/combi/sagnol/.local/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: _Py_ZeroStruct

Do I need a particular version of numpy to execute the testing suite ? Or is there another way to run the unit tests ?

@peendebak : I posted an issue on the OApackage repository about confusing locations for the documentation (readthedocs.io vs. http://pietereendebak.nl)

@peendebak : I would like to have a look at your unit tests. I tried to run
coverage run --source='./oapackage' -m pytest,
but numpy raises some error:
ImportError: /homes/combi/sagnol/.local/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: _Py_ZeroStruct

Do I need a particular version of numpy to execute the testing suite ? Or is there another way to run the unit tests ?

The minimal version of numpy is specified in the setup.py (1.13, although perhaps earlier versions of numpy work as well). Can you provide me with some more details of your system (e.g. platform, version of numpy installed, how did you install (pip or compile from source), send output of installation process, version of swig installed)

Can you also send me the output of the following commands?

python -c "import numpy; print(numpy); print(numpy.__version__')
python -c "import oapackage; print(oapackage)"
pytest - v

@gsagnol

@peendebak and @gsagnol - please review the "latest" and be sure that all the docs are consistent, then we will accept that version into the repository and the journal once everything is approved.

@peendebak I created an issue on the oapackage repo for the tests.

• On the PC of my institute, I am not able to run the tests. Here, I used a local information (pip install --user)
• On my laptop, the testing suite seems to work, but some tests fail. On my laptop I used a standard global installation without the --user flag.

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

@peendebak : Concerning the last "check-box", it seems that some doi's are missing in the software paper. For example,
The book "Orthogonal Arrays: Theory and Applications" of Hedayat et al. should have doi https://doi.org/10.1007/978-1-4612-1478-6

Moreover, this reference appears in two separate bib entries (once as a book, once as a website).

@peendebak : I created a number of issues in the source repository. This can be considered as my list of requests for a minor revision.

@gsagnol Thanks for the review! A couple of issues we already addressed (in particular the tests that failed) and we made a new release to pypi based on that. The other issues we will probably address after new year.

@eendebakpt - please let us know when these are done

Hi @eendebakpt - just checking on the post-holiday status of this...

@danielskatz We started addressing the remaining comments.

@eendebakpt - Is there any further update at this point?