update scikit-image dependency #117
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There's a bug that's been introduced with an interaction between python 3.6, numpy, and the version of scikit-image that's pinned here. This should fix that, and AFAICT `skimage` actually isn't used in the notebooks, so this upgrade shouldn't be breaking yeah? https://github.com/jakevdp/PythonDataScienceHandbook/search?utf8=%E2%9C%93&q=skimage&type= would fix jakevdp#108
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Gentlest of bumps :) |
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The new version of scikit-image changed the default behavior of |
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gah that's annoying...hmm, it looks like here's the deprecation message related to |
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hlapp
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The Mybinder.org link for Jake van der Plas' Python Data Science Handbook (PDSH) is currently broken (and has been for a while: jakevdp/PythonDataScienceHandbook#108). The root of the problem is an incompatibility between the version of scikit-image stated in the requirements.txt and the 3.6+ version of Python. Upgrading the scikit-image requirement has been stalled for > 6 months (see jakevdp/PythonDataScienceHandbook#117). The alternative is to force the Python runtime to Python 3.5, which is what one fork did: baldwint/PythonDataScienceHandbook@b233490 Here we're commenting out the link that we'd really want but that's broken (bad for learners), and instead use the link that uses the aforementioned fork. This obviously has to be a temporary fix only. Currently there is no sign that the problem will be fixed in the original repo by merging jakevdp/PythonDataScienceHandbook#117. One more long-term reliable solution to this could be to fork the original repo here and apply the same (trivial) fix as in the aforementioned fork. Alternatively, we may consider switching to another example.
hlapp
added a commit
to Reproducible-Science-Curriculum/sharing-RR-Jupyter
that referenced
this pull request
Aug 15, 2018
The Mybinder.org link for Jake van der Plas' Python Data Science Handbook (PDSH) is currently broken (and has been for a while: jakevdp/PythonDataScienceHandbook#108). The root of the problem is an incompatibility between the version of scikit-image stated in the requirements.txt and the 3.6+ version of Python. Upgrading the scikit-image requirement has been stalled for > 6 months (see jakevdp/PythonDataScienceHandbook#117). The alternative is to force the Python runtime to Python 3.5, which is what one fork did: baldwint/PythonDataScienceHandbook@b233490 We could switch to this fork, but this obviously would have to be a temporary fix only, and would almost be guaranteed to break again in the future. Currently there is no sign that the problem will be fixed in the original repo by merging jakevdp/PythonDataScienceHandbook#117. So instead of using a temporary fix and/or waiting for whenever the original repo will be fixed, this proposal switches to a notebooke "of our own", which has the advantages of having only few and relatively common dependencies, and being one that the learners just worked through, and now get to see a live-shared version of.
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Is there any way to keep the old skimage and allow the binder to actually build? |
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closing this since it was fixed in #145 ! |
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(though note that the underlying python 3.6/numpy/scikit-image bug is still there...) |
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There's a bug that's been introduced with an interaction between python 3.6, numpy, and the version of scikit-image that's pinned here. This should fix that, and AFAICT
skimageactually isn't used in the notebooks, so this upgrade shouldn't be breaking yeah?https://github.com/jakevdp/PythonDataScienceHandbook/search?utf8=%E2%9C%93&q=skimage&type=
would fix #108