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python packages updates: numpy, scipy, scikit-learn, pyflakes #10255

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merged 7 commits into from Oct 22, 2015
Merged

python packages updates: numpy, scipy, scikit-learn, pyflakes #10255

merged 7 commits into from Oct 22, 2015

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FRidh
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@FRidh FRidh commented Oct 6, 2015

Since 1.9.3 Python 3.5 is supported. This PR updates to 1.10.0 and enables numpy for Python 3.5.
numpy worked for me with all interpreter versions. I didn't check its dependents though with nox-review wip.

It might happen though that packages depending on numpy 1.10.0 will fail, especially when using Python 3.5.

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FRidh commented Oct 6, 2015

Failed due to an issue with the cache.
http://lists.science.uu.nl/pipermail/nix-dev/2015-October/018311.html

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FRidh commented Oct 8, 2015

@domenkozar I've tested that numpy builds and works, as well as a couple of dependents. However, because python 3.5 is now supported there are many more packages available that can fail. One-shot run on Hydra?

@FRidh FRidh changed the title pythonPackages numpy: 1.9.2 -> 1.10.0 and enable for Python 3.5 pythonPackages numpy: 1.9.2 -> 1.10.1 and enable for Python 3.5 Oct 12, 2015
@FRidh
pythonPackages numpy: 1.9.2 -> 1.10.1
0732a39
@FRidh
pythonPackages numpy: enable for Python 3.5
31f0478 
Since 1.9.3 numpy works with Python 3.5.
Packages depending on Numpy still might cause problems with Python 3.5.
@FRidh
python nibabel: remove failing test 1.10.1
d1975ca
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FRidh commented Oct 20, 2015

Travis:

The build failed due to running out of memory:

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http://hydra.nixos.org/jobset/nixpkgs/pr-10255

@FRidh
python-packages scipy: 0.15.1 -> 0.16.0
fb0bb02
@FRidh
python packages scikit-learn: 0.16.1 -> 0.17b1
9ada7aa 
Some tests in scikit-learn 0.16.1 fail with the new scipy 0.16 package.
This is known upstream and should be fixed in the next release.
scikit-learn/scikit-learn#5045

This commit disables the tests until the next scikit-learn release.
@FRidh
python pyflakes: 0.9.2 -> 1.0.0
fc80123
@FRidh
python pyflakes_0_8: init at 0.8.1
536949a
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FRidh commented Oct 20, 2015

@domenkozar

command `git rev-parse numpy' failed with exit status 32768 at /nix/store/l8dqx33lwbv7c67v8652n4r1zsx047c1-hydra-0.1pre1234-abcdef/libexec/hydra/lib/Hydra/Helper/Nix.pm line 413.

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fixed

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Looks good, merging

domenkozar added a commit that referenced this pull request Oct 22, 2015
@domenkozar
Merge pull request #10255 from FRidh/numpy
45d8f62 
pythonPackages numpy: 1.9.2 -> 1.10.1 and enable for Python 3.5
@domenkozar domenkozar merged commit 45d8f62 into NixOS:master Oct 22, 2015
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FRidh commented Oct 22, 2015

Thanks for the run @domenkozar
I had added some additional commits to this PR before Hydra did its work. The results can be seen at
http://hydra.nixos.org/eval/1227283?compare=trunk#tabs-now-fail

About the fails:

  • scikitlearn: i686 fails, these are upstream issues (Tests: bunch of failures with 0.17b1 i686 on Nix scikit-learn/scikit-learn#5534)
  • xray: 0.6.1 should be compatible with numpy 1.10 and Python 3.5. Let's update xray
  • tables: pytables is already an older version, could use an update. Not sure whether it solves the fails
  • pandas: 1 test fails with Python 2.7. Seems to be datetime related again. These issues are often do not arise when they perform their own tests with Travis.
  • swiften: failure seems to be unrelated. Any idea @Twey ?
  • x42-plugins: seems unrelated
  • ocropus: guess this is not yet numpy 1.10 compatible @domenkozar
  • musescore: unrelated, see musescore: 2.0.0 -> 2.0.1 #8111
  • reflex-transformers: haskell, guess it's unrelated
  • ceph-git: lack of memory, disregard result

I would like to add to this PR version updates of Pandas (#10296), PyTables and xray. Furthermore, I suggest we disable i686 tests for scikit-learn (@garbas) since upstream does not seem to be that much interested in i686.

@FRidh FRidh deleted the numpy branch October 22, 2015 14:01
@FRidh FRidh changed the title pythonPackages numpy: 1.9.2 -> 1.10.1 and enable for Python 3.5 python packages updates: numpy, scipy, scikit-learn, pyflakes Oct 22, 2015
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@FRidh sure, open a nother PR for Pandas, pytables and xray. We can disable scikit-learn for now.

This was referenced Oct 22, 2015
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garbas commented Oct 22, 2015

+1 for ignoring i686 platform until skikit-learn devs get around supporting it

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@FRidh @domenkozar @garbas @pSub