<div dir="ltr">Matthew, you are correct. A lot of things happened with random integer generation recently (including deprecating random_integers), but I believe those warnings should be squashed in the up and coming version of SciPy from what I remember.</div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Apr 4, 2016 at 6:47 PM, Matthew Brett <span dir="ltr"><<a href="mailto:matthew.brett@gmail.com" target="_blank">matthew.brett@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<div><div class="h5"><br>
On Mon, Apr 4, 2016 at 9:02 AM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>> wrote:<br>
> On Sun, Apr 3, 2016 at 2:11 AM, Matthew Brett <<a href="mailto:matthew.brett@gmail.com">matthew.brett@gmail.com</a>> wrote:<br>
>> On Fri, Mar 25, 2016 at 6:39 AM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>> wrote:<br>
>>> On Fri, Mar 25, 2016 at 3:02 AM, Robert T. McGibbon <<a href="mailto:rmcgibbo@gmail.com">rmcgibbo@gmail.com</a>> wrote:<br>
>>>> I suspect that many of the maintainers of major scipy-ecosystem projects are<br>
>>>> aware of these (or other similar) travis wheel caches, but would guess that<br>
>>>> the pool of travis-ci python users who weren't aware of these wheel caches<br>
>>>> is much much larger. So there will still be a lot of travis-ci clock cycles<br>
>>>> saved by manylinux wheels.<br>
>>>><br>
>>>> -Robert<br>
>>><br>
>>> Yes exactly. Availability of NumPy Linux wheels on PyPI is definitely something<br>
>>> I would suggest adding to the release notes. Hopefully this will help trigger<br>
>>> a general availability of wheels in the numpy-ecosystem :)<br>
>>><br>
>>> In the case of Travis CI, their VM images for Python already have a version<br>
>>> of NumPy installed, but having the latest version of NumPy and SciPy etc<br>
>>> available as Linux wheels would be very nice.<br>
>><br>
>> We're very nearly there now.<br>
>><br>
>> The latest versions of numpy, scipy, scikit-image, pandas, numexpr,<br>
>> statsmodels wheels for testing at<br>
>> <a href="http://ccdd0ebb5a931e58c7c5-aae005c4999d7244ac63632f8b80e089.r77.cf2.rackcdn.com/" rel="noreferrer" target="_blank">http://ccdd0ebb5a931e58c7c5-aae005c4999d7244ac63632f8b80e089.r77.cf2.rackcdn.com/</a><br>
>><br>
>> Please do test with:<br>
>> ...<br>
>><br>
>> We would love to get any feedback as to whether these work on your machines.<br>
><br>
> Hi Matthew,<br>
><br>
> Testing on a 64bit CentOS 6 machine with Python 3.5 compiled<br>
> from source under my home directory:<br>
><br>
><br>
> $ python3.5 -m pip install --upgrade pip<br>
> Requirement already up-to-date: pip in ./lib/python3.5/site-packages<br>
><br>
> $ python3.5 -m pip install<br>
> --trusted-host=<a href="http://ccdd0ebb5a931e58c7c5-aae005c4999d7244ac63632f8b80e089.r77.cf2.rackcdn.com" rel="noreferrer" target="_blank">ccdd0ebb5a931e58c7c5-aae005c4999d7244ac63632f8b80e089.r77.cf2.rackcdn.com</a><br>
> --find-links=<a href="http://ccdd0ebb5a931e58c7c5-aae005c4999d7244ac63632f8b80e089.r77.cf2.rackcdn.com" rel="noreferrer" target="_blank">http://ccdd0ebb5a931e58c7c5-aae005c4999d7244ac63632f8b80e089.r77.cf2.rackcdn.com</a><br>
> numpy scipy<br>
> Requirement already satisfied (use --upgrade to upgrade): numpy in<br>
> ./lib/python3.5/site-packages<br>
> Requirement already satisfied (use --upgrade to upgrade): scipy in<br>
> ./lib/python3.5/site-packages<br>
><br>
> $ python3.5 -m pip install<br>
> --trusted-host=<a href="http://ccdd0ebb5a931e58c7c5-aae005c4999d7244ac63632f8b80e089.r77.cf2.rackcdn.com" rel="noreferrer" target="_blank">ccdd0ebb5a931e58c7c5-aae005c4999d7244ac63632f8b80e089.r77.cf2.rackcdn.com</a><br>
> --find-links=<a href="http://ccdd0ebb5a931e58c7c5-aae005c4999d7244ac63632f8b80e089.r77.cf2.rackcdn.com" rel="noreferrer" target="_blank">http://ccdd0ebb5a931e58c7c5-aae005c4999d7244ac63632f8b80e089.r77.cf2.rackcdn.com</a><br>
> numpy scipy --upgrade<br>
> Collecting numpy<br>
> Downloading <a href="http://ccdd0ebb5a931e58c7c5-aae005c4999d7244ac63632f8b80e089.r77.cf2.rackcdn.com/numpy-1.11.0-cp35-cp35m-manylinux1_x86_64.whl" rel="noreferrer" target="_blank">http://ccdd0ebb5a931e58c7c5-aae005c4999d7244ac63632f8b80e089.r77.cf2.rackcdn.com/numpy-1.11.0-cp35-cp35m-manylinux1_x86_64.whl</a><br>
> (15.5MB)<br>
> 100% |████████████████████████████████| 15.5MB 42.1MB/s<br>
> Collecting scipy<br>
> Downloading <a href="http://ccdd0ebb5a931e58c7c5-aae005c4999d7244ac63632f8b80e089.r77.cf2.rackcdn.com/scipy-0.17.0-cp35-cp35m-manylinux1_x86_64.whl" rel="noreferrer" target="_blank">http://ccdd0ebb5a931e58c7c5-aae005c4999d7244ac63632f8b80e089.r77.cf2.rackcdn.com/scipy-0.17.0-cp35-cp35m-manylinux1_x86_64.whl</a><br>
> (40.8MB)<br>
> 100% |████████████████████████████████| 40.8MB 53.6MB/s<br>
> Installing collected packages: numpy, scipy<br>
> Found existing installation: numpy 1.10.4<br>
> Uninstalling numpy-1.10.4:<br>
> Successfully uninstalled numpy-1.10.4<br>
> Found existing installation: scipy 0.16.0<br>
> Uninstalling scipy-0.16.0:<br>
> Successfully uninstalled scipy-0.16.0<br>
> Successfully installed numpy-1.11.0 scipy-0.17.0<br>
><br>
><br>
> $ python3.5 -c 'import numpy; numpy.test("full")'<br>
> Running unit tests for numpy<br>
> NumPy version 1.11.0<br>
> NumPy relaxed strides checking option: False<br>
> NumPy is installed in /home/xxx/lib/python3.5/site-packages/numpy<br>
> Python version 3.5.0 (default, Sep 28 2015, 11:25:31) [GCC 4.4.7<br>
> 20120313 (Red Hat 4.4.7-16)]<br>
> nose version 1.3.7<br>
> .............................................................................................................................................................................................................................S....................................................................................................................................................................KKK....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................S....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K.................................................................................................................................................................................................................................................................................................................................................................................................................................................K.......................................................................................................................................................................................................................................................................................................................................................................................................................................................K......................K............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................<br>
> ----------------------------------------------------------------------<br>
> Ran 6332 tests in 243.029s<br>
><br>
> OK (KNOWNFAIL=7, SKIP=2)<br>
><br>
><br>
><br>
> So far so good, but there are a lot of deprecation warnings etc from SciPy,<br>
><br>
><br>
> $ python3.5 -c 'import scipy; scipy.test("full")'<br>
> Running unit tests for scipy<br>
> NumPy version 1.11.0<br>
> NumPy relaxed strides checking option: False<br>
> NumPy is installed in /home/xxx/lib/python3.5/site-packages/numpy<br>
> SciPy version 0.17.0<br>
> SciPy is installed in /home/xxx/lib/python3.5/site-packages/scipy<br>
> Python version 3.5.0 (default, Sep 28 2015, 11:25:31) [GCC 4.4.7<br>
> 20120313 (Red Hat 4.4.7-16)]<br>
> nose version 1.3.7<br>
> [snip]<br>
> /home/xxx/lib/python3.5/site-packages/numpy/lib/utils.py:99:<br>
> DeprecationWarning: `rand` is deprecated!<br>
> numpy.testing.rand is deprecated in numpy 1.11. Use numpy.random.rand instead.<br>
> warnings.warn(depdoc, DeprecationWarning)<br>
> [snip]<br>
> /home/xxx/lib/python3.5/site-packages/scipy/io/arff/tests/test_arffread.py:254:<br>
> DeprecationWarning: parsing timezone aware datetimes is deprecated;<br>
> this will raise an error in the future<br>
> ], dtype='datetime64[m]')<br>
> /home/xxx/lib/python3.5/site-packages/scipy/io/arff/arffread.py:638:<br>
> PendingDeprecationWarning: generator '_loadarff.<locals>.generator'<br>
> raised StopIteration<br>
> [snip]<br>
> /home/xxx/lib/python3.5/site-packages/scipy/sparse/tests/test_base.py:2425:<br>
> DeprecationWarning: This function is deprecated. Please call<br>
> randint(-5, 5 + 1) instead<br>
> I = np.random.random_integers(-M + 1, M - 1, size=NUM_SAMPLES)<br>
> [snip]<br>
> 0-th dimension must be fixed to 3 but got 15<br>
> [snip]<br>
> ----------------------------------------------------------------------<br>
> Ran 21407 tests in 741.602s<br>
><br>
> OK (KNOWNFAIL=130, SKIP=1775)<br>
><br>
><br>
> Hopefully I didn't miss anything important in hand editing the scipy output.<br>
<br>
</div></div>Thanks a lot for testing.<br>
<br>
I believe the deprecation warnings are expected, because numpy 1.11.0<br>
introduced a new deprecation warning when using `random_integers`.<br>
Scipy 0.17.0 is using `random_integers` in a few places.<br>
<br>
Best,<br>
<br>
Matthew<br>
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