From jni.soma at gmail.com  Sun Jan  1 19:04:49 2017
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 2 Jan 2017 11:04:49 +1100
Subject: [scikit-image] Future of nose and issues for scikit-image
In-Reply-To: <1483226766.3931153.833987329.7617F174@webmail.messagingengine.com>
References: <ec39bdce-02d6-17c7-0d3a-7d47e98297af@sciunto.org>
 <CAE-UAvS3TgKrJ=b3DDOY64of2h4sAygjYducLtW9S4EigspYyQ@mail.gmail.com>
 <08c990bf-f2f0-ab5e-4063-f4300e46900f@sciunto.org>
 <159565c1f38.273e.acf34a9c767d7bb498a799333be0433e@fastmail.com>
 <98FF2884-49FF-4421-A6C3-DE2B321A710E@gmail.com>
 <1483226766.3931153.833987329.7617F174@webmail.messagingengine.com>
Message-ID: <9019c557-d6ec-4d3f-858e-805ddbf0b853@Spark>

+1 for pytest.

Nelle, can you comment a bit on why scikit-learn effectively decided to roll their own test library? ;) Is it part of their general (and well-justified) aversion to new dependencies, or were there specific objections to pytest?

Pytest mostly works out of the box with tests written for nose. As far as I know the exceptions are:

- all the nose imports that St?fan pointed out (btw how did an import * make its way into our codebase???)
- it seems that yielding tests is deprecated, so that will require a few rewrites.

It's not a trivial effort to fix these, but I don't think it'll be any bigger than any other move.

Juan.

On 1 Jan 2017, 10:26 AM +1100, Stefan van der Walt <stefanv at berkeley.edu>, wrote:
> On Sat, Dec 31, 2016, at 15:05, Steven Silvester wrote:
> > I agree with St?fan that a forward-looking clean break would be best. ?It looks like a rather large undertaking though, judging from?https://github.com/matplotlib/matplotlib/pull/5405.
>
> Perhaps we are better off than matplotlib:
>
> $ git grep "from nose"
> skimage/_shared/testing.py:??? from nose.tools import assert_less
> skimage/_shared/testing.py:??? from nose.tools import assert_greater
> skimage/_shared/tests/test_testing.py:from nose.tools import (assert_true, assert_raises, assert_equal)
> skimage/draw/tests/test_draw3d.py:from nose.tools import raises
> skimage/io/tests/test_sift.py:from nose.tools import *
> skimage/novice/tests/test_novice.py:from nose.tools import assert_true
> skimage/segmentation/tests/test_quickshift.py:from nose.tools import assert_true
> skimage/util/tests/test_montage.py:from nose.tools import assert_equal, raises
> skimage/util/tests/test_shape.py:from nose.tools import raises
>
> St?fan
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
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From tcaswell at gmail.com  Mon Jan  2 21:09:45 2017
From: tcaswell at gmail.com (Thomas Caswell)
Date: Tue, 03 Jan 2017 02:09:45 +0000
Subject: [scikit-image] Future of nose and issues for scikit-image
In-Reply-To: <9019c557-d6ec-4d3f-858e-805ddbf0b853@Spark>
References: <ec39bdce-02d6-17c7-0d3a-7d47e98297af@sciunto.org>
 <CAE-UAvS3TgKrJ=b3DDOY64of2h4sAygjYducLtW9S4EigspYyQ@mail.gmail.com>
 <08c990bf-f2f0-ab5e-4063-f4300e46900f@sciunto.org>
 <159565c1f38.273e.acf34a9c767d7bb498a799333be0433e@fastmail.com>
 <98FF2884-49FF-4421-A6C3-DE2B321A710E@gmail.com>
 <1483226766.3931153.833987329.7617F174@webmail.messagingengine.com>
 <9019c557-d6ec-4d3f-858e-805ddbf0b853@Spark>
Message-ID: <CAA48SF8rtNS8n=OmSAi89qh8ODtZ6ka3OBAFpB7GfhMC81=Vsw@mail.gmail.com>

Parameterized tests in pytest are _way_ better than the yield based tests.
I use pytest fixtures pretty heavily at my day job and am super happy.

mpl's test suite on master currently runs under both as of
https://github.com/matplotlib/matplotlib/pull/6730 (we now have some pytest
only tests as well) and are probably a few days of effort away from
switching entirely (our tests.py script still runs the nose version).

The big advantage of supporting both (at least for a while) is that you can
get both to run and report they ran the same number of tests to be sure you
did not make any mistakes.  The test suite protects you when you refactor
the code, what protects you when you refactor the tests >:)

Tom

On Sun, Jan 1, 2017 at 7:36 PM Juan Nunez-Iglesias <jni.soma at gmail.com>
wrote:

> +1 for pytest.
>
> Nelle, can you comment a bit on why scikit-learn effectively decided to
> roll their own test library? ;) Is it part of their general (and
> well-justified) aversion to new dependencies, or were there specific
> objections to pytest?
>
> Pytest mostly works out of the box with tests written for nose. As far as
> I know the exceptions are:
>
> - all the nose imports that St?fan pointed out (btw how did an import *
> make its way into our codebase???)
> - it seems that yielding tests is deprecated, so that will require a few
> rewrites.
>
> It's not a trivial effort to fix these, but I don't think it'll be any
> bigger than any other move.
>
> Juan.
>
> On 1 Jan 2017, 10:26 AM +1100, Stefan van der Walt <stefanv at berkeley.edu>,
> wrote:
>
> On Sat, Dec 31, 2016, at 15:05, Steven Silvester wrote:
>
> I agree with St?fan that a forward-looking clean break would be best.  It
> looks like a rather large undertaking though, judging from
> https://github.com/matplotlib/matplotlib/pull/5405.
>
>
> Perhaps we are better off than matplotlib:
>
> $ git grep "from nose"
> skimage/_shared/testing.py:    from nose.tools import assert_less
> skimage/_shared/testing.py:    from nose.tools import assert_greater
> skimage/_shared/tests/test_testing.py:from nose.tools import (assert_true,
> assert_raises, assert_equal)
> skimage/draw/tests/test_draw3d.py:from nose.tools import raises
> skimage/io/tests/test_sift.py:from nose.tools import *
> skimage/novice/tests/test_novice.py:from nose.tools import assert_true
> skimage/segmentation/tests/test_quickshift.py:from nose.tools import
> assert_true
> skimage/util/tests/test_montage.py:from nose.tools import assert_equal,
> raises
> skimage/util/tests/test_shape.py:from nose.tools import raises
>
> St?fan
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
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From stefanv at berkeley.edu  Wed Jan  4 14:43:19 2017
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Wed, 04 Jan 2017 11:43:19 -0800
Subject: [scikit-image] GLCM and angles
In-Reply-To: <CAFTPLW96Qx3Um7d8deH2pm=UyLVLdgqqQWi85n9NEnKxbWANHw@mail.gmail.com>
References: <CAFTPLW96Qx3Um7d8deH2pm=UyLVLdgqqQWi85n9NEnKxbWANHw@mail.gmail.com>
Message-ID: <1483558999.3274087.837440361.59AD386C@webmail.messagingengine.com>

Hi Igor



On Thu, Dec 8, 2016, at 22:43, Igor Karlovits wrote:

> I would have a question regarding the results of graycoprops which is
> giving me the same results for all attributes (energy, ASM etc...) in
> angles of rotation of 135 and 90. Angles 0, 45 and 90 are ok (with an
> offset of 1) but the angle 135 is giving the same results as 90?


Apologies for the delay: can you give an example of the problem you
see?  If you believe this to be a bug, would you mind filing an issue
on GitHub?


Thanks!

St?fan




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From tcaswell at gmail.com  Wed Jan  4 21:49:05 2017
From: tcaswell at gmail.com (Thomas Caswell)
Date: Thu, 05 Jan 2017 02:49:05 +0000
Subject: [scikit-image] pixel value changes during reading image and
 showing images using skimage and matplotlib
In-Reply-To: <CAFyUc2A-Lc-QtDDJAiL+-Ux9KTiVjfg5SZWG-tOWiq+5Nk-4vw@mail.gmail.com>
References: <CAFyUc2CvU9S1apTmmd8xaXTYGY8fv=R_ZL0af+2nGhy1GxUG6Q@mail.gmail.com>
 <9abc3f6b-497c-b2b2-bc43-7e39824af6cb@nottingham.ac.uk>
 <CAFyUc2A-Lc-QtDDJAiL+-Ux9KTiVjfg5SZWG-tOWiq+5Nk-4vw@mail.gmail.com>
Message-ID: <CAA48SF9goSW8rjDnKmYgE+Um0YNPjpihsEoxi32PzHT_nbZTUw@mail.gmail.com>

plt.imread falls back to PIL/pillow for tiff reading which does not always
handle high-bit depth tiffs well.  I (as a lead mpl dev) would discourage
`plt.imread` for 'production' use, there are many better options out there
(ex skimage, http://imageio.github.io/ ,
http://soft-matter.github.io/pims/v0.3.3/  ,
http://imread.readthedocs.io/en/latest/  ).

Tom

On Sun, Dec 11, 2016 at 2:04 PM wine lover <winecoding at gmail.com> wrote:

> Hi Imanol,
>
> It works fine now, thanks for your suggestions.
>
> Regarding the second part of my question. If I read the image using
> matlibplot instead of skimage,
> i.e.,  output=plt.imread(os.path.join(image_path,raw_image_name))
>
> I found that the pixel values of output were all changed, and they becomes
> either 255. or 0. which causes the image shown as all black. What are the
> possible reasons for plt.imread. Thanks.
>
> Yuanyuan
>
> On Sun, Dec 11, 2016 at 4:54 AM, Imanol Luengo <
> imanol.luengo at nottingham.ac.uk> wrote:
>
> Dear Yuanyuan,
>
> The reason why you are looking at a *color* image is due to the colormaps:
>
> http://matplotlib.org/users/colormaps.html
>
> The default colormap (to map from numbers to colors) is not grayscale, as
> matplotlib is not primarly focus on images, and grayscale is not an
> *adequate* colormap to represent other types of plots.
>
> To properly visualize your image specify a colormap to the plot function:
>
>      plt.imshow(output, 'gray')
>
> Cheers,
>
> Imanol
>
> On 11/12/16 06:46, wine lover wrote:
>
> Dear All,
>
> I have a tif images, its type is float32, shape is (128*128) (a grayscale
> image). All the pixel values are of range [0.0, 1.0]
>
>  I am trying to read it using skimage and show it on screen using
> matplotlib.
>
> from skimage import ioimport matplotlib.pyplot as plt
> output=io.imread(os.path.join(image_path,raw_image_name))print(output.dtype)print(output.shape)print(output.max())print(output.min())
> plt.imshow(output)
> plt.show()
>
> The output image looks like color image instead of gray image as shown
> originally. I attached the screenshot as the capture-1.jpg.
>
> However, when I read the image using matplotlib instead,i.e.,
> output=plt.imread(os.path.join(image_path,raw_image_name)). I found that
> pixel value will become 255 and 0. The dtype is still float32. But when I
> print output, the pixel values are either 0. or 255.
>
> The output image will become black as shown in the second image
> (capture-2.jpg). I am confused how does this work? My guess is that there
> are some dtype changes happening during the reading image and showing
> image,
>
>
> Thanks,
>
> Yuanyuan
>
>
> _______________________________________________
> scikit-image mailing listscikit-image at python.orghttps://mail.python.org/mailman/listinfo/scikit-image
>
>
>
>
> This message and any attachment are intended solely for the addressee
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> message in error, please send it back to me, and immediately delete it.
>
> Please do not use, copy or disclose the information contained in this
> message or in any attachment.  Any views or opinions expressed by the
> author of this email do not necessarily reflect the views of the
> University of Nottingham.
>
> This message has been checked for viruses but the contents of an
> attachment may still contain software viruses which could damage your
> computer system, you are advised to perform your own checks. Email
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> permitted by UK legislation.
>
>
> _______________________________________________
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From fboulogne at sciunto.org  Thu Jan  5 04:30:32 2017
From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=)
Date: Thu, 5 Jan 2017 10:30:32 +0100
Subject: [scikit-image] Future of nose and issues for scikit-image
In-Reply-To: <CAA48SF8rtNS8n=OmSAi89qh8ODtZ6ka3OBAFpB7GfhMC81=Vsw@mail.gmail.com>
References: <ec39bdce-02d6-17c7-0d3a-7d47e98297af@sciunto.org>
 <CAE-UAvS3TgKrJ=b3DDOY64of2h4sAygjYducLtW9S4EigspYyQ@mail.gmail.com>
 <08c990bf-f2f0-ab5e-4063-f4300e46900f@sciunto.org>
 <159565c1f38.273e.acf34a9c767d7bb498a799333be0433e@fastmail.com>
 <98FF2884-49FF-4421-A6C3-DE2B321A710E@gmail.com>
 <1483226766.3931153.833987329.7617F174@webmail.messagingengine.com>
 <9019c557-d6ec-4d3f-858e-805ddbf0b853@Spark>
 <CAA48SF8rtNS8n=OmSAi89qh8ODtZ6ka3OBAFpB7GfhMC81=Vsw@mail.gmail.com>
Message-ID: <97bb74ab-b45d-4001-55db-80dfabdf2f8f@sciunto.org>

FYI, I created an issue for this task:

https://github.com/scikit-image/scikit-image/issues/2424

Best,

-- 
Fran?ois Boulogne.
http://www.sciunto.org
GPG: 32D5F22F


From m.p.romaniuk at gmail.com  Thu Jan  5 04:45:14 2017
From: m.p.romaniuk at gmail.com (Michal Romaniuk)
Date: Thu, 5 Jan 2017 10:45:14 +0100
Subject: [scikit-image] IO documentation
Message-ID: <CALxM84=Y2z4eWWMXR5h3iQVpq6EqzoVucYmou0BddzkMq7goCg@mail.gmail.com>

Hi everyone,

The IO documentation doesn't seem to be very good. It explains how plugins
work but it's scarce on examples e.g. on how to export jpeg image with a
specified compression level. The IO API docs don't give much detail either.
Some details can be found in the docs for external.tifffile but it takes
some searching to find it. For PIL the only way to figure out how to use it
seems to be looking at the source code - no modern docs as far as I can
tell (did I fail to use Google properly?).

Any thoughts?

Best wishes,
Michal
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From luecks at gmail.com  Thu Jan  5 09:33:17 2017
From: luecks at gmail.com (=?UTF-8?Q?Stefanie_L=C3=BCck?=)
Date: Thu, 5 Jan 2017 15:33:17 +0100
Subject: [scikit-image] GLCM strange results
Message-ID: <CAHvaZnYSufUmu1SPcGGarYP6UjwSreOzGmYMxSP9H_tzutVk_A@mail.gmail.com>

Hi everybody,

first of all, a happy to new year!

I am trying to extract GLCM features of my image but I don't understand the
results. The GLCM output images are looking quite different, nevertheless
that the source is quite similar.


I attached three example images and the corresponding GLCM output. I don't
really understand why the second example has much brighter values then the
other two images. Can anybody tell me what I am doing wrong?

Any help would be very appreciated,
thanks in advance,
Stefanie


Here is the code I used:

import cv2
import matplotlib.pyplot as plt

img = cv2.imread(crop_path + image, 0)
glcm_img = np.copy(img)
glcm_img[:] = 0
for i in range(glcm_img.shape[0]):
for j in range(glcm_img.shape[1]):
if i < 3 or j < 3:
continue
if i > (glcm_img.shape[0] - 4) or j > (glcm_img.shape[0] - 4):
continue
glcm_window = img[i - 3: i + 4, j - 3: j + 4]
glcm = greycomatrix(glcm_window, [1], [0], symmetric=True, normed=True)

contrast = greycoprops(glcm, 'dissimilarity')
glcm_img[i, j] = contrast
plt.imsave(glcm_path + image, glcm_img, cmap=plt.cm.gray)
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From luecks at gmail.com  Thu Jan  5 10:02:27 2017
From: luecks at gmail.com (=?UTF-8?Q?Stefanie_L=C3=BCck?=)
Date: Thu, 5 Jan 2017 16:02:27 +0100
Subject: [scikit-image] Image analysis pipeline improvement suggestions
In-Reply-To: <CAN1J6jW=BHzWBZ7MderdceLC=gbNdS+mWbVjzXoSdcmNvNUjxw@mail.gmail.com>
References: <CACi8E-B6EEA=zXKoOZHVNQf7oq-es=gPgvKQnzRzn_yvpiM=4g@mail.gmail.com>
 <CAN1J6jW=BHzWBZ7MderdceLC=gbNdS+mWbVjzXoSdcmNvNUjxw@mail.gmail.com>
Message-ID: <CAHvaZnbTsAKZi3LvvaerHA6AVnQUYgyKAXwXiBPemTjAaR-nyQ@mail.gmail.com>

Hi Simone,

unfortunately I can not contribute anything to your questions but would you
mind to share some of your experience with the hdf5 file format and
parallelization?
I am also analysing a lot of big microscopy images and would love to hear
your opinion or get advice for an image pipeline.

Best regards,
Stefanie



2016-12-28 23:37 GMT+01:00 Nathan Faggian <nathan.faggian at gmail.com>:

> Hi Simone,
>
> I have had a little experience with HDF5 and am interested to see where
> you go with this. I wonder if you could use "feather":
>     https://github.com/wesm/feather
>
> There was a recent post from Wes McKinney about feather, which sparked my
> interest:
>    http://wesmckinney.com/blog/high-perf-arrow-to-pandas/
>
> Do you use HDF5 to store intermediates? if so, I would try storing
> intermediates to a file format like feather and then reducing to a HDF5
> file at the end. The reduction should be IO bound and not dependent on RAM
> so would suit your cluster.
>
> If you need to read a large array then I think HDF5 supports that (for
> single write but multiple reads) without the need for MPI - so this could
> map well to a tool like distributed:
>     http://distributed.readthedocs.io/en/latest/
>
> Not sure this helps, there is an assumption (on my part) that your
> intermediate calculations are not terabytes in size.
>
> Good luck!
>
> Nathan
>
>
> On 29 December 2016 at 05:07, simone codeluppi <simone.codeluppi at gmail.com
> > wrote:
>
>> Hi all!
>>
>> I would like to pick your brain for some suggestion on how to modify my
>> image analysis pipeline.
>>
>> I am analyzing terabytes of image stacks generated using a microscope.
>> The current code I generated rely heavily on scikit-image, numpy and scipy.
>> In order to speed up the analysis the code runs on a HPC computer (
>> https://www.nsc.liu.se/systems/triolith/) with MPI (mpi4py) for
>> parallelization and hdf5 (h5py) for file storage. The development cycle of
>> the code has been pretty painful mainly due to my non familiarity with mpi
>> and problems in compiling parallel hdf5 (with many open/closing bugs).
>> However, the big drawback is that each core has only 2Gb of RAM (no shared
>> ram across nodes) and in order to run some of the processing steps i ended
>> up reserving one node (16 cores) but running only 3 cores in order to have
>> enough ram (image chunking won?t work in this case). As you can imagine
>> this is extremely inefficient and i end up getting low priority in the
>> queue system.
>>
>>
>> Our lab currently bought a new 4 nodes server with shared RAM running
>> hadoop. My goal is to move the parallelization of the processing to dask. I
>> tested it before in another system and works great. The drawback is that,
>> if I understood correctly, parallel hdf5 works only with MPI
>> (driver=?mpio?). Hdf5 gave me quite a bit of headache but works well in
>> keeping a good structure of the data and i can save everything as numpy
>> arrays?.very handy.
>>
>>
>> If I will move to hadoop/dask what do you think will be a good solution
>> for data storage? Do you have any additional suggestion that can improve
>> the layout of the pipeline? Any help will be greatly appreciated.
>>
>>
>> Simone
>> --
>> *Bad as he is, the Devil may be abus'd,*
>> *Be falsy charg'd, and causelesly accus'd,*
>> *When men, unwilling to be blam'd alone,*
>> *Shift off these Crimes on Him which are their*
>> *Own*
>>
>>                                                       *Daniel Defoe*
>>
>> simone.codeluppi at gmail.com
>>
>> simone at codeluppi.org
>>
>>
>> _______________________________________________
>> scikit-image mailing list
>> scikit-image at python.org
>> https://mail.python.org/mailman/listinfo/scikit-image
>>
>>
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>
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From simone.codeluppi at gmail.com  Fri Jan  6 12:13:28 2017
From: simone.codeluppi at gmail.com (simone codeluppi)
Date: Fri, 06 Jan 2017 17:13:28 +0000
Subject: [scikit-image] Image analysis pipeline improvement suggestions
In-Reply-To: <CAN1J6jW=BHzWBZ7MderdceLC=gbNdS+mWbVjzXoSdcmNvNUjxw@mail.gmail.com>
References: <CACi8E-B6EEA=zXKoOZHVNQf7oq-es=gPgvKQnzRzn_yvpiM=4g@mail.gmail.com>
 <CAN1J6jW=BHzWBZ7MderdceLC=gbNdS+mWbVjzXoSdcmNvNUjxw@mail.gmail.com>
Message-ID: <CACi8E-DQGTcphsxi6qpFiw4gpJRPnw-axhRKeZXTQTjS52U5Ww@mail.gmail.com>

Hi Nathan
thanks a lot for the infos!
I looked into it and it seems promising, I just need to understand if it is
possible to save numpy data into feather.

In the pipeline I developed, in the majority of the intermediate steps the
generated numpy arrays are saved as single file (as .lzma using
joblib.dump) that are then written on a single hdf5 file at the end of the
processing step. However, as it is now one of the steps require parallel
writing to the file. After your suggestion and some discussion on stack
overflow I think that the best solution will be to modify the code and skip
the parallel writing.

The main issue with the RAM however is related to some of the large image
stacks I need to filter (using scipy already made filters). Unfortunately
the only way out will be to chunk the images, process them on different
cores and then re-join them if the full image can fit in RAM.

Thanks a lot for the help!

Simone

On Wed, Dec 28, 2016 at 2:37 PM Nathan Faggian <nathan.faggian at gmail.com>
wrote:

> Hi Simone,
>
> I have had a little experience with HDF5 and am interested to see where
> you go with this. I wonder if you could use "feather":
>     https://github.com/wesm/feather
>
> There was a recent post from Wes McKinney about feather, which sparked my
> interest:
>    http://wesmckinney.com/blog/high-perf-arrow-to-pandas/
>
> Do you use HDF5 to store intermediates? if so, I would try storing
> intermediates to a file format like feather and then reducing to a HDF5
> file at the end. The reduction should be IO bound and not dependent on RAM
> so would suit your cluster.
>
> If you need to read a large array then I think HDF5 supports that (for
> single write but multiple reads) without the need for MPI - so this could
> map well to a tool like distributed:
>     http://distributed.readthedocs.io/en/latest/
>
> Not sure this helps, there is an assumption (on my part) that your
> intermediate calculations are not terabytes in size.
>
> Good luck!
>
> Nathan
>
>
> On 29 December 2016 at 05:07, simone codeluppi <simone.codeluppi at gmail.com
> > wrote:
>
> Hi all!
>
> I would like to pick your brain for some suggestion on how to modify my
> image analysis pipeline.
>
> I am analyzing terabytes of image stacks generated using a microscope. The
> current code I generated rely heavily on scikit-image, numpy and scipy. In
> order to speed up the analysis the code runs on a HPC computer (
> https://www.nsc.liu.se/systems/triolith/) with MPI (mpi4py) for
> parallelization and hdf5 (h5py) for file storage. The development cycle of
> the code has been pretty painful mainly due to my non familiarity with mpi
> and problems in compiling parallel hdf5 (with many open/closing bugs).
> However, the big drawback is that each core has only 2Gb of RAM (no shared
> ram across nodes) and in order to run some of the processing steps i ended
> up reserving one node (16 cores) but running only 3 cores in order to have
> enough ram (image chunking won?t work in this case). As you can imagine
> this is extremely inefficient and i end up getting low priority in the
> queue system.
>
>
> Our lab currently bought a new 4 nodes server with shared RAM running
> hadoop. My goal is to move the parallelization of the processing to dask. I
> tested it before in another system and works great. The drawback is that,
> if I understood correctly, parallel hdf5 works only with MPI
> (driver=?mpio?). Hdf5 gave me quite a bit of headache but works well in
> keeping a good structure of the data and i can save everything as numpy
> arrays?.very handy.
>
>
> If I will move to hadoop/dask what do you think will be a good solution
> for data storage? Do you have any additional suggestion that can improve
> the layout of the pipeline? Any help will be greatly appreciated.
>
>
> Simone
> --
> *Bad as he is, the Devil may be abus'd,*
> *Be falsy charg'd, and causelesly accus'd,*
> *When men, unwilling to be blam'd alone,*
> *Shift off these Crimes on Him which are their*
> *Own*
>
>                                                       *Daniel Defoe*
>
> simone.codeluppi at gmail.com
>
> simone at codeluppi.org
>
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>
> --
*Bad as he is, the Devil may be abus'd,*
*Be falsy charg'd, and causelesly accus'd,*
*When men, unwilling to be blam'd alone,*
*Shift off these Crimes on Him which are their*
*Own*

                                                      *Daniel Defoe*

simone.codeluppi at gmail.com

simone at codeluppi.org
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From jpboard2 at yahoo.com  Sun Jan  8 21:11:29 2017
From: jpboard2 at yahoo.com (James Board)
Date: Mon, 9 Jan 2017 02:11:29 +0000 (UTC)
Subject: [scikit-image] Compilation Problems
References: <462146064.760735.1483927889145.ref@mail.yahoo.com>
Message-ID: <462146064.760735.1483927889145@mail.yahoo.com>

I'm on a Red-Hat-like Linux machine and I tried to install scikit several ways and failed.  Here was one attempt:

> git clone https://github.com/scikit-image/scikit-image.git
> cd scikit-image
> python --version
Python 2.7.9

> pip install -e
Traceback (most recent call last):
  File "/usr/local/python/2.7.9/gnu//bin/pip", line 9, in <module>
    load_entry_point('pip==8.1.0', 'console_scripts', 'pip')()
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 568, in load_entry_point
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2720, in load_entry_point
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2380, in load
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2386, in resolve
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/__init__.py", line 15, in <module>
    from pip.vcs import git, mercurial, subversion, bazaar  # noqa
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/vcs/subversion.py", line 9, in <module>
    from pip.index import Link
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/index.py", line 30, in <module>
    from pip.wheel import Wheel, wheel_ext
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/wheel.py", line 39, in <module>
    from pip._vendor.distlib.scripts import ScriptMaker
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/_vendor/distlib/scripts.py", line 14, in <module>
    from .compat import sysconfig, detect_encoding, ZipFile
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/_vendor/distlib/compat.py", line 31, in <module>
    from urllib2 import (Request, urlopen, URLError, HTTPError,
ImportError: cannot import name HTTPSHandler

Here's another attempt that failed:

> easy_install --install-dir=/p/home/jpboard/SCIKIT -U scikit-image
Creating /p/home/jpboard/SCIKIT/site.py
Searching for scikit-image
Reading https://pypi.python.org/simple/scikit-image/
Download error on https://pypi.python.org/simple/scikit-image/: unknown url type: https -- Some packages may not be found!
Couldn't find index page for 'scikit-image' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading https://pypi.python.org/simple/
Download error on https://pypi.python.org/simple/: unknown url type: https -- Some packages may not be found!
No local packages or download links found for scikit-image
error: Could not find suitable distribution for Requirement.parse('scikit-image')

Can anyone tell what I'm doing wrong?   I tried all available options for me in the scikit documentation.  What should I do next?


From njs at pobox.com  Sun Jan  8 22:16:13 2017
From: njs at pobox.com (Nathaniel Smith)
Date: Sun, 8 Jan 2017 19:16:13 -0800
Subject: [scikit-image] Compilation Problems
In-Reply-To: <462146064.760735.1483927889145@mail.yahoo.com>
References: <462146064.760735.1483927889145.ref@mail.yahoo.com>
 <462146064.760735.1483927889145@mail.yahoo.com>
Message-ID: <CAPJVwB=gdA1JdFw8G9MkmQwtyJYNxNnF8rZZL=0yFfG_ExooKw@mail.gmail.com>

You appear to be using a self-built Python. Did you by chance forget
to install openssl-devel before building Python, so that you ended up
with a Python that has no ssl module?

-n

On Sun, Jan 8, 2017 at 6:11 PM, James Board via scikit-image
<scikit-image at python.org> wrote:
> I'm on a Red-Hat-like Linux machine and I tried to install scikit several ways and failed.  Here was one attempt:
>
>> git clone https://github.com/scikit-image/scikit-image.git
>> cd scikit-image
>> python --version
> Python 2.7.9
>
>> pip install -e
> Traceback (most recent call last):
>   File "/usr/local/python/2.7.9/gnu//bin/pip", line 9, in <module>
>     load_entry_point('pip==8.1.0', 'console_scripts', 'pip')()
>   File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 568, in load_entry_point
>   File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2720, in load_entry_point
>   File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2380, in load
>   File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2386, in resolve
>   File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/__init__.py", line 15, in <module>
>     from pip.vcs import git, mercurial, subversion, bazaar  # noqa
>   File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/vcs/subversion.py", line 9, in <module>
>     from pip.index import Link
>   File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/index.py", line 30, in <module>
>     from pip.wheel import Wheel, wheel_ext
>   File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/wheel.py", line 39, in <module>
>     from pip._vendor.distlib.scripts import ScriptMaker
>   File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/_vendor/distlib/scripts.py", line 14, in <module>
>     from .compat import sysconfig, detect_encoding, ZipFile
>   File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/_vendor/distlib/compat.py", line 31, in <module>
>     from urllib2 import (Request, urlopen, URLError, HTTPError,
> ImportError: cannot import name HTTPSHandler
>
> Here's another attempt that failed:
>
>> easy_install --install-dir=/p/home/jpboard/SCIKIT -U scikit-image
> Creating /p/home/jpboard/SCIKIT/site.py
> Searching for scikit-image
> Reading https://pypi.python.org/simple/scikit-image/
> Download error on https://pypi.python.org/simple/scikit-image/: unknown url type: https -- Some packages may not be found!
> Couldn't find index page for 'scikit-image' (maybe misspelled?)
> Scanning index of all packages (this may take a while)
> Reading https://pypi.python.org/simple/
> Download error on https://pypi.python.org/simple/: unknown url type: https -- Some packages may not be found!
> No local packages or download links found for scikit-image
> error: Could not find suitable distribution for Requirement.parse('scikit-image')
>
> Can anyone tell what I'm doing wrong?   I tried all available options for me in the scikit documentation.  What should I do next?
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image



-- 
Nathaniel J. Smith -- https://vorpus.org

From jpboard2 at yahoo.com  Tue Jan 10 10:33:08 2017
From: jpboard2 at yahoo.com (James Board)
Date: Tue, 10 Jan 2017 15:33:08 +0000 (UTC)
Subject: [scikit-image] Fw: Re:  Compilation Problems
References: <233536092.319170.1484062388065.ref@mail.yahoo.com>
Message-ID: <233536092.319170.1484062388065@mail.yahoo.com>

I don't have root access on this
machine and I personally didn't install the python
version.? I can't tell if the sysadmins installed
openssl-devel before building python.

How sure are you that this is causing my problem?? I
could build python and openssl-devel myself.? But
without root access, that could be a lot of work because
I'll have to track down each dependency manually.

Thank you for replying.


> 
> --------------------------------------------
> On Sun, 1/8/17, Nathaniel Smith <njs at pobox.com>
> wrote:
> 
>  Subject: Re: [scikit-image] Compilation Problems
>  To: "James Board" <jpboard2 at yahoo.com>
>  Cc: scikit-image at python.org
>  Date: Sunday, January 8, 2017, 10:16 PM
>  
>  You appear to be using a self-built
>  Python. Did you by chance forget
>  to install openssl-devel before building Python, so that
> you
>  ended up
>  with a Python that has no ssl module?
>  
>  -n
>  
>  On Sun, Jan 8, 2017 at 6:11 PM, James Board via
>  scikit-image
>  <scikit-image at python.org>
>  wrote:
>  > I'm on a Red-Hat-like Linux machine and I tried to
>  install scikit several ways and failed.? Here was one
>  attempt:
>  >
>  >> git clone https://github.com/scikit-image/scikit-image.git
>  >> cd scikit-image
>  >> python --version
>  > Python 2.7.9
>  >
>  >> pip install -e
>  > Traceback (most recent call last):
>  >???File
>  "/usr/local/python/2.7.9/gnu//bin/pip", line 9, in
>  <module>
>  >? ???load_entry_point('pip==8.1.0',
>  'console_scripts', 'pip')()
>  >???File
>  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
>  line 568, in load_entry_point
>  >???File
>  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
>  line 2720, in load_entry_point
>  >???File
>  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
>  line 2380, in load
>  >???File
>  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
>  line 2386, in resolve
>  >???File
>  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/__init__.py",
>  line 15, in <module>
>  >? ???from pip.vcs import git,
>  mercurial, subversion, bazaar? # noqa
>  >???File
>  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/vcs/subversion.py",
>  line 9, in <module>
>  >? ???from pip.index import Link
>  >???File
>  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/index.py",
>  line 30, in <module>
>  >? ???from pip.wheel import Wheel,
>  wheel_ext
>  >???File
>  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/wheel.py",
>  line 39, in <module>
>  >? ???from
>  pip._vendor.distlib.scripts import ScriptMaker
>  >???File
>  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/_vendor/distlib/scripts.py",
>  line 14, in <module>
>  >? ???from .compat import sysconfig,
>  detect_encoding, ZipFile
>  >???File
>  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/_vendor/distlib/compat.py",
>  line 31, in <module>
>  >? ???from urllib2 import (Request,
>  urlopen, URLError, HTTPError,
>  > ImportError: cannot import name HTTPSHandler
>  >
>  > Here's another attempt that failed:
>  >
>  >> easy_install --install-dir=/p/home/jpboard/SCIKIT
>  -U scikit-image
>  > Creating /p/home/jpboard/SCIKIT/site.py
>  > Searching for scikit-image
>  > Reading https://pypi.python.org/simple/scikit-image/
>  > Download error on
> https://pypi.python.org/simple/scikit-image/:
>  unknown url type: https -- Some packages may not be
>  found!
>  > Couldn't find index page for 'scikit-image' (maybe
>  misspelled?)
>  > Scanning index of all packages (this may take a
> while)
>  > Reading https://pypi.python.org/simple/
>  > Download error on https://pypi.python.org/simple/: unknown url type:
>  https -- Some packages may not be found!
>  > No local packages or download links found for
>  scikit-image
>  > error: Could not find suitable distribution for
>  Requirement.parse('scikit-image')
>  >
>  > Can anyone tell what I'm doing
>  wrong????I tried all available options for me
>  in the scikit documentation.? What should I do next?
>  >
>  > _______________________________________________
>  > scikit-image mailing list
>  > scikit-image at python.org
>  > https://mail.python.org/mailman/listinfo/scikit-image
>  
>  
>  
>  -- 
>  Nathaniel J. Smith -- https://vorpus.org
>  

From jpboard2 at yahoo.com  Tue Jan 10 11:56:29 2017
From: jpboard2 at yahoo.com (James Board)
Date: Tue, 10 Jan 2017 16:56:29 +0000 (UTC)
Subject: [scikit-image] Fw: Re: Compilation Problems
References: <1790865824.413838.1484067389133.ref@mail.yahoo.com>
Message-ID: <1790865824.413838.1484067389133@mail.yahoo.com>

I just tried both.  Here are the error messages:



pip install scikit-image --user
Traceback (most recent call last):
  File "/usr/local/python/2.7.9/gnu/bin/pip", line 9, in <module>
    load_entry_point('pip==8.1.0', 'console_scripts', 'pip')()
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 568, in load_entry_point
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2720, in load_entry_point
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2380, in load
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2386, in resolve
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/__init__.py", line 15, in <module>
    from pip.vcs import git, mercurial, subversion, bazaar  # noqa
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/vcs/subversion.py", line 9, in <module>
    from pip.index import Link
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/index.py", line 30, in <module>
    from pip.wheel import Wheel, wheel_ext
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/wheel.py", line 39, in <module>
    from pip._vendor.distlib.scripts import ScriptMaker
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/_vendor/distlib/scripts.py", line 14, in <module>
    from .compat import sysconfig, detect_encoding, ZipFile
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/_vendor/distlib/compat.py", line 31, in <module>
    from urllib2 import (Request, urlopen, URLError, HTTPError,
ImportError: cannot import name HTTPSHandler

And in the cloned directory:

> cd scikit-image
> pip install . --user
Traceback (most recent call last):
  File "/usr/local/python/2.7.9/gnu/bin/pip", line 9, in <module>
    load_entry_point('pip==8.1.0', 'console_scripts', 'pip')()
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 568, in load_entry_point
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2720, in load_entry_point
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2380, in load
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2386, in resolve
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/__init__.py", line 15, in <module>
    from pip.vcs import git, mercurial, subversion, bazaar  # noqa
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/vcs/subversion.py", line 9, in <module>
    from pip.index import Link
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/index.py", line 30, in <module>
    from pip.wheel import Wheel, wheel_ext
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/wheel.py", line 39, in <module>
    from pip._vendor.distlib.scripts import ScriptMaker
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/_vendor/distlib/scripts.py", line 14, in <module>
    from .compat import sysconfig, detect_encoding, ZipFile
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-8.1.0-py2.7.egg/pip/_vendor/distlib/compat.py", line 31, in <module>
    from urllib2 import (Request, urlopen, URLError, HTTPError,
ImportError: cannot import name HTTPSHandler




 

From jpboard2 at yahoo.com  Tue Jan 10 12:00:29 2017
From: jpboard2 at yahoo.com (James Board)
Date: Tue, 10 Jan 2017 17:00:29 +0000 (UTC)
Subject: [scikit-image] Fw: Re: Compilation Problems
References: <308740834.401096.1484067629670.ref@mail.yahoo.com>
Message-ID: <308740834.401096.1484067629670@mail.yahoo.com>

I'm not sure what you mean by anaconda.  There are two relevant software packages named anaconda.  From Wikipedia:

    1) Anaconda is the installer for Red Hat Enterprise Linux, Oracle Linux, Scientific Linux, CentOS and Fedora.

    2) Anaconda is a freemium[2] open source[3] distribution of the Python and R programming languages for large-scale data processing, predictive analytics, and scientific computing, that aims to simplify package management and deployment.[4][5][6][7][8] Its package management system is conda.

Which one are you referring to?  

--------------------------------------------
On Tue, 1/10/17, Josh Warner <silvertrumpet999 at gmail.com> wrote:

 Subject: Re: [scikit-image] Fw: Re: Compilation Problems
 To: "James Board" <jpboard2 at yahoo.com>
 Date: Tuesday, January 10, 2017, 10:39 AM
 
 The simplest way to
 handle this, if you don't have the privileges to get
 openssl-dev or even properly troubleshoot the system
 install, is to abandon the system Python in favor of
 Anaconda/Miniconda or another full distribution that can
 install and run exclusively in user space.
 Keeping all your packages
 easily up to date, dependency management, trivial virtual
 environments, etc. are other huge benefits of this
 approach.
 On Tue, Jan 10, 2017 at
 9:33 AM, James Board via scikit-image <scikit-image at python.org>
 wrote:
 I
 don't have root access on this
 
 machine and I personally didn't install the python
 
 version.? I can't tell if the sysadmins installed
 
 openssl-devel before building python.
 
 
 
 How sure are you that this is causing my problem?? I
 
 could build python and openssl-devel myself.? But
 
 without root access, that could be a lot of work because
 
 I'll have to track down each dependency manually.
 
 
 
 Thank you for replying.
 
 
 
 
 
 >
 
 > ------------------------------ --------------
 
 > On Sun, 1/8/17, Nathaniel Smith <njs at pobox.com>
 
 > wrote:
 
 >
 
 >? Subject: Re: [scikit-image] Compilation Problems
 
 >? To: "James Board" <jpboard2 at yahoo.com>
 
 >? Cc: scikit-image at python.org
 
 >? Date: Sunday, January 8, 2017, 10:16 PM
 
 >
 
 >? You appear to be using a self-built
 
 >? Python. Did you by chance forget
 
 >? to install openssl-devel before building Python, so
 that
 
 > you
 
 >? ended up
 
 >? with a Python that has no ssl module?
 
 >
 
 >? -n
 
 >
 
 >? On Sun, Jan 8, 2017 at 6:11 PM, James Board via
 
 >? scikit-image
 
 >? <scikit-image at python.org>
 
 >? wrote:
 
 >? > I'm on a Red-Hat-like Linux machine and I
 tried to
 
 >? install scikit several ways and failed.? Here was
 one
 
 >? attempt:
 
 >? >
 
 >? >> git clone https://github.com/scikit-
 image/scikit-image.git
 
 >? >> cd scikit-image
 
 >? >> python --version
 
 >? > Python 2.7.9
 
 >? >
 
 >? >> pip install -e
 
 >? > Traceback (most recent call last):
 
 >? >???File
 
 >? "/usr/local/python/2.7.9/gnu// bin/pip",
 line 9, in
 
 >? <module>
 
 >? >? ???load_entry_point('pip==8.1.
 0',
 
 >? 'console_scripts', 'pip')()
 
 >? >???File
 
 >? "build/bdist.linux-x86_64/egg/
 pkg_resources/__init__.py",
 
 >? line 568, in load_entry_point
 
 >? >???File
 
 >? "build/bdist.linux-x86_64/egg/
 pkg_resources/__init__.py",
 
 >? line 2720, in load_entry_point
 
 >? >???File
 
 >? "build/bdist.linux-x86_64/egg/
 pkg_resources/__init__.py",
 
 >? line 2380, in load
 
 >? >???File
 
 >? "build/bdist.linux-x86_64/egg/
 pkg_resources/__init__.py",
 
 >? line 2386, in resolve
 
 >? >???File
 
 >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/__
 init__.py",
 
 >? line 15, in <module>
 
 >? >? ???from pip.vcs import git,
 
 >? mercurial, subversion, bazaar? # noqa
 
 >? >???File
 
 >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/vcs/
 subversion.py",
 
 >? line 9, in <module>
 
 >? >? ???from pip.index import Link
 
 >? >???File
 
 >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/index.
 py",
 
 >? line 30, in <module>
 
 >? >? ???from pip.wheel import Wheel,
 
 >? wheel_ext
 
 >? >???File
 
 >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/wheel.
 py",
 
 >? line 39, in <module>
 
 >? >? ???from
 
 >? pip._vendor.distlib.scripts import ScriptMaker
 
 >? >???File
 
 >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/_
 vendor/distlib/scripts.py",
 
 >? line 14, in <module>
 
 >? >? ???from .compat import sysconfig,
 
 >? detect_encoding, ZipFile
 
 >? >???File
 
 >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/_
 vendor/distlib/compat.py",
 
 >? line 31, in <module>
 
 >? >? ???from urllib2 import (Request,
 
 >? urlopen, URLError, HTTPError,
 
 >? > ImportError: cannot import name HTTPSHandler
 
 >? >
 
 >? > Here's another attempt that failed:
 
 >? >
 
 >? >> easy_install --install-dir=/p/home/jpboard/
 SCIKIT
 
 >? -U scikit-image
 
 >? > Creating /p/home/jpboard/SCIKIT/site.py
 
 >? > Searching for scikit-image
 
 >? > Reading https://pypi.python.org/
 simple/scikit-image/
 
 >? > Download error on
 
 > https://pypi.python.org/
 simple/scikit-image/:
 
 >? unknown url type: https -- Some packages may not
 be
 
 >? found!
 
 >? > Couldn't find index page for
 'scikit-image' (maybe
 
 >? misspelled?)
 
 >? > Scanning index of all packages (this may take
 a
 
 > while)
 
 >? > Reading https://pypi.python.org/
 simple/
 
 >? > Download error on https://pypi.python.org/
 simple/: unknown url type:
 
 >? https -- Some packages may not be found!
 
 >? > No local packages or download links found for
 
 >? scikit-image
 
 >? > error: Could not find suitable distribution
 for
 
 >? Requirement.parse('scikit- image')
 
 >? >
 
 >? > Can anyone tell what I'm doing
 
 >? wrong????I tried all available options for me
 
 >? in the scikit documentation.? What should I do
 next?
 
 >? >
 
 >? > ______________________________
 _________________
 
 >? > scikit-image mailing list
 
 >? > scikit-image at python.org
 
 >? > https://mail.python.org/
 mailman/listinfo/scikit-image
 
 >
 
 >
 
 >
 
 >? --
 
 >? Nathaniel J. Smith -- https://vorpus.org
 
 >
 
 ______________________________ _________________
 
 scikit-image mailing list
 
 scikit-image at python.org
 
 https://mail.python.org/
 mailman/listinfo/scikit-image
 
 
 

From jpboard2 at yahoo.com  Tue Jan 10 12:15:35 2017
From: jpboard2 at yahoo.com (James Board)
Date: Tue, 10 Jan 2017 17:15:35 +0000 (UTC)
Subject: [scikit-image] Older versions of scikit-image
References: <1902422295.436436.1484068535708.ref@mail.yahoo.com>
Message-ID: <1902422295.436436.1484068535708@mail.yahoo.com>

Where can I download scikit-image version 0.93?  There is a list of versions here
    http://scikit-image.org/docs/dev/install.html
But the links to older versions don't take me to an actual download page.

From guziy.sasha at gmail.com  Tue Jan 10 10:43:58 2017
From: guziy.sasha at gmail.com (Oleksandr Huziy)
Date: Tue, 10 Jan 2017 10:43:58 -0500
Subject: [scikit-image] Fw: Re: Compilation Problems
In-Reply-To: <233536092.319170.1484062388065@mail.yahoo.com>
References: <233536092.319170.1484062388065.ref@mail.yahoo.com>
 <233536092.319170.1484062388065@mail.yahoo.com>
Message-ID: <CAN3p1sUxHfNWd-rdkPzaU7QbYhBKU=nM75R3zeFyExZJQVCU1w@mail.gmail.com>

Hi James:

Have you tried?

pip install scikit-image --user

Or with the cloned directory:
pip install . --user


Cheers





2017-01-10 10:33 GMT-05:00 James Board via scikit-image <
scikit-image at python.org>:

> I don't have root access on this
> machine and I personally didn't install the python
> version.  I can't tell if the sysadmins installed
> openssl-devel before building python.
>
> How sure are you that this is causing my problem?  I
> could build python and openssl-devel myself.  But
> without root access, that could be a lot of work because
> I'll have to track down each dependency manually.
>
> Thank you for replying.
>
>
> >
> > --------------------------------------------
> > On Sun, 1/8/17, Nathaniel Smith <njs at pobox.com>
> > wrote:
> >
> >  Subject: Re: [scikit-image] Compilation Problems
> >  To: "James Board" <jpboard2 at yahoo.com>
> >  Cc: scikit-image at python.org
> >  Date: Sunday, January 8, 2017, 10:16 PM
> >
> >  You appear to be using a self-built
> >  Python. Did you by chance forget
> >  to install openssl-devel before building Python, so that
> > you
> >  ended up
> >  with a Python that has no ssl module?
> >
> >  -n
> >
> >  On Sun, Jan 8, 2017 at 6:11 PM, James Board via
> >  scikit-image
> >  <scikit-image at python.org>
> >  wrote:
> >  > I'm on a Red-Hat-like Linux machine and I tried to
> >  install scikit several ways and failed.  Here was one
> >  attempt:
> >  >
> >  >> git clone https://github.com/scikit-image/scikit-image.git
> >  >> cd scikit-image
> >  >> python --version
> >  > Python 2.7.9
> >  >
> >  >> pip install -e
> >  > Traceback (most recent call last):
> >  >   File
> >  "/usr/local/python/2.7.9/gnu//bin/pip", line 9, in
> >  <module>
> >  >     load_entry_point('pip==8.1.0',
> >  'console_scripts', 'pip')()
> >  >   File
> >  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
> >  line 568, in load_entry_point
> >  >   File
> >  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
> >  line 2720, in load_entry_point
> >  >   File
> >  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
> >  line 2380, in load
> >  >   File
> >  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
> >  line 2386, in resolve
> >  >   File
> >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/
> pip-8.1.0-py2.7.egg/pip/__init__.py",
> >  line 15, in <module>
> >  >     from pip.vcs import git,
> >  mercurial, subversion, bazaar  # noqa
> >  >   File
> >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/
> pip-8.1.0-py2.7.egg/pip/vcs/subversion.py",
> >  line 9, in <module>
> >  >     from pip.index import Link
> >  >   File
> >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/
> pip-8.1.0-py2.7.egg/pip/index.py",
> >  line 30, in <module>
> >  >     from pip.wheel import Wheel,
> >  wheel_ext
> >  >   File
> >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/
> pip-8.1.0-py2.7.egg/pip/wheel.py",
> >  line 39, in <module>
> >  >     from
> >  pip._vendor.distlib.scripts import ScriptMaker
> >  >   File
> >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/
> pip-8.1.0-py2.7.egg/pip/_vendor/distlib/scripts.py",
> >  line 14, in <module>
> >  >     from .compat import sysconfig,
> >  detect_encoding, ZipFile
> >  >   File
> >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/
> pip-8.1.0-py2.7.egg/pip/_vendor/distlib/compat.py",
> >  line 31, in <module>
> >  >     from urllib2 import (Request,
> >  urlopen, URLError, HTTPError,
> >  > ImportError: cannot import name HTTPSHandler
> >  >
> >  > Here's another attempt that failed:
> >  >
> >  >> easy_install --install-dir=/p/home/jpboard/SCIKIT
> >  -U scikit-image
> >  > Creating /p/home/jpboard/SCIKIT/site.py
> >  > Searching for scikit-image
> >  > Reading https://pypi.python.org/simple/scikit-image/
> >  > Download error on
> > https://pypi.python.org/simple/scikit-image/:
> >  unknown url type: https -- Some packages may not be
> >  found!
> >  > Couldn't find index page for 'scikit-image' (maybe
> >  misspelled?)
> >  > Scanning index of all packages (this may take a
> > while)
> >  > Reading https://pypi.python.org/simple/
> >  > Download error on https://pypi.python.org/simple/: unknown url type:
> >  https -- Some packages may not be found!
> >  > No local packages or download links found for
> >  scikit-image
> >  > error: Could not find suitable distribution for
> >  Requirement.parse('scikit-image')
> >  >
> >  > Can anyone tell what I'm doing
> >  wrong?   I tried all available options for me
> >  in the scikit documentation.  What should I do next?
> >  >
> >  > _______________________________________________
> >  > scikit-image mailing list
> >  > scikit-image at python.org
> >  > https://mail.python.org/mailman/listinfo/scikit-image
> >
> >
> >
> >  --
> >  Nathaniel J. Smith -- https://vorpus.org
> >
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>



-- 
Sasha
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From jpboard2 at yahoo.com  Tue Jan 10 12:31:28 2017
From: jpboard2 at yahoo.com (James Board)
Date: Tue, 10 Jan 2017 17:31:28 +0000 (UTC)
Subject: [scikit-image] Fw: Re: Compilation Problems
References: <808182212.422794.1484069488444.ref@mail.yahoo.com>
Message-ID: <808182212.422794.1484069488444@mail.yahoo.com>

I made some progress.  I tried this command in the cloned version of scikit-image and it got fairly deep into the compilation process:

python setup.py install --prefix ~/SCIKIT

However, it ultimately failed with these error messages:

Processing dependencies for scikit-image==0.13.dev0
Searching for PyWavelets>=0.4.0
Reading https://pypi.python.org/simple/PyWavelets/
Download error on https://pypi.python.org/simple/PyWavelets/: unknown url type: https -- Some packages may not be found!
Couldn't find index page for 'PyWavelets' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading https://pypi.python.org/simple/
Download error on https://pypi.python.org/simple/: unknown url type: https -- Some packages may not be found!
No local packages or download links found for PyWavelets>=0.4.0
error: Could not find suitable distribution for Requirement.parse('PyWavelets>=0.4.0')

What is the cause of this? 


From guziy.sasha at gmail.com  Tue Jan 10 13:40:39 2017
From: guziy.sasha at gmail.com (Oleksandr Huziy)
Date: Tue, 10 Jan 2017 13:40:39 -0500
Subject: [scikit-image] Fw: Re: Compilation Problems
In-Reply-To: <808182212.422794.1484069488444@mail.yahoo.com>
References: <808182212.422794.1484069488444.ref@mail.yahoo.com>
 <808182212.422794.1484069488444@mail.yahoo.com>
Message-ID: <CAN3p1sX3Xu3GfP2m96iF2E3ziGmLfMKPOGsA3Jt9rrngSnSz2Q@mail.gmail.com>

Hi James:

Can you ask admins of the server to install openssl-devel? That could make
your task much easier..

Are you stuck with this python version? sometimes there might be several
python versions installed on a server, you could try python<Tab> to see
what else is there.

Cheers




2017-01-10 12:31 GMT-05:00 James Board via scikit-image <
scikit-image at python.org>:

> I made some progress.  I tried this command in the cloned version of
> scikit-image and it got fairly deep into the compilation process:
>
> python setup.py install --prefix ~/SCIKIT
>
> However, it ultimately failed with these error messages:
>
> Processing dependencies for scikit-image==0.13.dev0
> Searching for PyWavelets>=0.4.0
> Reading https://pypi.python.org/simple/PyWavelets/
> Download error on https://pypi.python.org/simple/PyWavelets/: unknown url
> type: https -- Some packages may not be found!
> Couldn't find index page for 'PyWavelets' (maybe misspelled?)
> Scanning index of all packages (this may take a while)
> Reading https://pypi.python.org/simple/
> Download error on https://pypi.python.org/simple/: unknown url type:
> https -- Some packages may not be found!
> No local packages or download links found for PyWavelets>=0.4.0
> error: Could not find suitable distribution for
> Requirement.parse('PyWavelets>=0.4.0')
>
> What is the cause of this?
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>



-- 
Sasha
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From stefanv at berkeley.edu  Tue Jan 10 14:10:46 2017
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Tue, 10 Jan 2017 11:10:46 -0800
Subject: [scikit-image] Fw: Re: Compilation Problems
In-Reply-To: <CAN3p1sUxHfNWd-rdkPzaU7QbYhBKU=nM75R3zeFyExZJQVCU1w@mail.gmail.com>
References: <233536092.319170.1484062388065.ref@mail.yahoo.com>
 <233536092.319170.1484062388065@mail.yahoo.com>
 <CAN3p1sUxHfNWd-rdkPzaU7QbYhBKU=nM75R3zeFyExZJQVCU1w@mail.gmail.com>
Message-ID: <1484075446.605305.843447977.62B541E2@webmail.messagingengine.com>

You may want to follow Nathaniel's suggestion and install a version of
Python that has SSL support.  Are you able to make a local Python
installation into your home directory?


St?fan



On Tue, Jan 10, 2017, at 07:43, Oleksandr Huziy wrote:

> Hi James:

> 

> Have you tried?

> 

> pip install scikit-image --user

> 

> Or with the cloned directory:

> pip install . --user

> 

> 

> Cheers

> 

> 

> 

> 

> 

> 2017-01-10 10:33 GMT-05:00 James Board via scikit-image <scikit-
> image at python.org>:
>> I don't have root access on this

>>  machine and I personally didn't install the python

>>  version.  I can't tell if the sysadmins installed

>>  openssl-devel before building python.

>> 

>>  How sure are you that this is causing my problem?  I

>>  could build python and openssl-devel myself.  But

>>  without root access, that could be a lot of work because

>>  I'll have to track down each dependency manually.

>> 

>>  Thank you for replying.

>> 

>> 

>>  >

>>  > --------------------------------------------

>>  > On Sun, 1/8/17, Nathaniel Smith <njs at pobox.com>

>>  > wrote:

>>  >

>>  >  Subject: Re: [scikit-image] Compilation Problems

>>  >  To: "James Board" <jpboard2 at yahoo.com>

>>  >  Cc: scikit-image at python.org

>>  >  Date: Sunday, January 8, 2017, 10:16 PM

>> 

>> >

>>  >  You appear to be using a self-built

>>  >  Python. Did you by chance forget

>>  >  to install openssl-devel before building Python, so that

>>  > you

>>  >  ended up

>>  >  with a Python that has no ssl module?

>>  >

>>  >  -n

>>  >

>>  >  On Sun, Jan 8, 2017 at 6:11 PM, James Board via

>>  >  scikit-image

>>  >  <scikit-image at python.org>

>>  >  wrote:

>>  >  > I'm on a Red-Hat-like Linux machine and I tried to

>>  >  install scikit several ways and failed.  Here was one

>>  >  attempt:

>>  >  >

>>  >  >> git clone https://github.com/scikit-image/scikit-image.git

>>  >  >> cd scikit-image

>>  >  >> python --version

>>  >  > Python 2.7.9

>>  >  >

>>  >  >> pip install -e

>>  >  > Traceback (most recent call last):

>>  >  >   File

>>  >  "/usr/local/python/2.7.9/gnu//bin/pip", line 9, in

>>  >  <module>

>>  >  >     load_entry_point('pip==8.1.0',

>>  >  'console_scripts', 'pip')()

>>  >  >   File

>>  >  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",

>>  >  line 568, in load_entry_point

>>  >  >   File

>>  >  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",

>>  >  line 2720, in load_entry_point

>>  >  >   File

>>  >  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",

>>  >  line 2380, in load

>>  >  >   File

>>  >  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",

>>  >  line 2386, in resolve

>>  >  >   File

>>  >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-
>>  >  8.1.0-py2.7.egg/pip/__init__.py",
>>  >  line 15, in <module>

>>  >  >     from pip.vcs import git,

>>  >  mercurial, subversion, bazaar  # noqa

>>  >  >   File

>>  >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-
>>  >  8.1.0-py2.7.egg/pip/vcs/subversion.py",
>>  >  line 9, in <module>

>>  >  >     from pip.index import Link

>>  >  >   File

>>  >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-
>>  >  8.1.0-py2.7.egg/pip/index.py",
>>  >  line 30, in <module>

>>  >  >     from pip.wheel import Wheel,

>>  >  wheel_ext

>>  >  >   File

>>  >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-
>>  >  8.1.0-py2.7.egg/pip/wheel.py",
>>  >  line 39, in <module>

>>  >  >     from

>>  >  pip._vendor.distlib.scripts import ScriptMaker

>>  >  >   File

>>  >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-
>>  >  8.1.0-py2.7.egg/pip/_vendor/distlib/scripts.py",
>>  >  line 14, in <module>

>>  >  >     from .compat import sysconfig,

>>  >  detect_encoding, ZipFile

>>  >  >   File

>>  >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip-
>>  >  8.1.0-py2.7.egg/pip/_vendor/distlib/compat.py",
>>  >  line 31, in <module>

>>  >  >     from urllib2 import (Request,

>>  >  urlopen, URLError, HTTPError,

>>  >  > ImportError: cannot import name HTTPSHandler

>>  >  >

>>  >  > Here's another attempt that failed:

>>  >  >

>>  >  >> easy_install --install-dir=/p/home/jpboard/SCIKIT

>>  >  -U scikit-image

>>  >  > Creating /p/home/jpboard/SCIKIT/site.py

>>  >  > Searching for scikit-image

>>  >  > Reading https://pypi.python.org/simple/scikit-image/

>>  >  > Download error on

>>  > https://pypi.python.org/simple/scikit-image/:

>>  >  unknown url type: https -- Some packages may not be

>>  >  found!

>>  >  > Couldn't find index page for 'scikit-image' (maybe

>>  >  misspelled?)

>>  >  > Scanning index of all packages (this may take a

>>  > while)

>>  >  > Reading https://pypi.python.org/simple/

>>  >  > Download error on https://pypi.python.org/simple/: unknown url
>>  >  > type:
>>  >  https -- Some packages may not be found!

>>  >  > No local packages or download links found for

>>  >  scikit-image

>>  >  > error: Could not find suitable distribution for

>>  >  Requirement.parse('scikit-image')

>>  >  >

>>  >  > Can anyone tell what I'm doing

>>  >  wrong?   I tried all available options for me

>>  >  in the scikit documentation.  What should I do next?

>>  >  >

>>  >  > _______________________________________________

>>  >  > scikit-image mailing list

>>  >  > scikit-image at python.org

>>  >  > https://mail.python.org/mailman/listinfo/scikit-image

>>  >

>>  >

>>  >

>>  >  --

>>  >  Nathaniel J. Smith -- https://vorpus.org

>>  >

>>  _______________________________________________

>>  scikit-image mailing list

>> scikit-image at python.org

>> https://mail.python.org/mailman/listinfo/scikit-image

> 

> 

> 

> -- 

> Sasha

> _________________________________________________

> scikit-image mailing list

> scikit-image at python.org

> https://mail.python.org/mailman/listinfo/scikit-image


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From stefanv at berkeley.edu  Tue Jan 10 14:11:39 2017
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Tue, 10 Jan 2017 11:11:39 -0800
Subject: [scikit-image] Older versions of scikit-image
In-Reply-To: <1902422295.436436.1484068535708@mail.yahoo.com>
References: <1902422295.436436.1484068535708.ref@mail.yahoo.com>
 <1902422295.436436.1484068535708@mail.yahoo.com>
Message-ID: <1484075499.605780.843449433.623897F1@webmail.messagingengine.com>

On Tue, Jan 10, 2017, at 09:15, James Board via scikit-image wrote:
> Where can I download scikit-image version 0.93?  There is a list of
> versions here
>     http://scikit-image.org/docs/dev/install.html
> But the links to older versions don't take me to an actual download page.

Do you have a specific need for such an old version?  Otherwise, you can
install via pip on most platforms (or conda, if you use that).

St?fan

From guziy.sasha at gmail.com  Tue Jan 10 14:15:18 2017
From: guziy.sasha at gmail.com (Oleksandr Huziy)
Date: Tue, 10 Jan 2017 14:15:18 -0500
Subject: [scikit-image] Fw: Re: Compilation Problems
In-Reply-To: <1484075446.605305.843447977.62B541E2@webmail.messagingengine.com>
References: <233536092.319170.1484062388065.ref@mail.yahoo.com>
 <233536092.319170.1484062388065@mail.yahoo.com>
 <CAN3p1sUxHfNWd-rdkPzaU7QbYhBKU=nM75R3zeFyExZJQVCU1w@mail.gmail.com>
 <1484075446.605305.843447977.62B541E2@webmail.messagingengine.com>
Message-ID: <CAN3p1sU9KCcvNEubQ0FgR_FuX7ohUMHAOxFTO7f6Nb3JK8vBTg@mail.gmail.com>

Hi Stefan:


> You may want to follow Nathaniel's suggestion and install a version of
> Python that has SSL support.  Are you able to make a local Python
> installation into your home directory?


I am afraid he would still need the openssl library or is it included in
the python sources?

Cheers



2017-01-10 14:10 GMT-05:00 Stefan van der Walt <stefanv at berkeley.edu>:

> You may want to follow Nathaniel's suggestion and install a version of
> Python that has SSL support.  Are you able to make a local Python
> installation into your home directory?
>
> St?fan
>
> On Tue, Jan 10, 2017, at 07:43, Oleksandr Huziy wrote:
>
> Hi James:
>
> Have you tried?
>
> pip install scikit-image --user
>
> Or with the cloned directory:
> pip install . --user
>
>
> Cheers
>
>
>
>
>
> 2017-01-10 10:33 GMT-05:00 James Board via scikit-image <
> scikit-image at python.org>:
>
> I don't have root access on this
> machine and I personally didn't install the python
> version.  I can't tell if the sysadmins installed
> openssl-devel before building python.
>
> How sure are you that this is causing my problem?  I
> could build python and openssl-devel myself.  But
> without root access, that could be a lot of work because
> I'll have to track down each dependency manually.
>
> Thank you for replying.
>
>
> >
> > --------------------------------------------
> > On Sun, 1/8/17, Nathaniel Smith <njs at pobox.com>
> > wrote:
> >
> >  Subject: Re: [scikit-image] Compilation Problems
> >  To: "James Board" <jpboard2 at yahoo.com>
> >  Cc: scikit-image at python.org
> >  Date: Sunday, January 8, 2017, 10:16 PM
>
> >
> >  You appear to be using a self-built
> >  Python. Did you by chance forget
> >  to install openssl-devel before building Python, so that
> > you
> >  ended up
> >  with a Python that has no ssl module?
> >
> >  -n
> >
> >  On Sun, Jan 8, 2017 at 6:11 PM, James Board via
> >  scikit-image
> >  <scikit-image at python.org>
> >  wrote:
> >  > I'm on a Red-Hat-like Linux machine and I tried to
> >  install scikit several ways and failed.  Here was one
> >  attempt:
> >  >
> >  >> git clone https://github.com/scikit-image/scikit-image.git
> >  >> cd scikit-image
> >  >> python --version
> >  > Python 2.7.9
> >  >
> >  >> pip install -e
> >  > Traceback (most recent call last):
> >  >   File
> >  "/usr/local/python/2.7.9/gnu//bin/pip", line 9, in
> >  <module>
> >  >     load_entry_point('pip==8.1.0',
> >  'console_scripts', 'pip')()
> >  >   File
> >  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
> >  line 568, in load_entry_point
> >  >   File
> >  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
> >  line 2720, in load_entry_point
> >  >   File
> >  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
> >  line 2380, in load
> >  >   File
> >  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
> >  line 2386, in resolve
> >  >   File
> >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip
> -8.1.0-py2.7.egg/pip/__init__.py",
> >  line 15, in <module>
> >  >     from pip.vcs import git,
> >  mercurial, subversion, bazaar  # noqa
> >  >   File
> >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip
> -8.1.0-py2.7.egg/pip/vcs/subversion.py",
> >  line 9, in <module>
> >  >     from pip.index import Link
> >  >   File
> >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip
> -8.1.0-py2.7.egg/pip/index.py",
> >  line 30, in <module>
> >  >     from pip.wheel import Wheel,
> >  wheel_ext
> >  >   File
> >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip
> -8.1.0-py2.7.egg/pip/wheel.py",
> >  line 39, in <module>
> >  >     from
> >  pip._vendor.distlib.scripts import ScriptMaker
> >  >   File
> >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip
> -8.1.0-py2.7.egg/pip/_vendor/distlib/scripts.py",
> >  line 14, in <module>
> >  >     from .compat import sysconfig,
> >  detect_encoding, ZipFile
> >  >   File
> >  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/pip
> -8.1.0-py2.7.egg/pip/_vendor/distlib/compat.py",
> >  line 31, in <module>
> >  >     from urllib2 import (Request,
> >  urlopen, URLError, HTTPError,
> >  > ImportError: cannot import name HTTPSHandler
> >  >
> >  > Here's another attempt that failed:
> >  >
> >  >> easy_install --install-dir=/p/home/jpboard/SCIKIT
> >  -U scikit-image
> >  > Creating /p/home/jpboard/SCIKIT/site.py
> >  > Searching for scikit-image
> >  > Reading https://pypi.python.org/simple/scikit-image/
> >  > Download error on
> > https://pypi.python.org/simple/scikit-image/:
> >  unknown url type: https -- Some packages may not be
> >  found!
> >  > Couldn't find index page for 'scikit-image' (maybe
> >  misspelled?)
> >  > Scanning index of all packages (this may take a
> > while)
> >  > Reading https://pypi.python.org/simple/
> >  > Download error on https://pypi.python.org/simple/: unknown url type:
> >  https -- Some packages may not be found!
> >  > No local packages or download links found for
> >  scikit-image
> >  > error: Could not find suitable distribution for
> >  Requirement.parse('scikit-image')
> >  >
> >  > Can anyone tell what I'm doing
> >  wrong?   I tried all available options for me
> >  in the scikit documentation.  What should I do next?
> >  >
> >  > _______________________________________________
> >  > scikit-image mailing list
> >  > scikit-image at python.org
> >  > https://mail.python.org/mailman/listinfo/scikit-image
> >
> >
> >
> >  --
> >  Nathaniel J. Smith -- https://vorpus.org
> >
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>
>
>
> --
> Sasha
> *_______________________________________________*
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>
>


-- 
Sasha
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From stefanv at berkeley.edu  Tue Jan 10 14:17:59 2017
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Tue, 10 Jan 2017 11:17:59 -0800
Subject: [scikit-image] Fw: Re: Compilation Problems
In-Reply-To: <CAN3p1sU9KCcvNEubQ0FgR_FuX7ohUMHAOxFTO7f6Nb3JK8vBTg@mail.gmail.com>
References: <233536092.319170.1484062388065.ref@mail.yahoo.com>
 <233536092.319170.1484062388065@mail.yahoo.com>
 <CAN3p1sUxHfNWd-rdkPzaU7QbYhBKU=nM75R3zeFyExZJQVCU1w@mail.gmail.com>
 <1484075446.605305.843447977.62B541E2@webmail.messagingengine.com>
 <CAN3p1sU9KCcvNEubQ0FgR_FuX7ohUMHAOxFTO7f6Nb3JK8vBTg@mail.gmail.com>
Message-ID: <1484075879.607141.843455369.5F6BCB71@webmail.messagingengine.com>

On Tue, Jan 10, 2017, at 11:15, Oleksandr Huziy wrote:

> I am afraid he would still need the openssl library or is it included
> in the python sources?


Ah, I see what you mean; I thought some of those binaries would be
static compiles, but I guess they may not be.  A simple experiment
should suffice to clear that up :)


St?fan


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From stefanv at berkeley.edu  Tue Jan 10 14:18:49 2017
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Tue, 10 Jan 2017 11:18:49 -0800
Subject: [scikit-image] Fw: Re: Compilation Problems
In-Reply-To: <308740834.401096.1484067629670@mail.yahoo.com>
References: <308740834.401096.1484067629670.ref@mail.yahoo.com>
 <308740834.401096.1484067629670@mail.yahoo.com>
Message-ID: <1484075929.607266.843456129.3F4B3F33@webmail.messagingengine.com>

On Tue, Jan 10, 2017, at 09:00, James Board via scikit-image wrote:
> I'm not sure what you mean by anaconda.  There are two relevant software
> packages named anaconda.  From Wikipedia:
> 
>     1) Anaconda is the installer for Red Hat Enterprise Linux, Oracle
>     Linux, Scientific Linux, CentOS and Fedora.
> 
>     2) Anaconda is a freemium[2] open source[3] distribution of the
>     Python and R programming languages for large-scale data processing,
>     predictive analytics, and scientific computing, that aims to simplify
>     package management and deployment.[4][5][6][7][8] Its package
>     management system is conda.
> 
> Which one are you referring to?  

I was referring to https://www.continuum.io/downloads

St?fan

From njs at vorpus.org  Tue Jan 10 15:13:06 2017
From: njs at vorpus.org (Nathaniel Smith)
Date: Tue, 10 Jan 2017 12:13:06 -0800
Subject: [scikit-image] Fw: Re: Compilation Problems
In-Reply-To: <CAPJVwB=h5YJpcdB0eHTUK5=VKNzXkZ9Mv6qCfctz1VD=1OMQ9A@mail.gmail.com>
References: <233536092.319170.1484062388065.ref@mail.yahoo.com>
 <233536092.319170.1484062388065@mail.yahoo.com>
 <CAPJVwB=h5YJpcdB0eHTUK5=VKNzXkZ9Mv6qCfctz1VD=1OMQ9A@mail.gmail.com>
Message-ID: <CAPJVwB=sK5X_PvWSwezTT5xRSopwJ1c2n4x_8+CyUcVM2ESTzw@mail.gmail.com>

The easy way to check if your Python has SSL support is to do:
  python -c "import ssl"
and see if you get an error message.

If you do you then it's probably worth complaining to whoever installed
that Python so that they at least know that there's a problem -- this is a
pretty serious kind of brokenness, as you're discovering.

I agree with other posters that the quick/easy fix is to install Anaconda.

-n

On Jan 10, 2017 7:33 AM, "James Board via scikit-image" <
scikit-image at python.org> wrote:

I don't have root access on this
machine and I personally didn't install the python
version.  I can't tell if the sysadmins installed
openssl-devel before building python.

How sure are you that this is causing my problem?  I
could build python and openssl-devel myself.  But
without root access, that could be a lot of work because
I'll have to track down each dependency manually.

Thank you for replying.


>
> --------------------------------------------
> On Sun, 1/8/17, Nathaniel Smith <njs at pobox.com>
> wrote:
>
>  Subject: Re: [scikit-image] Compilation Problems
>  To: "James Board" <jpboard2 at yahoo.com>
>  Cc: scikit-image at python.org
>  Date: Sunday, January 8, 2017, 10:16 PM
>
>  You appear to be using a self-built
>  Python. Did you by chance forget
>  to install openssl-devel before building Python, so that
> you
>  ended up
>  with a Python that has no ssl module?
>
>  -n
>
>  On Sun, Jan 8, 2017 at 6:11 PM, James Board via
>  scikit-image
>  <scikit-image at python.org>
>  wrote:
>  > I'm on a Red-Hat-like Linux machine and I tried to
>  install scikit several ways and failed.  Here was one
>  attempt:
>  >
>  >> git clone https://github.com/scikit-image/scikit-image.git
>  >> cd scikit-image
>  >> python --version
>  > Python 2.7.9
>  >
>  >> pip install -e
>  > Traceback (most recent call last):
>  >   File
>  "/usr/local/python/2.7.9/gnu//bin/pip", line 9, in
>  <module>
>  >     load_entry_point('pip==8.1.0',
>  'console_scripts', 'pip')()
>  >   File
>  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
>  line 568, in load_entry_point
>  >   File
>  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
>  line 2720, in load_entry_point
>  >   File
>  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
>  line 2380, in load
>  >   File
>  "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py",
>  line 2386, in resolve
>  >   File
>  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/
pip-8.1.0-py2.7.egg/pip/__init__.py",
>  line 15, in <module>
>  >     from pip.vcs import git,
>  mercurial, subversion, bazaar  # noqa
>  >   File
>  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/
pip-8.1.0-py2.7.egg/pip/vcs/subversion.py",
>  line 9, in <module>
>  >     from pip.index import Link
>  >   File
>  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/
pip-8.1.0-py2.7.egg/pip/index.py",
>  line 30, in <module>
>  >     from pip.wheel import Wheel,
>  wheel_ext
>  >   File
>  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/
pip-8.1.0-py2.7.egg/pip/wheel.py",
>  line 39, in <module>
>  >     from
>  pip._vendor.distlib.scripts import ScriptMaker
>  >   File
>  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/
pip-8.1.0-py2.7.egg/pip/_vendor/distlib/scripts.py",
>  line 14, in <module>
>  >     from .compat import sysconfig,
>  detect_encoding, ZipFile
>  >   File
>  "/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/
pip-8.1.0-py2.7.egg/pip/_vendor/distlib/compat.py",
>  line 31, in <module>
>  >     from urllib2 import (Request,
>  urlopen, URLError, HTTPError,
>  > ImportError: cannot import name HTTPSHandler
>  >
>  > Here's another attempt that failed:
>  >
>  >> easy_install --install-dir=/p/home/jpboard/SCIKIT
>  -U scikit-image
>  > Creating /p/home/jpboard/SCIKIT/site.py
>  > Searching for scikit-image
>  > Reading https://pypi.python.org/simple/scikit-image/
>  > Download error on
> https://pypi.python.org/simple/scikit-image/:
>  unknown url type: https -- Some packages may not be
>  found!
>  > Couldn't find index page for 'scikit-image' (maybe
>  misspelled?)
>  > Scanning index of all packages (this may take a
> while)
>  > Reading https://pypi.python.org/simple/
>  > Download error on https://pypi.python.org/simple/: unknown url type:
>  https -- Some packages may not be found!
>  > No local packages or download links found for
>  scikit-image
>  > error: Could not find suitable distribution for
>  Requirement.parse('scikit-image')
>  >
>  > Can anyone tell what I'm doing
>  wrong?   I tried all available options for me
>  in the scikit documentation.  What should I do next?
>  >
>  > _______________________________________________
>  > scikit-image mailing list
>  > scikit-image at python.org
>  > https://mail.python.org/mailman/listinfo/scikit-image
>
>
>
>  --
>  Nathaniel J. Smith -- https://vorpus.org
>
_______________________________________________
scikit-image mailing list
scikit-image at python.org
https://mail.python.org/mailman/listinfo/scikit-image
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From jpboard2 at yahoo.com  Tue Jan 10 15:32:57 2017
From: jpboard2 at yahoo.com (James Board)
Date: Tue, 10 Jan 2017 20:32:57 +0000 (UTC)
Subject: [scikit-image] Fw: Re: Compilation Problems
References: <1569728724.582577.1484080377931.ref@mail.yahoo.com>
Message-ID: <1569728724.582577.1484080377931@mail.yahoo.com>

I did get an error:

> python -c "import ssl"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/python/2.7.9/gnu/lib/python2.7/ssl.py", line 97, in <module>
    import _ssl             # if we can't import it, let the error propagate
ImportError: No module named _ssl

I'll let the sysadmins know.  Thanks.




--------------------------------------------
On Tue, 1/10/17, Nathaniel Smith <njs at vorpus.org> wrote:

 Subject: Re: [scikit-image] Fw: Re: Compilation Problems
 To: "James Board" <jpboard2 at yahoo.com>
 Cc: scikit-image at python.org
 Date: Tuesday, January 10, 2017, 3:13 PM
 
 The easy way to check if your
 Python has SSL support is to do:? python -c
 "import ssl"and see if you get an error
 message.?
 If you do you then it's probably worth
 complaining to whoever installed that Python so that they at
 least know that there's a problem -- this is a pretty
 serious kind of brokenness, as you're
 discovering.
 I agree with other posters that the quick/easy
 fix is to install Anaconda.?
 -n
 On Jan 10, 2017 7:33
 AM, "James Board via scikit-image" <scikit-image at python.org>
 wrote:
 I don't have root
 access on this
 
 machine and I personally didn't install the python
 
 version.? I can't tell if the sysadmins installed
 
 openssl-devel before building python.
 
 
 
 How sure are you that this is causing my problem?? I
 
 could build python and openssl-devel myself.? But
 
 without root access, that could be a lot of work because
 
 I'll have to track down each dependency manually.
 
 
 
 Thank you for replying.
 
 
 
 
 
 >
 
 > ------------------------------ --------------
 
 > On Sun, 1/8/17, Nathaniel Smith <njs at pobox.com>
 
 > wrote:
 
 >
 
 >? Subject: Re: [scikit-image] Compilation Problems
 
 >? To: "James Board" <jpboard2 at yahoo.com>
 
 >? Cc: scikit-image at python.org
 
 >? Date: Sunday, January 8, 2017, 10:16 PM
 
 >
 
 >? You appear to be using a self-built
 
 >? Python. Did you by chance forget
 
 >? to install openssl-devel before building Python, so
 that
 
 > you
 
 >? ended up
 
 >? with a Python that has no ssl module?
 
 >
 
 >? -n
 
 >
 
 >? On Sun, Jan 8, 2017 at 6:11 PM, James Board via
 
 >? scikit-image
 
 >? <scikit-image at python.org>
 
 >? wrote:
 
 >? > I'm on a Red-Hat-like Linux machine and I
 tried to
 
 >? install scikit several ways and failed.? Here was
 one
 
 >? attempt:
 
 >? >
 
 >? >> git clone https://github.com/scikit-
 image/scikit-image.git
 
 >? >> cd scikit-image
 
 >? >> python --version
 
 >? > Python 2.7.9
 
 >? >
 
 >? >> pip install -e
 
 >? > Traceback (most recent call last):
 
 >? >???File
 
 >? "/usr/local/python/2.7.9/gnu// bin/pip",
 line 9, in
 
 >? <module>
 
 >? >? ???load_entry_point('pip==8.1. 0',
 
 >? 'console_scripts', 'pip')()
 
 >? >???File
 
 >? "build/bdist.linux-x86_64/egg/
 pkg_resources/__init__.py",
 
 >? line 568, in load_entry_point
 
 >? >???File
 
 >? "build/bdist.linux-x86_64/egg/
 pkg_resources/__init__.py",
 
 >? line 2720, in load_entry_point
 
 >? >???File
 
 >? "build/bdist.linux-x86_64/egg/
 pkg_resources/__init__.py",
 
 >? line 2380, in load
 
 >? >???File
 
 >? "build/bdist.linux-x86_64/egg/
 pkg_resources/__init__.py",
 
 >? line 2386, in resolve
 
 >? >???File
 
 >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/__
 init__.py",
 
 >? line 15, in <module>
 
 >? >? ???from pip.vcs import git,
 
 >? mercurial, subversion, bazaar? # noqa
 
 >? >???File
 
 >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/vcs/
 subversion.py",
 
 >? line 9, in <module>
 
 >? >? ???from pip.index import Link
 
 >? >???File
 
 >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/index.
 py",
 
 >? line 30, in <module>
 
 >? >? ???from pip.wheel import Wheel,
 
 >? wheel_ext
 
 >? >???File
 
 >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/wheel.
 py",
 
 >? line 39, in <module>
 
 >? >? ???from
 
 >? pip._vendor.distlib.scripts import ScriptMaker
 
 >? >???File
 
 >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/_
 vendor/distlib/scripts.py",
 
 >? line 14, in <module>
 
 >? >? ???from .compat import sysconfig,
 
 >? detect_encoding, ZipFile
 
 >? >???File
 
 >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/_
 vendor/distlib/compat.py",
 
 >? line 31, in <module>
 
 >? >? ???from urllib2 import (Request,
 
 >? urlopen, URLError, HTTPError,
 
 >? > ImportError: cannot import name HTTPSHandler
 
 >? >
 
 >? > Here's another attempt that failed:
 
 >? >
 
 >? >> easy_install --install-dir=/p/home/jpboard/
 SCIKIT
 
 >? -U scikit-image
 
 >? > Creating /p/home/jpboard/SCIKIT/site.py
 
 >? > Searching for scikit-image
 
 >? > Reading https://pypi.python.org/
 simple/scikit-image/
 
 >? > Download error on
 
 > https://pypi.python.org/
 simple/scikit-image/:
 
 >? unknown url type: https -- Some packages may not be
 
 >? found!
 
 >? > Couldn't find index page for
 'scikit-image' (maybe
 
 >? misspelled?)
 
 >? > Scanning index of all packages (this may take a
 
 > while)
 
 >? > Reading https://pypi.python.org/
 simple/
 
 >? > Download error on https://pypi.python.org/
 simple/: unknown url type:
 
 >? https -- Some packages may not be found!
 
 >? > No local packages or download links found for
 
 >? scikit-image
 
 >? > error: Could not find suitable distribution for
 
 >? Requirement.parse('scikit- image')
 
 >? >
 
 >? > Can anyone tell what I'm doing
 
 >? wrong????I tried all available options for me
 
 >? in the scikit documentation.? What should I do
 next?
 
 >? >
 
 >? > ______________________________
 _________________
 
 >? > scikit-image mailing list
 
 >? > scikit-image at python.org
 
 >? > https://mail.python.org/
 mailman/listinfo/scikit-image
 
 >
 
 >
 
 >
 
 >? --
 
 >? Nathaniel J. Smith -- https://vorpus.org
 
 >
 
 ______________________________ _________________
 
 scikit-image mailing list
 
 scikit-image at python.org
 
 https://mail.python.org/
 mailman/listinfo/scikit-image
 
 
 

From jpboard2 at yahoo.com  Tue Jan 10 15:42:57 2017
From: jpboard2 at yahoo.com (James Board)
Date: Tue, 10 Jan 2017 20:42:57 +0000 (UTC)
Subject: [scikit-image] Fw: Re: Compilation Problems
References: <1462364104.587887.1484080977004.ref@mail.yahoo.com>
Message-ID: <1462364104.587887.1484080977004@mail.yahoo.com>

I did build my own version of python in my own directory (2.7.13) but it also doesn't seem to have SSL support.  I looked at the configure options, and I didn't see any option for SSL support.  I could easily rebuild that version and use it if I could figure out how to turn on SSL support.  However, it also doesn't have pip either.  

BTW, I'm not a regular python user so I'm sorry for asking dumb questions or for getting stuck on things that other users can easily do.


--------------------------------------------
On Tue, 1/10/17, Stefan van der Walt <stefanv at berkeley.edu> wrote:

 Subject: Re: [scikit-image] Fw: Re: Compilation Problems
 To: "Oleksandr Huziy" <guziy.sasha at gmail.com>, "James Board" <jpboard2 at yahoo.com>
 Cc: scikit-image at python.org
 Date: Tuesday, January 10, 2017, 2:10 PM
 
 You
 may want to follow Nathaniel's suggestion and install a
 version of Python that has SSL support.? Are you able to
 make a local Python installation into your home
 directory?
 
 
 
 St?fan
 
 
 
 On Tue, Jan 10, 2017, at
 07:43, Oleksandr Huziy wrote:
 
 Hi James:
 
 
 
 Have you tried?
 
 
 
 pip install scikit-image --user
 
 
 
 Or with the cloned directory:
 
 pip install . --user
 
 
 
 
 
 Cheers
 
 
 
 
 
 
 
 
 
 
 
 
 2017-01-10 10:33 GMT-05:00 James Board via
 scikit-image <scikit-image at python.org>:
 
 I don't have root
 access on this
 
  machine and I personally didn't install the
 python
 
  version.? I can't tell if the sysadmins
 installed
 
  openssl-devel before building python.
 
  
 
  How sure are you that this is causing my problem??
 I
 
  could build python and openssl-devel myself.? But
 
  without root access, that could be a lot of work
 because
 
  I'll have to track down each dependency
 manually.
 
  
 
  Thank you for replying.
 
  
 
  
 
  >
 
  > ------------------------------ --------------
 
  > On Sun, 1/8/17, Nathaniel Smith <njs at pobox.com>
 
  > wrote:
 
  >
 
  >? Subject: Re: [scikit-image] Compilation
 Problems
 
  >? To: "James Board" <jpboard2 at yahoo.com>
 
  >? Cc: scikit-image at python.org
 
  >? Date: Sunday, January 8, 2017, 10:16 PM
 
  
 
 >
 
  >? You appear to be using a self-built
 
  >? Python. Did you by chance forget
 
  >? to install openssl-devel before building
 Python, so that
 
  > you
 
  >? ended up
 
  >? with a Python that has no ssl module?
 
  >
 
  >? -n
 
  >
 
  >? On Sun, Jan 8, 2017 at 6:11 PM, James Board
 via
 
  >? scikit-image
 
  >? <scikit-image at python.org>
 
  >? wrote:
 
  >? > I'm on a Red-Hat-like Linux machine
 and I tried to
 
  >? install scikit several ways and failed.? Here
 was one
 
  >? attempt:
 
  >? >
 
  >? >> git clone https://github.com/scikit-
 image/scikit-image.git
 
  >? >> cd scikit-image
 
  >? >> python --version
 
  >? > Python 2.7.9
 
  >? >
 
  >? >> pip install -e
 
  >? > Traceback (most recent call last):
 
  >? >???File
 
  >? "/usr/local/python/2.7.9/gnu//
 bin/pip", line 9, in
 
  >? <module>
 
  >? >? ???load_entry_point('pip==8.1.
 0',
 
  >? 'console_scripts', 'pip')()
 
  >? >???File
 
  >? "build/bdist.linux-x86_64/egg/
 pkg_resources/__init__.py",
 
  >? line 568, in load_entry_point
 
  >? >???File
 
  >? "build/bdist.linux-x86_64/egg/
 pkg_resources/__init__.py",
 
  >? line 2720, in load_entry_point
 
  >? >???File
 
  >? "build/bdist.linux-x86_64/egg/
 pkg_resources/__init__.py",
 
  >? line 2380, in load
 
  >? >???File
 
  >? "build/bdist.linux-x86_64/egg/
 pkg_resources/__init__.py",
 
  >? line 2386, in resolve
 
  >? >???File
 
  >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/__
 init__.py",
 
  >? line 15, in <module>
 
  >? >? ???from pip.vcs import git,
 
  >? mercurial, subversion, bazaar? # noqa
 
  >? >???File
 
  >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/vcs/
 subversion.py",
 
  >? line 9, in <module>
 
  >? >? ???from pip.index import Link
 
  >? >???File
 
  >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/index.
 py",
 
  >? line 30, in <module>
 
  >? >? ???from pip.wheel import Wheel,
 
  >? wheel_ext
 
  >? >???File
 
  >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/wheel.
 py",
 
  >? line 39, in <module>
 
  >? >? ???from
 
  >? pip._vendor.distlib.scripts import
 ScriptMaker
 
  >? >???File
 
  >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/_
 vendor/distlib/scripts.py",
 
  >? line 14, in <module>
 
  >? >? ???from .compat import sysconfig,
 
  >? detect_encoding, ZipFile
 
  >? >???File
 
  >? "/usr/local/python/2.7.9/gnu/
 lib/python2.7/site-packages/ pip-8.1.0-py2.7.egg/pip/_
 vendor/distlib/compat.py",
 
  >? line 31, in <module>
 
  >? >? ???from urllib2 import (Request,
 
  >? urlopen, URLError, HTTPError,
 
  >? > ImportError: cannot import name
 HTTPSHandler
 
  >? >
 
  >? > Here's another attempt that failed:
 
  >? >
 
  >? >> easy_install
 --install-dir=/p/home/jpboard/ SCIKIT
 
  >? -U scikit-image
 
  >? > Creating /p/home/jpboard/SCIKIT/site.py
 
  >? > Searching for scikit-image
 
  >? > Reading https://pypi.python.org/
 simple/scikit-image/
 
  >? > Download error on
 
  > https://pypi.python.org/
 simple/scikit-image/:
 
  >? unknown url type: https -- Some packages may
 not be
 
  >? found!
 
  >? > Couldn't find index page for
 'scikit-image' (maybe
 
  >? misspelled?)
 
  >? > Scanning index of all packages (this may
 take a
 
  > while)
 
  >? > Reading https://pypi.python.org/
 simple/
 
  >? > Download error on https://pypi.python.org/
 simple/: unknown url type:
 
  >? https -- Some packages may not be found!
 
  >? > No local packages or download links found
 for
 
  >? scikit-image
 
  >? > error: Could not find suitable
 distribution for
 
  >? Requirement.parse('scikit- image')
 
  >? >
 
  >? > Can anyone tell what I'm doing
 
  >? wrong????I tried all available options for
 me
 
  >? in the scikit documentation.? What should I do
 next?
 
  >? >
 
  >? > ______________________________
 _________________
 
  >? > scikit-image mailing list
 
  >? > scikit-image at python.org
 
  >? > https://mail.python.org/
 mailman/listinfo/scikit-image
 
  >
 
  >
 
  >
 
  >? --
 
  >? Nathaniel J. Smith -- https://vorpus.org
 
  >
 
  ______________________________ _________________
 
  scikit-image mailing list
 
  scikit-image at python.org
 
  https://mail.python.org/
 mailman/listinfo/scikit-image
 
 
 
 
 
 
 
 
 
 
 -- 
 
 Sasha
 
 
 
 _______________________________________________
 
 scikit-image mailing list
 
 scikit-image at python.org
 
 https://mail.python.org/mailman/listinfo/scikit-image
 
 
 
 

From jpboard2 at yahoo.com  Tue Jan 10 15:43:36 2017
From: jpboard2 at yahoo.com (James Board)
Date: Tue, 10 Jan 2017 20:43:36 +0000 (UTC)
Subject: [scikit-image] Fw: Re:  Older versions of scikit-image
References: <2030920947.555909.1484081016551.ref@mail.yahoo.com>
Message-ID: <2030920947.555909.1484081016551@mail.yahoo.com>

I'm trying to build a software
environment for deep-learning that uses caffe, among many
other packages.? It seems to be fairly brittle: it's
real easy to break if the dependencies aren't exact.? I
don't know for sure that they absolutely must have
scikit-image 0.93, but that is what the developers are using
and I'm just trying to be safe with version numbers.


> --------------------------------------------
> On Tue, 1/10/17, Stefan van der Walt <stefanv at berkeley.edu>
> wrote:
> 
>  Subject: Re: [scikit-image] Older versions of scikit-image
>  To: "James Board" <jpboard2 at yahoo.com>,
> scikit-image at python.org
>  Date: Tuesday, January 10, 2017, 2:11 PM
>  
>  On Tue, Jan 10, 2017, at
>  09:15, James Board via scikit-image wrote:
>  >
>  Where can I download scikit-image version 0.93?? There is
> a
>  list of
>  > versions here
>  >? ???http://scikit-image.org/docs/dev/install.html
>  > But the links to older versions don't
>  take me to an actual download page.
>  
>  Do you have a specific need
>  for such an old version?? Otherwise, you can
>  install via pip on most platforms (or conda, if
>  you use that).
>  
>  St?fan

From jpboard2 at yahoo.com  Tue Jan 10 15:45:56 2017
From: jpboard2 at yahoo.com (James Board)
Date: Tue, 10 Jan 2017 20:45:56 +0000 (UTC)
Subject: [scikit-image] Fw: Re:  Fw: Re: Compilation Problems
References: <786854323.579927.1484081156224.ref@mail.yahoo.com>
Message-ID: <786854323.579927.1484081156224@mail.yahoo.com>

I can ask.? I think it might
already be installed.? I know that openssh is
installed.
 
> ssh -V
OpenSSH_7.2p2a, OpenSSL 1.0.2g? 1 Mar 2016

How can I tell if openssh-devel is installed?

Jim

> 
> --------------------------------------------
> On Tue, 1/10/17, Oleksandr Huziy <guziy.sasha at gmail.com>
> wrote:
> 
>  Subject: Re: [scikit-image] Fw: Re: Compilation Problems
>  To: "James Board" <jpboard2 at yahoo.com>
>  Cc: scikit-image at python.org
>  Date: Tuesday, January 10, 2017, 1:40 PM
>  
>  Hi
>  James:
>  Can you ask admins of
>  the server to install openssl-devel? That could make your
>  task much easier..
>  Are
>  you stuck with this python version? sometimes there might
> be
>  several python versions installed on a server, you could
> try
>  python<Tab> to see what else is there.
>  Cheers
>  
>  
>  
>  2017-01-10 12:31 GMT-05:00
>  James Board via scikit-image <scikit-image at python.org>:
>  I made some progress.? I tried
>  this command in the cloned version of scikit-image and it
>  got fairly deep into the compilation process:
>  
>  
>  
>  python setup.py install --prefix ~/SCIKIT
>  
>  
>  
>  However, it ultimately failed with these error messages:
>  
>  
>  
>  Processing dependencies for scikit-image==0.13.dev0
>  
>  Searching for PyWavelets>=0.4.0
>  
>  Reading https://pypi.python.org/
>  simple/PyWavelets/
>  
>  Download error on https://pypi.python.org/
>  simple/PyWavelets/: unknown url type: https -- Some
>  packages may not be found!
>  
>  Couldn't find index page for 'PyWavelets' (maybe
>  misspelled?)
>  
>  Scanning index of all packages
>  (this may take a while)
>  
>  Reading https://pypi.python.org/
>  simple/
>  
>  Download error on https://pypi.python.org/
>  simple/: unknown url type: https -- Some packages may
>  not be found!
>  
>  No local packages or download links found for
>  PyWavelets>=0.4.0
>  
>  error: Could not find suitable distribution for
>  Requirement.parse('PyWavelets> =0.4.0')
>  
>  
>  
>  What is the cause of this?
>  
>  
>  
>  ______________________________ _________________
>  
>  scikit-image mailing list
>  
>  scikit-image at python.org
>  
>  https://mail.python.org/
>  mailman/listinfo/scikit-image
>  
>  
>  
>  
>  -- 
>  Sasha
>  

From jpboard2 at yahoo.com  Wed Jan 11 06:49:16 2017
From: jpboard2 at yahoo.com (James Board)
Date: Wed, 11 Jan 2017 11:49:16 +0000 (UTC)
Subject: [scikit-image] Fw: Re: Compilation Problems
References: <373392517.946396.1484135356554.ref@mail.yahoo.com>
Message-ID: <373392517.946396.1484135356554@mail.yahoo.com>

It looks like openssh and openssh-devel are already installed:

> rpm -qa | grep -i openssl
libopenssl0_9_8-32bit-0.9.8j-0.102.2
openssl-0.9.8j-0.102.2
libopenssl-devel-0.9.8j-0.97.1
openssl-certs-2.7-0.6.1
libopenssl0_9_8-0.9.8j-0.102.2
libopenssl-devel-32bit-0.9.8j-0.97.1

I'll try to re-install python with the instructions from the stackoverflow thread about enabling openssh.

Jim


--------------------------------------------
On Tue, 1/10/17, Oleksandr Huziy <guziy.sasha at gmail.com> wrote:

 Subject: Re: [scikit-image] Fw: Re: Compilation Problems
 To: "James Board" <jpboard2 at yahoo.com>
 Date: Tuesday, January 10, 2017, 4:23 PM
 
 James:
 How can I tell on my own if
 openssh-devel is installed?
 Does rpm command work for you? If
 yes then:
 rpm -qa | grep -i
 openssl(copied from https://mail.google.com/mail/u/0/#inbox/15980ff09187ce6b)
 2017-01-10 15:38 GMT-05:00
 James Board <jpboard2 at yahoo.com>:
 I can ask.? I think it might already
 be installed.? I know that openssh is installed.
 
 
 
 > ssh -V
 
 OpenSSH_7.2p2a, OpenSSL 1.0.2g? 1 Mar 2016
 
 
 
 How can I tell on my own if openssh-devel is
 installed?
 
 
 
 Jim
 
 
 
 
 
 ------------------------------ --------------
 
 On Tue, 1/10/17, Oleksandr Huziy <guziy.sasha at gmail.com>
 wrote:
 
 
 
 ?Subject: Re: [scikit-image] Fw: Re: Compilation
 Problems
 
 ?To: "James Board" <jpboard2 at yahoo.com>
 
 ?Cc: scikit-image at python.org
 
 ?Date: Tuesday, January 10, 2017, 1:40 PM
 
 
 
 ?Hi
 
 ?James:
 
 ?Can you ask admins of
 
 ?the server to install openssl-devel? That could make
 your
 
 ?task much easier..
 
 ?Are
 
 ?you stuck with this python version? sometimes there might
 be
 
 ?several python versions installed on a server, you could
 try
 
 ?python<Tab> to see what else is there.
 
 ?Cheers
 
 
 
 
 
 
 
 ?2017-01-10 12:31 GMT-05:00
 
 ?James Board via scikit-image <scikit-image at python.org>:
 
 ?I made some progress.? I tried
 
 ?this command in the cloned version of scikit-image and
 it
 
 ?got fairly deep into the compilation process:
 
 
 
 
 
 
 
 ?python setup.py install --prefix ~/SCIKIT
 
 
 
 
 
 
 
 ?However, it ultimately failed with these error
 messages:
 
 
 
 
 
 
 
 ?Processing dependencies for scikit-image==0.13.dev0
 
 
 
 ?Searching for PyWavelets>=0.4.0
 
 
 
 ?Reading https://pypi.python.org/
 
 ?simple/PyWavelets/
 
 
 
 ?Download error on https://pypi.python.org/
 
 ?simple/PyWavelets/: unknown url type: https -- Some
 
 ?packages may not be found!
 
 
 
 ?Couldn't find index page for 'PyWavelets'
 (maybe
 
 ?misspelled?)
 
 
 
 ?Scanning index of all packages
 
 ?(this may take a while)
 
 
 
 ?Reading https://pypi.python.org/
 
 ?simple/
 
 
 
 ?Download error on https://pypi.python.org/
 
 ?simple/: unknown url type: https -- Some packages may
 
 ?not be found!
 
 
 
 ?No local packages or download links found for
 
 ?PyWavelets>=0.4.0
 
 
 
 ?error: Could not find suitable distribution for
 
 ?Requirement.parse('PyWavelets> =0.4.0')
 
 
 
 
 
 
 
 ?What is the cause of this?
 
 
 
 
 
 
 
 ?______________________________ _________________
 
 
 
 ?scikit-image mailing list
 
 
 
 ?scikit-image at python.org
 
 
 
 ?https://mail.python.org/
 
 ?mailman/listinfo/scikit-image
 
 
 
 
 
 
 
 
 
 ?--
 
 ?Sasha
 
 
 
 
 
 
 -- 
 Sasha
 

From njs at vorpus.org  Wed Jan 11 12:36:25 2017
From: njs at vorpus.org (Nathaniel Smith)
Date: Wed, 11 Jan 2017 09:36:25 -0800
Subject: [scikit-image] Fw: Re: Compilation Problems
In-Reply-To: <373392517.946396.1484135356554@mail.yahoo.com>
References: <373392517.946396.1484135356554.ref@mail.yahoo.com>
 <373392517.946396.1484135356554@mail.yahoo.com>
Message-ID: <CAPJVwB=_81f0TZ9Ztpb964-vTTKUmp3e4UODNbMAN+FAw1zA6Q@mail.gmail.com>

Watch out, openssh and openssl are different things...

On Jan 11, 2017 3:49 AM, "James Board via scikit-image" <
scikit-image at python.org> wrote:

> It looks like openssh and openssh-devel are already installed:
>
> > rpm -qa | grep -i openssl
> libopenssl0_9_8-32bit-0.9.8j-0.102.2
> openssl-0.9.8j-0.102.2
> libopenssl-devel-0.9.8j-0.97.1
> openssl-certs-2.7-0.6.1
> libopenssl0_9_8-0.9.8j-0.102.2
> libopenssl-devel-32bit-0.9.8j-0.97.1
>
> I'll try to re-install python with the instructions from the stackoverflow
> thread about enabling openssh.
>
> Jim
>
>
> --------------------------------------------
> On Tue, 1/10/17, Oleksandr Huziy <guziy.sasha at gmail.com> wrote:
>
>  Subject: Re: [scikit-image] Fw: Re: Compilation Problems
>  To: "James Board" <jpboard2 at yahoo.com>
>  Date: Tuesday, January 10, 2017, 4:23 PM
>
>  James:
>  How can I tell on my own if
>  openssh-devel is installed?
>  Does rpm command work for you? If
>  yes then:
>  rpm -qa | grep -i
>  openssl(copied from https://mail.google.com/mail/
> u/0/#inbox/15980ff09187ce6b)
>  2017-01-10 15:38 GMT-05:00
>  James Board <jpboard2 at yahoo.com>:
>  I can ask.  I think it might already
>  be installed.  I know that openssh is installed.
>
>
>
>  > ssh -V
>
>  OpenSSH_7.2p2a, OpenSSL 1.0.2g  1 Mar 2016
>
>
>
>  How can I tell on my own if openssh-devel is
>  installed?
>
>
>
>  Jim
>
>
>
>
>
>  ------------------------------ --------------
>
>  On Tue, 1/10/17, Oleksandr Huziy <guziy.sasha at gmail.com>
>  wrote:
>
>
>
>   Subject: Re: [scikit-image] Fw: Re: Compilation
>  Problems
>
>   To: "James Board" <jpboard2 at yahoo.com>
>
>   Cc: scikit-image at python.org
>
>   Date: Tuesday, January 10, 2017, 1:40 PM
>
>
>
>   Hi
>
>   James:
>
>   Can you ask admins of
>
>   the server to install openssl-devel? That could make
>  your
>
>   task much easier..
>
>   Are
>
>   you stuck with this python version? sometimes there might
>  be
>
>   several python versions installed on a server, you could
>  try
>
>   python<Tab> to see what else is there.
>
>   Cheers
>
>
>
>
>
>
>
>   2017-01-10 12:31 GMT-05:00
>
>   James Board via scikit-image <scikit-image at python.org>:
>
>   I made some progress.  I tried
>
>   this command in the cloned version of scikit-image and
>  it
>
>   got fairly deep into the compilation process:
>
>
>
>
>
>
>
>   python setup.py install --prefix ~/SCIKIT
>
>
>
>
>
>
>
>   However, it ultimately failed with these error
>  messages:
>
>
>
>
>
>
>
>   Processing dependencies for scikit-image==0.13.dev0
>
>
>
>   Searching for PyWavelets>=0.4.0
>
>
>
>   Reading https://pypi.python.org/
>
>   simple/PyWavelets/
>
>
>
>   Download error on https://pypi.python.org/
>
>   simple/PyWavelets/: unknown url type: https -- Some
>
>   packages may not be found!
>
>
>
>   Couldn't find index page for 'PyWavelets'
>  (maybe
>
>   misspelled?)
>
>
>
>   Scanning index of all packages
>
>   (this may take a while)
>
>
>
>   Reading https://pypi.python.org/
>
>   simple/
>
>
>
>   Download error on https://pypi.python.org/
>
>   simple/: unknown url type: https -- Some packages may
>
>   not be found!
>
>
>
>   No local packages or download links found for
>
>   PyWavelets>=0.4.0
>
>
>
>   error: Could not find suitable distribution for
>
>   Requirement.parse('PyWavelets> =0.4.0')
>
>
>
>
>
>
>
>   What is the cause of this?
>
>
>
>
>
>
>
>   ______________________________ _________________
>
>
>
>   scikit-image mailing list
>
>
>
>   scikit-image at python.org
>
>
>
>   https://mail.python.org/
>
>   mailman/listinfo/scikit-image
>
>
>
>
>
>
>
>
>
>   --
>
>   Sasha
>
>
>
>
>
>
>  --
>  Sasha
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
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From matthew.brett at gmail.com  Sat Jan 14 18:19:18 2017
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sat, 14 Jan 2017 15:19:18 -0800
Subject: [scikit-image] Oops - I broke travis-ci build temporarily
Message-ID: <CAH6Pt5rTKgaSy9Ktvs5xRYxO4Q_4Pg2mnh8KPcnK7ud+6Q7RpQ@mail.gmail.com>

Hi,

Sorry, I've been updating the travis-ci build, and in particular the
wheel sources, over at :

https://github.com/scikit-image/scikit-image/pull/2451

As part of that, I built a new version of the pyside wheel, for our
wheel repository, and this broke one of the current scikit image
travis build matrix entries:

https://travis-ci.org/scikit-image/scikit-image/jobs/191999862

That break will be fixed when #2451 is merged - just letting y'all know.

Cheers,

Matthew

From max.linke88 at gmail.com  Mon Jan 16 10:23:05 2017
From: max.linke88 at gmail.com (Max Linke)
Date: Mon, 16 Jan 2017 16:23:05 +0100
Subject: [scikit-image] GSOC 2017: NumFOCUS will be an umbrella organization
Message-ID: <40f85dfb-0635-a042-79b7-039d3dd347a9@gmail.com>

Hi

Organizations can start submitting applications for Google Summer of Code
2017 on January 19 (and the deadline is February 9)

https://developers.google.com/open-source/gsoc/timeline?hl=en

NumFOCUS will be applying again this year. If you want to work with us
please let me know and if you apply as an organization yourself or under a
different umbrella organization please tell me as well. If you participate
with us it would be great if you start to add possible projects to the
ideas page on github soon. We some general information for mentors on
github.

https://github.com/numfocus/gsoc/blob/master/CONTRIBUTING-mentors.md

We also have a template for ideas that might help. It lists the things
Google likes to see.

https://github.com/numfocus/gsoc/blob/master/2017/ideas-list-skeleton.md

In case you participated in earlier years with NumFOCUS there are some
small changes this year. Raniere won't be the admin this year. Instead I'm
going to be the admin. We are also planning to include two explicit rules
when a student should be failed, they have to communicate regularly and
commit code into your development branch at the end of the summer.

best, Max

From jpboard2 at yahoo.com  Tue Jan 17 13:32:12 2017
From: jpboard2 at yahoo.com (James Board)
Date: Tue, 17 Jan 2017 18:32:12 +0000 (UTC)
Subject: [scikit-image] Compilation Problems
References: <1272665361.4757618.1484677932491.ref@mail.yahoo.com>
Message-ID: <1272665361.4757618.1484677932491@mail.yahoo.com>

Making progress, but still no success.

I had my system admins re-install python with OpenSSL support.  Looks like it works.  I ran this command with no errors:

    >python -c "import ssl"

But I still run into problems installing scikit.  This was my install command

    > python setup.py install --prefix ~/SCIKIT

Here are the last few lines of error messages:

Processing dependencies for scikit-image==0.13.dev0
Searching for PyWavelets>=0.4.0
Reading https://pypi.python.org/simple/PyWavelets/
Download error on https://pypi.python.org/simple/PyWavelets/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:581) -- Some packages may not be found!
Couldn't find index page for 'PyWavelets' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading https://pypi.python.org/simple/
Download error on https://pypi.python.org/simple/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:581) -- Some packages may not be found!
No local packages or download links found for PyWavelets>=0.4.0
error: Could not find suitable distribution for Requirement.parse('PyWavelets>=0.4.0')

Does anyone know why this error occurs?


From jpboard2 at yahoo.com  Tue Jan 17 13:39:27 2017
From: jpboard2 at yahoo.com (James Board)
Date: Tue, 17 Jan 2017 18:39:27 +0000 (UTC)
Subject: [scikit-image] Compilation Problems
References: <1415623788.4763669.1484678367186.ref@mail.yahoo.com>
Message-ID: <1415623788.4763669.1484678367186@mail.yahoo.com>

I also tried to install scikit-image another way.  And got errors:

> pip install scikit-image --user

    Complete output from command /usr/local/python/2.7.9/gnu/bin/python -u -c "import setuptools, tokenize;__file__='/p/work2/workspace/guest/pip-build-L2pBBW/subprocess32/setup.py';
        exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /workspace/guest/pip-_PsWy1-record/install-record.txt
        --single-version-externally-managed --compile --user --prefix=:
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-2.7
    copying subprocess32.py -> build/lib.linux-x86_64-2.7
    running build_ext
    failed to import Cython: /usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/Cython-0.23.4-py2.7-linux-x86_64.egg/Cython/Compiler/Scanning.so: undefined symbol: PyUnicodeUCS4_DecodeUTF8
    error: Cython does not appear to be installed

    ----------------------------------------
Command "/usr/local/python/2.7.9/gnu/bin/python -u -c "import setuptools, tokenize;__file__='/p/work2/workspace/guest/pip-build-L2pBBW/subprocess32/setup.py';
    exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install
    --record /workspace/guest/pip-_PsWy1-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /p/work2/workspace/guest/pip-build-L2pBBW/subprocess32/
You are using pip version 8.1.0, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.



So, it complains about cython.  But cython is already installed:



> pip install cython --user
Requirement already satisfied (use --upgrade to upgrade): cython in /p/home/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/Cython-0.23.4-py2.7-linux-x86_64.egg


I'm not sure what to do next.

From stefanv at berkeley.edu  Tue Jan 17 14:00:23 2017
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Tue, 17 Jan 2017 11:00:23 -0800
Subject: [scikit-image] Compilation Problems
In-Reply-To: <1415623788.4763669.1484678367186@mail.yahoo.com>
References: <1415623788.4763669.1484678367186.ref@mail.yahoo.com>
 <1415623788.4763669.1484678367186@mail.yahoo.com>
Message-ID: <1484679623.3172255.850728120.0AFE666A@webmail.messagingengine.com>

Hi James

Please try:

pip uninstall cython
pip install cython

Thanks
St?fan

On Tue, Jan 17, 2017, at 10:39, James Board via scikit-image wrote:
> I also tried to install scikit-image another way.  And got errors:
> 
> > pip install scikit-image --user
> 
>     Complete output from command /usr/local/python/2.7.9/gnu/bin/python
>     -u -c "import setuptools,
>     tokenize;__file__='/p/work2/workspace/guest/pip-build-L2pBBW/subprocess32/setup.py';
>         exec(compile(getattr(tokenize, 'open',
>         open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))"
>         install --record
>         /workspace/guest/pip-_PsWy1-record/install-record.txt
>         --single-version-externally-managed --compile --user --prefix=:
>     running install
>     running build
>     running build_py
>     creating build
>     creating build/lib.linux-x86_64-2.7
>     copying subprocess32.py -> build/lib.linux-x86_64-2.7
>     running build_ext
>     failed to import Cython:
>     /usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/Cython-0.23.4-py2.7-linux-x86_64.egg/Cython/Compiler/Scanning.so:
>     undefined symbol: PyUnicodeUCS4_DecodeUTF8
>     error: Cython does not appear to be installed
> 
>     ----------------------------------------
> Command "/usr/local/python/2.7.9/gnu/bin/python -u -c "import setuptools,
> tokenize;__file__='/p/work2/workspace/guest/pip-build-L2pBBW/subprocess32/setup.py';
>     exec(compile(getattr(tokenize, 'open',
>     open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))"
>     install
>     --record /workspace/guest/pip-_PsWy1-record/install-record.txt
>     --single-version-externally-managed --compile --user --prefix="
>     failed with error code 1 in
>     /p/work2/workspace/guest/pip-build-L2pBBW/subprocess32/
> You are using pip version 8.1.0, however version 9.0.1 is available.
> You should consider upgrading via the 'pip install --upgrade pip'
> command.
> 
> 
> 
> So, it complains about cython.  But cython is already installed:
> 
> 
> 
> > pip install cython --user
> Requirement already satisfied (use --upgrade to upgrade): cython in
> /p/home/usr/local/python/2.7.9/gnu/lib/python2.7/site-packages/Cython-0.23.4-py2.7-linux-x86_64.egg
> 
> 
> I'm not sure what to do next.


From jpboard2 at yahoo.com  Wed Jan 18 15:43:28 2017
From: jpboard2 at yahoo.com (James Board)
Date: Wed, 18 Jan 2017 20:43:28 +0000 (UTC)
Subject: [scikit-image] Compilation Problems
References: <979621904.5605375.1484772208729.ref@mail.yahoo.com>
Message-ID: <979621904.5605375.1484772208729@mail.yahoo.com>

>
> Please try:
> 
> pip uninstall cython
> pip install cython
> 
> Thanks
> St?fan
 
I can't do that.  I don't have root access.

From matthew.brett at gmail.com  Wed Jan 18 16:00:53 2017
From: matthew.brett at gmail.com (Matthew Brett)
Date: Wed, 18 Jan 2017 13:00:53 -0800
Subject: [scikit-image] Compilation Problems
In-Reply-To: <979621904.5605375.1484772208729@mail.yahoo.com>
References: <979621904.5605375.1484772208729.ref@mail.yahoo.com>
 <979621904.5605375.1484772208729@mail.yahoo.com>
Message-ID: <CAH6Pt5rRUoF8DEcMzsE+on50dQuUD6nR2T9LpYAW7xDKUCG2cw@mail.gmail.com>

Hi,

On Wed, Jan 18, 2017 at 12:43 PM, James Board via scikit-image
<scikit-image at python.org> wrote:
>>
>> Please try:
>>
>> pip uninstall cython
>> pip install cython
>>
>> Thanks
>> St?fan
>
> I can't do that.  I don't have root access.

Try this:

pip install --user --ignore-installed cython

Then make sure that the Python user installs bin directory is on your path:

export PATH=$HOME/.local/bin:$PATH

Reload the path to make sure you're finding the right Cython:

hash -r

Now check you have the right Cython (in ~/.local/bin):

which cython

Cheers,

Matthew

From jpboard2 at yahoo.com  Thu Jan 19 11:57:02 2017
From: jpboard2 at yahoo.com (James Board)
Date: Thu, 19 Jan 2017 16:57:02 +0000 (UTC)
Subject: [scikit-image] Compilation Problems
References: <41323896.372154.1484845022694.ref@mail.yahoo.com>
Message-ID: <41323896.372154.1484845022694@mail.yahoo.com>

>
> Try
> this:
> 
> pip install --user --ignore-installed cython
> 
> Then make sure that the Python user installs
> bin directory is on your path:
> 
> export PATH=$HOME/.local/bin:$PATH
> 
> Reload the path to make sure
> you're finding the right Cython:
> 
> hash -r
> 
> Now
> check you have the right Cython (in ~/.local/bin):
> 
> which cython
 
That. fixed it.  Thanks, and thanks to all who helped me get scikit imstalled.

From siqueiraaf at gmail.com  Thu Jan 19 16:33:41 2017
From: siqueiraaf at gmail.com (Alexandre Fioravante de Siqueira)
Date: Thu, 19 Jan 2017 19:33:41 -0200
Subject: [scikit-image] skimage on GSoC 2017
In-Reply-To: <CANPz1oaj2Q5qEXE-DcEq1iOdDdS6WG1wojyM9RVNT1mZQdhNxA@mail.gmail.com>
References: <CANPz1oaG_1w=MK98XV2KRweF+K9Xuo9gLXQ8maWUOJ8aFxZp2Q@mail.gmail.com>
 <CANPz1oZ6+YMS6OGhBcFx6pRKP47OedhPbJLRuZ5DSmeeQw9Nkg@mail.gmail.com>
 <CANPz1oYu_ykdYEijzOKWk5swT8p3FHgaS7Ab8o2dwEQ1eASb1Q@mail.gmail.com>
 <CANPz1oaj2Q5qEXE-DcEq1iOdDdS6WG1wojyM9RVNT1mZQdhNxA@mail.gmail.com>
Message-ID: <CANPz1oYVcS2YuwtXOqbdxt4=W7zSujiem2GtaCOJK=biUU-_5Q@mail.gmail.com>

Dear all,
are we (scikit-image) planning to participate on Google Summer of Code [1]
this year?
Would it be good? If yes, I volunteer myself to be a mentor.
Kind regards,

Alex

[1]
https://opensource.googleblog.com/2017/01/now-accepting-organization-applications.html?m=1
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From stefanv at berkeley.edu  Thu Jan 19 17:38:40 2017
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Thu, 19 Jan 2017 14:38:40 -0800
Subject: [scikit-image] skimage on GSoC 2017
In-Reply-To: <CANPz1oYVcS2YuwtXOqbdxt4=W7zSujiem2GtaCOJK=biUU-_5Q@mail.gmail.com>
References: <CANPz1oaG_1w=MK98XV2KRweF+K9Xuo9gLXQ8maWUOJ8aFxZp2Q@mail.gmail.com>
 <CANPz1oZ6+YMS6OGhBcFx6pRKP47OedhPbJLRuZ5DSmeeQw9Nkg@mail.gmail.com>
 <CANPz1oYu_ykdYEijzOKWk5swT8p3FHgaS7Ab8o2dwEQ1eASb1Q@mail.gmail.com>
 <CANPz1oaj2Q5qEXE-DcEq1iOdDdS6WG1wojyM9RVNT1mZQdhNxA@mail.gmail.com>
 <CANPz1oYVcS2YuwtXOqbdxt4=W7zSujiem2GtaCOJK=biUU-_5Q@mail.gmail.com>
Message-ID: <1484865520.2006521.853433712.39B4C6E5@webmail.messagingengine.com>

Hi Alex



Last year, we chose not to participate: the time investment for
mentoring is significant.  On the other hand, we have gained some very
good contributors through GSoC, some of them still active.


If you are willing to lead the GSoC effort, and to put the time in to
mentor, I would happily support you in whichever way I can.


Best regards

St?fan





On Thu, Jan 19, 2017, at 13:33, Alexandre Fioravante de Siqueira wrote:
> Dear all,

> are we (scikit-image) planning to participate on Google Summer of Code
> [1] this year?
> Would it be good? If yes, I volunteer myself to be a mentor.

> Kind regards,

> 

> Alex

> 

> [1] https://opensource.googleblog.com/2017/01/now-accepting-organization-applications.html?m=1
> _________________________________________________

> scikit-image mailing list

> scikit-image at python.org

> https://mail.python.org/mailman/listinfo/scikit-image


-------------- next part --------------
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From max.linke88 at gmail.com  Thu Jan 19 17:43:41 2017
From: max.linke88 at gmail.com (Max Linke)
Date: Thu, 19 Jan 2017 23:43:41 +0100
Subject: [scikit-image] skimage on GSoC 2017
In-Reply-To: <1484865520.2006521.853433712.39B4C6E5@webmail.messagingengine.com>
References: <CANPz1oaG_1w=MK98XV2KRweF+K9Xuo9gLXQ8maWUOJ8aFxZp2Q@mail.gmail.com>
 <CANPz1oZ6+YMS6OGhBcFx6pRKP47OedhPbJLRuZ5DSmeeQw9Nkg@mail.gmail.com>
 <CANPz1oYu_ykdYEijzOKWk5swT8p3FHgaS7Ab8o2dwEQ1eASb1Q@mail.gmail.com>
 <CANPz1oaj2Q5qEXE-DcEq1iOdDdS6WG1wojyM9RVNT1mZQdhNxA@mail.gmail.com>
 <CANPz1oYVcS2YuwtXOqbdxt4=W7zSujiem2GtaCOJK=biUU-_5Q@mail.gmail.com>
 <1484865520.2006521.853433712.39B4C6E5@webmail.messagingengine.com>
Message-ID: <2d7821c8-a4bf-0f15-00ab-6465ca1ebcc9@gmail.com>

Hi

NumFOCUS will apply again as an umbrella organization. You are welcome
to participate with us this year.

https://github.com/numfocus/gsoc

@Alex the time commitment for a student will be on the order of
5-10 hours a week minimum if you have an student that can work 
independently.

best Max

On 01/19/2017 11:38 PM, Stefan van der Walt wrote:
> Hi Alex
>
> Last year, we chose not to participate: the time investment for
> mentoring is significant.  On the other hand, we have gained some very
> good contributors through GSoC, some of them still active.
>
> If you are willing to lead the GSoC effort, and to put the time in to
> mentor, I would happily support you in whichever way I can.
>
> Best regards
> St?fan
>
>
> On Thu, Jan 19, 2017, at 13:33, Alexandre Fioravante de Siqueira wrote:
>> Dear all,
>> are we (scikit-image) planning to participate on Google Summer of Code
>> [1] this year?
>> Would it be good? If yes, I volunteer myself to be a mentor.
>> Kind regards,
>>
>> Alex
>>
>> [1]
>> https://opensource.googleblog.com/2017/01/now-accepting-organization-applications.html?m=1
>> _________________________________________________
>> scikit-image mailing list
>> scikit-image at python.org <mailto:scikit-image at python.org>
>> https://mail.python.org/mailman/listinfo/scikit-image
>
>
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>

From fboulogne at sciunto.org  Sat Jan 21 01:20:52 2017
From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=)
Date: Sat, 21 Jan 2017 07:20:52 +0100
Subject: [scikit-image] Future of nose and issues for scikit-image
In-Reply-To: <97bb74ab-b45d-4001-55db-80dfabdf2f8f@sciunto.org>
References: <ec39bdce-02d6-17c7-0d3a-7d47e98297af@sciunto.org>
 <CAE-UAvS3TgKrJ=b3DDOY64of2h4sAygjYducLtW9S4EigspYyQ@mail.gmail.com>
 <08c990bf-f2f0-ab5e-4063-f4300e46900f@sciunto.org>
 <159565c1f38.273e.acf34a9c767d7bb498a799333be0433e@fastmail.com>
 <98FF2884-49FF-4421-A6C3-DE2B321A710E@gmail.com>
 <1483226766.3931153.833987329.7617F174@webmail.messagingengine.com>
 <9019c557-d6ec-4d3f-858e-805ddbf0b853@Spark>
 <CAA48SF8rtNS8n=OmSAi89qh8ODtZ6ka3OBAFpB7GfhMC81=Vsw@mail.gmail.com>
 <97bb74ab-b45d-4001-55db-80dfabdf2f8f@sciunto.org>
Message-ID: <44b7cb89-9ff0-0c17-6f7d-503f03400781@sciunto.org>

FYI, Nelle started a PR here:
https://github.com/scikit-image/scikit-image/pull/2468

-- 
Fran?ois Boulogne.
http://www.sciunto.org
GPG: 32D5F22F


From siqueiraaf at gmail.com  Sun Jan 22 07:13:09 2017
From: siqueiraaf at gmail.com (Alexandre Fioravante de Siqueira)
Date: Sun, 22 Jan 2017 10:13:09 -0200
Subject: [scikit-image] skimage on GSoC 2017
In-Reply-To: <2d7821c8-a4bf-0f15-00ab-6465ca1ebcc9@gmail.com>
References: <CANPz1oaG_1w=MK98XV2KRweF+K9Xuo9gLXQ8maWUOJ8aFxZp2Q@mail.gmail.com>
 <CANPz1oZ6+YMS6OGhBcFx6pRKP47OedhPbJLRuZ5DSmeeQw9Nkg@mail.gmail.com>
 <CANPz1oYu_ykdYEijzOKWk5swT8p3FHgaS7Ab8o2dwEQ1eASb1Q@mail.gmail.com>
 <CANPz1oaj2Q5qEXE-DcEq1iOdDdS6WG1wojyM9RVNT1mZQdhNxA@mail.gmail.com>
 <CANPz1oYVcS2YuwtXOqbdxt4=W7zSujiem2GtaCOJK=biUU-_5Q@mail.gmail.com>
 <1484865520.2006521.853433712.39B4C6E5@webmail.messagingengine.com>
 <2d7821c8-a4bf-0f15-00ab-6465ca1ebcc9@gmail.com>
Message-ID: <1485087189.3826.4.camel@gmail.com>

Dear Stefan and Max,
thank you very much for your insights. I'm back in Brazil now, in a
place with a very bad internet connection until Jan 31.
I don't believe I have that much time available... I'll check my
schedule for May~Aug and return to you soon.
Kind regards,

Alex 

On Thu, 2017-01-19 at 23:43 +0100, Max Linke wrote:
> Hi
> 
> NumFOCUS will apply again as an umbrella organization. You are welcome
> to participate with us this year.
> 
> https://github.com/numfocus/gsoc
> 
> @Alex the time commitment for a student will be on the order of
> 5-10 hours a week minimum if you have an student that can work 
> independently.
> 
> best Max
> 
> On 01/19/2017 11:38 PM, Stefan van der Walt wrote:
> > Hi Alex
> >
> > Last year, we chose not to participate: the time investment for
> > mentoring is significant.  On the other hand, we have gained some very
> > good contributors through GSoC, some of them still active.
> >
> > If you are willing to lead the GSoC effort, and to put the time in to
> > mentor, I would happily support you in whichever way I can.
> >
> > Best regards
> > St?fan
> >
> >
> > On Thu, Jan 19, 2017, at 13:33, Alexandre Fioravante de Siqueira wrote:
> >> Dear all,
> >> are we (scikit-image) planning to participate on Google Summer of Code
> >> [1] this year?
> >> Would it be good? If yes, I volunteer myself to be a mentor.
> >> Kind regards,
> >>
> >> Alex
> >>
> >> [1]
> >> https://opensource.googleblog.com/2017/01/now-accepting-organization-applications.html?m=1
> >> _________________________________________________
> >> scikit-image mailing list
> >> scikit-image at python.org <mailto:scikit-image at python.org>
> >> https://mail.python.org/mailman/listinfo/scikit-image
> >
> >
> >
> > _______________________________________________
> > scikit-image mailing list
> > scikit-image at python.org
> > https://mail.python.org/mailman/listinfo/scikit-image
> >
> 



From fboulogne at sciunto.org  Tue Jan 24 14:51:01 2017
From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=)
Date: Tue, 24 Jan 2017 20:51:01 +0100
Subject: [scikit-image] Need a review (for a long standing PR) and release
 manager
Message-ID: <0dfda563-4315-9ea6-6561-8b65fd2d44d7@sciunto.org>

Dear core devs,

This PR is opened for a while and we need a final second reviewer:
https://github.com/scikit-image/scikit-image/pull/2040
Please, take few minutes to approve the PR. It's part of the blocking
issues for 0.13 and we tried to ping several times.

There is still few issues and PR for 0.13. Egor and I did our best these
last weeks to reduce drastically the length of the list and some of them
can probably be postponed. Is there anyone who wants to manage the next
release? (Personally, I don't.want to).

Thank you.
Best,

-- 
Fran?ois Boulogne.
http://www.sciunto.org
GPG: 32D5F22F



From stefanv at berkeley.edu  Tue Jan 24 15:17:58 2017
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Tue, 24 Jan 2017 12:17:58 -0800
Subject: [scikit-image] Need a review (for a long standing PR) and
 release manager
In-Reply-To: <0dfda563-4315-9ea6-6561-8b65fd2d44d7@sciunto.org>
References: <0dfda563-4315-9ea6-6561-8b65fd2d44d7@sciunto.org>
Message-ID: <1485289078.1427586.858303800.1720C7C5@webmail.messagingengine.com>

Hi Fran?ois

On Tue, Jan 24, 2017, at 11:51, Fran?ois Boulogne wrote:
> This PR is opened for a while and we need a final second reviewer:
> https://github.com/scikit-image/scikit-image/pull/2040
> Please, take few minutes to approve the PR. It's part of the blocking
> issues for 0.13 and we tried to ping several times.

I think that issue has been approved enough times in words to go ahead
and merge (there's one conflict that needs to be sorted out).

> There is still few issues and PR for 0.13. Egor and I did our best these
> last weeks to reduce drastically the length of the list and some of them
> can probably be postponed. Is there anyone who wants to manage the next
> release? (Personally, I don't.want to).

You have done a great job at that, too---thank you very much.

I think Alexandre was interested in helping out with the release.  But
if he isn't available, I will put some time aside.

St?fan

From jni.soma at gmail.com  Tue Jan 24 17:44:07 2017
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Wed, 25 Jan 2017 09:44:07 +1100
Subject: [scikit-image] Need a review (for a long standing PR) and
 release manager
In-Reply-To: <1485289078.1427586.858303800.1720C7C5@webmail.messagingengine.com>
References: <0dfda563-4315-9ea6-6561-8b65fd2d44d7@sciunto.org>
 <1485289078.1427586.858303800.1720C7C5@webmail.messagingengine.com>
Message-ID: <dfea437c-653f-4e64-98d0-5e9257341a1a@Spark>

I'm happy to volunteer as release manager.

On 25 Jan 2017, 7:18 AM +1100, Stefan van der Walt <stefanv at berkeley.edu>, wrote:
> Hi Fran?ois
>
> On Tue, Jan 24, 2017, at 11:51, Fran?ois Boulogne wrote:
> > This PR is opened for a while and we need a final second reviewer:
> > https://github.com/scikit-image/scikit-image/pull/2040
> > Please, take few minutes to approve the PR. It's part of the blocking
> > issues for 0.13 and we tried to ping several times.
>
> I think that issue has been approved enough times in words to go ahead
> and merge (there's one conflict that needs to be sorted out).
>
> > There is still few issues and PR for 0.13. Egor and I did our best these
> > last weeks to reduce drastically the length of the list and some of them
> > can probably be postponed. Is there anyone who wants to manage the next
> > release? (Personally, I don't.want to).
>
> You have done a great job at that, too---thank you very much.
>
> I think Alexandre was interested in helping out with the release. But
> if he isn't available, I will put some time aside.
>
> St?fan
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
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From stefanv at berkeley.edu  Tue Jan 24 17:45:13 2017
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Tue, 24 Jan 2017 14:45:13 -0800
Subject: [scikit-image] Need a review (for a long standing PR) and
 release manager
In-Reply-To: <dfea437c-653f-4e64-98d0-5e9257341a1a@Spark>
References: <0dfda563-4315-9ea6-6561-8b65fd2d44d7@sciunto.org>
 <1485289078.1427586.858303800.1720C7C5@webmail.messagingengine.com>
 <dfea437c-653f-4e64-98d0-5e9257341a1a@Spark>
Message-ID: <1485297913.2385448.858461480.5A0F280A@webmail.messagingengine.com>

On Tue, Jan 24, 2017, at 14:44, Juan Nunez-Iglesias wrote:

> I'm happy to volunteer as release manager.



Going, going, gone!



Congratulations, Juan, and thank you.


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From siqueiraaf at gmail.com  Wed Jan 25 12:33:05 2017
From: siqueiraaf at gmail.com (Alexandre Fioravante de Siqueira)
Date: Wed, 25 Jan 2017 15:33:05 -0200
Subject: [scikit-image] Need a review (for a long standing PR) and
 release manager
In-Reply-To: <1485297913.2385448.858461480.5A0F280A@webmail.messagingengine.com>
References: <0dfda563-4315-9ea6-6561-8b65fd2d44d7@sciunto.org>
 <1485289078.1427586.858303800.1720C7C5@webmail.messagingengine.com>
 <dfea437c-653f-4e64-98d0-5e9257341a1a@Spark>
 <1485297913.2385448.858461480.5A0F280A@webmail.messagingengine.com>
Message-ID: <1485365585.4935.5.camel@gmail.com>

Dear all,

"""
I think Alexandre was interested in helping out with the release.  But
if he isn't available, I will put some time aside.
"""

I'm moving back to Brazil these days, so I'd be not useful for anything
within ~3 weeks (not on my working PC/poor internet access). I'm sorry
about that.

"""
I'm happy to volunteer as release manager.
"""

Thank you very much for that Juan!

Kind regards,

Alex


On Tue, 2017-01-24 at 14:45 -0800, Stefan van der Walt wrote:
> On Tue, Jan 24, 2017, at 14:44, Juan Nunez-Iglesias wrote:
> 
> > I'm happy to volunteer as release manager.
> > 
> 
> 
> Going, going, gone!
> 
> 
> 
> Congratulations, Juan, and thank you.
> 
> 
>