[ITK-users] SimpleITK, Python, Local User, Anaconda -- how to install without messing up shared libraries?

Tue Feb 2 16:26:20 EST 2016

Hello Robert,

We understand our documentation was not sufficiently clear, so we have
updated our installation instructions page
(http://www.itk.org/Wiki/SimpleITK/GettingStarted). Hopefully the
instructions are clearer now.

Instructions for anaconda:
0. See which virtual environments already exist:
   $ conda info -e
1. Assuming sitkpy doesn't exist, create it and install SimpleITK there:
   $ conda create -n sitkpy -c https://conda.binstar.org/simpleitk
python=3.4 anaconda SimpleITK
2. Activate the environment and start working:
   $ source activate sitkpy

If there is no binary distribution for your operating system, step 1
fails, then you will have to build from source using our conda-recipe:

   $ git clone https://github.com/conda/conda-recipes.git
   $ cd conda-recipes
   $ conda build simpleitk

This will take a while as it will download the source and compile
everything. We assume you have git and a supported compiler installed. For
more information on conda recipes see the conda documentation
http://conda.pydata.org/docs/building/recipe.html.

    Ziv 

On 2/2/16, 6:58 AM, "Robert.Atwood at diamond.ac.uk"
<Robert.Atwood at diamond.ac.uk> wrote:

>
>Hi, ITK people! 
>
>
>I don't maintain the Python installation at work so I know little about
>all the intricacies of python modules and distributions and path
>searching and so on.
>What I do know is that if I follow the instructions for including
>SimpleITK as on the web page for Anacoda installation, everyone gets very
>angry. 
>That is because it automatically resolves some dependencies in a way that
>breaks other people's applications, and it does this within the shared
>Python Anaconda installation on the cluster shared file system.
>
>It was suggested (strongly) that I "use the --user option of pip"  .
>However I cannot get this to do anything by following the pip instruction
>on the SimpleITK web site, I know nothing of eggs and wheels nor pipit
>nor "more complicated commands. "
>
>Does anyone know the magic incantation to do what I want?  Is there an
>Anaconda command that does it?
>
>
>Instructions from website with questions annotated:
>
>Wheels [ Recommended ]
>You need a recent version of pip ( >= 6.0, newer is better) to install
>wheels. Please go to pip homepage for more information about installation.
>Once you have pip, the package can be installed:
>$ pip install --allow-external SimpleITK --trusted-host www.simpleitk.org
>SimpleITK  --timeout 30 SimpleITK
>Note: We do have window wheels hosted on pypi, but due to size and Linux
>binary restrictions neither OS X nor Linux are hosted on pipit, so the
>more complicated command is needed(1).
>However, you may need to manually download the file(2) from SourceForge.
>And specify it (3) on the command line if the automatic search does not
>work.
>
>(1) What is the 'more complicated command' ???
>(2) Which file? An egg? Wheel? Huh?
>(3) Specify what? How (what is the syntax for specifying 'it' )?
>
>
>Output of session trying to follow the instructions.
>
>$ pip install --user --allow-external SimpleITK --trusted-host
>www.simpleitk.org SimpleITK  --timeout 30 SimpleITK
>Double requirement given: SimpleITK (already in SimpleITK,
>name='SimpleITK')
>You are using pip version 7.1.2, however version 8.0.2 is available.
>You should consider upgrading via the 'pip install --upgrade pip' command.
>[kny48981 at i12-ws011 6137]$ pip install --user --allow-external SimpleITK
>--trusted-host www.simpleitk.org   --timeout 30 SimpleITK
>Collecting SimpleITK
>  Could not find a version that satisfies the requirement SimpleITK (from
>versions: )
>No matching distribution found for SimpleITK
>You are using pip version 7.1.2, however version 8.0.2 is available.
>You should consider upgrading via the 'pip install --upgrade pip' command.
>[kny48981 at i12-ws011 6137]$ pip install --user --allow-external SimpleITK
>--trusted-host www.simpleitk.org SimpleITK
>Collecting SimpleITK
>  Could not find a version that satisfies the requirement SimpleITK (from
>versions: )
>No matching distribution found for SimpleITK
>You are using pip version 7.1.2, however version 8.0.2 is available.
>You should consider upgrading via the 'pip install --upgrade pip' command.
>[kny48981 at i12-ws011 6137]$ pip install --user --allow-external
>--trusted-host www.simpleitk.org SimpleITK
>Collecting www.simpleitk.org
>  Could not find a version that satisfies the requirement
>www.simpleitk.org (from versions: )
>No matching distribution found for www.simpleitk.org
>You are using pip version 7.1.2, however version 8.0.2 is available.
>You should consider upgrading via the 'pip install --upgrade pip' command.
>
>
>
>
>
>
>
>
>
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