[WIP] VTK 7 recipe supporting both Python 2 & 3

[grlee77]

Hi,

I spent some time the other day getting VTK 7 to build with Python 3 wrappers and wanted to share my efforts. I have marked this as work-in-progress because I am only sure that this recipe succeeds on 64-bit linux.

On OSX Yosemite, the build completed successfully (at least once I installed XCode), but for some reason the import failed during running the tests and the package was not installed. However, if I manually copy the VTK folder from the _build environment's site-packages folder into my primary environment's site-packages folder, it does seem to work properly.

The windows case has not been tested at all, but I attempted to add the appropriate flag for Python 2 vs. 3

[ccordoba12]

Please leave here gcc44 and g++44. Those are the versions we're using right now in centos5.

[ccordoba12]

Thanks a lot for working on this. Other than my minor comments, this seems good to go :-)

[satra]

+1 for merge works beautifully on os x.

[ccordoba12]

Will do :-)

[satra]

@ccordoba12 - hold that thought.

getting some rpath errors on pushing this to anaconda.org and installing with conda. looking into it.

[satra]

this is the error that's happening: nipy/mindboggle#69

[grlee77]

Hi Satra,
I verified that I can build mindboggle using this recipe on linux (Ubuntu 14.04) as long as I configure VTK_DIR to point to ~/anaconda/lib/cmake/vtk-7.0 instead of the one it found by default on the system path (or to the equivalent subfolder of whichever anaconda/env environment you are running)

Are you sure the VTK_DIR is getting set to this location during your os x build?

I am now trying this on a laptop with OS X at the moment, but the build is taking a while. For some reason, on my laptop, I have to comment out the cmake build requirement from meta.yml. Otherwise I get the following error. Did you encounter this?

+ cmake .. -DCMAKE_C_COMPILER=cc -DCMAKE_CXX_COMPILER=c++ -DVTK_REQUIRED_OBJCXX_FLAGS= -DVTK_USE_TK=OFF -DVTK_USE_COCOA=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/Users/lee8rx/anaconda/envs/_build -DCMAKE_INSTALL_RPATH:STRING=/Users/lee8rx/anaconda/envs/_build/lib -DBUILD_DOCUMENTATION=OFF -DVTK_HAS_FEENABLEEXCEPT=OFF -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=OFF -DBUILD_SHARED_LIBS=ON -DVTK_WRAP_PYTHON=ON -DPYTHON_EXECUTABLE=/Users/lee8rx/anaconda/envs/_build/bin/python -DPYTHON_INCLUDE_PATH=/Users/lee8rx/anaconda/envs/_build/include/python3.4m -DPYTHON_LIBRARY=/Users/lee8rx/anaconda/envs/_build/lib/libpython3.4m.dylib -DVTK_INSTALL_PYTHON_MODULE_DIR=/Users/lee8rx/anaconda/envs/_build/lib/python3.4/site-packages -DModule_vtkRenderingMatplotlib=ON -DVTK_USE_X=OFF -DVTK_PYTHON_VERSION=3
CMake Error: Could not find CMAKE_ROOT !!!
CMake has most likely not been installed correctly.
Modules directory not found in
/Users/lee8rx/anaconda/envs/_build/share/cmake-3.3
CMake Error: Error executing cmake::LoadCache(). Aborting.

I have cmake v3.4.3 already on my system, so removing the cmake requirement from meta.yml caused the system cmake to be used instead which works fine.

[satra]

@binarybottle - can you answer @grlee77 question?

[satra]

@grlee77 - did you try installing vtk7 from my conda repo, instead of building vtk locally with conda?

https://anaconda.org/satra/vtk

so the recipe builds fine on my local machine, but when i push to anaconda.org and someone downloads it they get the rpath error.

[grlee77]

@satra, @binarybottle
The OS X build of vtk_cpp_tools worked for me on OS X as well based on this recipe (I am on OS X Yosemite).

I uploaded a Python 3.4 build of VTK 7 for OS X here:
https://anaconda.org/grlee77/vtk/files
I will go ahead and upload Python 3.5 and 2.7 versions for OS X there as well once those builds complete. You can try installing from my channel via:
conda install --channel https://conda.anaconda.org/grlee77 vtk

Let's continue any further discussion of this back at nipy/mindboggle#69 as it seems the recipe itself is likely not the cause of the problem.

[satra]

@ccordoba12 - could someone from the continuum team help with this. i believe this is specific to conda-build and OSX.

[ccordoba12]

@satra, I'm in charge of compiling VTK in all platforms, so I'm your guy :-) Problem is I'm terribly busy until April 8th.

By reading the mindboggle issue very quickly, I think your problem is that CMake doesn't find the 10.6 SDK, which is necessary because conda-build sets MACOSX_DEPLOYMENT_TARGET precisely to 10.6.

If you're using command line tools, that SDK has to be placed in a particular location (I don't exactly remember which one right now), and if you're using XCode, it needs to be placed on another.

I hope this helps you to better understand your problem until I have some free time :-)

[hjmjohnson]

@ccordoba12 I am trying to build SimpleITK and VTK against anaconda, with similar issues with 10.6 SDK not being available.

I am running OS X 10.10.5, and Xcode 7.2.1.

CMake Warning at /scratch/johnsonhj/anaconda2/envs/_build/share/cmake-3.3/Modules/Platform/Darwin-Initialize.cmake:97 (message):
CMAKE_OSX_DEPLOYMENT_TARGET is '10.6' but the matching SDK does not exist
at:

"/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.6.sdk"

Instead using SDK:

"/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk".
Call Stack (most recent call first):
/scratch/johnsonhj/anaconda2/envs/_build/share/cmake-3.3/Modules/CMakeSystemSpecificInitialize.cmake:18 (include)
CMakeLists.txt:16 (project)

Are there instructions for setting up a compilation environment that is appropriate for the anaconda package building?

Thanks,
Hans

[mick-d]

Just for reference, after following the thread of PRs, the current easiest installation seems to be with conda-forge:

conda config --add channels conda-forge 
conda install vtk

[astrofrog]

@ccordoba12 - I know that VTK 7.0 on all platforms is currently not possible in conda-forge due to build time limitations on the CI services, but is there any chance that you could build and put VTK 7.0 in the defaults channel? :)