Merge pull request #154 from satra/enh/vtk8

[WIP] fix: first pass at transition to vtk 8.x

Author: satra

.circleci/config.yml

@@ -0,0 +1,43 @@
+version: 2
+jobs:
+  build:
+    docker:
+      - image: continuumio/miniconda3:4.5.4
+    environment:
+      ENV_NAME: mindboggle-env
+      vtk_cpp_tools: /src/mindboggle/vtk_cpp_tools/bin
+    working_directory: /src/mindboggle
+    steps:
+      - checkout
+      - run:
+          name: Install mindboggle
+          command: |
+            set -eu
+            apt-get update -qq && apt-get install -yq \
+                build-essential \
+                libgl1-mesa-dev \
+                libglu1-mesa-dev \
+                libsm-dev \
+                libx11-dev \
+                libxt-dev \
+                libxext-dev
+            ln -sv /usr/lib/x86_64-linux-gnu /usr/lib64
+            conda config --set show_channel_urls yes --set always_yes yes
+            conda config --add channels conda-forge
+            conda update conda conda-env
+            conda env create --quiet
+            source activate $ENV_NAME
+            conda info --envs
+            python setup.py install
+            mkdir $vtk_cpp_tools && cd $vtk_cpp_tools && cmake ../ && make
+      - run:
+          name: Test mindboggle
+          command: |
+            source activate $ENV_NAME
+            export MB=/opt/conda/envs/${ENV_NAME}/lib/python3.6/site-packages/mindboggle
+            export PATH=$PATH:$vtk_cpp_tools
+            python -m "nose" --with-doctest ${MB}/thirdparty/
+            python -m "nose" --with-doctest ${MB}/mio/
+            python -m "nose" --with-doctest ${MB}/guts/
+            python -m "nose" --with-doctest ${MB}/shapes/
+            python -m "nose" --with-doctest ${MB}/features/

.gitignore

@@ -44,3 +44,5 @@ _$*
 *.tar.gz
 *.Z 
 *.zip
+
+MANIFEST

circle.yml

@@ -13,16 +13,12 @@
 #-----------------------------------------------------------------------------
 name: mindboggle-env
 #-----------------------------------------------------------------------------
-# anaconda cloud channel for installing VTK 7.0.0:
-#-----------------------------------------------------------------------------
-channels:
-    - clinicalgraphics
-#-----------------------------------------------------------------------------
 # mindboggle dependencies:
 #-----------------------------------------------------------------------------
 dependencies:
-    - python=3.5.1
-    - vtk=7.0.0
+    - python>=3.5.1
+    - vtk>=7.0
+    - mesalib
     - matplotlib
     - numpy
     - scipy

environment.yml

@@ -16,7 +16,8 @@
                "Programming Language :: Python 3",
                "Topic :: Scientific/Engineering"]
 
-description  = "Automated human brain image feature extraction, labeling, and shape analysis"
+description  = ("Automated human brain image feature extraction, labeling, "
+                "and shape analysis")
 
 # Note: this long_description is actually a copy/paste from the top-level
 # README.rst, so that it shows up nicely on PyPI.  So please remember to edit
@@ -50,5 +51,5 @@
 PLATFORMS           = "Linux"
 VERSION             = __version__
 PROVIDES            = ["mindboggle"]
-#REQUIRES            = ["numpy (>={0})".format(NUMPY_MIN_VERSION)]
+REQUIRES            = ["nipype", "matplotlib", "colormath", "pandas"]
 

info.py

@@ -18,29 +18,13 @@
 if len(set(('develop', 'bdist_egg', 'bdist_rpm', 'bdist', 'bdist_dumb',
             'bdist_wininst', 'install_egg_info', 'egg_info', 'easy_install',
             )).intersection(sys.argv)) > 0:
-    # setup_egg imports setuptools setup, thus monkeypatching distguts.
-    # import setup_egg
     pass
 from distutils.core import setup
 
 # Get version and release info, which is all stored in info.py
 ver_file = pjoin(os.getcwd(), 'info.py')
 exec(open(ver_file).read())
 
-# Do dependency checking
-#package_check('numpy', NUMPY_MIN_VERSION)
-
-# extra_setuptools_args = {}
-# if 'setuptools' in sys.modules:
-#     extra_setuptools_args = dict(
-#         tests_require=['nose'],
-#         test_suite='nose.collector',
-#         zip_safe=False,
-#         extras_require = dict(
-#             doc='Sphinx>=0.3',
-#             test='nose>=0.10.1')
-#     )
-
 def main(**extra_args):
     setup(name=NAME,
           maintainer=MAINTAINER,
@@ -55,7 +39,7 @@ def main(**extra_args):
           author_email=AUTHOR_EMAIL,
           platforms=PLATFORMS,
           version=VERSION,
-          #requires=REQUIRES,
+          requires=REQUIRES,
           provides=PROVIDES,
           packages=['mindboggle',
                     'mindboggle.data',
@@ -77,4 +61,3 @@ def main(**extra_args):
 
 if __name__ == "__main__":
     main()
-    #main(**extra_setuptools_args)

setup.py

@@ -5,7 +5,7 @@ project(mindboggle_surfaces)
 ## "cmake .. -DVTK_DIR:STRING=/Users/arno/anaconda/lib/cmake/vtk-7.0"
 #set(VTK_DIR "/Users/arno/anaconda/lib/cmake/vtk-7.0")
 #find_package(VTK REQUIRED NO_MODULE)
-find_package(VTK 7.0 COMPONENTS vtkInteractionStyle vtkRenderingFreeType vtkRenderingOpenGL2 vtkRenderingVolumeOpenGL2 vtkIOLegacy vtkIOMINC vtkIOGeometry vtkImagingStencil vtkImagingMorphological vtkFiltersModeling NO_MODULE)
+find_package(VTK 8.1 COMPONENTS vtkInteractionStyle vtkRenderingFreeType vtkRenderingOpenGL2 vtkRenderingVolumeOpenGL2 vtkIOLegacy vtkIOMINC vtkIOGeometry vtkImagingStencil vtkImagingMorphological vtkFiltersModeling NO_MODULE)
 include(${VTK_USE_FILE})
 
 #if(COMMAND CMAKE_POLICY)