Merge pull request #143 from RemiLehe/robust_install

Close #142: pip install fails

Author: RemiLehe

.travis.yml

@@ -8,13 +8,10 @@ matrix:
   include:
     - os: linux
       python: "2.7"
-    - os: linux
-      python: "3.4"
     - os: linux
       python: "3.5"
-    - os: osx
-      language: cpp
-      env: TRAVIS_PYTHON_VERSION=2.7
+    - os: linux
+      python: "3.6"
 
 before_install:
   # Setup anaconda

MANIFEST.in

@@ -1,4 +1,5 @@
 include README.md
 include requirements.txt
+include opmd_viewer/openpmd_timeseries/cython_function.pyx
 include opmd_viewer/notebook_starter/openPMD_notebook
-include opmd_viewer/notebook_starter/Template_notebook.ipynb
+include opmd_viewer/notebook_starter/Template_notebook.ipynb

conda_recipe/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = "0.5.1" %}
+{% set version = "0.5.2" %}
 
 package:
   name: openpmd_viewer

opmd_viewer/__version__.py

@@ -1 +1 @@
-__version__ = "0.5.1"
+__version__ = "0.5.2"

opmd_viewer/openpmd_timeseries/particle_tracker.py

@@ -7,6 +7,7 @@
 Authors: Remi Lehe
 License: 3-Clause-BSD-LBNL
 """
+import warnings
 import numpy as np
 from .data_reader.particle_reader import read_species_data
 try:
@@ -103,6 +104,15 @@ def __init__(self, ts, species=None, t=None,
         self.species = species
         self.preserve_particle_index = preserve_particle_index
 
+        # Print a warning if the Cython function is unavailable
+        if not cython_function_available:
+            warnings.warn(
+            "\nUnable to compile particle tracking with Cython. \n"
+            "The ParticleTracker will still work, but will be slow. \n"
+            "For faster particle tracking: \n"
+            " - make sure that Cython is installed \n"
+            " - then reinstall openPMD-viewer")
+
     def extract_tracked_particles( self, file_handle, data_list,
                                     species, extensions ):
         """

requirements.txt

@@ -1,5 +1,4 @@
 numpy
 scipy
-Cython
 matplotlib
 h5py

setup.py

@@ -1,8 +1,6 @@
 import sys
 from setuptools import setup, find_packages
 from setuptools.command.test import test as TestCommand
-from Cython.Build import cythonize
-import numpy
 
 # Get the long description
 # If possible, use pypandoc to convert the README from Markdown
@@ -29,6 +27,18 @@ def run_tests(self):
         errcode = pytest.main([])
         sys.exit(errcode)
 
+# Try to compile the Cython function
+try:
+    import numpy
+    include_dirs = [numpy.get_include()]
+    from Cython.Build import cythonize
+    ext_modules = cythonize(
+      "opmd_viewer/openpmd_timeseries/cython_function.pyx")
+except ImportError:
+    # If the compilation fails, still install the package in a robust way
+    include_dirs = []
+    ext_modules = []
+
 # Main setup command
 setup(name='openPMD-viewer',
       version=__version__,
@@ -42,10 +52,8 @@ def run_tests(self):
       package_data={'opmd_viewer': ['notebook_starter/*.ipynb']},
       scripts=['opmd_viewer/notebook_starter/openPMD_notebook'],
       tests_require=['pytest', 'jupyter'],
-      setup_requires=['Cython', 'numpy'],
-      ext_modules = cythonize(
-        "opmd_viewer/openpmd_timeseries/cython_function.pyx"),
-      include_dirs=[numpy.get_include()],
+      ext_modules=ext_modules,
+      include_dirs=include_dirs,
       install_requires=install_requires,
       cmdclass={'test': PyTest},
       platforms='any',
@@ -60,6 +68,6 @@ def run_tests(self):
           'Topic :: Scientific/Engineering :: Visualization',
           'Topic :: Database :: Front-Ends',
           'Programming Language :: Python :: 2.7',
-          'Programming Language :: Python :: 3.4',
-          'Programming Language :: Python :: 3.5'],
+          'Programming Language :: Python :: 3.5',
+          'Programming Language :: Python :: 3.6'],
       )