Merge branch 'master' into release

.travis.yml

@@ -1,7 +1,7 @@
 language: python
 os: linux
 # To test filter plugins, need hdf5 1.8.11+, present in Trusty but not Precise.
-#dist: trusty
+dist: trusty
 # Required to get Trusty.
 #sudo: true
 python:
@@ -18,9 +18,7 @@ install:
     - "pip install -U pip virtualenv"
     # Ensures the system hdf5 headers/libs will be used whatever its version
     - "export HDF5_DIR=/usr/lib"
-    # Force Cython to be istalled before h5py.
-    - "pip install Cython>=0.19"
-    - "pip install --no-binary=h5py -r requirements.txt"
+    - "pip install -r requirements.txt"
     # Installing the plugin to arbitrary directory to check the install script.
     - "python setup.py install --h5plugin --h5plugin-dir ~/hdf5/lib"
     # Ensure it's installable and usable in virtualenv

README.rst

@@ -47,9 +47,12 @@ As a bonus, Bitshuffle ships with a dynamically loaded version of
 `h5py`'s LZF compression filter, such that the filter can be transparently
 used outside of python and in command line utilities such as ``h5dump``.
 
-.. [1] Chosen to fit comfortably within L1 cache as well as be well matched window of the LZF compression library.
+.. [1] Chosen to fit comfortably within L1 cache as well as be well matched
+       window of the LZF compression library.
 
-.. [2] Over applying bitshuffle to the full dataset then applying LZ4 compression, this has the tremendous advantage that the block is already in the L1 cache.
+.. [2] Over applying bitshuffle to the full dataset then applying LZ4
+       compression, this has the tremendous advantage that the block is
+       already in the L1 cache.
 
 .. _`dynamically loaded filters`: http://www.hdfgroup.org/HDF5/doc/Advanced/DynamicallyLoadedFilters/HDF5DynamicallyLoadedFilters.pdf
 
@@ -92,9 +95,11 @@ Comparing Bitshuffle to other compression algorithms and HDF5 filters:
 Installation for Python
 -----------------------
 
-Installation requires python 2.7+ or 3.3+, HDF5 1.8 or later, HDF5 for python,
-Numpy and Cython.  To use the dynamically loaded HDF5 filter requires HDF5
-1.8.11 or later.
+Installation requires python 2.7+ or 3.3+, HDF5 1.8.4 or later, HDF5 for python
+(h5py), Numpy and Cython. Bitshuffle must be linked against the same version of
+HDF5 as h5py, which in practice means h5py must be built from source_ rather
+than pre-built wheels [3]_. To use the dynamically loaded HDF5 filter requires
+HDF5 1.8.11 or later.
 
 To install::
 
@@ -113,6 +118,11 @@ If you get an error about missing source files when building the extensions,
 try upgrading setuptools.  There is a weird bug where setuptools prior to 0.7
 doesn't work properly with Cython in some cases.
 
+.. _source: http://docs.h5py.org/en/latest/build.html#source-installation
+
+.. [3] Typically you will be able to install Bitshuffle, but there will be
+       errors when creating and reading datasets.
+
 
 Usage from Python
 -----------------

bitshuffle/h5.pyx

@@ -100,7 +100,7 @@ def create_dataset(parent, name, shape, dtype, chunks=None, maxshape=None,
 
     tmp_shape = maxshape if maxshape is not None else shape
     # Validate chunk shape
-    chunks_larger = (-numpy.array([ i>=j 
+    chunks_larger = (numpy.array([ not i>=j
                      for i,j in zip(tmp_shape,chunks) if i is not None])).any()
     if isinstance(chunks, tuple) and chunks_larger:
         errmsg = ("Chunk shape must not be greater than data shape in any "

requirements.txt

@@ -1,5 +1,5 @@
-# order matter
+# Order matters
 setuptools>=0.7
 Cython>=0.19
 numpy>=1.6.1
-h5py>=2.4.0
+h5py>=2.4.0 --no-binary=h5py

setup.py

@@ -2,8 +2,6 @@
 # I didn't import unicode_literals. They break setuptools or Cython in python
 # 2.7, but python 3 seems to be happy with them.
 
-from distutils import ccompiler
-from distutils import spawn
 import glob
 import os
 from os import path
@@ -247,17 +245,21 @@ def finalize_options(self):
                 print("\n#################################")
                 print("# Compiling with OpenMP support #")
                 print("#################################\n")
-            self.libraries += ['gomp']
+            # More portable to pass -fopenmp to linker.
+            # self.libraries += ['gomp']
             for e in self.extensions:
                 if '-fopenmp' not in e.extra_compile_args:
                     e.extra_compile_args += ['-fopenmp']
+                if '-fopenmp' not in e.extra_link_args:
+                    e.extra_link_args += ['-fopenmp']
 
         # Required only by old version of setuptools < 18.0
         from Cython.Build import cythonize
         self.extensions = cythonize(self.extensions)
         for ext in self.extensions:
             ext._needs_stub = False
 
+
 # Don't install numpy/cython/hdf5 if not needed
 for cmd in ["sdist", "clean",
             "--help", "--help-commands", "--version"]:
@@ -269,6 +271,7 @@ def finalize_options(self):
 
 with open('requirements.txt') as f:
     requires = f.read().splitlines()
+    requires = [r.split()[0] for r in requires]
 
 # TODO hdf5 support should be an "extra". Figure out how to set this up.
 setup(
@@ -290,6 +293,7 @@ def finalize_options(self):
     description="Bitshuffle filter for improving typed data compression.",
     license="MIT",
     url="https://github.com/kiyo-masui/bitshuffle",
-    download_url="https://github.com/kiyo-masui/bitshuffle/tarball/%s" % VERSION,
+    download_url=("https://github.com/kiyo-masui/bitshuffle/tarball/%s"
+                  % VERSION),
     keywords=['compression', 'hdf5', 'numpy'],
 )