Merge pull request #566 from madsbk/version

Separating Bohrium and Bohrium API versions

VERSION

@@ -1 +1 @@
-0.10.0
+0.10.1

bridge/npbackend/bohrium/__init__.py

@@ -6,13 +6,16 @@
 
 if 'numpy_force' not in sys.modules:
     import numpy
+
     sys.modules['numpy_force'] = numpy
     del numpy
 
 # We import all of NumPy and overwrite with the objects we implement our self
 from numpy_force import *
 from numpy_force import testing
-
+import warnings
+import bohrium_api
+from .version import __version__, __version_info__
 from .array_create import *
 from .array_manipulation import *
 from .reorganization import *
@@ -29,7 +32,6 @@
 from .concatenate import *
 from .ufuncs import _handle__array_ufunc__
 from . import contexts
-from bohrium_api import stack_info as bh_info
 from . import interop_pyopencl
 from . import interop_pycuda
 from . import interop_numpy
@@ -44,18 +46,23 @@
 # However, NumPy and SciPy's functionality differ! Thus, the ND version cannot replace NumPy's 1D version.
 from .signal import correlate1d as correlate, convolve1d as convolve
 from .signal import correlate as correlate_scipy, convolve as convolve_scipy
-
 from numpy_force import dtype
+
 asarray = array
 asanyarray = array
 
+if __version_info__ > bohrium_api.__version_info__:
+    warnings.warn("The version of Bohrium API (%s) is newer than Bohrium (%s). Please upgrade "
+                  "Bohrium (e.g. `pip install bohrium --upgrade`)" % (__version__, bohrium_api.__version__))
+
 
 def replace_numpy(function):
     def wrapper(*args, **kwargs):
         with contexts.EnableBohrium():
             # Run your function/program
             result = function(*args, **kwargs)
         return result
+
     return wrapper
 
 
@@ -112,6 +119,7 @@ def wrapper(*args, **kwargs):
     def set_printoptions(*args, **kwargs):
         numpy.core.arrayprint.set_printoptions(*args, **kwargs)
 
+
     def get_printoptions(*args, **kwargs):
         return numpy.core.arrayprint.get_printoptions()
 

bridge/npbackend/bohrium/__main__.py

@@ -7,7 +7,8 @@
 import os
 import argparse
 import bohrium
-from . import bh_info
+import bohrium_api
+from . import version
 
 
 @bohrium.replace_numpy
@@ -49,7 +50,8 @@ def execfile_wrapper(path):
     execfile_wrapper(sys.argv[0])
 else:
     if args.info:
-        print(bh_info.pprint())
+        print("----\nBohrium version: %s" % version.__version__)
+        print(bohrium_api.stack_info.pprint())
 
         cmd = "import bohrium as bh; import numpy as np; assert((bh.arange(10) == np.arange(10)).all())"
         sys.stdout.write('Sanity Check: "%s"' % cmd)

bridge/npbackend/bohrium/interop_numpy.py

@@ -3,7 +3,7 @@
 ~~~~~~~~~~~~~
 """
 from .bhary import get_base
-from . import bh_info
+from bohrium_api import stack_info
 
 
 def get_array(bh_ary):
@@ -24,7 +24,7 @@ def get_array(bh_ary):
 
     """
 
-    if bh_info.is_proxy_in_stack():
+    if stack_info.is_proxy_in_stack():
         raise RuntimeError("Cannot directly access array data through a proxy.")
 
     if get_base(bh_ary) is not bh_ary:

bridge/npbackend/bohrium/interop_pycuda.py

@@ -2,10 +2,10 @@
 Interop PyCUDA
 ~~~~~~~~~~~~~~
 """
+from bohrium_api import stack_info
 from .bhary import get_base
 from ._bh import get_data_pointer
 from .backend_messaging import cuda_use_current_context
-from . import bh_info
 from . import contexts
 
 
@@ -19,11 +19,11 @@ def _import_pycuda_module():
     except ImportError:
         raise ImportError("Failed to import the `pycuda` module, please install PyCUDA")
 
-    if not bh_info.is_cuda_in_stack():
+    if not stack_info.is_cuda_in_stack():
         raise RuntimeError("No CUDA device in the Bohrium stack! "
                            "Try defining the environment variable `BH_STACK=cuda`.")
 
-    if bh_info.is_proxy_in_stack():
+    if stack_info.is_proxy_in_stack():
         raise RuntimeError("Cannot directly access the CUDA device through a proxy.")
     return pycuda
 

bridge/npbackend/bohrium/interop_pyopencl.py

@@ -2,9 +2,9 @@
 Interop PyOpenCL
 ~~~~~~~~~~~~~~~~
 """
+from bohrium_api import stack_info
 from .bhary import get_base
 from ._bh import get_data_pointer, set_data_pointer, get_device_context
-from . import bh_info
 
 
 def _import_pyopencl_module():
@@ -14,11 +14,11 @@ def _import_pyopencl_module():
     except ImportError:
         raise ImportError("Failed to import the `pyopencl` module, please install PyOpenCL")
 
-    if not bh_info.is_opencl_in_stack():
+    if not stack_info.is_opencl_in_stack():
         raise RuntimeError("No OpenCL device in the Bohrium stack! "
                            "Try defining the environment variable `BH_STACK=opencl`.")
 
-    if bh_info.is_proxy_in_stack():
+    if stack_info.is_proxy_in_stack():
         raise RuntimeError("Cannot directly access the OpenCL device through a proxy.")
     return pyopencl
 

bridge/npbackend/bohrium/nobh/bincount.py

@@ -1,10 +1,9 @@
 import math
 import numpy_force as np
-
+from bohrium_api import stack_info
 from .. import interop_pyopencl
 from .. import interop_pycuda
 from .. import array_create
-from .. import bh_info
 from .bincount_cython import bincount_cython
 
 
@@ -83,7 +82,7 @@ def bincount(x, weights=None, minlength=None):
     assert(np.issubdtype(x.dtype.type, np.integer))
     assert(np.issubdtype(x.dtype.type, np.integer))
 
-    if bh_info.is_proxy_in_stack():  # Cannot directly access array data through a proxy
+    if stack_info.is_proxy_in_stack():  # Cannot directly access array data through a proxy
         return np.bincount(x.copy2numpy(), weights=weights, minlength=minlength)
 
     try:

bridge/npbackend/bohrium/ufuncs.pyx

@@ -13,7 +13,7 @@ from . import _util
 from . import array_create
 from . import loop
 import numpy_force as np
-from bohrium_api import _info
+from bohrium_api import _info, stack_info
 from .numpy_backport import as_strided
 from ._util import dtype_equal
 from .bhary import fix_biclass_wrapper
@@ -354,7 +354,6 @@ class Ufunc(object):
                [ 9, 13]])
         """
         from . import _bh
-        from . import bh_info
 
         if out is not None:
             if bhary.check(out):
@@ -427,7 +426,7 @@ class Ufunc(object):
         else:
             # Let's sort the axis indexes by their stride
             # We use column major when a GPU is in the stack
-            column_major = bh_info.is_opencl_in_stack() or bh_info.is_cuda_in_stack()
+            column_major = stack_info.is_opencl_in_stack() or stack_info.is_cuda_in_stack()
             strides = []
             for i, s in enumerate(ary.strides):
                 if i in axis:

bridge/npbackend/setup.py

@@ -26,17 +26,59 @@
 from setuptools import setup, find_packages
 from setuptools.extension import Extension
 from setuptools.command.build_ext import build_ext as setup_build_ext
+from setuptools.command.build_py import build_py as setup_build_py
+from setuptools.command.sdist import sdist as setup_sdist
 import numbers
 import os
 import glob
 
+""" Beside the regular setup arguments, this script reads the follow environment variables:
+
+      * USE_CYTHON - if defined, this setup will cythonize all pyx files.
+    
+    NB: when running the source distribution command, `setup.py sdist`, do it from the same directory as `setup.py` 
+"""
+
 
 def script_path(*paths):
     prefix = os.path.abspath(os.path.dirname(__file__))
     assert len(prefix) > 0
     return os.path.join(prefix, *paths)
 
 
+def version_file_exist():
+    """Return whether the version.py file exist or not"""
+    ver_path = script_path("bohrium", "version.py")
+    return os.path.exists(ver_path)
+
+
+def get_version():
+    """Returns the version and version_info.
+        If the version.py file doesn't exist, the version of Bohrium API is returned.
+        NB: If the version.py file doesn't exist, this function must be called after the call to `setup()`.
+    """
+    ver_path = script_path("bohrium", "version.py")
+    if os.path.exists(ver_path):
+        print("Getting version from version.py")
+        # Loading `__version__` variable from the version file
+        with open(ver_path, "r") as f:
+            exec (f.read())
+        return (__version__, __version_info__)
+    else:
+        print("Getting version from bohrium_api")
+        import bohrium_api
+        return (bohrium_api.__version__, bohrium_api.__version_info__)
+
+
+def get_bohrium_api_required_string():
+    """Returns the install_requires/setup_requires string for `bohrium_api`"""
+    try:
+        ver_tuple = get_version()[1]
+        return "bohrium_api>=%d.%d.%d" % (ver_tuple[0], ver_tuple[1], ver_tuple[2])
+    except ImportError:
+        return "bohrium_api"  # If `bohrium_api` is not available, we expect PIP to install the newest package
+
+
 def get_pyx_extensions():
     """Find and compiles all cython extensions"""
     include_dirs = []
@@ -60,9 +102,34 @@ def get_pyx_extensions():
         return ret
 
 
+def gen_version_file_in_cmd(self, target_dir):
+    """We extend the setup commands to also generate the `version.py` file if it doesn't exist already"""
+    if not self.dry_run:
+        version, version_info = get_version()
+        if not version_file_exist():
+            self.mkpath(target_dir)
+            p = os.path.join(target_dir, 'version.py')
+            print("Generating '%s'" % p)
+            with open(p, 'w') as fobj:
+                fobj.write("__version__ = \"%s\"\n" % version)
+                fobj.write("__version_info__ = %s\n" % str(version_info))
+
+
+class BuildPy(setup_build_py):
+    def run(self):
+        gen_version_file_in_cmd(self, os.path.join(self.build_lib, 'bohrium'))
+        setup_build_py.run(self)
+
+
+class Sdist(setup_sdist):
+    def run(self):
+        gen_version_file_in_cmd(self, "bohrium")
+        setup_sdist.run(self)
+
+
 class BuildExt(setup_build_ext):
     """We delay the numpy and bohrium dependency to the build command.
-    Hopefully, PIP has installed them at this point."""
+       Hopefully, PIP has installed them at this point."""
 
     def run(self):
         if not self.dry_run:
@@ -77,12 +144,11 @@ class DelayedVersion(numbers.Number):
     """In order to delay the version evaluation that depend on `bohrium_api`, we use this class"""
 
     def __str__(self):
-        import bohrium_api
-        return bohrium_api.__version__
+        return get_version()[0]
 
 
 setup(
-    cmdclass={'build_ext': BuildExt},
+    cmdclass={'build_ext': BuildExt, 'build_py': BuildPy, 'sdist': Sdist},
     name='bohrium',
     version=DelayedVersion(),
     description='Bohrium Python/NumPy Backend',
@@ -126,8 +192,8 @@ def __str__(self):
     keywords='Bohrium, bh107, Python, C, HPC, MPI, PGAS, CUDA, OpenCL, OpenMP',
 
     # Dependencies
-    install_requires=['numpy>=1.7', 'bohrium_api'],
-    setup_requires=['numpy>=1.7', 'bohrium_api'],
+    install_requires=['numpy>=1.7', get_bohrium_api_required_string()],
+    setup_requires=['numpy>=1.7', get_bohrium_api_required_string()],
 
     # You can just specify the packages manually here if your project is
     # simple. Or you can use find_packages().

bridge/py_api/bohrium_api/__init__.py

@@ -7,7 +7,7 @@
 """
 import os
 from ._bh_api import _C_API  # Exposing the C_API of `_bh_api.c`
-from ._info import __version__
+from .version import __version__, __version_info__
 from . import stack_info
 
 

bridge/py_api/bohrium_api/stack_info.py

@@ -5,7 +5,7 @@
 import os
 from os.path import join
 from . import messaging
-from . import _info
+from .version import __version__, __version_info__
 
 # Some cached info
 _opencl_is_in_stack = None
@@ -34,11 +34,6 @@ def installed_through_pypi():
     return os.path.exists(os.path.join(os.path.dirname(os.path.realpath(__file__)), "config.ini"))
 
 
-def version():
-    """Return the version of Bohrium"""
-    return _info.__version__
-
-
 def header_dir():
     """Return the path to the C header directory"""
     return os.path.join(os.path.abspath(os.path.dirname(__file__)), "include")
@@ -47,8 +42,9 @@ def header_dir():
 def info():
     """Return a dict with all info"""
     return {
-        "config_path" : config_file_path(),
-        "version": version(),
+        "config_path": config_file_path(),
+        "version": __version__,
+        "version_info": __version_info__,
         "runtime_info": messaging.runtime_info(),
         "statistics": messaging.statistic(),
         "header_dir": header_dir(),
@@ -82,17 +78,15 @@ def is_proxy_in_stack():
 def pprint():
     """Pretty print Bohrium info"""
 
-    ret = ""
-    if not (is_opencl_in_stack() or is_cuda_in_stack()):
-        ret += "Note: in order to activate and retrieve GPU info, set the `BH_STACK=opencl` " \
-               "or `BH_STACK=cuda` environment variable.\n"
-
-    ret += """----
-Bohrium version: %s
+    ret = """----
+Bohrium API version: %s
 Installed through PyPI: %s
 Config file: %s
 Header dir: %s
 Backend stack:
 %s----
-""" % (version(), installed_through_pypi(), config_file_path(), header_dir(), messaging.runtime_info())
+""" % (__version__, installed_through_pypi(), config_file_path(), header_dir(), messaging.runtime_info())
+    if not (is_opencl_in_stack() or is_cuda_in_stack()):
+        ret += "Note: in order to activate and retrieve GPU info, set the `BH_STACK=opencl` " \
+               "or `BH_STACK=cuda` environment variable.\n"
     return ret

bridge/py_api/build.bash

@@ -17,7 +17,7 @@ if [[ -d "$VR_PATH" ]]; then
   echo "Using virtualenv: $VR_PATH"
 else
   echo "Create virtualenv: $VR_PATH"
-  ${PYTHON_EXECUTABLE} -m virtualenv -p ${PY_EXE} ${VR_PATH}
+  ${PYTHON_EXECUTABLE} -m virtualenv -p ${PY_EXE} --system-site-packages ${VR_PATH}
 fi
 
 source ${VR_PATH}/bin/activate