Source code for brian2.codegen.runtime.cython_rt.extension_manager

"""
Cython automatic extension builder/manager

Inspired by IPython's Cython cell magics, see:
https://github.com/ipython/ipython/blob/master/IPython/extensions/cythonmagic.py
"""


import glob
import hashlib
import importlib.util
import os
import shutil
import sys
import time
from distutils.command.build_ext import build_ext
from distutils.core import Distribution, Extension

import numpy

try:
    import Cython
    import Cython.Build as Cython_Build
    import Cython.Compiler as Cython_Compiler
    from Cython.Utils import get_cython_cache_dir as base_cython_cache_dir
except ImportError:
    Cython = None

from brian2.core.preferences import prefs
from brian2.utils.filelock import FileLock
from brian2.utils.logger import get_logger, std_silent
from brian2.utils.stringtools import deindent

__all__ = ["cython_extension_manager"]

logger = get_logger(__name__)


[docs]def get_cython_cache_dir(): cache_dir = prefs.codegen.runtime.cython.cache_dir if cache_dir is None and Cython is not None: cache_dir = os.path.join(base_cython_cache_dir(), "brian_extensions") return cache_dir
[docs]def get_cython_extensions(): return { ".pyx", ".pxd", ".pyd", ".cpp", ".c", ".so", ".o", ".o.d", ".lock", ".dll", ".obj", ".exp", ".lib", }
[docs]class CythonExtensionManager: def __init__(self): self._code_cache = {}
[docs] def create_extension( self, code, force=False, name=None, define_macros=None, include_dirs=None, library_dirs=None, runtime_library_dirs=None, extra_compile_args=None, extra_link_args=None, libraries=None, compiler=None, sources=None, owner_name="", ): if sources is None: sources = [] self._simplify_paths() if Cython is None: raise ImportError("Cython is not available") code = deindent(code) lib_dir = get_cython_cache_dir() if "~" in lib_dir: lib_dir = os.path.expanduser(lib_dir) try: os.makedirs(lib_dir) except OSError: if not os.path.exists(lib_dir): raise OSError( f"Couldn't create Cython cache directory '{lib_dir}', try setting" " the cache directly with prefs.codegen.runtime.cython.cache_dir." ) numpy_version = ".".join( numpy.__version__.split(".")[:2] ) # Only use major.minor version # avoid some issues when manually switching compilers CC = os.environ.get("CC", None) CXX = os.environ.get("CXX", None) key = ( code, sys.version_info, sys.executable, Cython.__version__, numpy_version, CC, CXX, ) if force: # Force a new module name by adding the current time to the # key which is hashed to determine the module name. key += (time.time(),) # Note the trailing comma (this is a tuple) if key in self._code_cache: return self._code_cache[key] if name is not None: module_name = name # py3compat.unicode_to_str(args.name) else: module_name = ( f"_cython_magic_{hashlib.md5(str(key).encode('utf-8')).hexdigest()}" ) if owner_name: logger.diagnostic(f'"{owner_name}" using Cython module "{module_name}"') module_path = os.path.join(lib_dir, module_name + self.so_ext) if prefs["codegen.runtime.cython.multiprocess_safe"]: lock = FileLock(os.path.join(lib_dir, f"{module_name}.lock")) with lock: module = self._load_module( module_path, define_macros=define_macros, include_dirs=include_dirs, library_dirs=library_dirs, extra_compile_args=extra_compile_args, extra_link_args=extra_link_args, libraries=libraries, code=code, lib_dir=lib_dir, module_name=module_name, runtime_library_dirs=runtime_library_dirs, compiler=compiler, key=key, sources=sources, ) return module else: return self._load_module( module_path, define_macros=define_macros, include_dirs=include_dirs, library_dirs=library_dirs, extra_compile_args=extra_compile_args, extra_link_args=extra_link_args, libraries=libraries, code=code, lib_dir=lib_dir, module_name=module_name, runtime_library_dirs=runtime_library_dirs, compiler=compiler, key=key, sources=sources, )
@property def so_ext(self): """The extension suffix for compiled modules.""" try: return self._so_ext except AttributeError: self._so_ext = self._get_build_extension().get_ext_filename("") return self._so_ext def _clear_distutils_mkpath_cache(self): """clear distutils mkpath cache prevents distutils from skipping re-creation of dirs that have been removed """ try: from distutils.dir_util import _path_created except ImportError: pass else: _path_created.clear() def _get_build_extension(self, compiler=None): self._clear_distutils_mkpath_cache() dist = Distribution() config_files = dist.find_config_files() try: config_files.remove("setup.cfg") except ValueError: pass dist.parse_config_files(config_files) build_extension = build_ext(dist) if compiler is not None: build_extension.compiler = compiler build_extension.finalize_options() return build_extension def _load_module( self, module_path, define_macros, include_dirs, library_dirs, extra_compile_args, extra_link_args, libraries, code, lib_dir, module_name, runtime_library_dirs, compiler, key, sources, ): have_module = os.path.isfile(module_path) if not have_module: if define_macros is None: define_macros = [] if include_dirs is None: include_dirs = [] if library_dirs is None: library_dirs = [] if runtime_library_dirs is None: runtime_library_dirs = [] if extra_compile_args is None: extra_compile_args = [] if extra_link_args is None: extra_link_args = [] if libraries is None: libraries = [] c_include_dirs = include_dirs if "numpy" in code: import numpy c_include_dirs.append(numpy.get_include()) # TODO: We should probably have a special folder just for header # files that are shared between different codegen targets import brian2.synapses as synapses synapses_dir = os.path.dirname(synapses.__file__) c_include_dirs.append(synapses_dir) pyx_file = os.path.join(lib_dir, f"{module_name}.pyx") # ignore Python 3 unicode stuff for the moment # pyx_file = py3compat.cast_bytes_py2(pyx_file, encoding=sys.getfilesystemencoding()) # with io.open(pyx_file, 'w', encoding='utf-8') as f: # f.write(code) with open(pyx_file, "w") as f: f.write(code) for source in sources: if not source.lower().endswith(".pyx"): raise ValueError( "Additional Cython source files need to have an .pyx ending" ) # Copy source and header file (if present) to library directory shutil.copyfile(source, os.path.join(lib_dir, os.path.basename(source))) name_without_ext = os.path.splitext(os.path.basename(source))[0] header_name = f"{name_without_ext}.pxd" if os.path.exists(os.path.join(os.path.dirname(source), header_name)): shutil.copyfile( os.path.join(os.path.dirname(source), header_name), os.path.join(lib_dir, header_name), ) final_sources = [ os.path.join(lib_dir, os.path.basename(source)) for source in sources ] extension = Extension( name=module_name, sources=[pyx_file], define_macros=define_macros, include_dirs=c_include_dirs, library_dirs=library_dirs, runtime_library_dirs=runtime_library_dirs, extra_compile_args=extra_compile_args, extra_link_args=extra_link_args, libraries=libraries, language="c++", ) build_extension = self._get_build_extension(compiler=compiler) try: opts = dict( quiet=True, annotate=False, force=True, ) # suppresses the output on stdout with std_silent(): build_extension.extensions = Cython_Build.cythonize( [extension] + final_sources, **opts ) build_extension.build_temp = os.path.dirname(pyx_file) build_extension.build_lib = lib_dir build_extension.run() if prefs["codegen.runtime.cython.delete_source_files"]: # we can delete the source files to save disk space cpp_file = os.path.join(lib_dir, f"{module_name}.cpp") try: os.remove(pyx_file) os.remove(cpp_file) temp_dir = os.path.join( lib_dir, os.path.dirname(pyx_file)[1:], f"{module_name}.*", ) for fname in glob.glob(temp_dir): os.remove(fname) except OSError as ex: logger.debug( "Deleting Cython source files failed with error:" f" {str(ex)}" ) except Cython_Compiler.Errors.CompileError: return # Temporarily insert the Cython directory to the Python path so that # code importing from an external module that was declared via # sources works sys.path.insert(0, lib_dir) spec = importlib.util.spec_from_file_location(module_name, module_path) module = importlib.util.module_from_spec(spec) spec.loader.exec_module(module) sys.path.pop(0) self._code_cache[key] = module return module def _simplify_paths(self): if "lib" in os.environ: os.environ["lib"] = simplify_path_env_var(os.environ["lib"]) if "include" in os.environ: os.environ["include"] = simplify_path_env_var(os.environ["include"])
cython_extension_manager = CythonExtensionManager()
[docs]def simplify_path_env_var(path): allpaths = path.split(os.pathsep) knownpaths = set() uniquepaths = [] for p in allpaths: if p not in knownpaths: knownpaths.add(p) uniquepaths.append(p) return os.pathsep.join(uniquepaths)