cython_compile.py was missing for some weird reason

wetb/utils/cython_compile/cython_compile.py

+'''
+Created on 10/07/2013
+
+@author: Mads M. Pedersen (mmpe@dtu.dk)
+
+
+Wrapper functions and decorators for compiling functions using Cython
+
+'''
+import inspect
+import os
+import re
+import shutil
+import subprocess
+import sys
+import numpy as np
+import warnings
+import imp
+
+
+
+def wrap(f, autodeclare, *args, **kwargs):
+    """
+    Wrapper function returned by the cython_compile and cython_compile_autodeclare decorators
+
+    :param f: Function to compile
+    :type f: function
+    :param py2pyx_func: py2pyx or py2pyx_autodeclare
+    :type py2pyx_func: function
+    """
+
+    # Generate name: "c:\documents\project\mymodule.py" -> mymodule_myfunction
+    # When called from ipython notebooks, filename is an object e.g: "<ipython-input-12-e897f9fefc0c>"
+    # therefore <,>,- is removed to make it a legal python module name
+    name = os.path.relpath(inspect.getabsfile(f), os.getcwd()).replace(".py", "")
+    name = name.replace("<", "").replace(">", "").replace("-", "")
+    name = "%s_%s" % (name, f.__name__)
+    if name.startswith(".."):
+        rel_dir = os.path.dirname(name) + os.path.sep
+        sys.path.append(rel_dir)
+        name = name[len(rel_dir):]
+        pass
+
+    module_name = name.replace(os.path.sep, ".")
+
+    # import compiled module_name if exists, otherwise compile and import
+    try:
+        cmodule = __import__(module_name, fromlist="*")
+        if cmodule.__name__ != module_name or not hasattr(cmodule, f.__name__):
+            raise ImportError()
+    except ImportError:
+        # Generate pyrex code lines
+        if autodeclare:
+            pyx_lines = py2pyx_autodeclare(f, args, kwargs.copy())
+        else:
+            # source lines except '@cython_compile'
+            source_lines = inspect.getsourcelines(f)[0][1:]
+            indent = source_lines[0].index("def")
+            pyx_lines = py2pyx([l[indent:] for l in source_lines])
+
+        # Write pyrex code lines to .pyx file
+        pyx_filename = name.replace("\\", "/") + ".pyx"
+        with open(pyx_filename, 'w') as fid:
+            fid.writelines(pyx_lines)
+
+        # compile, import compiled module_name and delete temporary files
+        cmodule = compile_and_cleanup(module_name, pyx_filename)
+    try:
+        cf = getattr(cmodule, f.__name__)
+        if kwargs == {}:
+            return cf(*args)
+        else:
+            return cf(*args, **kwargs)
+    except AttributeError:
+        warnings.warn(
+            "Compilation or import of %s failed. Python function used instead" %
+            f)
+        return f(*args, **kwargs)
+
+
+def cython_compile(f):
+    """Decorator for compilation, import and execution of the function, f.
+    Variables can be declared using Pure or cdef syntax, see module description
+    Example:
+    @cython_compile
+    def my_func(p):
+        pass
+    """
+    w = lambda *args, **kwargs: wrap(f, False, *args, **kwargs)
+    w.__name__ = f.__name__
+    return w
+
+
+def cython_compile_autodeclare(f):
+    """Decorator for autodeclaring, compilation, import and execution of the function, f.
+    Declared variables using cdef syntax overrides autodeclaration, see module description
+    Example:
+    @cython_compile_autocompile
+    def my_func(p):
+        pass
+    """
+    w = lambda *args, **kwargs: wrap(f, True, *args, **kwargs)
+    w.__name__ = f.__name__
+    return w
+
+
+def cython_import(import_module_name, compiler=None):
+    """Compiles and imports a module. Use it similar to the normal import
+    Example (import my_func from my_module):
+
+    from mmpe.cython_compile import cython_import
+    cython_import('my_module')
+    import my_module # import must be after cython_import statement
+    my_module.my_func()
+
+    """
+    module_name = import_module_name.split(".")[-1]
+    globals()[module_name] = __import__(import_module_name, fromlist=module_name)
+    pyd_module = eval(module_name)
+    if not is_compiled(pyd_module):
+
+        # Read py-module
+        file_name = import_module_name.replace(".", "/") + ".py"
+        for p in ["."] + sys.path:
+            if os.path.isfile(os.path.join(p, file_name)):
+                file_path = os.path.join(p, file_name).replace("\\", "/")
+                break
+        else:
+            raise IOError("Module %s cannot be found" % file_name)
+
+        fid = open(file_path)
+        pylines = fid.readlines()
+        fid.close()
+
+        # write pyrex file
+        pyx_filename = file_path.replace('.py', '.pyx')
+        fid = open(pyx_filename, 'w')
+        pyxlines = py2pyx(pylines)
+        fid.writelines(pyxlines)
+        fid.close()
+
+        # compile, import compiled module and delete temporary files
+        return compile_and_cleanup(import_module_name, pyx_filename, compiler)
+    return eval(module_name)
+
+
+def compile_and_cleanup(module, pyx_filename, compiler=None):
+    """compile, import compiled module and delete temporary files"""
+
+    # Generate setup.py script
+    fid = open('setup.py', 'w')
+    setup_str = """from distutils.core import setup
+from distutils.extension import Extension
+from Cython.Distutils import build_ext
+import numpy
+
+ext_modules = [Extension("%s", ["%s"], include_dirs = [numpy.get_include()])]
+
+setup(
+name = 'name',
+cmdclass = {'build_ext': build_ext},
+ext_modules = ext_modules
+)""" % (module, pyx_filename)
+    fid.write(setup_str)
+    fid.close()
+    if hasattr(sys, 'frozen'):
+        raise Exception ("Trying to compile %s in frozen application" % str(module))
+    # create compile command
+    import platform
+    if compiler is not None:
+        compiler_str = "--compiler=%s" % compiler
+    elif platform.architecture()[0] == "32bit" and os.name == 'nt' and "mingw" in os.environ['path'].lower():
+        compiler_str = "--compiler=mingw32"
+    else:
+        compiler_str = ""
+
+
+    if not hasattr(sys, 'frozen'):
+        bin_python = sys.executable
+        cmd = "%s setup.py build_ext --inplace %s" % (bin_python, compiler_str)
+
+        # compile
+        print ("compiling %s: %s" % (module, cmd))
+        proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True)
+        (out, err) = proc.communicate()
+
+    # Reload and check that module is compiled
+    try:
+        try:
+            del sys.modules[module]
+        except KeyError:
+            pass
+        cmodule = __import__(module, fromlist=module.split(".")[-1])
+        imp.reload(cmodule)
+
+    except ImportError:
+        cmodule = None
+
+    if cmodule is None or is_compiled(cmodule) == False:
+        line = '\n' + '=' * 79 + '\n'
+        sys.stderr.write("%s was not compiled correctly. It may result in slower execution" % module)
+        sys.stderr.write('%sstdout:\n%s' % (line, out.decode()))
+        sys.stderr.write('%sstderr:%s%s' % (line, line, err))
+
+    else:
+        print ("Compiling succeeded")
+        for f in ['setup.py', pyx_filename, pyx_filename.replace(".pyx", '.c')]:
+            if os.path.isfile(f):
+                os.remove(f)
+
+    # Clean up. Remove temporary files and folders
+    if os.path.isdir("build"):
+        try:
+            shutil.rmtree("build")
+        except:
+            pass
+
+    return cmodule
+
+
+def py2pyx_autodeclare(f, args, kwargs):
+    """Generate pyrex code of function f and its input arguments
+    This function invokes py2pyx and extends with autodeclarations:
+    - arguments: input arguments are declared based their values in args and kwargs
+    - cdef: Variables declared by cdef, overrides autodeclaration, e.g:
+        "def func(a): #cpdef func(int a):" -> "cpdef func(int a):" (independent of type of a)
+        "#cdef int a" - "cdef int a" (independent of type of a)
+    - assignment: Variables assigned in function, e.g.
+        "a = xxx"
+      are declared based on the type of eval(xxx)
+    - in: variables returned by iterators, e.g:
+        "for a in range(5)",
+        "for a,b in [(1,.2)]:"
+      are declared base on the type of the first element in eval(iterator), e.g. "type(eval(range(5)[0]))"
+    """
+
+    arg_names, _, _, defaults = inspect.getargspec(f)
+
+    # update kwargs with defaults
+    if defaults:
+        for k, v in zip(arg_names[::-1], defaults[::-1]):
+            if k not in kwargs:
+                kwargs[k] = v
+    kwargs.update(dict(zip(arg_names, args)))
+
+    # get pyx code lines using py2pyx
+    lines = inspect.getsourcelines(f)[0]
+    if lines[0].strip() == "@cython_compile_autodeclare":
+        lines = lines[1:]
+    lines = py2pyx(lines)
+
+    # prepare regular expressions
+    var_name = "(?:_*[a-zA-Z][a-zA-Z0-9_]*)"  # optional "_" + one alpha + [0..n] x alphanum. "?:" = no group
+    reg_args = re.compile("[ \t]*def +(?:%s) *\(([^:]*)\) *:" % (var_name))
+    reg_import = re.compile("[ \t]*c?import *(%s)(?: +as +(%s))?" % (var_name, var_name))
+    reg_cdef = re.compile("[ \t]*cdef +(?:(?:signed|unsigned|int|long|float|double|np\.ndarray\[.*\]) *)*(%s)" % var_name)
+    reg_assign = re.compile('[ \t]*(%s) *=(.*)' % var_name)
+    reg_in = re.compile('[ \t]*for +(%s(?:, *%s)*) +in +(.*):' % (var_name, var_name))
+
+
+    def declare_str(var_name, var_value):
+        """Generate declaration string '<type(var_value)> <var_name>' e.g:
+        declare_str('a',1) -> "long a"
+        """
+        if isinstance(var_value, (int)):
+            return "long long %s" % var_name
+        if isinstance(var_value, float):
+            return "double %s" % var_name
+        elif isinstance(var_value, np.ndarray):
+            return "np.ndarray[np.%s_t,ndim=%d] %s" % (var_value.dtype, len(var_value.shape), var_name)
+        else:
+            raise NotImplementedError(type(var_value))
+
+    defs = {}  # dict for known local variables
+    def_line = None  # line nr of "def func():". Autodeclaration of local field inserted below this line
+    for i, line in enumerate(lines):
+        if def_line is None and 'def' in line:
+            # first line containing "def" = function declaration line
+            def_line = i
+            match = reg_args.match(line)
+            if match is not None:
+                args = match.group(1).strip()  # line="   def func(xxx):#comment" -> args='xxx'
+                arg_strs = []
+                if args != "":
+                    for arg in args.split(','):
+                        arg_name = arg.split('=')[0].strip()
+                        arg_value = kwargs[arg_name]
+                        try:
+                            arg_strs.append(arg.strip().replace(arg_name, declare_str(arg_name, arg_value), 1))
+                        except NotImplementedError:
+                            arg_strs.append(arg)
+                # replace function declaration line
+                lines[i] = '%scpdef %s(%s):\n' % (" " * line.index('def'), f.__name__, ", ".join(arg_strs))
+        else:
+            #Import: import x as y
+            match = reg_import.match(line)
+            if match is not None:
+                # add imported moduled to kwargs -> enable evaluation of variables
+                import_module = match.group(1)
+                if match.group(2) is None:
+                    kwargs[import_module] = __import__(import_module)
+                else:
+                    # import xxx as y
+                    kwargs[match.group(2)] = __import__(import_module)
+                continue
+            #Cdef: cdef int x
+            match = reg_cdef.match(line)
+            if match is not None:
+                # line contains a 'cdef' declaration.
+                # Add to defs to avoid redeclaration
+                var_name = match.group(1)
+                if var_name not in defs:
+                    defs[var_name] = None
+                continue
+            #Assignment: x = y
+            match = reg_assign.match(line)
+            if match is not None:
+                # line contains an assignment, e.g. a = xxx.
+                # Try to evaluate xxx and declare a as type of eval(xxx)
+                try:
+                    var_name = match.group(1)
+                    if var_name not in defs:
+                        var_value = eval(match.group(2), globals(), kwargs)
+                        defs[var_name] = declare_str(
+                            var_name.strip(), var_value)
+                        kwargs[var_name] = var_value
+                except NotImplementedError:
+                    pass
+                continue
+            #In: For x in y
+            match = reg_in.match(line)
+            if match is not None:
+                # line contains 'for xxx in yyy:'.
+                # Try to evaluate yyy and declare xxx as type of first element
+                # of eval(yyy)
+                var_names = [v.strip() for v in match.group(1).split(",")]
+                var_values = eval(match.group(2), globals(), kwargs)[0]
+                if not isinstance(var_values, (list, tuple)):
+                    var_values = (var_values,)
+                for var_name, var_value in zip(var_names, var_values):
+                    try:
+                        if var_name not in defs:
+                            defs[var_name] = declare_str(var_name, var_value)
+                            kwargs[var_name] = var_value
+                    except NotImplementedError:
+                        pass
+    indent = lines[def_line + 1].replace(lines[def_line + 1].lstrip(), "")
+
+    # Insert declaration of local fields ordered by name just below function
+    # declaration
+    for key in sorted(defs.keys(), reverse=True):
+        if defs[key] is not None:
+            lines.insert(def_line + 1, "%scdef %s\n" % (indent, defs[key]))
+
+    return lines
+
+
+def py2pyx(pylines):
+    """Generate pyrex code lines from python code lines
+    - Adds import of cython and numpy
+    - searches every line for "#c". If found text before "#c" is replaced with text after "#c", e.g:
+    "def func(a): #cpdef func(int a):" -> "cpdef func(int a):
+    "#cdef int b" -> "cdef int b"
+    """
+    pyxlines = ['import cython\n', 'import numpy as np\n', 'cimport numpy as np\n']
+    for l in pylines:
+
+        if "#c" in l:
+            indent = l[:len(l) - len(l.lstrip())]
+            cdef = l[l.index("#c") + 1:]
+            l = indent + cdef
+        pyxlines.append(l)
+    return pyxlines
+
+
+def is_compiled(module):
+    return module.__file__.lower()[-4:] == ".pyd" or module.__file__.lower()[-3:] == ".so"