Added documenntation to the docs folder and edited the mac bash script in response to tests

numpy-1.6.2/numpy/numarray/alter_code1.py

@@ -0,0 +1,265 @@
+"""
+This module converts code written for numarray to run with numpy
+
+Makes the following changes:
+ * Changes import statements
+
+   import numarray.package
+       --> import numpy.numarray.package as numarray_package
+           with all numarray.package in code changed to numarray_package
+
+   import numarray --> import numpy.numarray as numarray
+   import numarray.package as <yyy> --> import numpy.numarray.package as <yyy>
+
+   from numarray import <xxx> --> from numpy.numarray import <xxx>
+   from numarray.package import <xxx>
+       --> from numpy.numarray.package import <xxx>
+
+   package can be convolve, image, nd_image, mlab, linear_algebra, ma,
+                  matrix, fft, random_array
+
+
+ * Makes search and replace changes to:
+   - .imaginary --> .imag
+   - .flat --> .ravel() (most of the time)
+   - .byteswapped() --> .byteswap(False)
+   - .byteswap() --> .byteswap(True)
+   - .info() --> numarray.info(self)
+   - .isaligned() --> .flags.aligned
+   - .isbyteswapped() --> (not .dtype.isnative)
+   - .typecode() --> .dtype.char
+   - .iscontiguous() --> .flags.contiguous
+   - .is_c_array() --> .flags.carray and .dtype.isnative
+   - .is_fortran_contiguous() --> .flags.fortran
+   - .is_f_array() --> .dtype.isnative and .flags.farray
+   - .itemsize() --> .itemsize
+   - .nelements() --> .size
+   - self.new(type) --> numarray.newobj(self, type)
+   - .repeat(r) --> .repeat(r, axis=0)
+   - .size() --> .size
+   - self.type() -- numarray.typefrom(self)
+   - .typecode() --> .dtype.char
+   - .stddev() --> .std()
+   - .togglebyteorder() --> numarray.togglebyteorder(self)
+   - .getshape() --> .shape
+   - .setshape(obj) --> .shape=obj
+   - .getflat() --> .ravel()
+   - .getreal() --> .real
+   - .setreal() --> .real =
+   - .getimag() --> .imag
+   - .setimag() --> .imag =
+   - .getimaginary() --> .imag
+   - .setimaginary() --> .imag
+
+"""
+__all__ = ['convertfile', 'convertall', 'converttree', 'convertsrc']
+
+import sys
+import os
+import re
+import glob
+
+def changeimports(fstr, name, newname):
+    importstr = 'import %s' % name
+    importasstr = 'import %s as ' % name
+    fromstr = 'from %s import ' % name
+    fromall=0
+
+    name_ = name
+    if ('.' in name):
+        name_ = name.replace('.','_')
+
+    fstr = re.sub(r'(import\s+[^,\n\r]+,\s*)(%s)' % name,
+                  "\\1%s as %s" % (newname, name), fstr)
+    fstr = fstr.replace(importasstr, 'import %s as ' % newname)
+    fstr = fstr.replace(importstr, 'import %s as %s' % (newname,name_))
+    if (name_ != name):
+        fstr = fstr.replace(name, name_)
+
+    ind = 0
+    Nlen = len(fromstr)
+    Nlen2 = len("from %s import " % newname)
+    while 1:
+        found = fstr.find(fromstr,ind)
+        if (found < 0):
+            break
+        ind = found + Nlen
+        if fstr[ind] == '*':
+            continue
+        fstr = "%sfrom %s import %s" % (fstr[:found], newname, fstr[ind:])
+        ind += Nlen2 - Nlen
+    return fstr, fromall
+
+flatindex_re = re.compile('([.]flat(\s*?[[=]))')
+
+
+def addimport(astr):
+    # find the first line with import on it
+    ind = astr.find('import')
+    start = astr.rfind(os.linesep, 0, ind)
+    astr = "%s%s%s%s" % (astr[:start], os.linesep,
+                         "import numpy.numarray as numarray",
+                         astr[start:])
+    return astr
+
+def replaceattr(astr):
+    astr = astr.replace(".imaginary", ".imag")
+    astr = astr.replace(".byteswapped()",".byteswap(False)")
+    astr = astr.replace(".byteswap()", ".byteswap(True)")
+    astr = astr.replace(".isaligned()", ".flags.aligned")
+    astr = astr.replace(".iscontiguous()",".flags.contiguous")
+    astr = astr.replace(".is_fortran_contiguous()",".flags.fortran")
+    astr = astr.replace(".itemsize()",".itemsize")
+    astr = astr.replace(".size()",".size")
+    astr = astr.replace(".nelements()",".size")
+    astr = astr.replace(".typecode()",".dtype.char")
+    astr = astr.replace(".stddev()",".std()")
+    astr = astr.replace(".getshape()", ".shape")
+    astr = astr.replace(".getflat()", ".ravel()")
+    astr = astr.replace(".getreal", ".real")
+    astr = astr.replace(".getimag", ".imag")
+    astr = astr.replace(".getimaginary", ".imag")
+
+    # preserve uses of flat that should be o.k.
+    tmpstr = flatindex_re.sub(r"@@@@\2",astr)
+    # replace other uses of flat
+    tmpstr = tmpstr.replace(".flat",".ravel()")
+    # put back .flat where it was valid
+    astr = tmpstr.replace("@@@@", ".flat")
+    return astr
+
+info_re = re.compile(r'(\S+)\s*[.]\s*info\s*[(]\s*[)]')
+new_re = re.compile(r'(\S+)\s*[.]\s*new\s*[(]\s*(\S+)\s*[)]')
+toggle_re = re.compile(r'(\S+)\s*[.]\s*togglebyteorder\s*[(]\s*[)]')
+type_re = re.compile(r'(\S+)\s*[.]\s*type\s*[(]\s*[)]')
+
+isbyte_re = re.compile(r'(\S+)\s*[.]\s*isbyteswapped\s*[(]\s*[)]')
+iscarr_re = re.compile(r'(\S+)\s*[.]\s*is_c_array\s*[(]\s*[)]')
+isfarr_re = re.compile(r'(\S+)\s*[.]\s*is_f_array\s*[(]\s*[)]')
+repeat_re = re.compile(r'(\S+)\s*[.]\s*repeat\s*[(]\s*(\S+)\s*[)]')
+
+setshape_re = re.compile(r'(\S+)\s*[.]\s*setshape\s*[(]\s*(\S+)\s*[)]')
+setreal_re = re.compile(r'(\S+)\s*[.]\s*setreal\s*[(]\s*(\S+)\s*[)]')
+setimag_re = re.compile(r'(\S+)\s*[.]\s*setimag\s*[(]\s*(\S+)\s*[)]')
+setimaginary_re = re.compile(r'(\S+)\s*[.]\s*setimaginary\s*[(]\s*(\S+)\s*[)]')
+def replaceother(astr):
+    # self.info() --> numarray.info(self)
+    # self.new(type) --> numarray.newobj(self, type)
+    # self.togglebyteorder() --> numarray.togglebyteorder(self)
+    # self.type() --> numarray.typefrom(self)
+    (astr, n1) = info_re.subn('numarray.info(\\1)', astr)
+    (astr, n2) = new_re.subn('numarray.newobj(\\1, \\2)', astr)
+    (astr, n3) = toggle_re.subn('numarray.togglebyteorder(\\1)', astr)
+    (astr, n4) = type_re.subn('numarray.typefrom(\\1)', astr)
+    if (n1+n2+n3+n4 > 0):
+        astr = addimport(astr)
+
+    astr = isbyte_re.sub('not \\1.dtype.isnative', astr)
+    astr = iscarr_re.sub('\\1.dtype.isnative and \\1.flags.carray', astr)
+    astr = isfarr_re.sub('\\1.dtype.isnative and \\1.flags.farray', astr)
+    astr = repeat_re.sub('\\1.repeat(\\2, axis=0)', astr)
+    astr = setshape_re.sub('\\1.shape = \\2', astr)
+    astr = setreal_re.sub('\\1.real = \\2', astr)
+    astr = setimag_re.sub('\\1.imag = \\2', astr)
+    astr = setimaginary_re.sub('\\1.imag = \\2', astr)
+    return astr
+
+import datetime
+def fromstr(filestr):
+    savestr = filestr[:]
+    filestr, fromall = changeimports(filestr, 'numarray', 'numpy.numarray')
+    base = 'numarray'
+    newbase = 'numpy.numarray'
+    for sub in ['', 'convolve', 'image', 'nd_image', 'mlab', 'linear_algebra',
+                'ma', 'matrix', 'fft', 'random_array']:
+        if sub != '':
+            sub = '.'+sub
+        filestr, fromall = changeimports(filestr, base+sub, newbase+sub)
+
+    filestr = replaceattr(filestr)
+    filestr = replaceother(filestr)
+    if savestr != filestr:
+        name = os.path.split(sys.argv[0])[-1]
+        today = datetime.date.today().strftime('%b %d, %Y')
+        filestr = '## Automatically adapted for '\
+                  'numpy.numarray %s by %s\n\n%s' % (today, name, filestr)
+        return filestr, 1
+    return filestr, 0
+
+def makenewfile(name, filestr):
+    fid = file(name, 'w')
+    fid.write(filestr)
+    fid.close()
+
+def convertfile(filename, orig=1):
+    """Convert the filename given from using Numarray to using NumPy
+
+    Copies the file to filename.orig and then over-writes the file
+    with the updated code
+    """
+    fid = open(filename)
+    filestr = fid.read()
+    fid.close()
+    filestr, changed = fromstr(filestr)
+    if changed:
+        if orig:
+            base, ext = os.path.splitext(filename)
+            os.rename(filename, base+".orig")
+        else:
+            os.remove(filename)
+        makenewfile(filename, filestr)
+
+def fromargs(args):
+    filename = args[1]
+    convertfile(filename)
+
+def convertall(direc=os.path.curdir, orig=1):
+    """Convert all .py files to use numpy.oldnumeric (from Numeric) in the directory given
+
+    For each file, a backup of <usesnumeric>.py is made as
+    <usesnumeric>.py.orig.  A new file named <usesnumeric>.py
+    is then written with the updated code.
+    """
+    files = glob.glob(os.path.join(direc,'*.py'))
+    for afile in files:
+        if afile[-8:] == 'setup.py': continue
+        convertfile(afile, orig)
+
+header_re = re.compile(r'(numarray/libnumarray.h)')
+
+def convertsrc(direc=os.path.curdir, ext=None, orig=1):
+    """Replace Numeric/arrayobject.h with numpy/oldnumeric.h in all files in the
+    directory with extension give by list ext (if ext is None, then all files are
+    replaced)."""
+    if ext is None:
+        files = glob.glob(os.path.join(direc,'*'))
+    else:
+        files = []
+        for aext in ext:
+            files.extend(glob.glob(os.path.join(direc,"*.%s" % aext)))
+    for afile in files:
+        fid = open(afile)
+        fstr = fid.read()
+        fid.close()
+        fstr, n = header_re.subn(r'numpy/libnumarray.h',fstr)
+        if n > 0:
+            if orig:
+                base, ext = os.path.splitext(afile)
+                os.rename(afile, base+".orig")
+            else:
+                os.remove(afile)
+            makenewfile(afile, fstr)
+
+def _func(arg, dirname, fnames):
+    convertall(dirname, orig=0)
+    convertsrc(dirname, ['h','c'], orig=0)
+
+def converttree(direc=os.path.curdir):
+    """Convert all .py files in the tree given
+
+    """
+    os.path.walk(direc, _func, None)
+
+
+if __name__ == '__main__':
+    converttree(sys.argv)