numpy · rgommers · Mar 6, 2011 · Mar 6, 2011 · Mar 7, 2011 · Mar 7, 2011
diff --git a/doc/TESTS.rst.txt b/doc/TESTS.rst.txt
@@ -46,7 +46,7 @@ can be turned on (recommended after installation and before upgrading) by
 starting the interpreter with the -Wd switch, or by::
 
   >>> import warnings
-  >>> wwarnings.simplefilter('always', DeprecationWarning)
+  >>> warnings.simplefilter('always', DeprecationWarning)
 
 The test method may take two or more arguments; the first is a string
 label specifying what should be tested and the second is an integer

diff --git a/doc/summarize.py b/doc/summarize.py
@@ -42,7 +42,6 @@
 
 # --- numpy.fft:
 fft fft.Tester fft.bench fft.fftpack fft.fftpack_lite fft.helper
-fft.refft fft.refft2 fft.refftn fft.irefft fft.irefft2 fft.irefftn
 fft.info fft.test
 
 # --- numpy.linalg:
@@ -67,10 +66,10 @@ def main():
     fn = os.path.join(CUR_DIR, 'dump.xml')
     if os.path.isfile(fn):
         import_phantom_module(fn)
-    
+
     # check
     documented, undocumented = check_numpy()
-    
+
     # report
     in_sections = {}
     for name, locations in documented.iteritems():
@@ -108,7 +107,7 @@ def check_numpy():
             if k.startswith('numpy.'):
                 d[k[6:]] = d[k]
                 del d[k]
-    
+
     return documented, undocumented
 
 def get_undocumented(documented, module, module_name=None, skip=[]):
@@ -123,24 +122,24 @@ def get_undocumented(documented, module, module_name=None, skip=[]):
 
     """
     undocumented = {}
-    
+
     if module_name is None:
         module_name = module.__name__
-    
+
     for name in dir(module):
         obj = getattr(module, name)
         if name.startswith('_'): continue
-        
+
         full_name = '.'.join([module_name, name])
 
         if full_name in skip: continue
         if full_name.startswith('numpy.') and full_name[6:] in skip: continue
         if not (inspect.ismodule(obj) or callable(obj) or inspect.isclass(obj)):
             continue
-        
+
         if full_name not in documented:
             undocumented[full_name] = True
-    
+
     return undocumented
 
 def format_in_columns(lst, max_columns):
@@ -160,9 +159,9 @@ def format_in_columns(lst, max_columns):
         nrows = len(lst)//ncols
     else:
         nrows = 1 + len(lst)//ncols
-    
+
     fmt = ' %%-%ds ' % (col_len-2)
-    
+
     lines = []
     for n in range(nrows):
         lines.append("".join([fmt % x for x in lst[n::nrows]]))

diff --git a/doc/swig/test/setup.py b/doc/swig/test/setup.py
@@ -7,11 +7,8 @@
 # Third-party modules - we depend on numpy for everything
 import numpy
 
-# Obtain the numpy include directory.  This logic works across numpy versions.
-try:
-    numpy_include = numpy.get_include()
-except AttributeError:
-    numpy_include = numpy.get_numpy_include()
+# Obtain the numpy include directory.
+numpy_include = numpy.get_include()
 
 # Array extension module
 _Array = Extension("_Array",

diff --git a/numpy/core/memmap.py b/numpy/core/memmap.py
@@ -278,11 +278,6 @@ def flush(self):
         if self._mmap is not None:
             self._mmap.flush()
 
-    def sync(self):
-        """This method is deprecated, use `flush`."""
-        warnings.warn("Use ``flush``.", DeprecationWarning)
-        self.flush()
-
     def _close(self):
         """Close the memmap file.  Only do this when deleting the object."""
         if self.base is self._mmap:
@@ -292,11 +287,6 @@ def _close(self):
             self._mmap.close()
             self._mmap = None
 
-    def close(self):
-        """Close the memmap file. Does nothing."""
-        warnings.warn("``close`` is deprecated on memmap arrays.  Use del",
-                      DeprecationWarning)
-
     def __del__(self):
         # We first check if we are the owner of the mmap, rather than
         # a view, so deleting a view does not call _close

diff --git a/numpy/core/tests/test_memmap.py b/numpy/core/tests/test_memmap.py
@@ -4,7 +4,7 @@
 
 from numpy import memmap
 from numpy import arange, allclose
-from numpy.testing import *
+from numpy.testing import TestCase, assert_, assert_array_equal
 
 class TestMemmap(TestCase):
     def setUp(self):
@@ -27,7 +27,7 @@ def test_roundtrip(self):
         # Read data back from file
         newfp = memmap(self.tmpfp, dtype=self.dtype, mode='r',
                        shape=self.shape)
-        assert allclose(self.data, newfp)
+        assert_(allclose(self.data, newfp))
         assert_array_equal(self.data, newfp)
 
     def test_open_with_filename(self):
@@ -71,10 +71,6 @@ def test_flush(self):
         fp[:] = self.data[:]
         fp.flush()
 
-        warnings.simplefilter('ignore', DeprecationWarning)
-        fp.sync()
-        warnings.simplefilter('default', DeprecationWarning)
-
     def test_del(self):
         # Make sure a view does not delete the underlying mmap
         fp_base = memmap(self.tmpfp, dtype=self.dtype, mode='w+',

diff --git a/numpy/fft/fftpack.py b/numpy/fft/fftpack.py
@@ -31,8 +31,7 @@
 
 """
 __all__ = ['fft','ifft', 'rfft', 'irfft', 'hfft', 'ihfft', 'rfftn',
-           'irfftn', 'rfft2', 'irfft2', 'fft2', 'ifft2', 'fftn', 'ifftn',
-           'refft', 'irefft','refftn','irefftn', 'refft2', 'irefft2']
+           'irfftn', 'rfft2', 'irfft2', 'fft2', 'ifft2', 'fftn', 'ifftn']
 
 from numpy.core import asarray, zeros, swapaxes, shape, conjugate, \
      take
@@ -1114,12 +1113,3 @@ def irfft2(a, s=None, axes=(-2,-1)):
     """
 
     return irfftn(a, s, axes)
-
-# Deprecated names
-from numpy import deprecate
-refft = deprecate(rfft, 'refft', 'rfft')
-irefft = deprecate(irfft, 'irefft', 'irfft')
-refft2 = deprecate(rfft2, 'refft2', 'rfft2')
-irefft2 = deprecate(irfft2, 'irefft2', 'irfft2')
-refftn = deprecate(rfftn, 'refftn', 'rfftn')
-irefftn = deprecate(irfftn, 'irefftn', 'irfftn')
diff --git a/numpy/lib/arraysetops.py b/numpy/lib/arraysetops.py
@@ -10,11 +10,6 @@
   union1d,
   setdiff1d
 
-:Deprecated:
-  unique1d,
-  intersect1d_nu,
-  setmember1d
-
 :Notes:
 
 For floating point arrays, inaccurate results may appear due to usual round-off
@@ -28,8 +23,8 @@
 
 :Author: Robert Cimrman
 """
-__all__ = ['ediff1d', 'unique1d', 'intersect1d', 'intersect1d_nu', 'setxor1d',
-           'setmember1d', 'union1d', 'setdiff1d', 'unique', 'in1d']
+__all__ = ['ediff1d', 'intersect1d', 'setxor1d', 'union1d', 'setdiff1d',
+           'unique', 'in1d']
 
 import numpy as np
 from numpy.lib.utils import deprecate
@@ -417,72 +412,3 @@ def setdiff1d(ar1, ar2, assume_unique=False):
         return aux
     else:
         return np.asarray(ar1)[aux == 0]
-
-@deprecate
-def unique1d(ar1, return_index=False, return_inverse=False):
-    """
-    This function is deprecated. Use unique() instead.
-    """
-    if return_index:
-        import warnings
-        warnings.warn("The order of the output arguments for "
-                      "`return_index` has changed.  Before, "
-                      "the output was (indices, unique_arr), but "
-                      "has now been reversed to be more consistent.")
-
-    ar = np.asanyarray(ar1).flatten()
-    if ar.size == 0:
-        if return_inverse and return_index:
-            return ar, np.empty(0, np.bool), np.empty(0, np.bool)
-        elif return_inverse or return_index:
-            return ar, np.empty(0, np.bool)
-        else:
-            return ar
-
-    if return_inverse or return_index:
-        perm = ar.argsort()
-        aux = ar[perm]
-        flag = np.concatenate(([True], aux[1:] != aux[:-1]))
-        if return_inverse:
-            iflag = np.cumsum(flag) - 1
-            iperm = perm.argsort()
-            if return_index:
-                return aux[flag], perm[flag], iflag[iperm]
-            else:
-                return aux[flag], iflag[iperm]
-        else:
-            return aux[flag], perm[flag]
-
-    else:
-        ar.sort()
-        flag = np.concatenate(([True], ar[1:] != ar[:-1]))
-        return ar[flag]
-
-@deprecate
-def intersect1d_nu(ar1, ar2):
-    """
-    This function is deprecated.  Use intersect1d()
-    instead.
-    """
-    # Might be faster than unique1d( intersect1d( ar1, ar2 ) )?
-    aux = np.concatenate((unique1d(ar1), unique1d(ar2)))
-    aux.sort()
-    return aux[aux[1:] == aux[:-1]]
-
-@deprecate
-def setmember1d(ar1, ar2):
-    """
-    This function is deprecated.  Use in1d(assume_unique=True)
-    instead.
-    """
-    # We need this to be a stable sort, so always use 'mergesort' here. The
-    # values from the first array should always come before the values from the
-    # second array.
-    ar = np.concatenate( (ar1, ar2 ) )
-    order = ar.argsort(kind='mergesort')
-    sar = ar[order]
-    equal_adj = (sar[1:] == sar[:-1])
-    flag = np.concatenate( (equal_adj, [False] ) )
-
-    indx = order.argsort(kind='mergesort')[:len( ar1 )]
-    return flag[indx]
diff --git a/numpy/lib/benchmarks/bench_arraysetops.py b/numpy/lib/benchmarks/bench_arraysetops.py
diff --git a/numpy/lib/npyio.py b/numpy/lib/npyio.py
@@ -1049,7 +1049,7 @@ def genfromtxt(fname, dtype=float, comments='#', delimiter=None,
     """
     Load data from a text file, with missing values handled as specified.
 
-    Each line past the first `skiprows` lines is split at the `delimiter`
+    Each line past the first `skip_header` lines is split at the `delimiter`
     character, and characters following the `comments` character are discarded.
 
     Parameters
@@ -1072,20 +1072,20 @@ def genfromtxt(fname, dtype=float, comments='#', delimiter=None,
         The numbers of lines to skip at the beginning of the file.
     skip_footer : int, optional
         The numbers of lines to skip at the end of the file
-    converters : variable or None, optional
+    converters : variable, optional
         The set of functions that convert the data of a column to a value.
         The converters can also be used to provide a default value
         for missing data: ``converters = {3: lambda s: float(s or 0)}``.
-    missing_values : variable or None, optional
+    missing_values : variable, optional
         The set of strings corresponding to missing data.
-    filling_values : variable or None, optional
+    filling_values : variable, optional
         The set of values to be used as default when the data are missing.
-    usecols : sequence or None, optional
+    usecols : sequence, optional
         Which columns to read, with 0 being the first.  For example,
         ``usecols = (1, 4, 5)`` will extract the 2nd, 5th and 6th columns.
     names : {None, True, str, sequence}, optional
         If `names` is True, the field names are read from the first valid line
-        after the first `skiprows` lines.
+        after the first `skip_header` lines.
         If `names` is a sequence or a single-string of comma-separated names,
         the names will be used to define the field names in a structured dtype.
         If `names` is None, the names of the dtype fields will be used, if any.
@@ -1218,9 +1218,10 @@ def genfromtxt(fname, dtype=float, comments='#', delimiter=None,
 
     # Get the first valid lines after the first skiprows ones ..
     if skiprows:
-        warnings.warn("The use of `skiprows` is deprecated.\n"\
-                      "Please use `skip_header` instead.",
-                      DeprecationWarning)
+        warnings.warn(\
+            "The use of `skiprows` is deprecated, it will be removed in numpy 2.0.\n" \
+            "Please use `skip_header` instead.",
+            DeprecationWarning)
         skip_header = skiprows
     # Skip the first `skip_header` rows
     for i in xrange(skip_header):
@@ -1343,9 +1344,10 @@ def genfromtxt(fname, dtype=float, comments='#', delimiter=None,
 
     # Process the deprecated `missing`
     if missing != asbytes(''):
-        warnings.warn("The use of `missing` is deprecated.\n"\
-                      "Please use `missing_values` instead.",
-                      DeprecationWarning)
+        warnings.warn(\
+            "The use of `missing` is deprecated, it will be removed in Numpy 2.0.\n" \
+            "Please use `missing_values` instead.",
+            DeprecationWarning)
         values = [str(_) for _ in missing.split(asbytes(","))]
         for entry in missing_values:
             entry.extend(values)