Numpy Deprecated Code Replacement

HISTORY.md

@@ -120,6 +120,8 @@
     `decision_tree()` and `hoeffding_tree()` (#2971).
 
   * Depend on `pkgbuild` for R bindings (#3081).
+
+  * Replaced Numpy deprecated code in Python bindings (#3126).
 
 ### mlpack 3.4.2
 ###### 2020-10-26

src/mlpack/bindings/python/mlpack/arma_numpy.pyx

@@ -32,6 +32,9 @@ isWin = (platform.system() == "Windows")
 cdef extern from "numpy/arrayobject.h":
   void PyArray_ENABLEFLAGS(numpy.ndarray arr, int flags)
   void PyArray_CLEARFLAGS(numpy.ndarray arr, int flags)
+  void* PyArray_DATA(numpy.ndarray arr)
+  numpy.npy_intp* PyArray_SHAPE(numpy.ndarray arr)
+  int PyArray_FLAGS(numpy.ndarray arr)
 
 cdef extern from "<mlpack/bindings/python/mlpack/arma_util.hpp>":
   void SetMemState[T](T& m, int state)
@@ -48,17 +51,19 @@ cdef arma.Mat[double]* numpy_to_mat_d(numpy.ndarray[numpy.double_t, ndim=2] X, \
   """
   Convert a numpy ndarray to a matrix.  The memory will still be owned by numpy.
   """
-  if not X.flags.c_contiguous or (not X.flags.owndata and not isWin):
+  cdef int flags = PyArray_FLAGS(X)
+  if not (flags & numpy.NPY_ARRAY_C_CONTIGUOUS) or \
+    (not (flags & numpy.NPY_ARRAY_OWNDATA) and not isWin):
     # If needed, make a copy where we own the memory.
     X = X.copy(order="C")
     takeOwnership = True
 
-  cdef arma.Mat[double]* m = new arma.Mat[double](<double*> X.data, X.shape[1],\
-      X.shape[0], isWin, False)
+  cdef arma.Mat[double]* m = new arma.Mat[double](<double*> PyArray_DATA(X),
+      PyArray_SHAPE(X)[1], PyArray_SHAPE(X)[0], isWin, False)
 
   # Take ownership of the memory, if we need to and we are not on Windows.
   if takeOwnership and not isWin:
-    PyArray_CLEARFLAGS(X, numpy.NPY_OWNDATA)
+    PyArray_CLEARFLAGS(X, numpy.NPY_ARRAY_OWNDATA)
     SetMemState[arma.Mat[double]](m[0], 0)
 
   return m
@@ -68,18 +73,20 @@ cdef arma.Mat[size_t]* numpy_to_mat_s(numpy.ndarray[numpy.npy_intp, ndim=2] X, \
   """
   Convert a numpy ndarray to a matrix.  The memory will still be owned by numpy.
   """
-  if not X.flags.c_contiguous or (not X.flags.owndata and not isWin):
+  cdef int flags = PyArray_FLAGS(X)
+  if not (flags & numpy.NPY_ARRAY_C_CONTIGUOUS) or \
+    (not (flags & numpy.NPY_ARRAY_OWNDATA) and not isWin):
     # If needed, make a copy where we own the memory, except on Windows where
     # we never copy.
     X = X.copy(order="C")
     takeOwnership = True
 
-  cdef arma.Mat[size_t]* m = new arma.Mat[size_t](<size_t*> X.data, X.shape[1],
-      X.shape[0], isWin, False)
+  cdef arma.Mat[size_t]* m = new arma.Mat[size_t](<size_t*> PyArray_DATA(X),
+      PyArray_SHAPE(X)[1], PyArray_SHAPE(X)[0], isWin, False)
 
   # Take ownership of the memory, if we need to.
   if takeOwnership and not isWin:
-    PyArray_CLEARFLAGS(X, numpy.NPY_OWNDATA)
+    PyArray_CLEARFLAGS(X, numpy.NPY_ARRAY_OWNDATA)
     SetMemState[arma.Mat[size_t]](m[0], 0)
 
   return m
@@ -101,7 +108,7 @@ cdef numpy.ndarray[numpy.double_t, ndim=2] mat_to_numpy_d(arma.Mat[double]& X) \
   # Transfer memory ownership, if needed.
   if GetMemState[arma.Mat[double]](X) == 0 and not isWin:
     SetMemState[arma.Mat[double]](X, 1)
-    PyArray_ENABLEFLAGS(output, numpy.NPY_OWNDATA)
+    PyArray_ENABLEFLAGS(output, numpy.NPY_ARRAY_OWNDATA)
 
   return output
 
@@ -122,7 +129,7 @@ cdef numpy.ndarray[numpy.npy_intp, ndim=2] mat_to_numpy_s(arma.Mat[size_t]& X) \
   # Transfer memory ownership, if needed.
   if GetMemState[arma.Mat[size_t]](X) == 0 and not isWin:
     SetMemState[arma.Mat[size_t]](X, 1)
-    PyArray_ENABLEFLAGS(output, numpy.NPY_OWNDATA)
+    PyArray_ENABLEFLAGS(output, numpy.NPY_ARRAY_OWNDATA)
 
   return output
 
@@ -132,18 +139,20 @@ cdef arma.Row[double]* numpy_to_row_d(numpy.ndarray[numpy.double_t, ndim=1] X, \
   Convert a numpy one-dimensional ndarray to a row.  The memory will still be
   owned by numpy.
   """
-  if not X.flags.c_contiguous or (not X.flags.owndata and not isWin):
+  cdef int flags = PyArray_FLAGS(X)
+  if not (flags & numpy.NPY_ARRAY_C_CONTIGUOUS) or \
+    (not (flags & numpy.NPY_ARRAY_OWNDATA) and not isWin):
     # If needed, make a copy where we own the memory, except on Windows where
     # we never copy.
     X = X.copy(order="C")
     takeOwnership = True
 
-  cdef arma.Row[double]* m = new arma.Row[double](<double*> X.data, X.shape[0],
-      isWin, False)
+  cdef arma.Row[double]* m = new arma.Row[double](<double*> PyArray_DATA(X),
+    PyArray_SHAPE(X)[0], isWin, False)
 
   # Transfer memory ownership, if needed.
   if takeOwnership and not isWin:
-    PyArray_CLEARFLAGS(X, numpy.NPY_OWNDATA)
+    PyArray_CLEARFLAGS(X, numpy.NPY_ARRAY_OWNDATA)
     SetMemState[arma.Row[double]](m[0], 0)
 
   return m
@@ -154,18 +163,20 @@ cdef arma.Row[size_t]* numpy_to_row_s(numpy.ndarray[numpy.npy_intp, ndim=1] X, \
   Convert a numpy one-dimensional ndarray to a row.  The memory will still be
   owned by numpy.
   """
-  if not X.flags.c_contiguous or (not X.flags.owndata and not isWin):
+  cdef int flags = PyArray_FLAGS(X)
+  if not (flags & numpy.NPY_ARRAY_C_CONTIGUOUS) or \
+    (not (flags & numpy.NPY_ARRAY_OWNDATA) and not isWin):
     # If needed, make a copy where we own the memory, except on Windows where
     # we never copy.
     X = X.copy(order="C")
     takeOwnership = True
 
-  cdef arma.Row[size_t]* m = new arma.Row[size_t](<size_t*> X.data, X.shape[0],
-      isWin, False)
+  cdef arma.Row[size_t]* m = new arma.Row[size_t](<size_t*> PyArray_DATA(X),
+      PyArray_SHAPE(X)[0], isWin, False)
 
   # Transfer memory ownership, if needed.
   if takeOwnership and not isWin:
-    PyArray_CLEARFLAGS(X, numpy.NPY_OWNDATA)
+    PyArray_CLEARFLAGS(X, numpy.NPY_ARRAY_OWNDATA)
     SetMemState[arma.Row[size_t]](m[0], 0)
 
   return m
@@ -185,7 +196,7 @@ cdef numpy.ndarray[numpy.double_t, ndim=1] row_to_numpy_d(arma.Row[double]& X) \
   # Transfer memory ownership, if needed.
   if GetMemState[arma.Row[double]](X) == 0 and not isWin:
     SetMemState[arma.Row[double]](X, 1)
-    PyArray_ENABLEFLAGS(output, numpy.NPY_OWNDATA)
+    PyArray_ENABLEFLAGS(output, numpy.NPY_ARRAY_OWNDATA)
 
   return output
 
@@ -205,7 +216,7 @@ cdef numpy.ndarray[numpy.npy_intp, ndim=1] row_to_numpy_s(arma.Row[size_t]& X) \
   # Transfer memory ownership, if needed.
   if GetMemState[arma.Row[size_t]](X) == 0 and not isWin:
     SetMemState[arma.Row[size_t]](X, 1)
-    PyArray_ENABLEFLAGS(output, numpy.NPY_OWNDATA)
+    PyArray_ENABLEFLAGS(output, numpy.NPY_ARRAY_OWNDATA)
 
   return output
 
@@ -215,18 +226,20 @@ cdef arma.Col[double]* numpy_to_col_d(numpy.ndarray[numpy.double_t, ndim=1] X, \
   Convert a numpy one-dimensional ndarray to a column vector.  The memory will
   still be owned by numpy.
   """
-  if not X.flags.c_contiguous or (not X.flags.owndata and not isWin):
+  cdef int flags = PyArray_FLAGS(X)
+  if not (flags & numpy.NPY_ARRAY_C_CONTIGUOUS) or \
+    (not (flags & numpy.NPY_ARRAY_OWNDATA) and not isWin):
     # If needed, make a copy where we own the memory, except on Windows where
     # we never copy.
     X = X.copy(order="C")
     takeOwnership = True
 
-  cdef arma.Col[double]* m = new arma.Col[double](<double*> X.data, X.shape[0],
-      isWin, False)
+  cdef arma.Col[double]* m = new arma.Col[double](<double*> PyArray_DATA(X),
+      PyArray_SHAPE(X)[0], isWin, False)
 
   # Transfer memory ownership, if needed.
   if takeOwnership and not isWin:
-    PyArray_CLEARFLAGS(X, numpy.NPY_OWNDATA)
+    PyArray_CLEARFLAGS(X, numpy.NPY_ARRAY_OWNDATA)
     SetMemState[arma.Col[double]](m[0], 0)
 
   return m
@@ -237,18 +250,20 @@ cdef arma.Col[size_t]* numpy_to_col_s(numpy.ndarray[numpy.npy_intp, ndim=1] X, \
   Convert a numpy one-dimensional ndarray to a column vector.  The memory will
   still be owned by numpy.
   """
-  if not X.flags.c_contiguous or (not X.flags.owndata and not isWin):
+  cdef int flags = PyArray_FLAGS(X)
+  if not (flags & numpy.NPY_ARRAY_C_CONTIGUOUS) or \
+    (not (flags & numpy.NPY_ARRAY_OWNDATA) and not isWin):
     # If needed, make a copy where we own the memory, except on Windows where
     # we never copy.
     X = X.copy(order="C")
     takeOwnership = True
 
-  cdef arma.Col[size_t]* m = new arma.Col[size_t](<size_t*> X.data, X.shape[0],
-      isWin, False)
+  cdef arma.Col[size_t]* m = new arma.Col[size_t](<size_t*> PyArray_DATA(X), 
+      PyArray_SHAPE(X)[0], isWin, False)
 
   # Transfer memory ownership, if needed.
   if takeOwnership and not isWin:
-    PyArray_CLEARFLAGS(X, numpy.NPY_OWNDATA)
+    PyArray_CLEARFLAGS(X, numpy.NPY_ARRAY_OWNDATA)
     SetMemState[arma.Col[size_t]](m[0], 0)
 
   return m
@@ -268,7 +283,7 @@ cdef numpy.ndarray[numpy.double_t, ndim=1] col_to_numpy_d(arma.Col[double]& X) \
   # Transfer memory ownership, if needed.
   if GetMemState[arma.Col[double]](X) == 0 and not isWin:
     SetMemState[arma.Col[double]](X, 1)
-    PyArray_ENABLEFLAGS(output, numpy.NPY_OWNDATA)
+    PyArray_ENABLEFLAGS(output, numpy.NPY_ARRAY_OWNDATA)
 
   return output
 
@@ -287,6 +302,6 @@ cdef numpy.ndarray[numpy.npy_intp, ndim=1] col_to_numpy_s(arma.Col[size_t]& X) \
   # Transfer memory ownership, if needed.
   if GetMemState[arma.Col[size_t]](X) == 0 and not isWin:
     SetMemState[arma.Col[size_t]](X, 1)
-    PyArray_ENABLEFLAGS(output, numpy.NPY_OWNDATA)
+    PyArray_ENABLEFLAGS(output, numpy.NPY_ARRAY_OWNDATA)
 
   return output

src/mlpack/bindings/python/print_input_processing.hpp

@@ -454,20 +454,25 @@ void PrintInputProcessing(
 
   /** We want to generate code like the following:
    *
+   * cdef extern from "numpy/arrayobject.h":
+   *   void* PyArray_DATA(np.ndarray arr)
    * if param_name is not None:
    *   param_name_tuple = to_matrix_with_info(param_name)
    *   if len(param_name_tuple[0].shape) < 2:
    *     param_name_tuple[0].shape = (param_name_tuple[0].size,)
    *   param_name_mat = arma_numpy.numpy_to_matrix_d(param_name_tuple[0])
    *   SetParamWithInfo[mat](p, \<const string\> 'param_name',
-   *       dereference(param_name_mat), &param_name_tuple[1][0])
+   *       dereference(param_name_mat), 
+   *       \<const cbool*\> PyArray_DATA(param_name_dims))
    *   p.SetPassed(\<const string\> 'param_name')
    */
   std::cout << prefix << "cdef np.ndarray " << d.name << "_dims" << std::endl;
   std::cout << prefix << "# Detect if the parameter was passed; set if so."
       << std::endl;
   if (!d.required)
   {
+    std::cout << prefix << "cdef extern from \"numpy/arrayobject.h\":" << std::endl;
+    std::cout << prefix << "  void* PyArray_DATA(np.ndarray arr)" << std::endl;
     std::cout << prefix << "if " << d.name << " is not None:" << std::endl;
     std::cout << prefix << "  " << d.name << "_tuple = to_matrix_with_info("
         << d.name << ", dtype=np.double, copy=p.Has('copy_all_inputs'))"
@@ -482,13 +487,15 @@ void PrintInputProcessing(
         << "_tuple[2]" << std::endl;
     std::cout << prefix << "  SetParamWithInfo[arma.Mat[double]](p, <const "
         << "string> '" << d.name << "', dereference(" << d.name << "_mat), "
-        << "<const cbool*> " << d.name << "_dims.data)" << std::endl;
+        << "<const cbool*> PyArray_DATA(" << d.name << "_dims))" << std::endl;
     std::cout << prefix << "  p.SetPassed(<const string> '" << d.name
         << "')" << std::endl;
     std::cout << prefix << "  del " << d.name << "_mat" << std::endl;
   }
   else
   {
+    std::cout << prefix << "cdef extern from \"numpy/arrayobject.h\":" << std::endl;
+    std::cout << prefix << "  void* PyArray_DATA(np.ndarray arr)" << std::endl;
     std::cout << prefix << d.name << "_tuple = to_matrix_with_info(" << d.name
         << ", dtype=np.double, copy=p.Has('copy_all_inputs'))"
         << std::endl;
@@ -502,7 +509,7 @@ void PrintInputProcessing(
         << std::endl;
     std::cout << prefix << "SetParamWithInfo[arma.Mat[double]](p, <const "
         << "string> '" << d.name << "', dereference(" << d.name << "_mat), "
-        << "<const cbool*> " << d.name << "_dims.data)" << std::endl;
+        << "<const cbool*> PyArray_DATA(" << d.name << "_dims))" << std::endl;
     std::cout << prefix << "p.SetPassed(<const string> '" << d.name << "')"
         << std::endl;
     std::cout << prefix << "del " << d.name << "_mat" << std::endl;

src/mlpack/bindings/python/setup.py.in

@@ -78,6 +78,7 @@ else:
                   # CMAKE_CXX_FLAGS seems to have an extra space.
                   extra_compile_args=extra_args,
                   extra_link_args=extra_link_args,
+                  define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
                   undef_macros=[] if len("${DISABLE_CFLAGS}") == 0 \
                       else '${DISABLE_CFLAGS}'.split(' ')) \
         for name in pyxs if name == module]
@@ -96,6 +97,7 @@ else:
                   # CMAKE_CXX_FLAGS seems to have an extra space.
                   extra_compile_args=extra_args,
                   extra_link_args=extra_link_args,
+                  define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
                   undef_macros=[] if len("${DISABLE_CFLAGS}") == 0 \
                       else '${DISABLE_CFLAGS}'.split(' ')) \
         for name in pyxs]