Merge pull request #358 from larsmans/buffer-doc

Docs: how to implement PEP 3118, the buffer protocol

docs/src/userguide/buffer.rst

+.. _buffer:
+
+Implementing the buffer protocol
+================================
+
+Cython objects can expose memory buffers to Python code
+by implementing the "buffer protocol".
+This chapter shows how to implement the protocol
+and make use of the memory managed by an extension type from NumPy.
+
+
+A matrix class
+--------------
+
+The following Cython/C++ code implements a matrix of floats,
+where the number of columns is fixed at construction time
+but rows can be added dynamically.
+
+::
+
+    # matrix.pyx
+    from libcpp.vector cimport vector
+
+    cdef class Matrix:
+        cdef unsigned ncols
+        cdef vector[float] v
+
+        def __cinit__(self, unsigned ncols):
+            self.ncols = ncols
+
+        def add_row(self):
+            """Adds a row, initially zero-filled."""
+            self.v.extend(self.ncols)
+
+There are no members to do anything productive with the matrices' contents.
+We could implement custom ``__getitem__``, ``__setitem__``, etc. for this,
+but instead we'll use the buffer protocol to expose the matrix's data to Python
+so we can use NumPy to do useful work.
+
+Implementing the buffer protocol requires adding two members,
+``__getbuffer__`` and ``__releasebuffer__``,
+which Cython handles specially.
+
+::
+
+    from cpython cimport Py_buffer
+    from libcpp.vector cimport vector
+
+    cdef class Matrix:
+        cdef Py_ssize_t ncols
+        cdef Py_ssize_t shape[2]
+        cdef Py_ssize_t strides[2]
+        cdef vector[float] v
+
+        def __cinit__(self, Py_ssize_t ncols):
+            self.ncols = ncols
+
+        def add_row(self):
+            """Adds a row, initially zero-filled."""
+            self.v.resize(self.v.size() + self.ncols)
+
+        def __getbuffer__(self, Py_buffer *buffer, int flags):
+            cdef Py_ssize_t itemsize = sizeof(self.v[0])
+
+            self.shape[0] = self.v.size()
+            self.shape[1] = self.ncols
+
+            # Stride 1 is the distance, in bytes, between two items in a row;
+            # this is the distance between two adjance items in the vector.
+            # Stride 0 is the distance between the first elements of adjacent rows.
+            self.strides[1] = <Py_ssize_t>(  <char *>&(self.v[1])
+                                           - <char *>&(self.v[0]))
+            self.strides[0] = self.ncols * self.strides[1]
+
+            buffer.buf = <char *>&(self.v[0])
+            buffer.format = 'f'
+            buffer.internal = NULL
+            buffer.itemsize = itemsize
+            buffer.len = self.v.size() * itemsize
+            buffer.ndim = 2
+            buffer.obj = self
+            buffer.readonly = 0
+            buffer.shape = self.shape
+            buffer.strides = self.strides
+            buffer.suboffsets = NULL
+
+        def __releasebuffer__(self, Py_buffer *buffer):
+            pass
+
+The method ``Matrix.__getbuffer__`` fills a descriptor structure,
+called a ``Py_buffer``, that is defined by the Python C-API.
+It contains a pointer to the actual buffer in memory,
+as well as metadata about the shape of the array and the strides
+(step sizes to get from one element or row to the next).
+Its ``shape`` and ``strides`` members are pointers
+that must be point to arrays of ``Py_ssize_t[ndim]``.
+These arrays have to stay alive as long as any buffer views the data,
+so we store them on the ``Matrix`` object as members.
+
+The code is not yet complete, but we can already compile it
+and test the basic functionality.
+
+::
+
+    >>> from matrix import Matrix
+    >>> import numpy as np
+    >>> m = Matrix(10)
+    >>> np.asarray(m)
+    array([], shape=(0, 10), dtype=float32)
+    >>> m.add_row()
+    >>> a = np.asarray(m)
+    >>> a[:] = 1
+    >>> m.add_row()
+    >>> a = np.asarray(m)
+    >>> a
+    array([[ 1.,  1.,  1.,  1.,  1.,  1.,  1.,  1.,  1.,  1.],
+           [ 0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.]], dtype=float32)
+
+Now we can view the ``Matrix`` as a NumPy ``ndarray``,
+and modify its contents using standard NumPy operations.
+
+
+Memory safety and reference counting
+------------------------------------
+
+The ``Matrix`` class as implemented so far is unsafe.
+The ``add_row`` operation can move the underlying buffer,
+which invalidates any NumPy (or other) view on the data.
+If you try to access values after an ``add_row`` call,
+you'll get outdated values or a segfault.
+
+This is where ``__releasebuffer__`` comes in.
+We can add a reference count to each matrix,
+and lock it for mutation whenever a view exists.
+
+::
+
+    cdef class Matrix:
+        # ...
+        cdef int view_count
+
+        def __cinit__(self, Py_ssize_t ncols):
+            self.ncols = ncols
+            self.view_count = 0
+
+        def add_row(self):
+            if self.view_count > 0:
+                raise ValueError("can't add row while being viewed")
+            self.v.resize(self.v.size() + self.ncols)
+
+        def __getbuffer__(self, Py_buffer *buffer, int flags):
+            # ... as before
+
+            self.view_count += 1
+
+        def __releasebuffer__(self, Py_buffer *buffer):
+            self.view_count -= 1
+
+
+Flags
+-----
+We skipped some input validation in the code.
+The ``flags`` argument to ``__getbuffer__`` comes from ``np.asarray``
+(and other clients) and is an OR of boolean flags
+that describe the kind of array that is requested.
+Strictly speaking, if the flags contain ``PyBUF_ND``, ``PyBUF_SIMPLE``,
+or ``PyBUF_F_CONTIGUOUS``, ``__getbuffer__`` must raise a ``BufferError``.
+These macros can be ``cimport``'d from the pseudo-package ``cython``.
+
+(The matrix-in-vector structure actually conforms to ``PyBUF_ND``,
+but that would prohibit ``__getbuffer__`` from filling in the strides.
+A single-row matrix is F-contiguous, but a larger matrix is not.)
+
+
+References
+----------
+
+The buffer interface used here is set out in
+`PEP 3118, Revising the buffer protocol
+<http://legacy.python.org/dev/peps/pep-3118/>`_
+
+A tutorial for using this API from C is on Jake Vanderplas's blog,
+`An Introduction to the Python Buffer Protocol
+<https://jakevdp.github.io/blog/2014/05/05/introduction-to-the-python-buffer-protocol/>`_.
+
+Reference documentation is available for
+`Python 3 <https://docs.python.org/3/c-api/buffer.html>`_
+and `Python 2 <https://docs.python.org/2.7/c-api/buffer.html>`_.
+The Py2 documentation also describes an older buffer protocol
+that is no longer in use;
+since Python 2.6, the PEP 3118 protocol has been implemented,
+and the older protocol is only relevant for legacy code.

docs/src/userguide/index.rst

@@ -19,6 +19,7 @@ Contents:
    limitations
    pyrex_differences
    memoryviews
+   buffer
    parallelism
    debugging
 

docs/src/userguide/special_methods.rst

@@ -372,6 +372,7 @@ Descriptor objects (see note 2)
         accessible from Python. It is described in the Python/C API Reference Manual
         of Python 2.x under sections 6.6 and 10.6. It was superseded by the new
         PEP 3118 buffer protocol in Python 2.6 and is no longer available in Python 3.
+        For a how-to guide to the new API, see :ref:`buffer`.
 
 .. note:: (2) Descriptor objects are part of the support mechanism for new-style
         Python classes. See the discussion of descriptors in the Python documentation.