Merge branch '0.22.x' into release-candidate

CHANGES.rst

@@ -58,7 +58,7 @@ Other changes
 * ``_`` is no longer considered a cacheable builtin as it could interfere with
   gettext.
 
-* Cythonize-computed metadata now cached in the generate C files.
+* Cythonize-computed metadata now cached in the generated C files.
 
 * Several corrections and extensions in numpy, cpython, and libcpp pxd files.
 

Cython/Compiler/ExprNodes.py

@@ -6767,6 +6767,13 @@ class ListNode(SequenceNode):
             else:
                 offset = ''
             for i, arg in enumerate(self.args):
+                if arg.type.is_array:
+                    code.globalstate.use_utility_code(UtilityCode.load_cached("IncludeStringH", "StringTools.c"))
+                    code.putln("memcpy(&(%s[%s%s]), %s, sizeof(%s[0]));" % (
+                        self.result(), i, offset,
+                        arg.result(), self.result()
+                    ))
+                else:
                     code.putln("%s[%s%s] = %s;" % (
                         self.result(),
                         i,

Cython/Compiler/ModuleNode.py

@@ -552,10 +552,9 @@ class ModuleNode(Nodes.Node, Nodes.BlockNode):
         code.putln("/* Generated by Cython %s */" % Version.watermark)
         code.putln("")
         if metadata:
-            code.putln("/* Cython Metadata */")
-            code.putln("/*")
+            code.putln("/* BEGIN: Cython Metadata")
             code.putln(json.dumps(metadata, indent=4))
-            code.putln("*/")
+            code.putln("END: Cython Metadata */")
             code.putln("")
         code.putln("#define PY_SSIZE_T_CLEAN")
 

Cython/Utility/Profile.c

@@ -35,20 +35,25 @@
   #endif
 
   #define __Pyx_TraceDeclarations(codeobj)                            \
-  static PyCodeObject *$frame_code_cname = NULL; if (codeobj != NULL) $frame_code_cname = (PyCodeObject*) codeobj;   \
+  static PyCodeObject *$frame_code_cname = NULL;                      \
   CYTHON_FRAME_MODIFIER PyFrameObject *$frame_cname = NULL;           \
-  int __Pyx_use_tracing = 0;
+  int __Pyx_use_tracing = 0;                                          \
+  if (codeobj) $frame_code_cname = (PyCodeObject*) codeobj;
 
   #define __Pyx_TraceCall(funcname, srcfile, firstlineno)                            \
-  if (unlikely(PyThreadState_GET()->use_tracing &&                                   \
-          (PyThreadState_GET()->c_profilefunc || (CYTHON_TRACE && PyThreadState_GET()->c_tracefunc)))) {      \
+  {   PyThreadState* tstate = PyThreadState_GET();                                   \
+      if (unlikely(tstate->use_tracing) && !tstate->tracing &&                       \
+              (tstate->c_profilefunc || (CYTHON_TRACE && tstate->c_tracefunc))) {    \
           __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&$frame_code_cname, &$frame_cname, funcname, srcfile, firstlineno);  \
+      }                                                                              \
   }
 
   #define __Pyx_TraceException()                                                           \
-  if (unlikely(__Pyx_use_tracing) && PyThreadState_GET()->use_tracing &&                   \
-          (PyThreadState_GET()->c_profilefunc || (CYTHON_TRACE && PyThreadState_GET()->c_tracefunc))) {  \
+  if (likely(!__Pyx_use_tracing)); else {                                                  \
       PyThreadState* tstate = PyThreadState_GET();                                         \
+      if (tstate->use_tracing &&                                                           \
+              (tstate->c_profilefunc || (CYTHON_TRACE && tstate->c_tracefunc))) {          \
+          tstate->tracing++;                                                               \
           tstate->use_tracing = 0;                                                         \
           PyObject *exc_info = __Pyx_GetExceptionTuple();                                  \
           if (exc_info) {                                                                  \
@@ -60,11 +65,15 @@
               Py_DECREF(exc_info);                                                         \
           }                                                                                \
           tstate->use_tracing = 1;                                                         \
+          tstate->tracing--;                                                               \
+      }                                                                                    \
   }
 
   #define __Pyx_TraceReturn(result)                                                       \
-  if (unlikely(__Pyx_use_tracing) && PyThreadState_GET()->use_tracing) {             \
+  if (likely(!__Pyx_use_tracing)); else {                                                 \
       PyThreadState* tstate = PyThreadState_GET();                                        \
+      if (tstate->use_tracing) {                                                          \
+          tstate->tracing++;                                                              \
           tstate->use_tracing = 0;                                                        \
           if (CYTHON_TRACE && tstate->c_tracefunc)                                        \
               tstate->c_tracefunc(                                                        \
@@ -74,6 +83,8 @@
                   tstate->c_profileobj, $frame_cname, PyTrace_RETURN, (PyObject*)result); \
           CYTHON_FRAME_DEL;                                                               \
           tstate->use_tracing = 1;                                                        \
+          tstate->tracing--;                                                              \
+      }                                                                                   \
   }
 
   static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno); /*proto*/
@@ -90,12 +101,16 @@
 
 #if CYTHON_TRACE
   #define __Pyx_TraceLine(lineno)                                                          \
-  if (unlikely(__Pyx_use_tracing) && unlikely(PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_tracefunc)) {    \
+  if (likely(!__Pyx_use_tracing)); else {                                                  \
       PyThreadState* tstate = PyThreadState_GET();                                         \
+      if (unlikely(tstate->use_tracing && tstate->c_tracefunc)) {                          \
           $frame_cname->f_lineno = lineno;                                                 \
+          tstate->tracing++;                                                               \
           tstate->use_tracing = 0;                                                         \
           tstate->c_tracefunc(tstate->c_traceobj, $frame_cname, PyTrace_LINE, NULL);       \
           tstate->use_tracing = 1;                                                         \
+          tstate->tracing--;                                                               \
+      }                                                                                    \
   }
 #else
   #define __Pyx_TraceLine(lineno)
@@ -136,17 +151,18 @@ static int __Pyx_TraceSetupAndCall(PyCodeObject** code,
 #endif
     }
     (*frame)->f_lineno = firstlineno;
+    retval = 1;
+    tstate->tracing++;
     tstate->use_tracing = 0;
     #if CYTHON_TRACE
     if (tstate->c_tracefunc)
-        tstate->c_tracefunc(tstate->c_traceobj, *frame, PyTrace_CALL, NULL);
-    if (!tstate->c_profilefunc)
-        retval = 1;
-    else
+        retval = tstate->c_tracefunc(tstate->c_traceobj, *frame, PyTrace_CALL, NULL) == 0;
+    if (retval && tstate->c_profilefunc)
     #endif
         retval = tstate->c_profilefunc(tstate->c_profileobj, *frame, PyTrace_CALL, NULL) == 0;
     tstate->use_tracing = (tstate->c_profilefunc ||
                            (CYTHON_TRACE && tstate->c_tracefunc));
+    tstate->tracing--;
     return tstate->use_tracing && retval;
 }
 

docs/src/userguide/buffer.rst

@@ -66,23 +66,23 @@ which Cython handles specially.
             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.
+            # this is the distance between two adjacent 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.format = 'f'                     # float
+            buffer.internal = NULL                  # see References
             buffer.itemsize = itemsize
-            buffer.len = self.v.size() * itemsize
+            buffer.len = self.v.size() * itemsize   # product(shape) * itemsize
             buffer.ndim = 2
             buffer.obj = self
             buffer.readonly = 0
             buffer.shape = self.shape
             buffer.strides = self.strides
-            buffer.suboffsets = NULL
+            buffer.suboffsets = NULL                # for pointer arrays only
 
         def __releasebuffer__(self, Py_buffer *buffer):
             pass

runtests.py

@@ -102,6 +102,7 @@ EXT_DEP_MODULES = {
     'tag:pstats': 'pstats',
     'tag:posix' : 'posix',
     'tag:array' : 'array',
+    'tag:coverage': 'coverage',
     'tag:ipython': 'IPython',
     'tag:jedi': 'jedi',
 }

tests/bugs.txt

@@ -14,6 +14,8 @@ inherited_final_method
 tryfinallychaining        # also see FIXME in "yield_from_pep380" test
 cimport_alias_subclass
 
+coverage     # depends on newer coverage.py version
+
 # CPython regression tests that don't current work:
 pyregr.test_signal
 pyregr.test_capi

tests/run/carray_coercion.pyx

@@ -67,6 +67,57 @@ def from_int_array_array():
     return v
 
 
+def assign_int_array_array():
+    """
+    >>> assign_int_array_array()
+    [[11, 12, 13], [21, 22, 23]]
+    """
+    cdef int[2][3] v = [[11, 12, 13], [21, 22, 23]]
+    return v
+
+
+def assign_int_array_array_from_tuples():
+    """
+    >>> assign_int_array_array_from_tuples()
+    [[11, 12, 13], [21, 22, 23]]
+    """
+    cdef int[2][3] v = ([11, 12, 13], [21, 22, 23])
+    return v
+
+
+''' FIXME: this currently crashes:
+def assign_int_array_array_from_tuples():
+    """
+    >>> assign_int_array_array_from_tuples()
+    [[11, 12, 13], [21, 22, 23]]
+    """
+    cdef int[2][3] v = ((11, 12, 13), (21, 22, 23))
+    return v
+'''
+
+
+def build_from_list_of_arrays():
+    """
+    >>> build_from_list_of_arrays()
+    [[11, 12, 13], [21, 22, 23]]
+    """
+    cdef int[3] x = [11, 12, 13]
+    cdef int[3] y = [21, 22, 23]
+    cdef int[2][3] v = [x, y]
+    return v
+
+
+def build_from_tuple_of_arrays():
+    """
+    >>> build_from_tuple_of_arrays()
+    [[11, 12, 13], [21, 22, 23]]
+    """
+    cdef int[3] x = [11, 12, 13]
+    cdef int[3] y = [21, 22, 23]
+    cdef int[2][3] v = (x, y)
+    return v
+
+
 ctypedef struct MyStructType:
     int x
     double y

tests/run/coverage.srctree

+# mode: run
+# tag: coverage,trace
+
+"""
+PYTHON setup.py build_ext -i
+PYTHON coverage_test.py
+"""
+
+######## setup.py ########
+
+from distutils.core import setup
+from Cython.Build import cythonize
+
+setup(ext_modules = cythonize('coverage_test_cy.py'))
+
+
+######## coverage_test_cy.py ########
+# cython: linetrace=True
+# distutils: define_macros=CYTHON_TRACE=1
+
+def func1(a, b):
+    x = 1               #  5
+    c = func2(a) + b    #  6
+    return x + c        #  7
+
+
+def func2(a):
+    return a * 2        # 11
+
+
+######## coverage_test.py ########
+
+try:
+    # io.StringIO in Py2.x cannot handle str ...
+    from StringIO import StringIO
+except ImportError:
+    from io import StringIO
+
+from coverage import coverage
+
+import coverage_test_cy
+
+
+def run_coverage():
+    cov = coverage()
+    cov.start()
+    assert coverage_test_cy.func1(1, 2) == 5
+    assert coverage_test_cy.func2(2) == 4
+    cov.stop()
+
+    out = StringIO()
+    cov.report([coverage_test_cy], file=out)
+    lines = out.getvalue().splitlines()
+    assert any('coverage_test_cy' in line for line in lines), "coverage_test_cy not found in coverage"
+
+    mod_file, exec_lines, excl_lines, missing_lines, _ = cov.analysis2(coverage_test_cy)
+    assert 'coverage_test_cy' in mod_file
+
+    executed = set(exec_lines) - set(missing_lines)
+    assert all(line in executed for line in [5, 6, 7, 11]), '%s / %s' % (exec_lines, missing_lines)
+
+
+if __name__ == '__main__':
+    run_coverage()

tests/run/numpy_math.pyx

@@ -37,7 +37,8 @@ def test_fp_classif():
     assert not npmath.isnan(d_zero)
     assert not npmath.isnan(f_zero)
 
-    assert npmath.isinf(npmath.INFINITY)
+    assert npmath.isinf(npmath.INFINITY) == 1
+    assert npmath.isinf(-npmath.INFINITY) == -1
     assert npmath.isnan(npmath.NAN)
 
     assert npmath.signbit(npmath.copysign(1., -1.))