numpy · charris · Sep 2, 2016 · Jan 23, 2016 · Jan 29, 2016 · Jan 30, 2016
diff --git a/.travis.yml b/.travis.yml
@@ -61,7 +61,7 @@ matrix:
     - python: 2.7
       env: USE_WHEEL=1
     - python: 3.5
-      env: USE_WHEEL=1
+      env: USE_WHEEL=1 RUN_FULL_TESTS=1
     - python: 3.5
       env: USE_SDIST=1
     - python: 2.7

diff --git a/doc/release/1.12.0-notes.rst b/doc/release/1.12.0-notes.rst
@@ -319,6 +319,19 @@ is regular quicksort but changing to a heapsort when not enough progress is
 made. This retains the good quicksort performance while changing the worst case
 runtime from ``O(N^2)`` to ``O(N*log(N))``.
 
+stacklevel of warnings increased
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+The stacklevel for python based warnings was increased so that most warnings
+will report the offending line of the user code instead of the line the
+warning itself is given. Passing of stacklevel is now tested to ensure that
+new warnings will recieve the ``stacklevel`` argument.
+
+This causes warnings with the "default" or "module" filter to be shown once
+for every offending user code line or user module instead of only once. On
+python versions before 3.4, this can cause warnings to appear that were falsly
+ignored before, which may be surprising especially in test suits.
+
+
 Deprecations
 ============
 

diff --git a/numpy/_import_tools.py b/numpy/_import_tools.py
@@ -166,7 +166,7 @@ def __call__(self,*packages, **options):
         # 2014-10-29, 1.10
         warnings.warn('pkgload and PackageLoader are obsolete '
                 'and will be removed in a future version of numpy',
-                DeprecationWarning)
+                DeprecationWarning, stacklevel=2)
         frame = self.parent_frame
         self.info_modules = {}
         if options.get('force', False):

diff --git a/numpy/core/_methods.py b/numpy/core/_methods.py
@@ -56,7 +56,7 @@ def _mean(a, axis=None, dtype=None, out=None, keepdims=False):
     rcount = _count_reduce_items(arr, axis)
     # Make this warning show up first
     if rcount == 0:
-        warnings.warn("Mean of empty slice.", RuntimeWarning)
+        warnings.warn("Mean of empty slice.", RuntimeWarning, stacklevel=2)
 
     # Cast bool, unsigned int, and int to float64 by default
     if dtype is None and issubclass(arr.dtype.type, (nt.integer, nt.bool_)):
@@ -79,7 +79,8 @@ def _var(a, axis=None, dtype=None, out=None, ddof=0, keepdims=False):
     rcount = _count_reduce_items(arr, axis)
     # Make this warning show up on top.
     if ddof >= rcount:
-        warnings.warn("Degrees of freedom <= 0 for slice", RuntimeWarning)
+        warnings.warn("Degrees of freedom <= 0 for slice", RuntimeWarning,
+                      stacklevel=2)
 
     # Cast bool, unsigned int, and int to float64 by default
     if dtype is None and issubclass(arr.dtype.type, (nt.integer, nt.bool_)):

diff --git a/numpy/core/fromnumeric.py b/numpy/core/fromnumeric.py
@@ -2647,7 +2647,7 @@ def rank(a):
     warnings.warn(
         "`rank` is deprecated; use the `ndim` attribute or function instead. "
         "To find the rank of a matrix see `numpy.linalg.matrix_rank`.",
-        VisibleDeprecationWarning)
+        VisibleDeprecationWarning, stacklevel=2)
     try:
         return a.ndim
     except AttributeError:

diff --git a/numpy/core/numeric.py b/numpy/core/numeric.py
@@ -1181,7 +1181,8 @@ def alterdot():
 
     """
     # 2014-08-13, 1.10
-    warnings.warn("alterdot no longer does anything.", DeprecationWarning)
+    warnings.warn("alterdot no longer does anything.",
+                  DeprecationWarning, stacklevel=2)
 
 
 def restoredot():
@@ -1205,7 +1206,8 @@ def restoredot():
 
     """
     # 2014-08-13, 1.10
-    warnings.warn("restoredot no longer does anything.", DeprecationWarning)
+    warnings.warn("restoredot no longer does anything.",
+                  DeprecationWarning, stacklevel=2)
 
 
 def tensordot(a, b, axes=2):
@@ -2260,8 +2262,8 @@ def warn_if_insufficient(width, binwdith):
         if width is not None and width < binwidth:
             warnings.warn(
                 "Insufficient bit width provided. This behavior "
-                "will raise an error in the future.", DeprecationWarning
-            )
+                "will raise an error in the future.", DeprecationWarning,
+                stacklevel=3)
 
     if num == 0:
         return '0' * (width or 1)

diff --git a/numpy/core/setup.py b/numpy/core/setup.py
@@ -179,7 +179,7 @@ def check_complex(config, mathlibs):
 
     try:
         if os.uname()[0] == "Interix":
-            warnings.warn("Disabling broken complex support. See #1365")
+            warnings.warn("Disabling broken complex support. See #1365", stacklevel=2)
             return priv, pub
     except:
         # os.uname not available on all platforms. blanket except ugly but safe

diff --git a/numpy/core/setup_common.py b/numpy/core/setup_common.py
@@ -94,7 +94,7 @@ def check_api_version(apiversion, codegen_dir):
                )
         warnings.warn(msg % (apiversion, curapi_hash, apiversion, api_hash,
                              __file__),
-                      MismatchCAPIWarning)
+                      MismatchCAPIWarning, stacklevel=2)
 # Mandatory functions: if not found, fail the build
 MANDATORY_FUNCS = ["sin", "cos", "tan", "sinh", "cosh", "tanh", "fabs",
         "floor", "ceil", "sqrt", "log10", "log", "exp", "asin",

diff --git a/numpy/core/tests/test_deprecations.py b/numpy/core/tests/test_deprecations.py
@@ -641,7 +641,7 @@ def test_assert_deprecated(self):
                       lambda: None)
 
         def foo():
-            warnings.warn("foo", category=DeprecationWarning)
+            warnings.warn("foo", category=DeprecationWarning, stacklevel=2)
 
         test_case_instance.assert_deprecated(foo)
         test_case_instance.tearDown()

diff --git a/numpy/ctypeslib.py b/numpy/ctypeslib.py
@@ -119,7 +119,7 @@ def load_library(libname, loader_path):
         if ctypes.__version__ < '1.0.1':
             import warnings
             warnings.warn("All features of ctypes interface may not work " \
-                          "with ctypes < 1.0.1")
+                          "with ctypes < 1.0.1", stacklevel=2)
 
         ext = os.path.splitext(libname)[1]
         if not ext:

diff --git a/numpy/distutils/command/config.py b/numpy/distutils/command/config.py
@@ -431,7 +431,7 @@ def get_output(self, body, headers=None, include_dirs=None,
                       "use it anymore, and avoid configuration checks \n" \
                       "involving running executable on the target machine.\n" \
                       "+++++++++++++++++++++++++++++++++++++++++++++++++\n",
-                      DeprecationWarning)
+                      DeprecationWarning, stacklevel=2)
         from distutils.ccompiler import CompileError, LinkError
         self._check_compiler()
         exitcode, output = 255, ''

diff --git a/numpy/distutils/command/egg_info.py b/numpy/distutils/command/egg_info.py
@@ -10,7 +10,7 @@ def run(self):
             import warnings
             warnings.warn("`build_src` is being run, this may lead to missing "
                           "files in your sdist!  See numpy issue gh-7127 for "
-                          "details", UserWarning)
+                          "details", UserWarning, stacklevel=2)
 
         # We need to ensure that build_src has been executed in order to give
         # setuptools' egg_info command real filenames instead of functions which

diff --git a/numpy/distutils/core.py b/numpy/distutils/core.py
@@ -176,18 +176,21 @@ def _check_append_library(libraries, item):
                     if item[1] is libitem[1]:
                         return
                     warnings.warn("[0] libraries list contains %r with"
-                                  " different build_info" % (item[0],))
+                                  " different build_info" % (item[0],),
+                                  stacklevel=2)
                     break
             else:
                 if item==libitem[0]:
                     warnings.warn("[1] libraries list contains %r with"
-                                  " no build_info" % (item[0],))
+                                  " no build_info" % (item[0],),
+                                  stacklevel=2)
                     break
         else:
             if is_sequence(item):
                 if item[0]==libitem:
                     warnings.warn("[2] libraries list contains %r with"
-                                  " no build_info" % (item[0],))
+                                  " no build_info" % (item[0],),
+                                  stacklevel=2)
                     break
             else:
                 if item==libitem:
@@ -201,10 +204,12 @@ def _check_append_ext_library(libraries, lib_name, build_info):
                 if item[1] is build_info:
                     return
                 warnings.warn("[3] libraries list contains %r with"
-                              " different build_info" % (lib_name,))
+                              " different build_info" % (lib_name,),
+                              stacklevel=2)
                 break
         elif item==lib_name:
             warnings.warn("[4] libraries list contains %r with"
-                          " no build_info" % (lib_name,))
+                          " no build_info" % (lib_name,),
+                          stacklevel=2)
             break
     libraries.append((lib_name, build_info))
diff --git a/numpy/distutils/cpuinfo.py b/numpy/distutils/cpuinfo.py
@@ -117,7 +117,7 @@ def __init__(self):
             fo = open('/proc/cpuinfo')
         except EnvironmentError:
             e = get_exception()
-            warnings.warn(str(e), UserWarning)
+            warnings.warn(str(e), UserWarning, stacklevel=2)
         else:
             for line in fo:
                 name_value = [s.strip() for s in line.split(':', 1)]

diff --git a/numpy/distutils/extension.py b/numpy/distutils/extension.py
@@ -63,7 +63,7 @@ def __init__ (
         if isinstance(self.swig_opts, basestring):
             import warnings
             msg = "swig_opts is specified as a string instead of a list"
-            warnings.warn(msg, SyntaxWarning)
+            warnings.warn(msg, SyntaxWarning, stacklevel=2)
             self.swig_opts = self.swig_opts.split()
 
         # Python 2.3 distutils new features

diff --git a/numpy/distutils/fcompiler/gnu.py b/numpy/distutils/fcompiler/gnu.py
@@ -137,7 +137,7 @@ def get_flags_linker_so(self):
                 os.environ['MACOSX_DEPLOYMENT_TARGET'] = target
                 if target == '10.3':
                     s = 'Env. variable MACOSX_DEPLOYMENT_TARGET set to 10.3'
-                    warnings.warn(s)
+                    warnings.warn(s, stacklevel=2)
 
             opt.extend(['-undefined', 'dynamic_lookup', '-bundle'])
         else:

diff --git a/numpy/distutils/misc_util.py b/numpy/distutils/misc_util.py
@@ -2206,7 +2206,7 @@ def default_config_dict(name = None, parent_name = None, local_path=None):
                   'deprecated default_config_dict(%r,%r,%r)'
                   % (name, parent_name, local_path,
                      name, parent_name, local_path,
-                     ))
+                     ), stacklevel=2)
     c = Configuration(name, parent_name, local_path)
     return c.todict()
 

diff --git a/numpy/distutils/system_info.py b/numpy/distutils/system_info.py
@@ -573,7 +573,7 @@ def get_info(self, notfound_action=0):
             if notfound_action:
                 if not self.has_info():
                     if notfound_action == 1:
-                        warnings.warn(self.notfounderror.__doc__)
+                        warnings.warn(self.notfounderror.__doc__, stacklevel=2)
                     elif notfound_action == 2:
                         raise self.notfounderror(self.notfounderror.__doc__)
                     else:
@@ -642,7 +642,7 @@ def get_paths(self, section, key):
         ret = []
         for d in dirs:
             if len(d) > 0 and not os.path.isdir(d):
-                warnings.warn('Specified path %s is invalid.' % d)
+                warnings.warn('Specified path %s is invalid.' % d, stacklevel=2)
                 continue
 
             if d not in ret:
@@ -1104,7 +1104,7 @@ def calc_info(self):
     Could not find lapack library within the ATLAS installation.
 *********************************************************************
 """
-            warnings.warn(message)
+            warnings.warn(message, stacklevel=2)
             self.set_info(**info)
             return
 
@@ -1135,7 +1135,7 @@ def calc_info(self):
     numpy/INSTALL.txt.
 *********************************************************************
 """ % (lapack_lib, sz / 1024)
-                warnings.warn(message)
+                warnings.warn(message, stacklevel=2)
             else:
                 info['language'] = 'f77'
 
@@ -1420,7 +1420,7 @@ def get_atlas_version(**config):
 when building extension libraries that use ATLAS.
 Make sure that -lgfortran is used for C++ extensions.
 *****************************************************
-""")
+""", stacklevel=2)
                 dict_append(info, language='f90',
                             define_macros=[('ATLAS_REQUIRES_GFORTRAN', None)])
     except Exception:  # failed to get version from file -- maybe on Windows
@@ -1531,7 +1531,7 @@ def calc_info(self):
             info = atlas_info
 
         else:
-            warnings.warn(AtlasNotFoundError.__doc__)
+            warnings.warn(AtlasNotFoundError.__doc__, stacklevel=2)
             need_blas = 1
             need_lapack = 1
             dict_append(info, define_macros=[('NO_ATLAS_INFO', 1)])
@@ -1542,10 +1542,10 @@ def calc_info(self):
             if lapack_info:
                 dict_append(info, **lapack_info)
             else:
-                warnings.warn(LapackNotFoundError.__doc__)
+                warnings.warn(LapackNotFoundError.__doc__, stacklevel=2)
                 lapack_src_info = get_info('lapack_src')
                 if not lapack_src_info:
-                    warnings.warn(LapackSrcNotFoundError.__doc__)
+                    warnings.warn(LapackSrcNotFoundError.__doc__, stacklevel=2)
                     return
                 dict_append(info, libraries=[('flapack_src', lapack_src_info)])
 
@@ -1554,10 +1554,10 @@ def calc_info(self):
             if blas_info:
                 dict_append(info, **blas_info)
             else:
-                warnings.warn(BlasNotFoundError.__doc__)
+                warnings.warn(BlasNotFoundError.__doc__, stacklevel=2)
                 blas_src_info = get_info('blas_src')
                 if not blas_src_info:
-                    warnings.warn(BlasSrcNotFoundError.__doc__)
+                    warnings.warn(BlasSrcNotFoundError.__doc__, stacklevel=2)
                     return
                 dict_append(info, libraries=[('fblas_src', blas_src_info)])
 
@@ -1634,7 +1634,7 @@ def calc_info(self):
         if atlas_info:
             info = atlas_info
         else:
-            warnings.warn(AtlasNotFoundError.__doc__)
+            warnings.warn(AtlasNotFoundError.__doc__, stacklevel=2)
             need_blas = 1
             dict_append(info, define_macros=[('NO_ATLAS_INFO', 1)])
 
@@ -1643,10 +1643,10 @@ def calc_info(self):
             if blas_info:
                 dict_append(info, **blas_info)
             else:
-                warnings.warn(BlasNotFoundError.__doc__)
+                warnings.warn(BlasNotFoundError.__doc__, stacklevel=2)
                 blas_src_info = get_info('blas_src')
                 if not blas_src_info:
-                    warnings.warn(BlasSrcNotFoundError.__doc__)
+                    warnings.warn(BlasSrcNotFoundError.__doc__, stacklevel=2)
                     return
                 dict_append(info, libraries=[('fblas_src', blas_src_info)])
 

diff --git a/numpy/lib/format.py b/numpy/lib/format.py
@@ -556,7 +556,7 @@ def write_array(fp, array, version=None, allow_pickle=True, pickle_kwargs=None):
     # this warning can be removed when 1.9 has aged enough
     if version != (2, 0) and used_ver == (2, 0):
         warnings.warn("Stored array in format 2.0. It can only be"
-                      "read by NumPy >= 1.9", UserWarning)
+                      "read by NumPy >= 1.9", UserWarning, stacklevel=2)
 
     if array.itemsize == 0:
         buffersize = 0
@@ -759,7 +759,7 @@ def open_memmap(filename, mode='r+', dtype=None, shape=None,
             # this warning can be removed when 1.9 has aged enough
             if version != (2, 0) and used_ver == (2, 0):
                 warnings.warn("Stored array in format 2.0. It can only be"
-                              "read by NumPy >= 1.9", UserWarning)
+                              "read by NumPy >= 1.9", UserWarning, stacklevel=2)
             offset = fp.tell()
         finally:
             fp.close()