Merge pull request #7148 from seberg/stacklevel+tests

ENH,TST: Bump stacklevel and add tests for warnings

34 files changed, 181 insertions, 86 deletions

diff --git a/numpy/_import_tools.py b/numpy/_import_tools.py
index eda0284fe..18ac78d29 100644
--- a/numpy/_import_tools.py
+++ b/numpy/_import_tools.py
@@ -166,7 +166,7 @@ class PackageLoader(object):
         # 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
index 5fc2bc445..54e267541 100644
--- 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
index d07c5c08b..99173d105 100644
--- 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
index 8db4e1302..81ed0178a 100644
--- 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 binary_repr(num, width=None):
         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
index c6c1f6c03..bec358480 100644
--- 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
index ba7521e30..90b592999 100644
--- 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
index e03edb2ea..47870581a 100644
--- a/numpy/core/tests/test_deprecations.py
+++ b/numpy/core/tests/test_deprecations.py
@@ -641,7 +641,7 @@ class TestTestDeprecated(object):
                       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
index 36bcf2764..bf34ce38b 100644
--- a/numpy/ctypeslib.py
+++ b/numpy/ctypeslib.py
@@ -119,7 +119,7 @@ else:
         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
index ea1cd3e24..e43fb631b 100644
--- a/numpy/distutils/command/config.py
+++ b/numpy/distutils/command/config.py
@@ -431,7 +431,7 @@ int main (void)
                       "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
index 972a27df3..7176f9212 100644
--- a/numpy/distutils/command/egg_info.py
+++ b/numpy/distutils/command/egg_info.py
@@ -10,7 +10,7 @@ class egg_info(_egg_info):
             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
index 3f0fd464a..d9e125368 100644
--- 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
index 020f2c02f..03860c151 100644
--- a/numpy/distutils/cpuinfo.py
+++ b/numpy/distutils/cpuinfo.py
@@ -117,7 +117,7 @@ class LinuxCPUInfo(CPUInfoBase):
             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
index ebb263bd1..935f3eec9 100644
--- a/numpy/distutils/extension.py
+++ b/numpy/distutils/extension.py
@@ -63,7 +63,7 @@ class Extension(old_Extension):
         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
index 9697aa8db..fd49db492 100644
--- a/numpy/distutils/fcompiler/gnu.py
+++ b/numpy/distutils/fcompiler/gnu.py
@@ -137,7 +137,7 @@ class GnuFCompiler(FCompiler):
                 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
index 2cd185332..0070678d3 100644
--- 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
index c3a62464b..286154e8f 100644
--- a/numpy/distutils/system_info.py
+++ b/numpy/distutils/system_info.py
@@ -573,7 +573,7 @@ class system_info(object):
             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 @@ class system_info(object):
         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 @@ class atlas_info(system_info):
     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 @@ class atlas_info(system_info):
     numpy/INSTALL.txt.
 *********************************************************************
 """ % (lapack_lib, sz / 1024)
-                warnings.warn(message)
+                warnings.warn(message, stacklevel=2)
             else:
                 info['language'] = 'f77'
 
@@ -1420,7 +1420,7 @@ Linkage with ATLAS requires gfortran. Use
 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 @@ class lapack_opt_info(system_info):
             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 @@ class lapack_opt_info(system_info):
             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 @@ class lapack_opt_info(system_info):
             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 @@ class blas_opt_info(system_info):
         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 @@ class blas_opt_info(system_info):
             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
index e62677bd8..633aee675 100644
--- 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()
diff --git a/numpy/lib/function_base.py b/numpy/lib/function_base.py
index a866ed767..b74e04028 100644
--- a/numpy/lib/function_base.py
+++ b/numpy/lib/function_base.py
@@ -1383,7 +1383,7 @@ def select(condlist, choicelist, default=0):
         # 2014-02-24, 1.9
         warnings.warn("select with an empty condition list is not possible"
                       "and will be deprecated",
-                      DeprecationWarning)
+                      DeprecationWarning, stacklevel=2)
         return np.asarray(default)[()]
 
     choicelist = [np.asarray(choice) for choice in choicelist]
@@ -1418,7 +1418,7 @@ def select(condlist, choicelist, default=0):
         msg = "select condlists containing integer ndarrays is deprecated " \
             "and will be removed in the future. Use `.astype(bool)` to " \
             "convert to bools."
-        warnings.warn(msg, DeprecationWarning)
+        warnings.warn(msg, DeprecationWarning, stacklevel=2)
 
     if choicelist[0].ndim == 0:
         # This may be common, so avoid the call.
@@ -2692,7 +2692,7 @@ def cov(m, y=None, rowvar=True, bias=False, ddof=None, fweights=None,
         fact = w_sum - ddof*sum(w*aweights)/w_sum
 
     if fact <= 0:
-        warnings.warn("Degrees of freedom <= 0 for slice", RuntimeWarning)
+        warnings.warn("Degrees of freedom <= 0 for slice", RuntimeWarning, stacklevel=2)
         fact = 0.0
 
     X -= avg[:, None]
@@ -2766,7 +2766,7 @@ def corrcoef(x, y=None, rowvar=1, bias=np._NoValue, ddof=np._NoValue):
     if bias is not np._NoValue or ddof is not np._NoValue:
         # 2015-03-15, 1.10
         warnings.warn('bias and ddof have no effect and are deprecated',
-                      DeprecationWarning)
+                      DeprecationWarning, stacklevel=2)
     c = cov(x, y, rowvar)
     try:
         d = diag(c)
@@ -3774,7 +3774,7 @@ def _median(a, axis=None, out=None, overwrite_input=False):
         if rout.ndim == 0:
             if n == True:
                 warnings.warn("Invalid value encountered in median",
-                              RuntimeWarning)
+                              RuntimeWarning, stacklevel=3)
                 if out is not None:
                     out[...] = a.dtype.type(np.nan)
                     rout = out
@@ -3783,7 +3783,7 @@ def _median(a, axis=None, out=None, overwrite_input=False):
         elif np.count_nonzero(n.ravel()) > 0:
             warnings.warn("Invalid value encountered in median for" +
                           " %d results" % np.count_nonzero(n.ravel()),
-                          RuntimeWarning)
+                          RuntimeWarning, stacklevel=3)
             rout[n] = np.nan
         return rout
     else:
@@ -4039,7 +4039,7 @@ def _percentile(a, q, axis=None, out=None,
 
     if np.any(n):
         warnings.warn("Invalid value encountered in percentile",
-                              RuntimeWarning)
+                      RuntimeWarning, stacklevel=3)
         if zerod:
             if ap.ndim == 1:
                 if out is not None:
@@ -4403,7 +4403,7 @@ def delete(arr, obj, axis=None):
         # 2013-09-24, 1.9
         warnings.warn(
             "in the future the special handling of scalars will be removed "
-            "from delete and raise an error", DeprecationWarning)
+            "from delete and raise an error", DeprecationWarning, stacklevel=2)
         if wrap:
             return wrap(arr)
         else:
@@ -4470,7 +4470,7 @@ def delete(arr, obj, axis=None):
     if obj.dtype == bool:
         warnings.warn(
             "in the future insert will treat boolean arrays and array-likes "
-            "as boolean index instead of casting it to integer", FutureWarning)
+            "as boolean index instead of casting it to integer", FutureWarning, stacklevel=2)
         obj = obj.astype(intp)
     if isinstance(_obj, (int, long, integer)):
         # optimization for a single value
@@ -4498,7 +4498,7 @@ def delete(arr, obj, axis=None):
             # 2013-09-24, 1.9
             warnings.warn(
                 "using a non-integer array as obj in delete will result in an "
-                "error in the future", DeprecationWarning)
+                "error in the future", DeprecationWarning, stacklevel=2)
             obj = obj.astype(intp)
         keep = ones(N, dtype=bool)
 
@@ -4509,13 +4509,13 @@ def delete(arr, obj, axis=None):
             warnings.warn(
                 "in the future out of bounds indices will raise an error "
                 "instead of being ignored by `numpy.delete`.",
-                DeprecationWarning)
+                DeprecationWarning, stacklevel=2)
             obj = obj[inside_bounds]
         positive_indices = obj >= 0
         if not positive_indices.all():
             warnings.warn(
                 "in the future negative indices will not be ignored by "
-                "`numpy.delete`.", FutureWarning)
+                "`numpy.delete`.", FutureWarning, stacklevel=2)
             obj = obj[positive_indices]
 
         keep[obj, ] = False
@@ -4642,7 +4642,7 @@ def insert(arr, obj, values, axis=None):
         # 2013-09-24, 1.9
         warnings.warn(
             "in the future the special handling of scalars will be removed "
-            "from insert and raise an error", DeprecationWarning)
+            "from insert and raise an error", DeprecationWarning, stacklevel=2)
         arr = arr.copy(order=arrorder)
         arr[...] = values
         if wrap:
@@ -4664,7 +4664,7 @@ def insert(arr, obj, values, axis=None):
             warnings.warn(
                 "in the future insert will treat boolean arrays and "
                 "array-likes as a boolean index instead of casting it to "
-                "integer", FutureWarning)
+                "integer", FutureWarning, stacklevel=2)
             indices = indices.astype(intp)
             # Code after warning period:
             #if obj.ndim != 1:
@@ -4714,7 +4714,7 @@ def insert(arr, obj, values, axis=None):
         # 2013-09-24, 1.9
         warnings.warn(
             "using a non-integer array as obj in insert will result in an "
-            "error in the future", DeprecationWarning)
+            "error in the future", DeprecationWarning, stacklevel=2)
         indices = indices.astype(intp)
 
     indices[indices < 0] += N
diff --git a/numpy/lib/nanfunctions.py b/numpy/lib/nanfunctions.py
index c2fc92ebf..7f7aea9bc 100644
--- a/numpy/lib/nanfunctions.py
+++ b/numpy/lib/nanfunctions.py
@@ -236,7 +236,7 @@ def nanmin(a, axis=None, out=None, keepdims=np._NoValue):
         # Fast, but not safe for subclasses of ndarray
         res = np.fmin.reduce(a, axis=axis, out=out, **kwargs)
         if np.isnan(res).any():
-            warnings.warn("All-NaN axis encountered", RuntimeWarning)
+            warnings.warn("All-NaN axis encountered", RuntimeWarning, stacklevel=2)
     else:
         # Slow, but safe for subclasses of ndarray
         a, mask = _replace_nan(a, +np.inf)
@@ -248,7 +248,7 @@ def nanmin(a, axis=None, out=None, keepdims=np._NoValue):
         mask = np.all(mask, axis=axis, **kwargs)
         if np.any(mask):
             res = _copyto(res, np.nan, mask)
-            warnings.warn("All-NaN axis encountered", RuntimeWarning)
+            warnings.warn("All-NaN axis encountered", RuntimeWarning, stacklevel=2)
     return res
 
 
@@ -343,7 +343,7 @@ def nanmax(a, axis=None, out=None, keepdims=np._NoValue):
         # Fast, but not safe for subclasses of ndarray
         res = np.fmax.reduce(a, axis=axis, out=out, **kwargs)
         if np.isnan(res).any():
-            warnings.warn("All-NaN slice encountered", RuntimeWarning)
+            warnings.warn("All-NaN slice encountered", RuntimeWarning, stacklevel=2)
     else:
         # Slow, but safe for subclasses of ndarray
         a, mask = _replace_nan(a, -np.inf)
@@ -355,7 +355,7 @@ def nanmax(a, axis=None, out=None, keepdims=np._NoValue):
         mask = np.all(mask, axis=axis, **kwargs)
         if np.any(mask):
             res = _copyto(res, np.nan, mask)
-            warnings.warn("All-NaN axis encountered", RuntimeWarning)
+            warnings.warn("All-NaN axis encountered", RuntimeWarning, stacklevel=2)
     return res
 
 
@@ -821,7 +821,7 @@ def nanmean(a, axis=None, dtype=None, out=None, keepdims=np._NoValue):
 
     isbad = (cnt == 0)
     if isbad.any():
-        warnings.warn("Mean of empty slice", RuntimeWarning)
+        warnings.warn("Mean of empty slice", RuntimeWarning, stacklevel=2)
         # NaN is the only possible bad value, so no further
         # action is needed to handle bad results.
     return avg
@@ -835,7 +835,7 @@ def _nanmedian1d(arr1d, overwrite_input=False):
     c = np.isnan(arr1d)
     s = np.where(c)[0]
     if s.size == arr1d.size:
-        warnings.warn("All-NaN slice encountered", RuntimeWarning)
+        warnings.warn("All-NaN slice encountered", RuntimeWarning, stacklevel=3)
         return np.nan
     elif s.size == 0:
         return np.median(arr1d, overwrite_input=overwrite_input)
@@ -887,7 +887,7 @@ def _nanmedian_small(a, axis=None, out=None, overwrite_input=False):
     a = np.ma.masked_array(a, np.isnan(a))
     m = np.ma.median(a, axis=axis, overwrite_input=overwrite_input)
     for i in range(np.count_nonzero(m.mask.ravel())):
-        warnings.warn("All-NaN slice encountered", RuntimeWarning)
+        warnings.warn("All-NaN slice encountered", RuntimeWarning, stacklevel=3)
     if out is not None:
         out[...] = m.filled(np.nan)
         return out
@@ -1161,7 +1161,7 @@ def _nanpercentile1d(arr1d, q, overwrite_input=False, interpolation='linear'):
     c = np.isnan(arr1d)
     s = np.where(c)[0]
     if s.size == arr1d.size:
-        warnings.warn("All-NaN slice encountered", RuntimeWarning)
+        warnings.warn("All-NaN slice encountered", RuntimeWarning, stacklevel=3)
         if q.ndim == 0:
             return np.nan
         else:
@@ -1317,7 +1317,7 @@ def nanvar(a, axis=None, dtype=None, out=None, ddof=0, keepdims=np._NoValue):
 
     isbad = (dof <= 0)
     if np.any(isbad):
-        warnings.warn("Degrees of freedom <= 0 for slice.", RuntimeWarning)
+        warnings.warn("Degrees of freedom <= 0 for slice.", RuntimeWarning, stacklevel=2)
         # NaN, inf, or negative numbers are all possible bad
         # values, so explicitly replace them with NaN.
         var = _copyto(var, np.nan, isbad)
diff --git a/numpy/lib/npyio.py b/numpy/lib/npyio.py
index 534aa695c..0b2fdfaba 100644
--- a/numpy/lib/npyio.py
+++ b/numpy/lib/npyio.py
@@ -944,7 +944,7 @@ def loadtxt(fname, dtype=float, comments='#', delimiter=None,
             # End of lines reached
             first_line = ''
             first_vals = []
-            warnings.warn('loadtxt: Empty input file: "%s"' % fname)
+            warnings.warn('loadtxt: Empty input file: "%s"' % fname, stacklevel=2)
         N = len(usecols or first_vals)
 
         dtype_types, packing = flatten_dtype(dtype)
@@ -1542,7 +1542,7 @@ def genfromtxt(fname, dtype=float, comments='#', delimiter=None,
         # return an empty array if the datafile is empty
         first_line = asbytes('')
         first_values = []
-        warnings.warn('genfromtxt: Empty input file: "%s"' % fname)
+        warnings.warn('genfromtxt: Empty input file: "%s"' % fname, stacklevel=2)
 
     # Should we take the first values as names ?
     if names is True:
@@ -1827,7 +1827,7 @@ def genfromtxt(fname, dtype=float, comments='#', delimiter=None,
                 raise ValueError(errmsg)
             # Issue a warning ?
             else:
-                warnings.warn(errmsg, ConversionWarning)
+                warnings.warn(errmsg, ConversionWarning, stacklevel=2)
 
     # Strip the last skip_footer data
     if skip_footer > 0:
diff --git a/numpy/lib/polynomial.py b/numpy/lib/polynomial.py
index d178ba4b3..81c72749a 100644
--- a/numpy/lib/polynomial.py
+++ b/numpy/lib/polynomial.py
@@ -588,7 +588,7 @@ def polyfit(x, y, deg, rcond=None, full=False, w=None, cov=False):
     # warn on rank reduction, which indicates an ill conditioned matrix
     if rank != order and not full:
         msg = "Polyfit may be poorly conditioned"
-        warnings.warn(msg, RankWarning)
+        warnings.warn(msg, RankWarning, stacklevel=2)
 
     if full:
         return c, resids, rank, s, rcond
diff --git a/numpy/lib/utils.py b/numpy/lib/utils.py
index a2191468f..133704d13 100644
--- a/numpy/lib/utils.py
+++ b/numpy/lib/utils.py
@@ -96,7 +96,7 @@ class _Deprecate(object):
 
         def newfunc(*args,**kwds):
             """`arrayrange` is deprecated, use `arange` instead!"""
-            warnings.warn(depdoc, DeprecationWarning)
+            warnings.warn(depdoc, DeprecationWarning, stacklevel=2)
             return func(*args, **kwds)
 
         newfunc = _set_function_name(newfunc, old_name)
@@ -152,7 +152,7 @@ def deprecate(*args, **kwargs):
     >>> olduint(6)
     /usr/lib/python2.5/site-packages/numpy/lib/utils.py:114:
     DeprecationWarning: uint32 is deprecated
-      warnings.warn(str1, DeprecationWarning)
+      warnings.warn(str1, DeprecationWarning, stacklevel=2)
     6
 
     """
@@ -1016,7 +1016,7 @@ class SafeEval(object):
     def __init__(self):
         # 2014-10-15, 1.10
         warnings.warn("SafeEval is deprecated in 1.10 and will be removed.",
-                      DeprecationWarning)
+                      DeprecationWarning, stacklevel=2)
 
     def visit(self, node):
         cls = node.__class__
diff --git a/numpy/linalg/linalg.py b/numpy/linalg/linalg.py
index db50a5eec..a05b0ee8e 100644
--- a/numpy/linalg/linalg.py
+++ b/numpy/linalg/linalg.py
@@ -737,12 +737,12 @@ def qr(a, mode='reduced'):
             msg = "".join((
                     "The 'full' option is deprecated in favor of 'reduced'.\n",
                     "For backward compatibility let mode default."))
-            warnings.warn(msg, DeprecationWarning)
+            warnings.warn(msg, DeprecationWarning, stacklevel=2)
             mode = 'reduced'
         elif mode in ('e', 'economic'):
             # 2013-04-01, 1.8
             msg = "The 'economic' option is deprecated.",
-            warnings.warn(msg, DeprecationWarning)
+            warnings.warn(msg, DeprecationWarning, stacklevel=2)
             mode = 'economic'
         else:
             raise ValueError("Unrecognized mode '%s'" % mode)
diff --git a/numpy/ma/core.py b/numpy/ma/core.py
index b1e48c156..1bf41b3d8 100644
--- a/numpy/ma/core.py
+++ b/numpy/ma/core.py
@@ -3210,7 +3210,8 @@ class MaskedArray(ndarray):
                                 "of fill_value at 0. Discarding "
                                 "heterogeneous fill_value and setting "
                                 "all to {fv!s}.".format(indx=indx,
-                                    fv=dout._fill_value[0]))
+                                    fv=dout._fill_value[0]),
+                                stacklevel=2)
                         dout._fill_value = dout._fill_value.flat[0]
                 dout._isfield = True
             # Update the mask if needed
@@ -4195,7 +4196,7 @@ class MaskedArray(ndarray):
             raise TypeError("Only length-1 arrays can be converted "
                             "to Python scalars")
         elif self._mask:
-            warnings.warn("Warning: converting a masked element to nan.")
+            warnings.warn("Warning: converting a masked element to nan.", stacklevel=2)
             return np.nan
         return float(self.item())
 
@@ -6909,7 +6910,7 @@ def rank(obj):
     # 2015-04-12, 1.10.0
     warnings.warn(
         "`rank` is deprecated; use the `ndim` function instead. ",
-        np.VisibleDeprecationWarning)
+        np.VisibleDeprecationWarning, stacklevel=2)
     return np.ndim(getdata(obj))
 
 rank.__doc__ = np.rank.__doc__
diff --git a/numpy/ma/extras.py b/numpy/ma/extras.py
index aefdd4e49..a05ea476b 100644
--- a/numpy/ma/extras.py
+++ b/numpy/ma/extras.py
@@ -1344,7 +1344,7 @@ def corrcoef(x, y=None, rowvar=True, bias=np._NoValue, allow_masked=True,
     msg = 'bias and ddof have no effect and are deprecated'
     if bias is not np._NoValue or ddof is not np._NoValue:
         # 2015-03-15, 1.10
-        warnings.warn(msg, DeprecationWarning)
+        warnings.warn(msg, DeprecationWarning, stacklevel=2)
     # Get the data
     (x, xnotmask, rowvar) = _covhelper(x, y, rowvar, allow_masked)
     # Compute the covariance matrix
diff --git a/numpy/ma/mrecords.py b/numpy/ma/mrecords.py
index 6c9a4ea73..6b7acf469 100644
--- a/numpy/ma/mrecords.py
+++ b/numpy/ma/mrecords.py
@@ -743,7 +743,7 @@ def fromtextfile(fname, delimitor=None, commentchar='#', missingchar='',
         if len(vartypes) != nfields:
             msg = "Attempting to %i dtypes for %i fields!"
             msg += " Reverting to default."
-            warnings.warn(msg % (len(vartypes), nfields))
+            warnings.warn(msg % (len(vartypes), nfields), stacklevel=2)
             vartypes = _guessvartypes(_variables[0])
 
     # Construct the descriptor.
diff --git a/numpy/ma/tests/test_core.py b/numpy/ma/tests/test_core.py
index cbab5ad5b..7cac90628 100644
--- a/numpy/ma/tests/test_core.py
+++ b/numpy/ma/tests/test_core.py
@@ -2450,12 +2450,12 @@ class TestMaskedArrayInPlaceArithmetics(TestCase):
                     x /= t(2)
                     assert_equal(x, y)
                 except (DeprecationWarning, TypeError) as e:
-                    warnings.warn(str(e))
+                    warnings.warn(str(e), stacklevel=1)
                 try:
                     xm /= t(2)
                     assert_equal(xm, y)
                 except (DeprecationWarning, TypeError) as e:
-                    warnings.warn(str(e))
+                    warnings.warn(str(e), stacklevel=1)
 
                 if issubclass(t, np.integer):
                     assert_equal(len(sup.log), 2, "Failed on type=%s." % t)
@@ -2485,7 +2485,7 @@ class TestMaskedArrayInPlaceArithmetics(TestCase):
                     x /= a
                     assert_equal(x, y / a)
                 except (DeprecationWarning, TypeError) as e:
-                    warnings.warn(str(e))
+                    warnings.warn(str(e), stacklevel=1)
                 try:
                     xm /= a
                     assert_equal(xm, y / a)
@@ -2494,7 +2494,7 @@ class TestMaskedArrayInPlaceArithmetics(TestCase):
                         mask_or(mask_or(m, a.mask), (a == t(0)))
                     )
                 except (DeprecationWarning, TypeError) as e:
-                    warnings.warn(str(e))
+                    warnings.warn(str(e), stacklevel=1)
 
                 if issubclass(t, np.integer):
                     assert_equal(len(sup.log), 2, "Failed on type=%s." % t)
diff --git a/numpy/polynomial/chebyshev.py b/numpy/polynomial/chebyshev.py
index 2537bea32..dd346fbda 100644
--- a/numpy/polynomial/chebyshev.py
+++ b/numpy/polynomial/chebyshev.py
@@ -1782,7 +1782,7 @@ def chebfit(x, y, deg, rcond=None, full=False, w=None):
     # warn on rank reduction
     if rank != order and not full:
         msg = "The fit may be poorly conditioned"
-        warnings.warn(msg, pu.RankWarning)
+        warnings.warn(msg, pu.RankWarning, stacklevel=2)
 
     if full:
         return c, [resids, rank, s, rcond]
diff --git a/numpy/polynomial/hermite.py b/numpy/polynomial/hermite.py
index e234c8e23..06d68668f 100644
--- a/numpy/polynomial/hermite.py
+++ b/numpy/polynomial/hermite.py
@@ -1558,7 +1558,7 @@ def hermfit(x, y, deg, rcond=None, full=False, w=None):
     # warn on rank reduction
     if rank != order and not full:
         msg = "The fit may be poorly conditioned"
-        warnings.warn(msg, pu.RankWarning)
+        warnings.warn(msg, pu.RankWarning, stacklevel=2)
 
     if full:
         return c, [resids, rank, s, rcond]
diff --git a/numpy/polynomial/hermite_e.py b/numpy/polynomial/hermite_e.py
index 8fdcbf666..a846b167c 100644
--- a/numpy/polynomial/hermite_e.py
+++ b/numpy/polynomial/hermite_e.py
@@ -1555,7 +1555,7 @@ def hermefit(x, y, deg, rcond=None, full=False, w=None):
     # warn on rank reduction
     if rank != order and not full:
         msg = "The fit may be poorly conditioned"
-        warnings.warn(msg, pu.RankWarning)
+        warnings.warn(msg, pu.RankWarning, stacklevel=2)
 
     if full:
         return c, [resids, rank, s, rcond]
diff --git a/numpy/polynomial/laguerre.py b/numpy/polynomial/laguerre.py
index d459551ae..60728c5f9 100644
--- a/numpy/polynomial/laguerre.py
+++ b/numpy/polynomial/laguerre.py
@@ -1557,7 +1557,7 @@ def lagfit(x, y, deg, rcond=None, full=False, w=None):
     # warn on rank reduction
     if rank != order and not full:
         msg = "The fit may be poorly conditioned"
-        warnings.warn(msg, pu.RankWarning)
+        warnings.warn(msg, pu.RankWarning, stacklevel=2)
 
     if full:
         return c, [resids, rank, s, rcond]
diff --git a/numpy/polynomial/legendre.py b/numpy/polynomial/legendre.py
index 54e9895db..ec6c2f8bf 100644
--- a/numpy/polynomial/legendre.py
+++ b/numpy/polynomial/legendre.py
@@ -1585,7 +1585,7 @@ def legfit(x, y, deg, rcond=None, full=False, w=None):
     # warn on rank reduction
     if rank != order and not full:
         msg = "The fit may be poorly conditioned"
-        warnings.warn(msg, pu.RankWarning)
+        warnings.warn(msg, pu.RankWarning, stacklevel=2)
 
     if full:
         return c, [resids, rank, s, rcond]
diff --git a/numpy/polynomial/polynomial.py b/numpy/polynomial/polynomial.py
index c310d659d..3ed6b67a4 100644
--- a/numpy/polynomial/polynomial.py
+++ b/numpy/polynomial/polynomial.py
@@ -1493,7 +1493,7 @@ def polyfit(x, y, deg, rcond=None, full=False, w=None):
     # warn on rank reduction
     if rank != order and not full:
         msg = "The fit may be poorly conditioned"
-        warnings.warn(msg, pu.RankWarning)
+        warnings.warn(msg, pu.RankWarning, stacklevel=2)
 
     if full:
         return c, [resids, rank, s, rcond]
diff --git a/numpy/tests/test_warnings.py b/numpy/tests/test_warnings.py
new file mode 100644
index 000000000..dcae60a81
--- /dev/null
+++ b/numpy/tests/test_warnings.py
@@ -0,0 +1,86 @@
+"""
+Tests which scan for certain occurances in the code, they may not find
+all of these occurances but should catch almost all.
+"""
+
+
+from __future__ import division, absolute_import, print_function
+
+
+import sys
+if sys.version_info >= (3, 4):
+    from pathlib import Path
+    import ast
+    import tokenize
+    import numpy
+    from numpy.testing import run_module_suite
+    from numpy.testing.decorators import slow
+
+
+    class ParseCall(ast.NodeVisitor):
+        def __init__(self):
+            self.ls = []
+
+        def visit_Attribute(self, node):
+            ast.NodeVisitor.generic_visit(self, node)
+            self.ls.append(node.attr)
+
+        def visit_Name(self, node):
+            self.ls.append(node.id)
+
+
+    class FindFuncs(ast.NodeVisitor):
+        def __init__(self, filename):
+            super().__init__()
+            self.__filename = filename
+
+        def visit_Call(self, node):
+            p = ParseCall()
+            p.visit(node.func)
+            ast.NodeVisitor.generic_visit(self, node)
+
+            if p.ls[-1] == 'simplefilter' or p.ls[-1] == 'filterwarnings':
+                if node.args[0].s == "ignore":
+                    raise AssertionError(
+                        "ignore filter should not be used; found in "
+                        "{} on line {}".format(self.__filename, node.lineno))
+
+            if p.ls[-1] == 'warn' and (
+                    len(p.ls) == 1 or p.ls[-2] == 'warnings'):
+
+                if "testing/tests/test_warnings.py" is self.__filename:
+                    # This file
+                    return
+
+                # See if stacklevel exists:
+                if len(node.args) == 3:
+                    return
+                args = {kw.arg for kw in node.keywords}
+                if "stacklevel" in args:
+                    return
+                raise AssertionError(
+                    "warnings should have an appropriate stacklevel; found in "
+                    "{} on line {}".format(self.__filename, node.lineno))
+
+
+    @slow
+    def test_warning_calls():
+        # combined "ignore" and stacklevel error
+        base = Path(numpy.__file__).parent
+
+        for path in base.rglob("*.py"):
+            if base / "testing" in path.parents:
+                continue
+            if path == base / "__init__.py":
+                continue
+            if path == base / "random" / "__init__.py":
+                continue
+            # use tokenize to auto-detect encoding on systems where no
+            # default encoding is defined (e.g. LANG='C')
+            with tokenize.open(str(path)) as file:
+                tree = ast.parse(file.read())
+                FindFuncs(path).visit(tree)
+
+
+    if __name__ == "__main__":
+        run_module_suite()