BUG: Increment stacklevel for warnings to account for NEP-18 overrides (#13589)

* Increment stacklevel for warnings to account for NEP-18 overrides

For NumPy functions that make use of `__array_function__`, the appropriate the
stack level for warnings should generally be increased by 1 to account for
the override function defined in numpy.core.overrides.

Fixes GH-13329

* Update numpy/lib/type_check.py

Co-Authored-By: Sebastian Berg <sebastian@sipsolutions.net>

8 files changed, 44 insertions, 37 deletions

diff --git a/numpy/core/fromnumeric.py b/numpy/core/fromnumeric.py
index 58da8a54b..cbbee463a 100644
--- a/numpy/core/fromnumeric.py
+++ b/numpy/core/fromnumeric.py
@@ -2145,7 +2145,7 @@ def sum(a, axis=None, dtype=None, out=None, keepdims=np._NoValue,
         warnings.warn(
             "Calling np.sum(generator) is deprecated, and in the future will give a different result. "
             "Use np.sum(np.fromiter(generator)) or the python sum builtin instead.",
-            DeprecationWarning, stacklevel=2)
+            DeprecationWarning, stacklevel=3)
 
         res = _sum_(a)
         if out is not None:
@@ -3569,5 +3569,5 @@ 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, stacklevel=2)
+        VisibleDeprecationWarning, stacklevel=3)
     return ndim(a)
diff --git a/numpy/lib/function_base.py b/numpy/lib/function_base.py
index 7fa51d683..2a6d39abc 100644
--- a/numpy/lib/function_base.py
+++ b/numpy/lib/function_base.py
@@ -682,7 +682,7 @@ 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, stacklevel=2)
+                      DeprecationWarning, stacklevel=3)
         return np.asarray(default)[()]
 
     choicelist = [np.asarray(choice) for choice in choicelist]
@@ -717,7 +717,7 @@ 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, stacklevel=2)
+        warnings.warn(msg, DeprecationWarning, stacklevel=3)
 
     if choicelist[0].ndim == 0:
         # This may be common, so avoid the call.
@@ -2443,7 +2443,7 @@ def cov(m, y=None, rowvar=True, bias=False, ddof=None, fweights=None,
 
     if fact <= 0:
         warnings.warn("Degrees of freedom <= 0 for slice",
-                      RuntimeWarning, stacklevel=2)
+                      RuntimeWarning, stacklevel=3)
         fact = 0.0
 
     X -= avg[:, None]
@@ -2522,7 +2522,7 @@ def corrcoef(x, y=None, rowvar=True, 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, stacklevel=2)
+                      DeprecationWarning, stacklevel=3)
     c = cov(x, y, rowvar)
     try:
         d = diag(c)
@@ -4304,7 +4304,7 @@ 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, stacklevel=2)
+            "from delete and raise an error", DeprecationWarning, stacklevel=3)
         if wrap:
             return wrap(arr)
         else:
@@ -4373,7 +4373,7 @@ 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, stacklevel=2)
+                      "to integer", FutureWarning, stacklevel=3)
         obj = obj.astype(intp)
     if isinstance(_obj, (int, long, integer)):
         # optimization for a single value
@@ -4401,7 +4401,7 @@ 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, stacklevel=2)
+                "error in the future", DeprecationWarning, stacklevel=3)
             obj = obj.astype(intp)
         keep = ones(N, dtype=bool)
 
@@ -4412,13 +4412,13 @@ 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, stacklevel=2)
+                DeprecationWarning, stacklevel=3)
             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, stacklevel=2)
+                "`numpy.delete`.", FutureWarning, stacklevel=3)
             obj = obj[positive_indices]
 
         keep[obj, ] = False
@@ -4543,7 +4543,7 @@ 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, stacklevel=2)
+            "from insert and raise an error", DeprecationWarning, stacklevel=3)
         arr = arr.copy(order=arrorder)
         arr[...] = values
         if wrap:
@@ -4567,7 +4567,7 @@ 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, stacklevel=2)
+                "integer", FutureWarning, stacklevel=3)
             indices = indices.astype(intp)
             # Code after warning period:
             #if obj.ndim != 1:
@@ -4617,7 +4617,7 @@ 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, stacklevel=2)
+            "error in the future", DeprecationWarning, stacklevel=3)
         indices = indices.astype(intp)
 
     indices[indices < 0] += N
diff --git a/numpy/lib/histograms.py b/numpy/lib/histograms.py
index ee9a3053c..5bcedc7f4 100644
--- a/numpy/lib/histograms.py
+++ b/numpy/lib/histograms.py
@@ -148,7 +148,8 @@ def _hist_bin_stone(x, range):
     nbins_upper_bound = max(100, int(np.sqrt(n)))
     nbins = min(_range(1, nbins_upper_bound + 1), key=jhat)
     if nbins == nbins_upper_bound:
-        warnings.warn("The number of bins estimated may be suboptimal.", RuntimeWarning, stacklevel=2)
+        warnings.warn("The number of bins estimated may be suboptimal.",
+                      RuntimeWarning, stacklevel=3)
     return ptp_x / nbins
 
 
@@ -279,7 +280,7 @@ def _ravel_and_check_weights(a, weights):
     if a.dtype == np.bool_:
         warnings.warn("Converting input from {} to {} for compatibility."
                       .format(a.dtype, np.uint8),
-                      RuntimeWarning, stacklevel=2)
+                      RuntimeWarning, stacklevel=3)
         a = a.astype(np.uint8)
 
     if weights is not None:
@@ -888,7 +889,7 @@ def histogram(a, bins=10, range=None, normed=None, weights=None,
             warnings.warn(
                     "The normed argument is ignored when density is provided. "
                     "In future passing both will result in an error.",
-                    DeprecationWarning, stacklevel=2)
+                    DeprecationWarning, stacklevel=3)
         normed = None
 
     if density:
@@ -904,7 +905,7 @@ def histogram(a, bins=10, range=None, normed=None, weights=None,
                 "density=True will produce the same result anyway. "
                 "The argument will be removed in a future version of "
                 "numpy.",
-                np.VisibleDeprecationWarning, stacklevel=2)
+                np.VisibleDeprecationWarning, stacklevel=3)
 
         # this normalization is incorrect, but
         db = np.array(np.diff(bin_edges), float)
@@ -915,7 +916,7 @@ def histogram(a, bins=10, range=None, normed=None, weights=None,
             warnings.warn(
                     "Passing normed=False is deprecated, and has no effect. "
                     "Consider passing the density argument instead.",
-                    DeprecationWarning, stacklevel=2)
+                    DeprecationWarning, stacklevel=3)
         return n, bin_edges
 
 
diff --git a/numpy/lib/nanfunctions.py b/numpy/lib/nanfunctions.py
index 77c851fcf..f497aca63 100644
--- a/numpy/lib/nanfunctions.py
+++ b/numpy/lib/nanfunctions.py
@@ -165,7 +165,8 @@ def _remove_nan_1d(arr1d, overwrite_input=False):
     c = np.isnan(arr1d)
     s = np.nonzero(c)[0]
     if s.size == arr1d.size:
-        warnings.warn("All-NaN slice encountered", RuntimeWarning, stacklevel=4)
+        warnings.warn("All-NaN slice encountered", RuntimeWarning,
+                      stacklevel=5)
         return arr1d[:0], True
     elif s.size == 0:
         return arr1d, overwrite_input
@@ -318,7 +319,8 @@ def nanmin(a, axis=None, out=None, keepdims=np._NoValue):
         # which do not implement isnan (gh-9009), or fmin correctly (gh-8975)
         res = np.fmin.reduce(a, axis=axis, out=out, **kwargs)
         if np.isnan(res).any():
-            warnings.warn("All-NaN slice encountered", RuntimeWarning, stacklevel=2)
+            warnings.warn("All-NaN slice encountered", RuntimeWarning,
+                          stacklevel=3)
     else:
         # Slow, but safe for subclasses of ndarray
         a, mask = _replace_nan(a, +np.inf)
@@ -330,7 +332,8 @@ 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, stacklevel=2)
+            warnings.warn("All-NaN axis encountered", RuntimeWarning,
+                          stacklevel=3)
     return res
 
 
@@ -431,7 +434,8 @@ def nanmax(a, axis=None, out=None, keepdims=np._NoValue):
         # which do not implement isnan (gh-9009), or fmax correctly (gh-8975)
         res = np.fmax.reduce(a, axis=axis, out=out, **kwargs)
         if np.isnan(res).any():
-            warnings.warn("All-NaN slice encountered", RuntimeWarning, stacklevel=2)
+            warnings.warn("All-NaN slice encountered", RuntimeWarning,
+                          stacklevel=3)
     else:
         # Slow, but safe for subclasses of ndarray
         a, mask = _replace_nan(a, -np.inf)
@@ -443,7 +447,8 @@ 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, stacklevel=2)
+            warnings.warn("All-NaN axis encountered", RuntimeWarning,
+                          stacklevel=3)
     return res
 
 
@@ -947,7 +952,7 @@ 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, stacklevel=2)
+        warnings.warn("Mean of empty slice", RuntimeWarning, stacklevel=3)
         # NaN is the only possible bad value, so no further
         # action is needed to handle bad results.
     return avg
@@ -959,7 +964,7 @@ def _nanmedian1d(arr1d, overwrite_input=False):
     See nanmedian for parameter usage
     """
     arr1d, overwrite_input = _remove_nan_1d(arr1d,
-        overwrite_input=overwrite_input)
+                                            overwrite_input=overwrite_input)
     if arr1d.size == 0:
         return np.nan
 
@@ -1002,7 +1007,8 @@ 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, stacklevel=3)
+        warnings.warn("All-NaN slice encountered", RuntimeWarning,
+                      stacklevel=4)
     if out is not None:
         out[...] = m.filled(np.nan)
         return out
@@ -1547,7 +1553,8 @@ 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, stacklevel=2)
+        warnings.warn("Degrees of freedom <= 0 for slice.", RuntimeWarning,
+                      stacklevel=3)
         # 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/polynomial.py b/numpy/lib/polynomial.py
index 1f08abf36..2c72f623c 100644
--- a/numpy/lib/polynomial.py
+++ b/numpy/lib/polynomial.py
@@ -634,7 +634,7 @@ 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, stacklevel=3)
+        warnings.warn(msg, RankWarning, stacklevel=4)
 
     if full:
         return c, resids, rank, s, rcond
diff --git a/numpy/lib/shape_base.py b/numpy/lib/shape_base.py
index 8ebe7a695..1b66f3a3e 100644
--- a/numpy/lib/shape_base.py
+++ b/numpy/lib/shape_base.py
@@ -578,7 +578,7 @@ def expand_dims(a, axis):
         # 2017-05-17, 1.13.0
         warnings.warn("Both axis > a.ndim and axis < -a.ndim - 1 are "
                       "deprecated and will raise an AxisError in the future.",
-                      DeprecationWarning, stacklevel=2)
+                      DeprecationWarning, stacklevel=3)
     # When the deprecation period expires, delete this if block,
     if axis < 0:
         axis = axis + a.ndim + 1
diff --git a/numpy/lib/type_check.py b/numpy/lib/type_check.py
index 2b254b6c0..ac4b03a6c 100644
--- a/numpy/lib/type_check.py
+++ b/numpy/lib/type_check.py
@@ -541,6 +541,9 @@ def real_if_close(a, tol=100):
 
 
 def _asscalar_dispatcher(a):
+    # 2018-10-10, 1.16
+    warnings.warn('np.asscalar(a) is deprecated since NumPy v1.16, use '
+                  'a.item() instead', DeprecationWarning, stacklevel=3)
     return (a,)
 
 
@@ -569,10 +572,6 @@ def asscalar(a):
     >>> np.asscalar(np.array([24]))
     24
     """
-
-    # 2018-10-10, 1.16
-    warnings.warn('np.asscalar(a) is deprecated since NumPy v1.16, use '
-                  'a.item() instead', DeprecationWarning, stacklevel=1)
     return a.item()
 
 #-----------------------------------------------------------------------------
diff --git a/numpy/linalg/linalg.py b/numpy/linalg/linalg.py
index 0aa8d5ca9..27ec62403 100644
--- a/numpy/linalg/linalg.py
+++ b/numpy/linalg/linalg.py
@@ -890,12 +890,12 @@ 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, stacklevel=2)
+            warnings.warn(msg, DeprecationWarning, stacklevel=3)
             mode = 'reduced'
         elif mode in ('e', 'economic'):
             # 2013-04-01, 1.8
             msg = "The 'economic' option is deprecated."
-            warnings.warn(msg, DeprecationWarning, stacklevel=2)
+            warnings.warn(msg, DeprecationWarning, stacklevel=3)
             mode = 'economic'
         else:
             raise ValueError("Unrecognized mode '%s'" % mode)
@@ -2245,7 +2245,7 @@ def lstsq(a, b, rcond="warn"):
                       "To use the future default and silence this warning "
                       "we advise to pass `rcond=None`, to keep using the old, "
                       "explicitly pass `rcond=-1`.",
-                      FutureWarning, stacklevel=2)
+                      FutureWarning, stacklevel=3)
         rcond = -1
     if rcond is None:
         rcond = finfo(t).eps * max(n, m)