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-rw-r--r--.lgtm.yml9
-rw-r--r--numpy/core/_internal.py4
-rw-r--r--numpy/core/records.py4
-rw-r--r--numpy/core/src/multiarray/buffer.c21
-rw-r--r--numpy/core/src/multiarray/multiarraymodule.c2
-rw-r--r--numpy/core/tests/test_deprecations.py5
-rw-r--r--numpy/core/tests/test_multiarray.py115
-rw-r--r--numpy/core/tests/test_scalarbuffer.py8
-rw-r--r--numpy/lib/_datasource.py8
-rw-r--r--numpy/lib/polynomial.py6
-rw-r--r--numpy/lib/tests/test__datasource.py23
-rw-r--r--numpy/polynomial/_polybase.py4
-rwxr-xr-xtools/travis-test.sh24
13 files changed, 167 insertions, 66 deletions
diff --git a/.lgtm.yml b/.lgtm.yml
new file mode 100644
index 000000000..c0a9cf59a
--- /dev/null
+++ b/.lgtm.yml
@@ -0,0 +1,9 @@
+path_classifiers:
+ library:
+ - tools
+ generated:
+ # The exports defined in __init__.py are defined in the Cython module
+ # np.random.mtrand. By excluding this file we suppress a number of
+ # "undefined export" alerts
+ - numpy/random/__init__.py
+
diff --git a/numpy/core/_internal.py b/numpy/core/_internal.py
index 1cf89aab0..ce7ef7060 100644
--- a/numpy/core/_internal.py
+++ b/numpy/core/_internal.py
@@ -9,7 +9,7 @@ from __future__ import division, absolute_import, print_function
import re
import sys
-from numpy.compat import basestring
+from numpy.compat import basestring, unicode
from .multiarray import dtype, array, ndarray
try:
import ctypes
@@ -294,7 +294,7 @@ def _newnames(datatype, order):
"""
oldnames = datatype.names
nameslist = list(oldnames)
- if isinstance(order, str):
+ if isinstance(order, (str, unicode)):
order = [order]
seen = set()
if isinstance(order, (list, tuple)):
diff --git a/numpy/core/records.py b/numpy/core/records.py
index 612d39322..a483871ba 100644
--- a/numpy/core/records.py
+++ b/numpy/core/records.py
@@ -42,7 +42,7 @@ import warnings
from . import numeric as sb
from . import numerictypes as nt
-from numpy.compat import isfileobj, bytes, long
+from numpy.compat import isfileobj, bytes, long, unicode
from .arrayprint import get_printoptions
# All of the functions allow formats to be a dtype
@@ -174,7 +174,7 @@ class format_parser(object):
if (names):
if (type(names) in [list, tuple]):
pass
- elif isinstance(names, str):
+ elif isinstance(names, (str, unicode)):
names = names.split(',')
else:
raise NameError("illegal input names %s" % repr(names))
diff --git a/numpy/core/src/multiarray/buffer.c b/numpy/core/src/multiarray/buffer.c
index 0325f3c6a..d549a3029 100644
--- a/numpy/core/src/multiarray/buffer.c
+++ b/numpy/core/src/multiarray/buffer.c
@@ -175,6 +175,14 @@ _is_natively_aligned_at(PyArray_Descr *descr,
return 1;
}
+/*
+ * Fill in str with an appropriate PEP 3118 format string, based on
+ * descr. For structured dtypes, calls itself recursively. Each call extends
+ * str at offset then updates offset, and uses descr->byteorder, (and
+ * possibly the byte order in obj) to determine the byte-order char.
+ *
+ * Returns 0 for success, -1 for failure
+ */
static int
_buffer_format_string(PyArray_Descr *descr, _tmp_string_t *str,
PyObject* obj, Py_ssize_t *offset,
@@ -195,8 +203,8 @@ _buffer_format_string(PyArray_Descr *descr, _tmp_string_t *str,
PyObject *item, *subarray_tuple;
Py_ssize_t total_count = 1;
Py_ssize_t dim_size;
+ Py_ssize_t old_offset;
char buf[128];
- int old_offset;
int ret;
if (PyTuple_Check(descr->subarray->shape)) {
@@ -230,15 +238,15 @@ _buffer_format_string(PyArray_Descr *descr, _tmp_string_t *str,
return ret;
}
else if (PyDataType_HASFIELDS(descr)) {
- int base_offset = *offset;
+ Py_ssize_t base_offset = *offset;
_append_str(str, "T{");
for (k = 0; k < PyTuple_GET_SIZE(descr->names); ++k) {
PyObject *name, *item, *offset_obj, *tmp;
PyArray_Descr *child;
char *p;
- Py_ssize_t len;
- int new_offset;
+ Py_ssize_t len, new_offset;
+ int ret;
name = PyTuple_GET_ITEM(descr->names, k);
item = PyDict_GetItem(descr->fields, name);
@@ -266,8 +274,11 @@ _buffer_format_string(PyArray_Descr *descr, _tmp_string_t *str,
}
/* Insert child item */
- _buffer_format_string(child, str, obj, offset,
+ ret = _buffer_format_string(child, str, obj, offset,
active_byteorder);
+ if (ret < 0) {
+ return -1;
+ }
/* Insert field name */
#if defined(NPY_PY3K)
diff --git a/numpy/core/src/multiarray/multiarraymodule.c b/numpy/core/src/multiarray/multiarraymodule.c
index 6e57f1d6d..dc571dfcb 100644
--- a/numpy/core/src/multiarray/multiarraymodule.c
+++ b/numpy/core/src/multiarray/multiarraymodule.c
@@ -2020,7 +2020,7 @@ array_fromstring(PyObject *NPY_UNUSED(ignored), PyObject *args, PyObject *keywds
if (DEPRECATE(
"The binary mode of fromstring is deprecated, as it behaves "
"surprisingly on unicode inputs. Use frombuffer instead") < 0) {
- Py_DECREF(descr);
+ Py_XDECREF(descr);
return NULL;
}
}
diff --git a/numpy/core/tests/test_deprecations.py b/numpy/core/tests/test_deprecations.py
index 5d66d963f..10ef16800 100644
--- a/numpy/core/tests/test_deprecations.py
+++ b/numpy/core/tests/test_deprecations.py
@@ -518,3 +518,8 @@ class TestPositiveOnNonNumerical(_DeprecationTestCase):
# 2018-06-28, 1.16.0
def test_positive_on_non_number(self):
self.assert_deprecated(operator.pos, args=(np.array('foo'),))
+
+class TestFromstring(_DeprecationTestCase):
+ # 2017-10-19, 1.14
+ def test_fromstring(self):
+ self.assert_deprecated(np.fromstring, args=('\x00'*80,))
diff --git a/numpy/core/tests/test_multiarray.py b/numpy/core/tests/test_multiarray.py
index 1511f5b6b..d751657db 100644
--- a/numpy/core/tests/test_multiarray.py
+++ b/numpy/core/tests/test_multiarray.py
@@ -4748,55 +4748,72 @@ class TestRecord(object):
# Error raised when multiple fields have the same name
assert_raises(ValueError, test_assign)
- if sys.version_info[0] >= 3:
- def test_bytes_fields(self):
- # Bytes are not allowed in field names and not recognized in titles
- # on Py3
- assert_raises(TypeError, np.dtype, [(b'a', int)])
- assert_raises(TypeError, np.dtype, [(('b', b'a'), int)])
-
- dt = np.dtype([((b'a', 'b'), int)])
- assert_raises(TypeError, dt.__getitem__, b'a')
-
- x = np.array([(1,), (2,), (3,)], dtype=dt)
- assert_raises(IndexError, x.__getitem__, b'a')
-
- y = x[0]
- assert_raises(IndexError, y.__getitem__, b'a')
-
- def test_multiple_field_name_unicode(self):
- def test_assign_unicode():
- dt = np.dtype([("\u20B9", "f8"),
- ("B", "f8"),
- ("\u20B9", "f8")])
-
- # Error raised when multiple fields have the same name(unicode included)
- assert_raises(ValueError, test_assign_unicode)
-
- else:
- def test_unicode_field_titles(self):
- # Unicode field titles are added to field dict on Py2
- title = u'b'
- dt = np.dtype([((title, 'a'), int)])
- dt[title]
- dt['a']
- x = np.array([(1,), (2,), (3,)], dtype=dt)
- x[title]
- x['a']
- y = x[0]
- y[title]
- y['a']
-
- def test_unicode_field_names(self):
- # Unicode field names are converted to ascii on Python 2:
- encodable_name = u'b'
- assert_equal(np.dtype([(encodable_name, int)]).names[0], b'b')
- assert_equal(np.dtype([(('a', encodable_name), int)]).names[0], b'b')
-
- # But raises UnicodeEncodeError if it can't be encoded:
- nonencodable_name = u'\uc3bc'
- assert_raises(UnicodeEncodeError, np.dtype, [(nonencodable_name, int)])
- assert_raises(UnicodeEncodeError, np.dtype, [(('a', nonencodable_name), int)])
+ @pytest.mark.skipif(sys.version_info[0] < 3, reason="Not Python 3")
+ def test_bytes_fields(self):
+ # Bytes are not allowed in field names and not recognized in titles
+ # on Py3
+ assert_raises(TypeError, np.dtype, [(b'a', int)])
+ assert_raises(TypeError, np.dtype, [(('b', b'a'), int)])
+
+ dt = np.dtype([((b'a', 'b'), int)])
+ assert_raises(TypeError, dt.__getitem__, b'a')
+
+ x = np.array([(1,), (2,), (3,)], dtype=dt)
+ assert_raises(IndexError, x.__getitem__, b'a')
+
+ y = x[0]
+ assert_raises(IndexError, y.__getitem__, b'a')
+
+ @pytest.mark.skipif(sys.version_info[0] < 3, reason="Not Python 3")
+ def test_multiple_field_name_unicode(self):
+ def test_assign_unicode():
+ dt = np.dtype([("\u20B9", "f8"),
+ ("B", "f8"),
+ ("\u20B9", "f8")])
+
+ # Error raised when multiple fields have the same name(unicode included)
+ assert_raises(ValueError, test_assign_unicode)
+
+ @pytest.mark.skipif(sys.version_info[0] >= 3, reason="Not Python 2")
+ def test_unicode_field_titles(self):
+ # Unicode field titles are added to field dict on Py2
+ title = u'b'
+ dt = np.dtype([((title, 'a'), int)])
+ dt[title]
+ dt['a']
+ x = np.array([(1,), (2,), (3,)], dtype=dt)
+ x[title]
+ x['a']
+ y = x[0]
+ y[title]
+ y['a']
+
+ @pytest.mark.skipif(sys.version_info[0] >= 3, reason="Not Python 2")
+ def test_unicode_field_names(self):
+ # Unicode field names are converted to ascii on Python 2:
+ encodable_name = u'b'
+ assert_equal(np.dtype([(encodable_name, int)]).names[0], b'b')
+ assert_equal(np.dtype([(('a', encodable_name), int)]).names[0], b'b')
+
+ # But raises UnicodeEncodeError if it can't be encoded:
+ nonencodable_name = u'\uc3bc'
+ assert_raises(UnicodeEncodeError, np.dtype, [(nonencodable_name, int)])
+ assert_raises(UnicodeEncodeError, np.dtype, [(('a', nonencodable_name), int)])
+
+ def test_fromarrays_unicode(self):
+ # A single name string provided to fromarrays() is allowed to be unicode
+ # on both Python 2 and 3:
+ x = np.core.records.fromarrays([[0], [1]], names=u'a,b', formats=u'i4,i4')
+ assert_equal(x['a'][0], 0)
+ assert_equal(x['b'][0], 1)
+
+ def test_unicode_order(self):
+ # Test that we can sort with order as a unicode field name in both Python 2 and
+ # 3:
+ name = u'b'
+ x = np.array([1, 3, 2], dtype=[(name, int)])
+ x.sort(order=name)
+ assert_equal(x[u'b'], np.array([1, 2, 3]))
def test_field_names(self):
# Test unicode and 8-bit / byte strings can be used
diff --git a/numpy/core/tests/test_scalarbuffer.py b/numpy/core/tests/test_scalarbuffer.py
index 6d57a5014..9e75fec3e 100644
--- a/numpy/core/tests/test_scalarbuffer.py
+++ b/numpy/core/tests/test_scalarbuffer.py
@@ -5,7 +5,7 @@ import sys
import numpy as np
import pytest
-from numpy.testing import assert_, assert_equal
+from numpy.testing import assert_, assert_equal, assert_raises
# PEP3118 format strings for native (standard alignment and byteorder) types
scalars_and_codes = [
@@ -77,3 +77,9 @@ class TestScalarPEP3118(object):
mv_a = memoryview(a)
assert_equal(mv_x.itemsize, mv_a.itemsize)
assert_equal(mv_x.format, mv_a.format)
+
+ def test_invalid_buffer_format(self):
+ # datetime64 cannot be used in a buffer yet
+ dt = np.dtype([('a', int), ('b', 'M8[s]')])
+ a = np.empty(1, dt)
+ assert_raises((ValueError, BufferError), memoryview, a[0])
diff --git a/numpy/lib/_datasource.py b/numpy/lib/_datasource.py
index 6f1295f09..ab00b1444 100644
--- a/numpy/lib/_datasource.py
+++ b/numpy/lib/_datasource.py
@@ -37,6 +37,7 @@ from __future__ import division, absolute_import, print_function
import os
import sys
+import warnings
import shutil
import io
@@ -85,9 +86,10 @@ def _python2_bz2open(fn, mode, encoding, newline):
if "t" in mode:
# BZ2File is missing necessary functions for TextIOWrapper
- raise ValueError("bz2 text files not supported in python2")
- else:
- return bz2.BZ2File(fn, mode)
+ warnings.warn("Assuming latin1 encoding for bz2 text file in Python2",
+ RuntimeWarning, stacklevel=5)
+ mode = mode.replace("t", "")
+ return bz2.BZ2File(fn, mode)
def _python2_gzipopen(fn, mode, encoding, newline):
""" Wrapper to open gzip in text mode.
diff --git a/numpy/lib/polynomial.py b/numpy/lib/polynomial.py
index 0e691f56e..9f3b84732 100644
--- a/numpy/lib/polynomial.py
+++ b/numpy/lib/polynomial.py
@@ -396,7 +396,11 @@ def polyfit(x, y, deg, rcond=None, full=False, w=None, cov=False):
Fit a polynomial ``p(x) = p[0] * x**deg + ... + p[deg]`` of degree `deg`
to points `(x, y)`. Returns a vector of coefficients `p` that minimises
- the squared error.
+ the squared error in the order `deg`, `deg-1`, ... `0`.
+
+ The `Polynomial.fit <numpy.polynomial.polynomial.Polynomial.fit>` class
+ method is recommended for new code as it is more stable numerically. See
+ the documentation of the method for more information.
Parameters
----------
diff --git a/numpy/lib/tests/test__datasource.py b/numpy/lib/tests/test__datasource.py
index 32812990c..70fff3bb0 100644
--- a/numpy/lib/tests/test__datasource.py
+++ b/numpy/lib/tests/test__datasource.py
@@ -2,11 +2,14 @@ from __future__ import division, absolute_import, print_function
import os
import sys
+import pytest
from tempfile import mkdtemp, mkstemp, NamedTemporaryFile
from shutil import rmtree
-from numpy.testing import assert_, assert_equal, assert_raises, SkipTest
import numpy.lib._datasource as datasource
+from numpy.testing import (
+ assert_, assert_equal, assert_raises, assert_warns, SkipTest
+ )
if sys.version_info[0] >= 3:
import urllib.request as urllib_request
@@ -161,6 +164,24 @@ class TestDataSourceOpen(object):
fp.close()
assert_equal(magic_line, result)
+ @pytest.mark.skipif(sys.version_info[0] >= 3, reason="Python 2 only")
+ def test_Bz2File_text_mode_warning(self):
+ try:
+ import bz2
+ except ImportError:
+ # We don't have the bz2 capabilities to test.
+ raise SkipTest
+ # Test datasource's internal file_opener for BZip2 files.
+ filepath = os.path.join(self.tmpdir, 'foobar.txt.bz2')
+ fp = bz2.BZ2File(filepath, 'w')
+ fp.write(magic_line)
+ fp.close()
+ with assert_warns(RuntimeWarning):
+ fp = self.ds.open(filepath, 'rt')
+ result = fp.readline()
+ fp.close()
+ assert_equal(magic_line, result)
+
class TestDataSourceExists(object):
def setup(self):
diff --git a/numpy/polynomial/_polybase.py b/numpy/polynomial/_polybase.py
index 9f4d30e53..ccbf30bda 100644
--- a/numpy/polynomial/_polybase.py
+++ b/numpy/polynomial/_polybase.py
@@ -860,7 +860,9 @@ class ABCPolyBase(object):
-------
new_series : series
A series that represents the least squares fit to the data and
- has the domain specified in the call.
+ has the domain and window specified in the call. If the
+ coefficients for the unscaled and unshifted basis polynomials are
+ of interest, do ``new_series.convert().coef``.
[resid, rank, sv, rcond] : list
These values are only returned if `full` = True
diff --git a/tools/travis-test.sh b/tools/travis-test.sh
index 11863b5fe..97b192813 100755
--- a/tools/travis-test.sh
+++ b/tools/travis-test.sh
@@ -125,6 +125,22 @@ run_test()
fi
if [ -n "$RUN_COVERAGE" ]; then
+ # move back up to the source dir because we want to execute
+ # gcov on the source files after the tests have gone through
+ # the code paths
+ cd ..
+
+ # execute gcov on source files
+ find . -name '*.gcno' -type f -exec gcov -pb {} +
+
+ # move the C line coverage report files to the same path
+ # as the Python report data
+ mv *.gcov empty
+
+ # move back to the previous path for good measure
+ # as the Python coverage data is there
+ cd empty
+
# Upload coverage files to codecov
bash <(curl -s https://codecov.io/bash) -X gcov -X coveragepy
fi
@@ -153,6 +169,14 @@ if [ -n "$USE_WHEEL" ] && [ $# -eq 0 ]; then
$PIP install -U virtualenv
# ensure some warnings are not issued
export CFLAGS=$CFLAGS" -Wno-sign-compare -Wno-unused-result"
+ # adjust gcc flags if C coverage requested
+ if [ -n "$RUN_COVERAGE" ]; then
+ export NPY_DISTUTILS_APPEND_FLAGS=1
+ export CC='gcc --coverage'
+ export F77='gfortran --coverage'
+ export F90='gfortran --coverage'
+ export LDFLAGS='--coverage'
+ fi
$PYTHON setup.py bdist_wheel
# Make another virtualenv to install into
virtualenv --python=`which $PYTHON` venv-for-wheel
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