Merge branch 'master' into npy-2.1

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,7 +1,7 @@
 <!-- Please be sure you are following the instructions in the dev guidelines
-http://www.numpy.org/devdocs/dev/gitwash/development_workflow.html
+http://www.numpy.org/devdocs/dev/development_workflow.html
 -->
 
 <!-- We'd appreciate it if your commit message is properly formatted
-http://www.numpy.org/devdocs/dev/gitwash/development_workflow.html#writing-the-commit-message
+http://www.numpy.org/devdocs/dev/development_workflow.html#writing-the-commit-message
 -->

.gitignore

@@ -142,6 +142,7 @@ numpy/core/src/npysort/binsearch.c
 numpy/core/src/npysort/heapsort.c
 numpy/core/src/npysort/mergesort.c
 numpy/core/src/npysort/quicksort.c
+numpy/core/src/npysort/radixsort.c
 numpy/core/src/npysort/selection.c
 numpy/core/src/npysort/timsort.c
 numpy/core/src/npysort/sort.c

.mailmap

@@ -204,7 +204,8 @@ Warren Weckesser <[email protected]> Warren Weckesser <warren.wecke
 Weitang Li <[email protected]> wtli@Dirac <[email protected]>
 Weitang Li <[email protected]> wtli <[email protected]>
 Wendell Smith <[email protected]> Wendell Smith <[email protected]>
-William Spotz <[email protected]@localhost> [email protected] <[email protected]@localhost>
+Bill Spotz <[email protected]> William Spotz <[email protected]@localhost>
+Bill Spotz <[email protected]> [email protected] <[email protected]@localhost>
 Wim Glenn <[email protected]> wim glenn <[email protected]>
 Wojtek Ruszczewski <[email protected]> wrwrwr <[email protected]>
 Yuji Kanagawa <[email protected]> kngwyu <[email protected]>

LICENSE.txt

@@ -28,33 +28,3 @@ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-
-The NumPy repository and source distributions bundle several libraries that are
-compatibly licensed.  We list these here.
-
-Name: Numpydoc
-Files: doc/sphinxext/numpydoc/*
-License: 2-clause BSD
-  For details, see doc/sphinxext/LICENSE.txt
-
-Name: scipy-sphinx-theme
-Files: doc/scipy-sphinx-theme/*
-License: 3-clause BSD, PSF and Apache 2.0
-  For details, see doc/scipy-sphinx-theme/LICENSE.txt
-
-Name: lapack-lite
-Files: numpy/linalg/lapack_lite/*
-License: 3-clause BSD
-  For details, see numpy/linalg/lapack_lite/LICENSE.txt
-
-Name: tempita
-Files: tools/npy_tempita/*
-License: BSD derived
-  For details, see tools/npy_tempita/license.txt
-
-Name: dragon4
-Files: numpy/core/src/multiarray/dragon4.c
-License: One of a kind
-  For license text, see numpy/core/src/multiarray/dragon4.c

LICENSES_bundled.txt

@@ -0,0 +1,27 @@
+The NumPy repository and source distributions bundle several libraries that are
+compatibly licensed.  We list these here.
+
+Name: Numpydoc
+Files: doc/sphinxext/numpydoc/*
+License: 2-clause BSD
+  For details, see doc/sphinxext/LICENSE.txt
+
+Name: scipy-sphinx-theme
+Files: doc/scipy-sphinx-theme/*
+License: 3-clause BSD, PSF and Apache 2.0
+  For details, see doc/scipy-sphinx-theme/LICENSE.txt
+
+Name: lapack-lite
+Files: numpy/linalg/lapack_lite/*
+License: 3-clause BSD
+  For details, see numpy/linalg/lapack_lite/LICENSE.txt
+
+Name: tempita
+Files: tools/npy_tempita/*
+License: BSD derived
+  For details, see tools/npy_tempita/license.txt
+
+Name: dragon4
+Files: numpy/core/src/multiarray/dragon4.c
+License: One of a kind
+  For license text, see numpy/core/src/multiarray/dragon4.c

MANIFEST.in

@@ -7,6 +7,7 @@
 include MANIFEST.in
 include pytest.ini
 include *.txt
+include README.md
 include site.cfg.example
 recursive-include numpy/random/mtrand *.pyx *.pxd
 # Add build support that should go in sdist, but not go in bdist/be installed
@@ -39,3 +40,6 @@ prune benchmarks/numpy
 # Exclude generated files
 prune */__pycache__
 global-exclude *.pyc *.pyo *.pyd *.swp *.bak *~
+# Exclude license file that we append to the main license when running
+# `python setup.py sdist`
+exclude LICENSES_bundled.txt

README.md

@@ -11,11 +11,13 @@
 
 NumPy is the fundamental package needed for scientific computing with Python.
 
-- **Website (including documentation):** https://www.numpy.org
+- **Website:** https://www.numpy.org
+- **Documentation:** http://docs.scipy.org/
 - **Mailing list:** https://mail.python.org/mailman/listinfo/numpy-discussion
-- **Source:** https://github.com/numpy/numpy
-- **Bug reports:** https://github.com/numpy/numpy/issues
+- **Source code:** https://github.com/numpy/numpy
 - **Contributing:** https://www.numpy.org/devdocs/dev/index.html
+- **Bug reports:** https://github.com/numpy/numpy/issues
+- **Report a security vulnerability:** https://tidelift.com/docs/security
 
 It provides:
 

azure-pipelines.yml

@@ -28,8 +28,8 @@ jobs:
            F77=gfortran-5 F90=gfortran-5 \
            CFLAGS='-UNDEBUG -std=c99' python3 runtests.py --mode=full -- -rsx --junitxml=junit/test-results.xml"
     displayName: 'Run 32-bit Ubuntu Docker Build / Tests'
-    continueOnError: true
   - task: PublishTestResults@2
+    condition: succeededOrFailed()
     inputs:
       testResultsFiles: '**/test-*.xml'
       failTaskOnFailedTests: true
@@ -101,8 +101,8 @@ jobs:
     displayName: 'Run Refuide Check'
   - script: python runtests.py --mode=full -- -rsx --junitxml=junit/test-results.xml
     displayName: 'Run Full NumPy Test Suite'
-    continueOnError: true
   - task: PublishTestResults@2
+    condition: succeededOrFailed()
     inputs:
       testResultsFiles: '**/test-*.xml'
       failTaskOnFailedTests: true
@@ -204,8 +204,8 @@ jobs:
     displayName: 'For gh-12667; Windows DLL resolution'
   - script: python runtests.py -n --show-build-log --mode=$(TEST_MODE) -- -rsx --junitxml=junit/test-results.xml
     displayName: 'Run NumPy Test Suite'
-    continueOnError: true
   - task: PublishTestResults@2
+    condition: succeededOrFailed()
     inputs:
       testResultsFiles: '**/test-*.xml'
       failTaskOnFailedTests: true
@@ -217,8 +217,8 @@ jobs:
   steps:
   - script: source tools/pypy-test.sh
     displayName: 'Run PyPy3 Build / Tests'
-    continueOnError: true
   - task: PublishTestResults@2
+    condition: succeededOrFailed()
     inputs:
       testResultsFiles: '**/test-*.xml'
       testRunTitle: 'Publish test results for PyPy3'

benchmarks/benchmarks/bench_function_base.py

@@ -95,6 +95,17 @@ def time_select_larger(self):
         np.select(self.cond_large, ([self.d, self.e] * 10))
 
 
+def memoize(f):
+    _memoized = {}
+    def wrapped(*args):
+        if args not in _memoized:
+            _memoized[args] = f(*args)
+
+        return _memoized[args].copy()
+
+    return f
+
+
 class SortGenerator(object):
     # The size of the unsorted area in the "random unsorted area"
     # benchmarks
@@ -103,6 +114,7 @@ class SortGenerator(object):
     BUBBLE_SIZE = 100
 
     @staticmethod
+    @memoize
     def random(size, dtype):
         """
         Returns a randomly-shuffled array.
@@ -112,27 +124,31 @@ def random(size, dtype):
         return arr
 
     @staticmethod
+    @memoize
     def ordered(size, dtype):
         """
         Returns an ordered array.
         """
         return np.arange(size, dtype=dtype)
 
     @staticmethod
+    @memoize
     def reversed(size, dtype):
         """
         Returns an array that's in descending order.
         """
         return np.arange(size-1, -1, -1, dtype=dtype)
 
     @staticmethod
+    @memoize
     def uniform(size, dtype):
         """
         Returns an array that has the same value everywhere.
         """
         return np.ones(size, dtype=dtype)
 
     @staticmethod
+    @memoize
     def swapped_pair(size, dtype, swap_frac):
         """
         Returns an ordered array, but one that has ``swap_frac * size``
@@ -145,6 +161,7 @@ def swapped_pair(size, dtype, swap_frac):
         return a
 
     @staticmethod
+    @memoize
     def sorted_block(size, dtype, block_size):
         """
         Returns an array with blocks that are all sorted.
@@ -159,6 +176,7 @@ def sorted_block(size, dtype, block_size):
         return np.array(b)
 
     @classmethod
+    @memoize
     def random_unsorted_area(cls, size, dtype, frac, area_size=None):
         """
         This type of array has random unsorted areas such that they
@@ -176,6 +194,7 @@ def random_unsorted_area(cls, size, dtype, frac, area_size=None):
         return a
 
     @classmethod
+    @memoize
     def random_bubble(cls, size, dtype, bubble_num, bubble_size=None):
         """
         This type of array has ``bubble_num`` random unsorted areas.
@@ -197,7 +216,7 @@ class Sort(Benchmark):
         # In NumPy 1.17 and newer, 'merge' can be one of several
         # stable sorts, it isn't necessarily merge sort.
         ['quick', 'merge', 'heap'],
-        ['float64', 'int64', 'uint64'],
+        ['float64', 'int64', 'int16'],
         [
             ('random',),
             ('ordered',),
@@ -206,15 +225,15 @@ class Sort(Benchmark):
             ('sorted_block', 10),
             ('sorted_block', 100),
             ('sorted_block', 1000),
-            ('swapped_pair', 0.01),
-            ('swapped_pair', 0.1),
-            ('swapped_pair', 0.5),
-            ('random_unsorted_area', 0.5),
-            ('random_unsorted_area', 0.1),
-            ('random_unsorted_area', 0.01),
-            ('random_bubble', 1),
-            ('random_bubble', 5),
-            ('random_bubble', 10),
+            # ('swapped_pair', 0.01),
+            # ('swapped_pair', 0.1),
+            # ('swapped_pair', 0.5),
+            # ('random_unsorted_area', 0.5),
+            # ('random_unsorted_area', 0.1),
+            # ('random_unsorted_area', 0.01),
+            # ('random_bubble', 1),
+            # ('random_bubble', 5),
+            # ('random_bubble', 10),
         ],
     ]
     param_names = ['kind', 'dtype', 'array_type']
@@ -227,10 +246,10 @@ def setup(self, kind, dtype, array_type):
         array_class = array_type[0]
         self.arr = getattr(SortGenerator, array_class)(self.ARRAY_SIZE, dtype, *array_type[1:])
 
-    def time_sort_inplace(self, kind, dtype, array_type):
-        self.arr.sort(kind=kind)
-
     def time_sort(self, kind, dtype, array_type):
+        # Using np.sort(...) instead of arr.sort(...) because it makes a copy.
+        # This is important because the data is prepared once per benchmark, but
+        # used across multiple runs.
         np.sort(self.arr, kind=kind)
 
     def time_argsort(self, kind, dtype, array_type):

doc/C_STYLE_GUIDE.rst.txt

@@ -138,7 +138,7 @@ Code lay-out
   the open paren, no spaces inside the parens, no spaces before
   commas, one space after each comma.
 
-* Always put spaces around assignment, Boolean and comparison
+* Always put spaces around the assignment, Boolean and comparison
   operators.  In expressions using a lot of operators, add spaces
   around the outermost (lowest priority) operators.