Merge branch 'master' into config-load-dll

.appveyor.yml

@@ -8,6 +8,10 @@ max_jobs: 100
 cache:
   - '%LOCALAPPDATA%\pip\Cache'
 
+matrix:
+  allow_failures:
+    - USE_PYTEST: true
+
 environment:
   global:
       MINGW_32: C:\mingw-w64\i686-6.3.0-posix-dwarf-rt_v5-rev1\mingw32\bin
@@ -17,8 +21,14 @@ environment:
       APPVEYOR_SAVE_CACHE_ON_ERROR: true
       APPVEYOR_SKIP_FINALIZE_ON_EXIT: true
       TEST_TIMEOUT: 1000
+      NPY_NUM_BUILD_JOBS: 4
 
   matrix:
+    - PYTHON: C:\Python34-x64
+      PYTHON_VERSION: 3.4
+      PYTHON_ARCH: 64
+      USE_PYTEST: true
+
     - PYTHON: C:\Python36
       PYTHON_VERSION: 3.6
       PYTHON_ARCH: 32
@@ -29,40 +39,11 @@ environment:
       PYTHON_ARCH: 64
       TEST_MODE: fast
 
-    - PYTHON: C:\Python34-x64
-      PYTHON_VERSION: 3.4
-      PYTHON_ARCH: 64
-      TEST_MODE: fast
-
     - PYTHON: C:\Python36-x64
       PYTHON_VERSION: 3.6
       PYTHON_ARCH: 64
       TEST_MODE: full
 
-    - PYTHON: C:\Python27
-      PYTHON_VERSION: 2.7
-      PYTHON_ARCH: 32
-      SKIP_NOTAG: true
-      TEST_MODE: full
-
-    - PYTHON: C:\Python34
-      PYTHON_VERSION: 3.4
-      PYTHON_ARCH: 32
-      SKIP_NOTAG: true
-      TEST_MODE: full
-
-    - PYTHON: C:\Python35-x64
-      PYTHON_VERSION: 3.5
-      PYTHON_ARCH: 64
-      SKIP_NOTAG: true
-      TEST_MODE: full
-
-    - PYTHON: C:\Python35
-      PYTHON_VERSION: 3.5
-      PYTHON_ARCH: 32
-      SKIP_NOTAG: true
-      TEST_MODE: full
-
 init:
   - "ECHO %PYTHON% %PYTHON_VERSION% %PYTHON_ARCH%"
   - "ECHO \"%APPVEYOR_SCHEDULED_BUILD%\""
@@ -74,22 +55,16 @@ init:
   - ps: if ($env:APPVEYOR_PULL_REQUEST_NUMBER -and $env:APPVEYOR_BUILD_NUMBER -ne ((Invoke-RestMethod `
         https://ci.appveyor.com/api/projects/$env:APPVEYOR_ACCOUNT_NAME/$env:APPVEYOR_PROJECT_SLUG/history?recordsNumber=50).builds | `
         Where-Object pullRequestId -eq $env:APPVEYOR_PULL_REQUEST_NUMBER)[0].buildNumber) { `
-          Write-Host "There are newer queued builds for this pull request, skipping build."
-          Exit-AppveyorBuild
+          raise "There are newer queued builds for this pull request, skipping build."
         }
-  - ps: |
-      If (($env:SKIP_NOTAG -eq "true") -and ($env:APPVEYOR_REPO_TAG -ne "true")) {
-          Write-Host "Skipping build, not at a tag."
-          Exit-AppveyorBuild
-      }
 
 install:
-  # Show size of cache
-  - C:\cygwin\bin\du -hs "%LOCALAPPDATA%\pip\Cache"
   # Prepend newly installed Python to the PATH of this build (this cannot be
   # done from inside the powershell script as it would require to restart
   # the parent CMD process).
   - SET PATH=%PYTHON%;%PYTHON%\Scripts;%PATH%
+  - if [%PYTHON_ARCH%]==[32] SET PATH=%MINGW_32%;%PATH% & SET OPENBLAS=%OPENBLAS_32%
+  - if [%PYTHON_ARCH%]==[64] SET PATH=%MINGW_64%;%PATH% & SET OPENBLAS=%OPENBLAS_64%
 
   # Check that we have the expected version and architecture for Python
   - python --version
@@ -101,72 +76,61 @@ install:
   # Install "openblas.a" to PYTHON\lib
   # Library provided by Matthew Brett at https://github.com/matthew-brett/build-openblas
   - ps: |
-      $PYTHON_ARCH = $env:PYTHON_ARCH
-      $PYTHON = $env:PYTHON
-      If ($PYTHON_ARCH -eq 32) {
-          $OPENBLAS = $env:OPENBLAS_32
-      } Else {
-          $OPENBLAS = $env:OPENBLAS_64
-      }
       $clnt = new-object System.Net.WebClient
       $file = "$(New-TemporaryFile).zip"
       $tmpdir = New-TemporaryFile | %{ rm $_; mkdir $_ }
-      $destination = "$PYTHON\lib\openblas.a"
+      $destination = "$env:PYTHON\lib\openblas.a"
 
       echo $file
       echo $tmpdir
-      echo $OPENBLAS
+      echo $env:OPENBLAS
 
-      $clnt.DownloadFile($OPENBLAS,$file)
+      $clnt.DownloadFile($env:OPENBLAS, $file)
       Get-FileHash $file | Format-List
 
       Expand-Archive $file $tmpdir      
 
-      rm $tmpdir\$PYTHON_ARCH\lib\*.dll.a
-      $lib = ls $tmpdir\$PYTHON_ARCH\lib\*.a | ForEach { ls $_ } | Select-Object -first 1
+      rm $tmpdir\$env:PYTHON_ARCH\lib\*.dll.a
+      $lib = ls $tmpdir\$env:PYTHON_ARCH\lib\*.a | ForEach { ls $_ } | Select-Object -first 1
       echo $lib
 
       cp $lib $destination
       ls $destination
 
   # Upgrade to the latest pip.
-  - '%CMD_IN_ENV% python -m pip install -U pip setuptools wheel'
+  - 'python -m pip install -U pip setuptools wheel'
 
   # Install the numpy test dependencies.
-  - '%CMD_IN_ENV% pip install -U --timeout 5 --retries 2 -r tools/ci/appveyor/requirements.txt'
+  - 'pip install -U --timeout 5 --retries 2 -r tools/ci/appveyor/requirements.txt'
 
 build_script:
   # Here, we add MinGW to the path to be able to link an OpenBLAS.dll
   # We then use the import library from the DLL to compile with MSVC
   - ps: |
-      $PYTHON_ARCH = $env:PYTHON_ARCH
-      If ($PYTHON_ARCH -eq 32) {
-          $MINGW = $env:MINGW_32 
+      If ($env:USE_PYTEST -eq "true") {
+          pip install -e .
       } Else {
-          $MINGW = $env:MINGW_64
-      }
-      $env:Path += ";$MINGW"
-      $env:NPY_NUM_BUILD_JOBS = "4"
-      mkdir dist
-      pip wheel -v -v -v --wheel-dir=dist .
-
-      # For each wheel that pip has placed in the "dist" directory
-      # First, upload the wheel to the "artifacts" tab and then
-      # install the wheel. If we have only built numpy (as is the case here),
-      # then there will be one wheel to install.
-      
-      # This method is more representative of what will be distributed,
-      # because it actually tests what the built wheels will be rather than
-      # what 'setup.py install' will do and at it uploads the wheels so that
-      # they can be inspected.
-
-      ls dist -r | Foreach-Object {
-          appveyor PushArtifact $_.FullName
-          pip install $_.FullName
+          pip wheel -v -v -v --wheel-dir=dist .
+
+          # For each wheel that pip has placed in the "dist" directory
+          # First, upload the wheel to the "artifacts" tab and then
+          # install the wheel. If we have only built numpy (as is the case here),
+          # then there will be one wheel to install.
+          
+          # This method is more representative of what will be distributed,
+          # because it actually tests what the built wheels will be rather than
+          # what 'setup.py install' will do and at it uploads the wheels so that
+          # they can be inspected.
+
+          ls dist -r | Foreach-Object {
+              appveyor PushArtifact $_.FullName
+              pip install $_.FullName
+          }
       }
 
 test_script:
-  - python runtests.py -v -n -m %TEST_MODE%
+  - if [%USE_PYTEST%]==[true] pytest -n3 --junitxml=junit-results.xml
+  - if [%USE_PYTEST%]==[] python runtests.py -v -n -m %TEST_MODE%
 
 after_build:
   # Remove old or huge cache files to hopefully not exceed the 1GB cache limit.

.gitignore

@@ -19,13 +19,15 @@ pmip
 .sw[nop]
 *.tmp
 *.vim
+.vscode
 tags
 cscope.out
 # gnu global
 GPATH
 GRTAGS
 GSYMS
 GTAGS
+.cache
 
 # Compiled source #
 ###################
@@ -71,6 +73,7 @@ doc/cdoc/build
 # The shelf plugin uses this dir
 ./.shelf
 MANIFEST
+.cache
 
 # Paver generated files #
 #########################

MANIFEST.in

@@ -4,6 +4,7 @@
 # data, etc files to distribution. Avoid using MANIFEST.in for that.
 #
 include MANIFEST.in
+include pytest.ini
 include *.txt
 include site.cfg.example
 include numpy/random/mtrand/generate_mtrand_c.py

doc/EXAMPLE_DOCSTRING.rst.txt

@@ -33,7 +33,7 @@ Returns
 -------
 out : ndarray
     The drawn samples, arranged according to `shape`.  If the
-    shape given is (m,n,...), then the shape of `out` is is
+    shape given is (m,n,...), then the shape of `out` is
     (m,n,...,N).
 
     In other words, each entry ``out[i,j,...,:]`` is an N-dimensional

doc/release/1.15.0-notes.rst

@@ -12,6 +12,8 @@ New functions
 
 * `np.gcd` and `np.lcm`, to compute the greatest common divisor and least
   common multiple.
+* `np.ma.stack`, the `np.stack` array-joining function generalized to masked
+  arrays.
 
 
 Deprecations
@@ -53,7 +55,51 @@ builtin arbitrary-precision `Decimal` and `long` types.
 Improvements
 ============
 
+``histogram`` and ``histogramdd` functions have moved to ``np.lib.histograms``
+------------------------------------------------------------------------------
+These were originally found in ``np.lib.function_base``. They are still
+available under their un-scoped ``np.histogram(dd)`` names, and
+to maintain compatibility, aliased at ``np.lib.function_base.histogram(dd)``.
+
+Code that does ``from np.lib.function_base import *`` will need to be updated
+with the new location, and should consider not using ``import *`` in future.
+
+``histogram`` will accept NaN values when explicit bins are given
+-----------------------------------------------------------------
+Previously it would fail when trying to compute a finite range for the data.
+Since the range is ignored anyway when the bins are given explcitly, this error
+was needless.
+
+Note that calling `histogram` on NaN values continues to raise the
+`RuntimeWarning`s typical of working with nan values, which can be silenced
+as usual with `errstate`.
+
+``histogram`` works on datetime types, when explicit bin edges are given
+------------------------------------------------------------------------
+Dates, times, and timedeltas can now be histogrammed. The bin edges must be
+passed explicitly, and are not yet computed automatically.
+
+``np.r_`` works with 0d arrays, and ``np.ma.mr_` works with ``np.ma.masked``
+----------------------------------------------------------------------------
+0d arrays passed to the `r_` and `mr_` concatenation helpers are now treated as
+though they are arrays of length 1. Previously, passing these was an error.
+As a result, ``np.ma.mr_`` now works correctly on the ``masked`` constant.
+
+``np.ptp`` accepts a ``keepdims`` argument, and extended axis tuples
+--------------------------------------------------------------------
+``np.ptp`` (peak-to-peak) can now work over multiple axes, just like `max` and
+`min`.
+
+``MaskedArray.astype`` now is identical to ``ndarray.astype``
+-------------------------------------------------------------
+This means it takes all the same arguments, making more code written for
+ndarray work for masked array too.
+
+Enable AVX2/AVX512 at compile time
+-------------------------------------------------------------
+Change to simd.inc.src to use AVX2 or AVX512 at compile time. Solving the gap
+that if compile numpy for avx2 (or 512) with -march=native, still get the SSE
+code for the simd functions even though rest of the code gets AVX2.
 
 Changes
 =======
-

doc/source/reference/c-api.coremath.rst

@@ -237,7 +237,7 @@ of floating point round-off error.
 
 Like for other types, NumPy includes a typedef npy_half for the 16 bit
 float.  Unlike for most of the other types, you cannot use this as a
-normal type in C, since is is a typedef for npy_uint16.  For example,
+normal type in C, since it is a typedef for npy_uint16.  For example,
 1.0 looks like 0x3c00 to C, and if you do an equality comparison
 between the different signed zeros, you will get -0.0 != 0.0
 (0x8000 != 0x0000), which is incorrect.

numpy/add_newdocs.py

@@ -4055,7 +4055,7 @@ def luf(lamdaexpr, *args, **kwargs):
 
 add_newdoc('numpy.core.multiarray', 'ndarray', ('ptp',
     """
-    a.ptp(axis=None, out=None)
+    a.ptp(axis=None, out=None, keepdims=False)
 
     Peak to peak (maximum - minimum) value along a given axis.
 

numpy/conftest.py

@@ -5,6 +5,8 @@
 
 import warnings
 import pytest
+import numpy
+import importlib
 
 from numpy.core.multiarray_tests import get_fpu_mode
 
@@ -52,3 +54,33 @@ def check_fpu_mode(request):
         raise AssertionError("FPU precision mode changed from {0:#x} to {1:#x}"
                              " when collecting the test".format(old_mode, 
                                                                 new_mode))
+
+
+def pytest_addoption(parser):
+    parser.addoption("--runslow", action="store_true",
+                     default=False, help="run slow tests")
+
+
+def pytest_collection_modifyitems(config, items):
+    if config.getoption("--runslow"):
+        # --runslow given in cli: do not skip slow tests
+        return
+    skip_slow = pytest.mark.skip(reason="need --runslow option to run")
+    for item in items:
+        if "slow" in item.keywords:
+            item.add_marker(skip_slow)
+
+
+@pytest.fixture(autouse=True)
+def add_np(doctest_namespace):
+    doctest_namespace['np'] = numpy
+
+
+for module, replacement in {
+    'numpy.testing.decorators': 'numpy.testing.pytest_tools.decorators',
+    'numpy.testing.utils': 'numpy.testing.pytest_tools.utils',
+}.items():
+    module = importlib.import_module(module)
+    replacement = importlib.import_module(replacement)
+    module.__dict__.clear()
+    module.__dict__.update(replacement.__dict__)

numpy/core/_methods.py

@@ -142,3 +142,10 @@ def _std(a, axis=None, dtype=None, out=None, ddof=0, keepdims=False):
         ret = um.sqrt(ret)
 
     return ret
+
+def _ptp(a, axis=None, out=None, keepdims=False):
+    return um.subtract(
+        umr_maximum(a, axis, None, out, keepdims),
+        umr_minimum(a, axis, None, None, keepdims),
+        out
+    )