Merge branch 'master' into sparse-row-slice

.circleci/config.yml

@@ -112,10 +112,10 @@ jobs:
             export CCACHE_COMPRESS=1
             export NPY_NUM_BUILD_JOBS=`pypy3 -c 'import multiprocessing as mp; print(mp.cpu_count())'`
             export PATH=/usr/lib/ccache:$PATH
-            # XXX: use "numpy>=1.15.0" when it's released
             pypy3 -mpip install --upgrade pip setuptools wheel
-            pypy3 -mpip install --no-build-isolation --extra-index https://antocuni.github.io/pypy-wheels/ubuntu pytest pytest-xdist Tempita "Cython>=0.28.2" mpmath
-            pypy3 -mpip install --no-build-isolation git+https://github.com/numpy/numpy.git@db552b5b6b37f2ff085b304751d7a2ebed26adc9
+            pypy3 -mpip install Cython>=0.28.5
+            pypy3 -mpip install numpy>=1.15.0
+            pypy3 -mpip install --no-build-isolation --extra-index https://antocuni.github.io/pypy-wheels/ubuntu pytest pytest-xdist Tempita mpmath
       - run:
           name: build
           command: |
@@ -137,6 +137,8 @@ jobs:
           command: |
             # CircleCI has 4G memory limit, play it safe
             export SCIPY_AVAILABLE_MEM=1G
+            # Try to limit per-process GC memory usage
+            export PYPY_GC_MAX=900MB
             pypy3 runtests.py -- -rfEX -n 3 --durations=30
 
 

.mailmap

@@ -68,6 +68,7 @@ Behzad Nouri <behzadnouri@gmail.com> behzad nouri <behzadnouri@gmail.com>
 Benjamin Root <> weathergod <>
 Benny Malengier <benny.malengier@gmail.com> Benny <benny.malengier@gmail.com>
 Bhavika Tekwani <bhavicka.7992@gmail.com> bhavikat <bhavicka.7992@gmail.com>
+Blair Azzopardi <blairuk@gmail.com> bsdz <blairuk@gmail.com>
 Brett R. Murphy <bmurphy@enthought.com> brettrmurphy <bmurphy@enthought.com>
 Brian Hawthorne <brian.hawthorne@localhost> brian.hawthorne <brian.hawthorne@localhost>
 Brian Newsom <brian.newsom@colorado.edu> Brian Newsom <Brian.Newsom@Colorado.edu>

CONTRIBUTING.rst

@@ -2,7 +2,7 @@
 SciPy pull request guidelines
 =============================
 
-Pull requests are always welcome, and the Scipy community appreciates
+Pull requests are always welcome, and the SciPy community appreciates
 any help you give. Note that a code of conduct applies to all spaces
 managed by the SciPy project, including issues and pull requests:
 https://github.com/scipy/scipy/blob/master/doc/source/dev/conduct/code_of_conduct.rst.

HACKING.rst.txt

@@ -261,7 +261,7 @@ following, a *SciPy module* is defined as a Python package, say
   for instance ``yyy/_somemodule.py``.
 
 * User-visible functions should have good documentation following
-  the Numpy documentation style, see `how to document`_
+  the NumPy documentation style, see `how to document`_
 
 * The ``__init__.py`` of the module should contain the main reference
   documentation in its docstring. This is connected to the Sphinx
@@ -277,7 +277,7 @@ following, a *SciPy module* is defined as a Python package, say
 
 See the existing Scipy submodules for guidance.
 
-For further details on Numpy distutils, see:
+For further details on NumPy distutils, see:
 
   https://github.com/numpy/numpy/blob/master/doc/DISTUTILS.rst.txt
 
@@ -356,7 +356,7 @@ command ``source scipy-dev/bin/activate``, and ``deactivate`` to exit from the
 virtual environment and back to your previous shell.  With scipy-dev
 activated, install first Scipy's dependencies::
 
-    $ pip install Numpy pytest Cython
+    $ pip install NumPy pytest Cython
 
 After that, you can install a development version of Scipy, for example via::
 

README.rst

@@ -13,6 +13,9 @@ SciPy
 .. image:: https://codecov.io/gh/scipy/scipy/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/scipy/scipy
 
+.. image:: https://dev.azure.com/scipy-org/SciPy/_apis/build/status/scipy.scipy?branchName=master
+  :target: https://dev.azure.com/scipy-org/SciPy/_build/latest?definitionId=1?branchName=master
+
 SciPy (pronounced "Sigh Pie") is open-source software for mathematics,
 science, and engineering.  It includes modules for statistics, optimization,
 integration, linear algebra, Fourier transforms, signal and image processing,

THANKS.txt

@@ -80,7 +80,7 @@ Martin Teichmann for improving scipy.special.ellipk & agm accuracy,
     and for linalg.qr_multiply.
 Jeff Armstrong for discrete state-space and linear time-invariant functionality
     in scipy.signal, and sylvester/riccati/lyapunov solvers in scipy.linalg.
-Mark Wiebe for fixing type casting after changes in Numpy.
+Mark Wiebe for fixing type casting after changes in NumPy.
 Andrey Smirnov for improvements to FIR filter design.
 Anthony Scopatz for help with code review and merging.
 Lars Buitinck for improvements to scipy.sparse and various other modules.

azure-pipelines.yml

@@ -0,0 +1,126 @@
+trigger:
+  # start a new build for every push
+  batch: False
+  branches:
+    include:
+      - master
+      - maintenance/*
+
+jobs:
+- job: Linux_Python_36_32bit_full
+  pool:
+    vmIMage: 'ubuntu-16.04'
+  steps:
+  - script: |
+           docker pull i386/ubuntu:bionic
+           docker run -v $(pwd):/scipy i386/ubuntu:bionic /bin/bash -c "cd scipy && \
+           apt-get -y update && \
+           apt-get -y install python3.6-dev python3-pip pkg-config libpng-dev libjpeg8-dev libfreetype6-dev && \
+           pip3 install setuptools wheel numpy cython==0.29 pytest pytest-timeout pytest-xdist pytest-env pytest-faulthandler Pillow mpmath matplotlib && \
+           apt-get -y install gfortran-5 wget && \
+           cd .. && \
+           mkdir openblas && cd openblas && \
+           wget https://3f23b170c54c2533c070-1c8a9b3114517dc5fe17b7c3f8c63a43.ssl.cf2.rackcdn.com/openblas-0.3.0-Linux-i686.tar.gz && \
+           tar zxvf openblas-0.3.0-Linux-i686.tar.gz && \
+           cp -r ./usr/local/lib/* /usr/lib && \
+           cp ./usr/local/include/* /usr/include && \
+           cd ../scipy && \
+           F77=gfortran-5 F90=gfortran-5 python3 runtests.py --mode=full -- -n auto -rsx --junitxml=junit/test-results.xml"
+    displayName: 'Run 32-bit Ubuntu Docker Build / Tests'
+  - task: PublishTestResults@2
+    inputs:
+      testResultsFiles: '**/test-*.xml'
+      testRunTitle: 'Publish test results for Python 3.6-32 bit full Linux'
+- job: Windows
+  pool:
+    vmIMage: 'VS2017-Win2016'
+  variables:
+      OPENBLAS_32: https://3f23b170c54c2533c070-1c8a9b3114517dc5fe17b7c3f8c63a43.ssl.cf2.rackcdn.com/openblas-5f998ef_gcc7_1_0_win32.zip
+      OPENBLAS_64: https://3f23b170c54c2533c070-1c8a9b3114517dc5fe17b7c3f8c63a43.ssl.cf2.rackcdn.com/openblas-5f998ef_gcc7_1_0_win64.zip
+  strategy:
+    maxParallel: 4
+    matrix:
+        Python36-32bit-full:
+          PYTHON_VERSION: '3.6'
+          PYTHON_ARCH: 'x86'
+          TEST_MODE: full
+          OPENBLAS: $(OPENBLAS_32)
+          BITS: 32
+        Python35-64bit-full:
+          PYTHON_VERSION: '3.5'
+          PYTHON_ARCH: 'x64'
+          TEST_MODE: full
+          OPENBLAS: $(OPENBLAS_64)
+          BITS: 64
+        Python36-64bit-full:
+          PYTHON_VERSION: '3.6'
+          PYTHON_ARCH: 'x64'
+          TEST_MODE: full
+          OPENBLAS: $(OPENBLAS_64)
+          BITS: 64
+        Python37-64bit-full:
+          PYTHON_VERSION: '3.7'
+          PYTHON_ARCH: 'x64'
+          TEST_MODE: full
+          OPENBLAS: $(OPENBLAS_64)
+          BITS: 64
+  steps:
+  - task: UsePythonVersion@0
+    inputs:
+      versionSpec: $(PYTHON_VERSION)
+      addToPath: true
+      architecture: $(PYTHON_ARCH)
+  - script: python -m pip install --upgrade pip setuptools wheel
+    displayName: 'Install tools'
+  - powershell: |
+      $wc = New-Object net.webclient;
+      $wc.Downloadfile("$(OPENBLAS)", "openblas.zip")
+      $tmpdir = New-TemporaryFile | %{ rm $_; mkdir $_ }
+      Expand-Archive "openblas.zip" $tmpdir
+      $pyversion = python -c "from __future__ import print_function; import sys; print(sys.version.split()[0])"
+      Write-Host "Python Version: $pyversion"
+      $target = "C:\\hostedtoolcache\\windows\\Python\\$pyversion\\$(PYTHON_ARCH)\\lib\\openblas.a"
+      Write-Host "target path: $target"
+      cp $tmpdir\$(BITS)\lib\libopenblas_5f998ef_gcc7_1_0.a $target
+    displayName: 'Download / Install OpenBLAS'
+  - powershell: |
+      # NOTE: can probably (eventually) abstract this 
+      # upstream in Microsoft repo to support x86 natively
+      choco install -y mingw --forcex86 --force
+    displayName: 'Install 32-bit mingw for 32-bit builds'
+    condition: eq(variables['BITS'], 32)
+  - script: python -m pip install numpy cython==0.28.5 pytest pytest-timeout pytest-xdist pytest-env pytest-faulthandler Pillow mpmath matplotlib
+    displayName: 'Install dependencies'
+  - powershell: |
+      # need a version of NumPy distutils that can build
+      # with msvc + mingw-gfortran
+      $NumpyDir = $((python -c 'import os; import numpy; print(os.path.dirname(numpy.__file__))') | Out-String).Trim()
+      rm -r -Force "$NumpyDir\distutils"
+      $tmpdir = New-TemporaryFile | %{ rm $_; mkdir $_ }
+      git clone -q --depth=1 -b master https://github.com/numpy/numpy.git $tmpdir
+      mv $tmpdir\numpy\distutils $NumpyDir
+    displayName: 'Replace NumPy distutils'
+  - powershell: |
+      If ($(BITS) -eq 32) {
+          # 32-bit build requires careful adjustments
+          # until Microsoft has a switch we can use
+          # directly for i686 mingw
+          $env:NPY_DISTUTILS_APPEND_FLAGS = 1
+          $env:CFLAGS = "-m32"
+          $env:LDFLAGS = "-m32"
+          $env:PATH = "C:\\tools\\mingw32\\bin;" + $env:PATH
+          refreshenv
+      }
+
+      mkdir dist
+      pip wheel --no-build-isolation -v -v -v --wheel-dir=dist .
+      ls dist -r | Foreach-Object {
+          pip install $_.FullName
+      }
+    displayName: 'Build SciPy'
+  - script: python runtests.py -n --mode=$(TEST_MODE) -- -n auto -rsx --junitxml=junit/test-results.xml
+    displayName: 'Run SciPy Test Suite'
+  - task: PublishTestResults@2
+    inputs:
+      testResultsFiles: '**/test-*.xml'
+      testRunTitle: 'Publish test results for Python $(python.version)'

benchmarks/README.rst

@@ -4,19 +4,19 @@
 SciPy benchmarks
 ================
 
-Benchmarking Scipy with Airspeed Velocity.
+Benchmarking SciPy with Airspeed Velocity.
 
 
 Usage
 -----
 
 Airspeed Velocity manages building and Python virtualenvs by itself,
 unless told otherwise. Some of the benchmarking features in
-``runtests.py`` also tell ASV to use the Scipy compiled by
+``runtests.py`` also tell ASV to use the SciPy compiled by
 ``runtests.py``. To run the benchmarks, you do not need to install a
-development version of Scipy to your current Python environment.
+development version of SciPy to your current Python environment.
 
-Run a benchmark against currently checked out Scipy version (don't record the
+Run a benchmark against currently checked out SciPy version (don't record the
 result)::
 
     python runtests.py --bench sparse.Arithmetic
@@ -54,15 +54,15 @@ See `ASV documentation`_ for basics on how to write benchmarks.
 
 Some things to consider:
 
-- When importing things from Scipy on the top of the test files, do it as::
+- When importing things from SciPy on the top of the test files, do it as::
 
       try:
           from scipy.sparse.linalg import onenormest
       except ImportError:
           pass
 
   The benchmark files need to be importable also when benchmarking old versions
-  of Scipy. The benchmarks themselves don't need any guarding against missing
+  of SciPy. The benchmarks themselves don't need any guarding against missing
   features --- only the top-level imports.
 
 - Try to keep the runtime of the benchmark reasonable.

doc/API.rst.txt

@@ -1,4 +1,4 @@
-API - importing from Scipy
+API - importing from SciPy
 ==========================
 
 In Python the distinction between what is the public API of a library and what
@@ -25,12 +25,12 @@ rules for what is and isn't public in Python are:
           case; the presence of underscores do mark something as private, but
           the absence of underscores do not mark something as public.
 
-In Scipy there are modules whose names don't start with an underscore, but that
+In SciPy there are modules whose names don't start with an underscore, but that
 should be considered private.  To clarify which modules these are we define
-below what the public API is for Scipy, and give some recommendations for how
-to import modules/functions/objects from Scipy.
+below what the public API is for SciPy, and give some recommendations for how
+to import modules/functions/objects from SciPy.
 
-Guidelines for importing functions from Scipy
+Guidelines for importing functions from SciPy
 ---------------------------------------------
 
 The scipy namespace itself only contains functions imported from numpy.  These
@@ -77,7 +77,7 @@ API definition
 
 Every submodule listed below is public.  That means that these submodules are
 unlikely to be renamed or changed in an incompatible way, and if that is
-necessary a deprecation warning will be raised for one Scipy release before the
+necessary a deprecation warning will be raised for one SciPy release before the
 change is made.
 
 * `scipy.cluster`

doc/README.txt

@@ -7,7 +7,7 @@ The easy way to build the documentation is to run
 
     python setup.py build_sphinx
 
-This will first build Scipy in-place, and then generate documentation for it.
+This will first build SciPy in-place, and then generate documentation for it.
 
 Another way
 -----------
@@ -16,5 +16,5 @@ Another way
 2. Run ``make html`` or ``make dist``
 
 Note that ``make html`` builds the documentation for the currently installed
-version of Scipy, not the one corresponding to the source code here.
+version of SciPy, not the one corresponding to the source code here.