Merge branch 'master' into implement-numpy-implementation

.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

.lgtm.yml

@@ -16,3 +16,6 @@ extraction:
     index:
       build_command:
         - python3 setup.py build
+
+queries:
+  - include: py/file-not-closed

.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]>

.travis.yml

@@ -53,6 +53,11 @@ matrix:
     - python: 3.6
       env:
        - PYTHONOPTIMIZE=2
+       - BLAS=None
+       - LAPACK=None
+       - ATLAS=None
+       - NPY_BLAS_ORDER=mkl,blis,openblas,atlas,accelerate,blas
+       - NPY_LAPACK_ORDER=MKL,OPENBLAS,ATLAS,ACCELERATE,LAPACK
        - USE_ASV=1
     - python: 3.5
       dist: trusty # remove after April 2019

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'

doc/Makefile

@@ -10,10 +10,14 @@
 PYVER:=$(shell python3 -c 'from sys import version_info as v; print("{0}.{1}".format(v[0], v[1]))')
 PYTHON = python$(PYVER)
 
+NUMPYVER:=$(shell python3 -c "import numpy; print(numpy.version.git_revision[:10])")
+GITVER ?= $(shell cd ..; python3 -c "from setup import git_version; \
+				print(git_version()[:10])")
+
 # You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = LANG=C sphinx-build
-PAPER         =
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= LANG=C sphinx-build
+PAPER         ?=
 
 FILES=
 
@@ -24,7 +28,7 @@ ALLSPHINXOPTS   = -WT --keep-going -d build/doctrees $(PAPEROPT_$(PAPER)) \
   $(SPHINXOPTS) source
 
 .PHONY: help clean html web pickle htmlhelp latex changes linkcheck \
-        dist dist-build gitwash-update
+        dist dist-build gitwash-update version-check
 
 #------------------------------------------------------------------------------
 
@@ -44,6 +48,18 @@ help:
 clean:
 	-rm -rf build/* source/reference/generated
 
+version-check:
+ifeq "$(GITVER)" "Unknown"
+	# @echo sdist build with unlabeled sources
+else ifneq ($(NUMPYVER),$(GITVER))
+	@echo installed numpy $(NUMPYVER) != current repo git version \'$(GITVER)\'
+	@echo use '"make dist"' or '"GITVER=$(NUMPYVER) make $(MAKECMDGOALS) ..."'
+	@exit 1
+else
+	# for testing
+	# @echo installed numpy $(NUMPYVER) matches git version $(GITVER); exit 1
+endif
+
 gitwash-update:
 	rm -rf source/dev/gitwash
 	install -d source/dev/gitwash
@@ -119,7 +135,7 @@ build/generate-stamp: $(wildcard source/reference/*.rst)
 	mkdir -p build
 	touch build/generate-stamp
 
-html: generate
+html: generate version-check
 	mkdir -p build/html build/doctrees
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) build/html $(FILES)
 	$(PYTHON) postprocess.py html build/html/*.html
@@ -132,7 +148,7 @@ html-scipyorg:
 	@echo
 	@echo "Build finished. The HTML pages are in build/html."
 
-pickle: generate
+pickle: generate version-check
 	mkdir -p build/pickle build/doctrees
 	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) build/pickle $(FILES)
 	@echo
@@ -142,7 +158,7 @@ pickle: generate
 
 web: pickle
 
-htmlhelp: generate
+htmlhelp: generate version-check
 	mkdir -p build/htmlhelp build/doctrees
 	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) build/htmlhelp $(FILES)
 	@echo
@@ -153,11 +169,11 @@ htmlhelp-build: htmlhelp build/htmlhelp/numpy.chm
 %.chm: %.hhp
 	-hhc.exe $^
 
-qthelp: generate
+qthelp: generate version-check
 	mkdir -p build/qthelp build/doctrees
 	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) build/qthelp $(FILES)
 
-latex: generate
+latex: generate version-check
 	mkdir -p build/latex build/doctrees
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) build/latex $(FILES)
 	$(PYTHON) postprocess.py tex build/latex/*.tex
@@ -167,18 +183,18 @@ latex: generate
 	@echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
 	      "run these through (pdf)latex."
 
-coverage: build
+coverage: build version-check
 	mkdir -p build/coverage build/doctrees
 	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) build/coverage $(FILES)
 	@echo "Coverage finished; see c.txt and python.txt in build/coverage"
 
-changes: generate
+changes: generate version-check
 	mkdir -p build/changes build/doctrees
 	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) build/changes $(FILES)
 	@echo
 	@echo "The overview file is in build/changes."
 
-linkcheck: generate
+linkcheck: generate version-check
 	mkdir -p build/linkcheck build/doctrees
 	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) build/linkcheck $(FILES)
 	@echo