Merge branch 'master' into lijunzh-open_memmap_docs

* master: (25 commits)
  BUG: fix unravel_index when dimension is greater than 'intp'
  MANT: refactor unravel_index for code repetition (numpy#13446)
  BLD, TST: implicit func errors
  DOC: document existance of linalg backends
  BLD: streamlined library names in site.cfg sections (numpy#13157)
  MAINT: fixed typo 'wtihout' from numpy/core/shape_base.py
  BUG: fixing bugs in AVX exp/log while handling special value floats (numpy#13415)
  update sequence
  Add analysis check
  BUG: blindly add TypeError to accepted exceptions
  MAINT: fixed several PYTHONOPTIMIZE=2 failures
  BUG: fixed PYTHONOPTIMIZE run
  MAINT: fixed typo 'Mismacth' from numpy.core.setup_common.py
  MAINT: fixed last issues and questions according to numpy#13132
  MAINT: improve efficiency of pad by avoiding use of apply_along_axis
  DOC: dimension sizes are non-negative, not positive
  BUILD, BUG: fix from review, fix bug in git_version
  MAINT: mention 'make dist' in error messsage
  BUILD: allow version-check to pass if GITVER is Unknown (sdist build)
  BUILD: fail documentation build if numpy version does not match
  ...

.lgtm.yml

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

.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

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

doc/source/reference/arrays.ndarray.rst

@@ -9,7 +9,7 @@ The N-dimensional array (:class:`ndarray`)
 An :class:`ndarray` is a (usually fixed-size) multidimensional
 container of items of the same type and size. The number of dimensions
 and items in an array is defined by its :attr:`shape <ndarray.shape>`,
-which is a :class:`tuple` of *N* positive integers that specify the
+which is a :class:`tuple` of *N* non-negative integers that specify the
 sizes of each dimension. The type of items in the array is specified by
 a separate :ref:`data-type object (dtype) <arrays.dtypes>`, one of which
 is associated with each ndarray.

doc/source/reference/routines.linalg.rst

@@ -5,6 +5,19 @@
 Linear algebra (:mod:`numpy.linalg`)
 ************************************
 
+The NumPy linear algebra functions rely on BLAS and LAPACK to provide efficient
+low level implementations of standard linear algebra algorithms. Those
+libraries may be provided by NumPy itself using C versions of a subset of their
+reference implementations but, when possible, highly optimized libraries that
+take advantage of specialized processor functionality are preferred. Examples
+of such libraries are OpenBLAS_, MKL (TM), and ATLAS. Because those libraries
+are multithreaded and processor dependent, environmental variables and external
+packages such as threadpoolctl_ may be needed to control the number of threads
+or specify the processor architecture.
+
+.. _OpenBLAS: https://www.openblas.net/
+.. _threadpoolctl: https://github.com/joblib/threadpoolctl
+
 .. currentmodule:: numpy
 
 Matrix and vector products

doc/source/user/building.rst

@@ -118,12 +118,70 @@ means that g77 has been used. If libgfortran.so is a dependency, gfortran
 has been used. If both are dependencies, this means both have been used, which
 is almost always a very bad idea.
 
+Accelerated BLAS/LAPACK libraries
+---------------------------------
+
+NumPy searches for optimized linear algebra libraries such as BLAS and LAPACK.
+There are specific orders for searching these libraries, as described below.
+
+BLAS
+~~~~
+
+The default order for the libraries are:
+
+1. MKL
+2. BLIS
+3. OpenBLAS
+4. ATLAS
+5. Accelerate (MacOS)
+6. BLAS (NetLIB)
+
+
+If you wish to build against OpenBLAS but you also have BLIS available one
+may predefine the order of searching via the environment variable
+``NPY_BLAS_ORDER`` which is a comma-separated list of the above names which
+is used to determine what to search for, for instance::
+
+      NPY_BLAS_ORDER=ATLAS,blis,openblas,MKL python setup.py build
+
+will prefer to use ATLAS, then BLIS, then OpenBLAS and as a last resort MKL.
+If neither of these exists the build will fail (names are compared
+lower case).
+
+LAPACK
+~~~~~~
+
+The default order for the libraries are:
+
+1. MKL
+2. OpenBLAS
+3. ATLAS
+4. Accelerate (MacOS)
+5. LAPACK (NetLIB)
+
+
+If you wish to build against OpenBLAS but you also have MKL available one
+may predefine the order of searching via the environment variable
+``NPY_LAPACK_ORDER`` which is a comma-separated list of the above names,
+for instance::
+
+      NPY_LAPACK_ORDER=ATLAS,openblas,MKL python setup.py build
+
+will prefer to use ATLAS, then OpenBLAS and as a last resort MKL.
+If neither of these exists the build will fail (names are compared
+lower case).
+
+
 Disabling ATLAS and other accelerated libraries
------------------------------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Usage of ATLAS and other accelerated libraries in NumPy can be disabled
 via::
 
+    NPY_BLAS_ORDER= NPY_LAPACK_ORDER= python setup.py build
+
+or::
+
     BLAS=None LAPACK=None ATLAS=None python setup.py build
 
 

numpy/core/setup_common.py

@@ -81,7 +81,7 @@ def get_api_versions(apiversion, codegen_dir):
     return curapi_hash, apis_hash[apiversion]
 
 def check_api_version(apiversion, codegen_dir):
-    """Emits a MismacthCAPIWarning if the C API version needs updating."""
+    """Emits a MismatchCAPIWarning if the C API version needs updating."""
     curapi_hash, api_hash = get_api_versions(apiversion, codegen_dir)
 
     # If different hash, it means that the api .txt files in

numpy/core/shape_base.py

@@ -832,7 +832,7 @@ def block(arrays):
 
 # Theses helper functions are mostly used for testing.
 # They allow us to write tests that directly call `_block_slicing`
-# or `_block_concatenate` wtihout blocking large arrays to forse the wisdom
+# or `_block_concatenate` without blocking large arrays to forse the wisdom
 # to trigger the desired path.
 def _block_setup(arrays):
     """