Merge branch 'master' of github.com:JuliaLang/julia

Conflicts:
	base/Makefile
	base/export.jl
	base/pkg.jl
	base/sysimg.jl
	src/ccall.cpp
	src/gf.c
	test/Makefile
	test/file.jl

.gitignore

@@ -23,5 +23,6 @@
 *.creator
 *.user
 *.orig
+*.swp
 
 /usr

.travis.yml

@@ -11,8 +11,8 @@ before_install:
  - sudo add-apt-repository ppa:staticfloat/julia-deps -y
  - sudo apt-get update -qq -y
  - sudo apt-get install gfortran llvm-3.1-dev libsuitesparse-dev libncurses5-dev libopenblas-dev libarpack2-dev libfftw3-dev libpcre3-dev libglpk-dev lighttpd libgmp-dev libunwind7-dev libreadline-dev -y
-script: make $BUILDOPTS PREFIX=/tmp/julia install
-after_script:
+script:
+ - make $BUILDOPTS PREFIX=/tmp/julia install
  - cd .. && mv julia julia2
  - cd /tmp/julia/share/julia/test && /tmp/julia/bin/julia runtests.jl all
  - cd - && mv julia2 julia

CONTRIBUTING.md

@@ -14,11 +14,13 @@ Hi! Thanks for checking out Julia. If you have questions or problems, the [Julia
 
 ## Submitting your contributions
 
+Julia now has a [package manager](https://github.com/JuliaLang/METADATA.jl). Most developers writing julia libraries are encouraged to provide them as a julia package. In case you are contributing to the core functionality or the base libraries, the process is as follows.
+
 The Julia team uses [GitHub issues](https://github.com/JuliaLang/julia/issues) to track and discuss problems, feature requests, and pull requests.
 
-You can make pull requests for incomplete features to get code review, in which case we have a convention of prefixing the pull request title with "RFC:" to indicate that the work is incomplete so it doesn't accidentally get merged into the master branch before it's ready.
+You can make pull requests for incomplete features to get code review. The convention is to prefix the pull request title with "WIP:" or "RFC:" as appropriate to indicate that the work is incomplete, so that it is not accidentally merged.
 
-Before submitting, make sure that all tests pass by running `make testall`. Even better, add your own tests for your change or feature to the test files in `test/`. If your contribution includes changes to Makefiles or external dependencies, make sure you can build Julia from a clean tree using `git clean -fdx` or equivalent (be careful – this command will delete any files lying around that aren't checked into git).
+Before submitting, make sure that all tests pass by running `make testall`. Add your own tests for the new functionality in `test/`. If your contribution includes changes to Makefiles or external dependencies, make sure you can build Julia from a clean tree using `git clean -fdx` or equivalent (be careful – this command will delete any files lying around that aren't checked into git). Make sure that [Travis](http:https://www.travis-ci.org) greenlights the pull request with a `Good to merge` message.
 
 *By contributing code to Julia, you are agreeing to release it under the [MIT License](https://github.com/JuliaLang/julia/tree/master/LICENSE.md).*
 
@@ -29,9 +31,14 @@ While getting familiar with Julia, remember to check out [the docs](http:https://docs.
 ## Resources
 
 * Julia
- - [Julia](http:https://julialang.org)
- - [Julia Manual and Library Guide](http:https://docs.julialang.org/en/latest/)
- - [Julia dev list](https://groups.google.com/forum/?fromgroups#!forum/julia-dev)
+ - **Homepage:** <http:https://julialang.org>
+ - **Mailing lists:** <http:https://julialang.org/mailing_lists>
+ - **IRC:** <http:https://webchat.freenode.net/?channels=julia>
+ - **Source code:** <https://github.com/JuliaLang/julia>
+ - **Git clone URL:** <git:https://github.com/JuliaLang/julia.git>
+ - **Documentation:** <http:https://julialang.org/manual/>
+* Design of Julia
+ - [Julia: A Fast Dynamic Language for Technical Computing](http:https://julialang.org/images/julia-dynamic-2012-tr.pdf)
 * Working with Types
  - [Some Type Patterns](https://github.com/JuliaLang/julia/wiki/Code-Patterns)
  - [The Type Hierarchy](https://github.com/JuliaLang/julia/wiki/Types-Hierarchy)

Make.inc

@@ -18,7 +18,7 @@ JL_PRIVATE_LIBDIR = lib/julia
 JL_LIBDIR = lib
 
 # If we're on debian, default to arch-dependent library dirs
-ifeq ($(USE_DEBIAN), 1)
+ifeq ($(MULTIARCH_INSTALL), 1)
 MULTIARCH = $(shell gcc -print-multiarch)
 JL_PRIVATE_LIBDIR = lib/$(MULTIARCH)/julia
 JL_LIBDIR = lib/$(MULTIARCH)/

Makefile

@@ -4,7 +4,7 @@ include $(JULIAHOME)/Make.inc
 all: default
 default: release
 
-DIRS = $(BUILD)/bin $(BUILD)/$(JL_LIBDIR) $(BUILD)/$(JL_PRIVATE_LIBDIR) $(BUILD)/share/julia
+DIRS = $(BUILD)/bin $(BUILD)/lib $(BUILD)/$(JL_PRIVATE_LIBDIR) $(BUILD)/share/julia
 
 $(foreach dir,$(DIRS),$(eval $(call dir_target,$(dir))))
 $(foreach link,extras base test doc examples ui,$(eval $(call symlink_target,$(link),$(BUILD)/share/julia)))
@@ -17,7 +17,7 @@ endif
 debug release: | $(DIRS) $(BUILD)/share/julia/extras $(BUILD)/share/julia/base $(BUILD)/share/julia/test $(BUILD)/share/julia/doc $(BUILD)/share/julia/examples $(BUILD)/share/julia/ui
  @$(MAKEs) julia-$@
  @export JL_PRIVATE_LIBDIR=$(JL_PRIVATE_LIBDIR) && \
- $(MAKEs) JULIA_EXECUTABLE=$(JULIA_EXECUTABLE_$@) $(BUILD)/$(JL_PRIVATE_LIBDIR)/sys.ji
+ $(MAKEs) LD_LIBRARY_PATH=$(BUILD)/lib JULIA_EXECUTABLE=$(JULIA_EXECUTABLE_$@) $(BUILD)/$(JL_PRIVATE_LIBDIR)/sys.ji
 
 julia-debug julia-release:
  @-git submodule update
@@ -47,17 +47,16 @@ JL_PRIVATE_LIBS = amd arpack cholmod colamd fftw3 fftw3f fftw3_threads \
 
 PREFIX ?= julia-$(JULIA_COMMIT)
 install: release
- @$(MAKEs) -C test/unicode
  @for subdir in "sbin" "bin" "etc" $(JL_LIBDIR) $(JL_PRIVATE_LIBDIR) "share/julia" ; do \
  mkdir -p $(PREFIX)/$$subdir ; \
  done
  cp $(BUILD)/bin/*julia* $(PREFIX)/bin
- cd $(PREFIX)/bin && ln -s julia-release-$(DEFAULT_REPL) julia
+ cd $(PREFIX)/bin && ln -sf julia-release-$(DEFAULT_REPL) julia
  -for suffix in $(JL_LIBS) ; do \
- cp -a $(BUILD)/lib/lib$${suffix}.* $(PREFIX)/$(JL_PRIVATE_LIBDIR) ; \
+ cp -a $(BUILD)/$(JL_LIBDIR)/lib$${suffix}*.$(SHLIB_EXT)* $(PREFIX)/$(JL_PRIVATE_LIBDIR) ; \
  done
  -for suffix in $(JL_PRIVATE_LIBS) ; do \
- cp -a $(BUILD)/lib/lib$${suffix}.* $(PREFIX)/$(JL_PRIVATE_LIBDIR) ; \
+ cp -a $(BUILD)/lib/lib$${suffix}*.$(SHLIB_EXT)* $(PREFIX)/$(JL_PRIVATE_LIBDIR) ; \
  done
  # Copy system image
 ifneq ($(OS), WINNT)
@@ -79,7 +78,7 @@ dist:
 # -$(MAKE) -C deps clean-openblas
  $(MAKE) install OPENBLAS_DYNAMIC_ARCH=1
 ifeq ($(OS), Darwin)
- -./contrib/fixup-libgfortran.sh $(PREFIX)/$(JL_LIBDIR) $(PREFIX)/$(JL_PRIVATE_LIBDIR)
+ -./contrib/fixup-libgfortran.sh $(PREFIX)/$(JL_PRIVATE_LIBDIR)
 endif
  tar zcvf julia-$(JULIA_COMMIT)-$(OS)-$(ARCH).tar.gz julia-$(JULIA_COMMIT)
  rm -fr julia-$(JULIA_COMMIT)
@@ -92,7 +91,6 @@ clean: | $(CLEAN_TARGETS)
  @$(MAKE) -C extras clean
  @$(MAKE) -C src clean
  @$(MAKE) -C ui clean
- @$(MAKE) -C test/unicode clean
  @for buildtype in "release" "debug" ; do \
  for repltype in "basic" "readline"; do \
  rm -f julia-$${buildtype}-$${repltype}; \

README.md

@@ -5,7 +5,7 @@
   (_) | (_) (_) | A fresh approach to technical computing
   _ _ _| |_ __ _ |
   | | | | | | |/ _` | | http:https://julialang.org
-  | | |_| | | | (_| | | julia-dev@googlegroups.com
+  | | |_| | | | (_| | | julia-users@googlegroups.com
   _/ |\__'_|_|_|\__'_| | #julia on freenode
  |__/ |
 
@@ -21,7 +21,8 @@ This is the GitHub repository of Julia source code, including instructions for c
 
 - **Homepage:** <http:https://julialang.org>
 - **Binaries:** <https://github.com/JuliaLang/julia/downloads>
-- **Mailing list:** <http:https://groups.google.com/group/julia-users/>
+- **Packages:** <https://github.com/JuliaLang/METADATA.jl>
+- **Mailing lists:** <http:https://julialang.org/mailing_lists>
 - **IRC:** <http:https://webchat.freenode.net/?channels=julia>
 - **Source code:** <https://github.com/JuliaLang/julia>
 - **Git clone URL:** <git:https://github.com/JuliaLang/julia.git>

base/.gitignore

@@ -1,5 +1,4 @@
 /pcre_h.jl
 /errno_h.jl
-os_detect.jl
 /build_h.jl
 /file_constants.jl

base/Makefile

@@ -3,28 +3,24 @@ include ../Make.inc
 
 PCRE_CONST = 0x[0-9a-fA-F]+|[-+]?\s*[0-9]+
 
-all: pcre_h.jl errno_h.jl os_detect.jl build_h.jl file_constants.jl
+all: pcre_h.jl errno_h.jl build_h.jl file_constants.jl
 
 pcre_h.jl:
  $(QUIET_PERL) $(CC) -E -dM $(shell $(PCRE_CONFIG) --prefix)/include/pcre.h | perl -nle '/^\s*#define\s+PCRE_(\w*)\s*\(?($(PCRE_CONST))\)?\s*$$/ and print "const $$1 = int32($$2)"' | sort > $@
 
 errno_h.jl:
  $(QUIET_PERL) echo '#include "errno.h"' | $(CC) -E -dM - | perl -nle 'print "const $$1 = int32($$2)" if /^#define\s+(E\w+)\s+(\d+)\s*$$/' | sort > $@
 
-os_detect.jl: ../src/os_detect.h
- $(QUIET_PERL) $(CC) -E -P -DJULIA ../src/os_detect.h | perl -p -e 's/\\n/\n/g' > $@
-
 file_constants.jl: ../src/file_constants.h
  $(QUIET_PERL) ${CC} -E -P -DJULIA ../src/file_constants.h | perl -nle 'print "$$1" if /^(\s*const\s+[A-z_]+\s+=\s+[0-9A-z_]+\s*)$$/' > $@
 
-
-build_h.jl: ../Make.inc
- @echo "libblas_name = \"$(LIBBLASNAME)\"" > $@
- @echo "liblapack_name = \"$(LIBLAPACKNAME)\"" >> $@
+build_h.jl: ../Make.inc ../src/os_detect.h
+ $(QUIET_PERL) $(CC) -E -P -DJULIA ../src/os_detect.h | grep OS_NAME > $@
+ @echo "const libblas_name = \"$(LIBBLASNAME)\"" >> $@
+ @echo "const liblapack_name = \"$(LIBLAPACKNAME)\"" >> $@
 
 clean:
  rm -f *# *~
  rm -f pcre_h.jl
  rm -f errno_h.jl
- rm -f os_detect.jl
  rm -f build_h.jl

base/abstractarray.jl

@@ -53,6 +53,75 @@ function trailingsize(A, n)
  return s
 end
 
+## Bounds checking ##
+function check_bounds(sz::Int, I::Integer)
+ if I < 1 || I > sz
+ throw(BoundsError())
+ end
+end
+
+function check_bounds(sz::Int, I::AbstractVector{Bool})
+ if length(I) > sz
+ throw(BoundsError())
+ end
+end
+
+function check_bounds{T<:Integer}(sz::Int, I::Ranges{T})
+ if min(I) < 1 || max(I) > sz
+ throw(BoundsError())
+ end
+end
+
+function check_bounds{T <: Integer}(sz::Int, I::AbstractVector{T})
+ for i in I
+ if i < 1 || i > sz
+ throw(BoundsError())
+ end
+ end
+end
+
+function check_bounds(A::AbstractVector, I::AbstractVector{Bool})
+ if !isequal(size(A), size(I)) throw(BoundsError()) end
+end
+
+function check_bounds(A::AbstractArray, I::AbstractVector{Bool})
+ if !isequal(size(A), size(I)) throw(BoundsError()) end
+end
+
+function check_bounds(A::AbstractArray, I::AbstractArray{Bool})
+ if !isequal(size(A), size(I)) throw(BoundsError()) end
+end
+
+check_bounds(A::AbstractVector, I::Indices) = check_bounds(length(A), I)
+
+function check_bounds(A::AbstractMatrix, I::Indices, J::Indices)
+ check_bounds(size(A,1), I)
+ check_bounds(size(A,2), J)
+end
+
+function check_bounds(A::AbstractArray, I::Indices, J::Indices)
+ check_bounds(size(A,1), I)
+ sz = size(A,2)
+ for i = 3:ndims(A)
+ sz *= size(A, i) # TODO: sync. with decision on issue #1030
+ end
+ check_bounds(sz, J)
+end
+
+function check_bounds(A::AbstractArray, I::Indices...)
+ n = length(I)
+ if n > 0
+ for dim = 1:(n-1)
+ check_bounds(size(A,dim), I[dim])
+ end
+ sz = size(A,n)
+ for i = n+1:ndims(A)
+ sz *= size(A,i) # TODO: sync. with decision on issue #1030
+ end
+ check_bounds(sz, I[n])
+ end
+end
+
 ## Constructors ##
 
 # default arguments to similar()
@@ -810,7 +879,7 @@ function (!=)(A::AbstractArray, B::AbstractArray)
 end
 
 (<)(A::AbstractArray, B::AbstractArray) =
- error("< not defined for arrays. Try .< or isless.")
+ error("Not defined. To compare arrays, try .< .> .<= .>= or isless.")
 
 (==)(A::AbstractArray, B) = error("Not defined. Try .== or isequal.")
 
@@ -858,6 +927,48 @@ for (f, op) = ((:cumsum, :+), (:cumprod, :*) )
  @eval ($f)(A::AbstractArray) = ($f)(A, 1)
 end
 
+for (f, op) = ((:cummin, :min), (:cummax, :max))
+ @eval function ($f)(v::AbstractVector)
+ n = length(v)
+ cur_val = v[1]
+ res = similar(v, n)
+ res[1] = cur_val
+ for i in 2:n
+ cur_val = ($op)(v[i], cur_val)
+ res[i] = cur_val
+ end
+ return res
+ end
+
+ @eval function ($f)(A::AbstractArray, axis::Integer)
+ dimsA = size(A)
+ ndimsA = ndims(A)
+ axis_size = dimsA[axis]
+ axis_stride = 1
+ for i = 1:(axis-1)
+ axis_stride *= size(A,i)
+ end
+
+ if axis_size <= 1
+ return A
+ end
+
+ B = similar(A)
+
+ for i = 1:length(A)
+ if div(i-1, axis_stride) % axis_size == 0
+ B[i] = A[i]
+ else
+ B[i] = ($op)(A[i], B[i-axis_stride])
+ end
+ end
+
+ return B
+ end
+
+ @eval ($f)(A::AbstractArray) = ($f)(A, 1)
+end
+
 ## ipermute in terms of permute ##
 
 function ipermute(A::AbstractArray,perm)