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

.gitignore

@@ -4,7 +4,7 @@
 
 /*.tar.gz
 /tmp
-/dist
+/dist*
 
 /julia
 /julia-*

.gitmodules

@@ -7,3 +7,6 @@
 [submodule "deps/Rmath"]
  path = deps/Rmath
  url = git:https://github.com/JuliaLang/Rmath.git
+[submodule "doc/juliadoc"]
+ path = doc/juliadoc
+ url = git:https://github.com/JuliaLang/JuliaDoc.git

.mailmap

@@ -100,3 +100,7 @@ Blake Johnson <[email protected]> <[email protected]>
 
 Marcus Silva <[email protected]> <[email protected]> 
 Marcus Silva <[email protected]> <[email protected]>
+
+Amit Murthy <[email protected]> <[email protected]>
+
+Tanmay Mohapatra <[email protected]> <[email protected]>

.travis.yml

@@ -4,6 +4,10 @@ compiler:
  - gcc
 notifications:
  email: false
+ webhooks:
+ urls:
+ - https://128.52.160.154/travis-hook
+ on_failure: never
 before_install:
  - BUILDOPTS="LLVM_CONFIG=llvm-config-3.2 USE_QUIET=0 USE_BLAS64=0"; for lib in LLVM ZLIB SUITESPARSE ARPACK BLAS FFTW LAPACK GMP MPFR PCRE LIBUNWIND READLINE GRISU OPENLIBM RMATH; do export BUILDOPTS="$BUILDOPTS USE_SYSTEM_$lib=1"; done
  - sudo apt-get update -qq -y

FAQ.md

@@ -0,0 +1,78 @@
+# Frequently-asked questions
+
+### Sessions and the REPL
+
+#### How do I delete an object in memory?
+
+Julia does not have an analog of MATLAB's `clear` function; once a name is defined in a Julia session (technically, in module `Main`), it is always present.
+
+If memory usage is your concern, you can always replace objects with ones that consume less memory.
+For example, if `A` is a gigabyte-sized array that you no longer need, you can free the memory with `A = 0`.
+The memory will be released the next time the garbage collector runs; you can force this to happen with `gc()`.
+
+#### How can I modify the declaration of a type/immutable in my session?
+
+Perhaps you've defined a type and and then realize you need to add a new field.
+If you try this at the REPL, you get the error
+```
+ERROR: invalid redefinition of constant MyType
+```
+Types in module `Main` cannot be redefined.
+
+While this can be inconvenient when you are developing new code, there's an excellent workaround.
+Modules can be replaced by redefining them, and so if you wrap all your new code inside a module you can redefine types and constants.
+You can't import the type names into `Main` and then expect to be able to redefine them there, but you can use the module name to resolve the scope.
+In other words, while developing you might use a workflow something like this:
+```julia
+include("mynewcode.jl") # this defines a module MyModule
+obj1 = MyModule.ObjConstructor(a, b)
+obj2 = MyModule.somefunction(obj1)
+# Got an error. Change something in "mynewcode.jl"
+include("mynewcode.jl") # reload the module
+obj1 = MyModule.ObjConstructor(a, b) # old objects are no longer valid, must reconstruct
+obj2 = MyModule.somefunction(obj1) # this time it worked!
+obj3 = MyModule.someotherfunction(obj2, c)
+...
+```
+
+### Developing Julia
+
+#### How do I debug julia's C code? (running the julia REPL from within a debugger like gdb)
+
+First, you should build the debug version of julia with `make debug`.
+Below, lines starting with `(gdb)` mean things you should type at the gdb prompt.
+
+##### From the shell
+
+The main challenge is that Julia and gdb each need to have their own terminal, so you can interact with them both.
+The first time you do this, you'll need to define a script, here called `oterm`, containing the following lines:
+```
+ps
+sleep 600000
+```
+Make it executable with `chmod +x oterm`.
+
+Now:
+
+- From a shell (called shell 1), type `xterm -e oterm &`. You'll see a new window pop up; this will be called terminal 2.
+- From within shell 1, `gdb julia-debug-basic`. You can find this executable within `julia/usr/bin`.
+- From within shell 1, `(gdb) tty /dev/pts/#` where `#` is the number shown after `pts/` in terminal 2.
+- From within shell 1, `(gdb) run`
+- From within terminal 2, issue any preparatory commands in Julia that you need to get to the step you want to debug
+- From within shell 1, hit Ctrl-C
+- From within shell 1, insert your breakpoint, e.g., `(gdb) b codegen.cpp:2244`
+- From within shell 1, `(gdb) c` to resume execution of julia
+- From within terminal 2, issue the command that you want to debug. Shell 1 will stop at your breakpoint.
+
+
+##### Within emacs
+
+- `M-x gdb`, then enter `julia-debug-basic` (this is easiest from within julia/usr/bin, or you can specify the full path)
+- `(gdb) run`
+- Now you'll see the Julia prompt. Run any commands in Julia you need to get to the step you want to debug.
+- Under emacs' "Signals" menu choose BREAK---this will return you to the `(gdb)` prompt
+- Set a breakpoint, e.g.,
+`(gdb) b codegen.cpp:2244`
+- Go back to the Julia prompt via
+`(gdb) c`
+- Execute the Julia command you want to see running.

Make.inc

@@ -1,5 +1,9 @@
 # -*- mode: makefile-gmake -*-
 
+USE_MKL = 0
+#MKLROOT = /opt/intel/composerxe/mkl/
+MKLLIB = $(MKLROOT)/lib/intel64
+
 # include twice to pickup user definitions
 ifeq (exists, $(shell [ -e $(JULIAHOME)/Make.user ] && echo exists ))
 include $(JULIAHOME)/Make.user 
@@ -29,7 +33,9 @@ endif
 
 ifeq ($(XC_HOST),)
 CROSS_COMPILE=
+HOSTCC = $(CC)
 else
+HOSTCC = gcc
 override OPENBLAS_DYNAMIC_ARCH = 1
 override CROSS_COMPILE=$(XC_HOST)-
 ifneq (,$(findstring mingw,$(XC_HOST)))
@@ -56,7 +62,7 @@ endif
 
 ifeq ($(OS), WINNT)
 fPIC = 
-PATH := ${PATH}:${BUILD}/lib:${BUILD}/lib/julia
+PATH := ${PATH}:${BUILD}/lib:${BUILD}/lib/julia:/c/Program Files/7-zip
 EXE = .exe
 else
 fPIC = -fPIC
@@ -90,7 +96,6 @@ endif
 endif
 
 ifeq ($(USEGCC),1)
-HOSTCC = gcc
 CC = $(CROSS_COMPILE)gcc
 CXX = $(CROSS_COMPILE)g++
 JCFLAGS = -std=gnu99 -pipe $(fPIC) -fno-strict-aliasing -D_FILE_OFFSET_BITS=64
@@ -100,7 +105,6 @@ SHIPFLAGS = -O3 -falign-functions
 endif
 
 ifeq ($(USECLANG),1)
-HOSTCC = clang
 CC = $(CROSS_COMPILE)clang
 CXX = $(CROSS_COMPILE)clang++
 JCFLAGS = -pipe $(fPIC) -fno-strict-aliasing -D_FILE_OFFSET_BITS=64
@@ -114,26 +118,6 @@ JCFLAGS += -D_LARGEFILE_SOURCE -D_DARWIN_USE_64_BIT_INODE=1
 endif
 endif
 
-BUILD_MACHINE := $(shell $(HOSTCC) -dumpmachine)
-ARCH := $(shell $(CC) -dumpmachine | sed "s/\([^-]*\).*$$/\1/")
-ifeq ($(ARCH),mingw32)
-$(error "the mingw32 compiler you are using fails the openblas testsuite. please see the README.windows document for a replacement")
-endif
-ifeq ($(OS),Darwin)
-ifeq ($(OS),$(BUILD_OS))
-## Mac is a nifty dual-arch platform (or was until 10.8), so we detect the currently running OS arch instead
-## of the compiler "-dumpmachine" result, like I believe the compiler does, and make a substitution
-ARCH := $(shell uname -m)
-BUILD_MACHINE := $(ARCH)$(shell echo $(BUILD_MACHINE) | sed "s/[^-]*\(.*\)$$/\1/")
-endif
-endif
-
-ifeq ($(USEGCC),1)
-ifneq ($(ARCH), ppc64)
- SHIPFLAGS += -momit-leaf-frame-pointer
-endif
-endif
-
 FC = $(CROSS_COMPILE)gfortran
 JFFLAGS = -O2 $(fPIC)
 CPP = $(CC) -E
@@ -174,15 +158,34 @@ ifeq (exists, $(shell [ -e $(JULIAHOME)/Make.user ] && echo exists ))
 include $(JULIAHOME)/Make.user
 endif
 
-# Snow Leopard specific configuration
-ifeq ($(OS), Darwin)
-ifeq ($(OSXVER), 10.6)
-USE_SYSTEM_LIBM=1
-USE_SYSTEM_BLAS=1
+# ===========================================================================
+
+BUILD_MACHINE := $(shell $(HOSTCC) -dumpmachine)
+ARCH := $(shell $(CC) -dumpmachine | sed "s/\([^-]*\).*$$/\1/")
+ifeq ($(ARCH),mingw32)
+$(error "the mingw32 compiler you are using fails the openblas testsuite. please see the README.windows document for a replacement")
+endif
+ifeq ($(BUILD_OS),Darwin)
+## Mac is a rather amazing 64-bit user-space on 32-bit kernel architecture, so to determine arch we detect
+## the capabilities of the hardware, rather than the compiler or kernel, and make a substitution
+ifeq ($(ARCH),x86_64)
+ARCH = i686
+else ifeq ($(ARCH),i386)
+ARCH = i686
+endif
+ifeq ($(ARCH),i686)
+ifeq ($(shell sysctl -n hw.cpu64bit_capable),1)
+ARCH = x86_64
+endif
+BUILD_MACHINE := $(ARCH)$(shell echo $(BUILD_MACHINE) | sed "s/[^-]*\(.*\)$$/\1/")
 endif
 endif
 
-# ===========================================================================
+ifeq ($(USEGCC),1)
+ifneq ($(ARCH), ppc64)
+ SHIPFLAGS += -momit-leaf-frame-pointer
+endif
+endif
 
 ifeq ($(USE_SYSTEM_LIBUNWIND), 1)
 LIBUNWIND=-lunwind-generic -lunwind
@@ -223,8 +226,8 @@ ifeq ($(USE_SYSTEM_BLAS), 1)
 ifeq ($(OS), Darwin)
 USE_BLAS64 = 0
 USE_SYSTEM_LAPACK = 0
-LIBBLAS = -framework vecLib -lBLAS
-LIBBLASNAME = libBLAS
+LIBBLAS = -L$(BUILD)/lib -lgfortblas
+LIBBLASNAME = libgfortblas
 else
 LIBBLAS = -lblas
 LIBBLASNAME = libblas
@@ -244,7 +247,7 @@ ifeq ($(USE_SYSTEM_LAPACK), 1)
 LIBLAPACK = -llapack
 LIBLAPACKNAME = liblapack
 else
-LIBLAPACK = -L$(BUILD)/lib -llapack
+LIBLAPACK = -L$(BUILD)/lib -llapack $(LIBBLAS)
 LIBLAPACKNAME = liblapack
 endif
 endif
@@ -348,22 +351,21 @@ endif
 
 # MKL
 
-USE_MKL = 0
-MKLLIB = $$MKLROOT/lib/intel64
-
 ifeq ($(USE_MKL), 1)
-USE_BLAS64 = 0
 USE_SYSTEM_BLAS=1
 USE_SYSTEM_LAPACK=1
-LIBBLAS = -L$(MKLLIB) -lmkl_rt
-LIBLAPACK = -L$(MKLLIB) -lmkl_rt
 LIBBLASNAME = libmkl_rt
 LIBLAPACKNAME = libmkl_rt
+MKL_LDFLAGS = -L$(MKLLIB) -lmkl_rt
 ifneq ($(strip $(MKLLIB)),)
  ifeq ($(OS), Linux)
- RPATH += -Wl,-rpath,$(MKLLIB)
+ RPATH_MKL = -Wl,-rpath,$(MKLLIB)
+ RPATH += $(RPATH_MKL)
+ MKL_LDFLAGS += $(RPATH_MKL)
  endif
 endif
+LIBBLAS = $(MKL_LDFLAGS)
+LIBLAPACK = $(MKL_LDFLAGS)
 endif
 
 # ATLAS

Makefile

@@ -13,17 +13,17 @@ VERSDIR = v`cut -d. -f1-2 < VERSION`
 all: default
 default: release
 
-DIRS = $(BUILD)/bin $(BUILD)/lib $(BUILD)/$(JL_PRIVATE_LIBDIR) $(BUILD)/share/julia
+DIRS = $(BUILD)/bin $(BUILD)/lib $(BUILD)/$(JL_PRIVATE_LIBDIR) $(BUILD)/share/julia $(BUILD)/share/julia/man/man1
 
 $(foreach dir,$(DIRS),$(eval $(call dir_target,$(dir))))
-$(foreach link,extras base test doc examples,$(eval $(call symlink_target,$(link),$(BUILD)/share/julia)))
+$(foreach link,base test doc examples,$(eval $(call symlink_target,$(link),$(BUILD)/share/julia)))
 
 QUIET_MAKE =
 ifeq ($(USE_QUIET), 1)
 QUIET_MAKE = -s
 endif
 
-debug release: | $(DIRS) $(BUILD)/share/julia/extras $(BUILD)/share/julia/base $(BUILD)/share/julia/test $(BUILD)/share/julia/doc $(BUILD)/share/julia/examples
+debug release: | $(DIRS) $(BUILD)/share/julia/base $(BUILD)/share/julia/test $(BUILD)/share/julia/doc $(BUILD)/share/julia/examples
  @$(MAKE) $(QUIET_MAKE) julia-$@
  @export JL_PRIVATE_LIBDIR=$(JL_PRIVATE_LIBDIR) && \
  $(MAKE) $(QUIET_MAKE) LD_LIBRARY_PATH=$(BUILD)/lib:$(LD_LIBRARY_PATH) JULIA_EXECUTABLE="$(JULIA_EXECUTABLE_$@)" $(BUILD)/$(JL_PRIVATE_LIBDIR)/sys.ji
@@ -44,12 +44,16 @@ endif
 $(BUILD)/share/julia/helpdb.jl: doc/helpdb.jl | $(BUILD)/share/julia
  @cp $< $@
 
+$(BUILD)/share/man/man1/julia.1: doc/man/julia.1 | $(BUILD)/share/julia
+ @mkdir -p $(BUILD)/share/man/man1
+ @cp $< $@
+
 COMMIT:
  @#this is a .PHONY target so that it will always run
  echo `git rev-parse --short HEAD`-$(OS)-$(ARCH) \(`date +"%Y-%m-%d %H:%M:%S"`\) > COMMIT
 
 # use sys.ji if it exists, otherwise run two stages
-$(BUILD)/$(JL_PRIVATE_LIBDIR)/sys.ji: VERSION base/*.jl base/pkg/*.jl base/linalg/*.jl $(BUILD)/share/julia/helpdb.jl
+$(BUILD)/$(JL_PRIVATE_LIBDIR)/sys.ji: VERSION base/*.jl base/pkg/*.jl base/linalg/*.jl base/sparse/*.jl $(BUILD)/share/julia/helpdb.jl $(BUILD)/share/man/man1/julia.1
  @$(MAKE) $(QUIET_MAKE) COMMIT
  $(QUIET_JULIA) cd base && \
  (test -f $(BUILD)/$(JL_PRIVATE_LIBDIR)/sys.ji || $(call spawn,$(JULIA_EXECUTABLE)) -bf sysimg.jl) && $(call spawn,$(JULIA_EXECUTABLE)) -f sysimg.jl || echo "*** This error is usually fixed by running 'make clean'. If the error persists, try 'make cleanall'. ***"
@@ -115,14 +119,18 @@ ifeq ($(OS), Darwin)
  -./contrib/mac/fixup-libgfortran.sh $(PREFIX)/$(JL_PRIVATE_LIBDIR)
 endif
 ifeq ($(OS), WINNT)
- -[ -e dist-extras/7za.exe ] && cp dist-extras/7za.exe $(PREFIX)/bin/7z.exe
- -[ -e dist-extras/PortableGit-1.8.1.2-preview20130201.7z ] && \
- mkdir $(PREFIX)/Git && \
- 7z x dist-extras/PortableGit-1.8.1.2-preview20130201.7z -o"$(PREFIX)/Git"
+ [ ! -d dist-extras ] || ( cd dist-extras && \
+ cp 7z.exe 7z.dll libexpat-1.dll zlib1.dll ../$(PREFIX)/bin && \
+  mkdir ../$(PREFIX)/Git && \
+  7z x PortableGit.7z -o"../$(PREFIX)/Git" )
 ifeq ($(BUILD_OS),WINNT)
  cp $(call pathsearch,libgfortran-3.dll,$(PATH)) $(PREFIX)/$(JL_LIBDIR) ;
  cp $(call pathsearch,libquadmath-0.dll,$(PATH)) $(PREFIX)/$(JL_LIBDIR) ;
+ifeq ($(ARCH),i686)
  cp $(call pathsearch,libgcc_s_sjlj-1.dll,$(PATH)) $(PREFIX)/$(JL_LIBDIR) ;
+else
+ cp $(call pathsearch,libgcc_s_seh-1.dll,$(PATH)) $(PREFIX)/$(JL_LIBDIR) ;
+endif
  cp $(call pathsearch,libstdc++-6.dll,$(PATH)) $(PREFIX)/$(JL_LIBDIR) ;
  #cp $(call pathsearch,libssp-0.dll,$(PATH)) $(PREFIX)/$(JL_LIBDIR) ;
 else
@@ -136,6 +144,7 @@ endif
  cp $(call wine_pathsearch,libstdc++-6.dll,$(WINE_PATH)) $(PREFIX)/$(JL_LIBDIR) ;
  cp $(call wine_pathsearch,libssp-0.dll,$(WINE_PATH)) $(PREFIX)/$(JL_LIBDIR) ;
 endif
+ cd $(PREFIX)/bin && rm -f llvm* llc.exe lli.exe opt.exe LTO.exe bugpoint.exe macho-dump.exe
  7z a -mx9 julia-$(JULIA_COMMIT)-$(OS)-$(ARCH).zip julia-$(JULIA_COMMIT)
 else
  tar zcvf julia-$(JULIA_COMMIT)-$(OS)-$(ARCH).tar.gz julia-$(JULIA_COMMIT)
@@ -154,6 +163,8 @@ clean: | $(CLEAN_TARGETS)
  @rm -f julia
  @rm -f *~ *# *.tar.gz
  @rm -fr $(BUILD)/$(JL_PRIVATE_LIBDIR)
+# Temporarily add this line to the Makefile to remove extras
+ @rm -fr $(BUILD)/share/julia/extras
 
 cleanall: clean
  @$(MAKE) -C src clean-flisp clean-support
@@ -182,9 +193,32 @@ test-%: release
 # download target for some hardcoded windows dependencies
 .PHONY: win-extras, wine_path
 win-extras:
+ [ -d dist-extras ] || mkdir dist-extras
+ifneq (,$(filter $(ARCH), i386 i686))
  cd dist-extras && \
- wget -O 7za920.zip https://downloads.sourceforge.net/sevenzip/7za920.zip && \
- wget -O PortableGit-1.8.1.2-preview20130201.7z https://msysgit.googlecode.com/files/PortableGit-1.8.1.2-preview20130201.7z
+ wget -O 7z920.exe https://downloads.sourceforge.net/sevenzip/7z920.exe && \
+ 7z x -y 7z920.exe 7z.exe 7z.dll && \
+ wget -O mingw-libexpat.rpm https://download.opensuse.org/repositories/windows:/mingw:/win32/SLE_11_SP2/noarch/mingw32-libexpat-2.0.1-4.15.noarch.rpm && \
+ wget -O mingw-zlib.rpm https://download.opensuse.org/repositories/windows:/mingw:/win32/SLE_11_SP2/noarch/mingw32-zlib-1.2.7-1.16.noarch.rpm
+else ifeq ($(ARCH),x86_64)
+ cd dist-extras && \
+ wget -O 7z920-x64.msi https://downloads.sourceforge.net/sevenzip/7z920-x64.msi && \
+ 7z x -y 7z920-x64.msi _7z.exe _7z.dll && \
+ mv _7z.dll 7z.dll && \
+ mv _7z.exe 7z.exe && \
+ wget -O mingw-libexpat.rpm https://download.opensuse.org/repositories/windows:/mingw:/win64/SLE_11_SP2/noarch/mingw64-libexpat-2.0.1-3.15.noarch.rpm && \
+ wget -O mingw-zlib.rpm https://download.opensuse.org/repositories/windows:/mingw:/win64/SLE_11_SP2/noarch/mingw64-zlib-1.2.7-1.19.noarch.rpm
+else
+$(error no win-extras target for ARCH=$(ARCH))
+endif
+ cd dist-extras && \
+ chmod a+x 7z.exe && \
+ 7z x -y mingw-libexpat.rpm -so > mingw-libexpat.cpio && \
+ 7z e -y mingw-libexpat.cpio && \
+ 7z x -y mingw-zlib.rpm -so > mingw-zlib.cpio && \
+ 7z e -y mingw-zlib.cpio && \
+ wget -O PortableGit.7z https://msysgit.googlecode.com/files/PortableGit-1.8.3-preview20130601.7z
+
 wine_path:
  $(info $(WINE_PATH))
  @echo "wine cmd /c \"set \$$PATH=...\";%PATH% && program"