Merge branch 'master' into sparse-find-next

Author: fredrikekre

.travis.yml

@@ -1,33 +1,41 @@
 language: cpp
-sudo: false
+sudo: required
 dist: trusty
 matrix:
   include:
     - os: linux
       env: ARCH="i686"
-      compiler: "g++ -m32"
+      compiler: "g++-5 -m32"
       addons:
         apt:
+          sources:
+            - ubuntu-toolchain-r-test
           packages:
             - libssl1.0.0
             - bar
             - time
-            - gcc-multilib
-            - g++-multilib
+            - binutils
+            - gcc-5
+            - g++-5
+            - gcc-5-multilib
+            - g++-5-multilib
             - make:i386
             - libssl-dev:i386
-            - gfortran
-            - gfortran-multilib
+            - gfortran-5
+            - gfortran-5-multilib
     - os: linux
       env: ARCH="x86_64"
-      compiler: "g++ -m64"
+      compiler: "g++-5 -m64"
       addons:
         apt:
+          sources:
+            - ubuntu-toolchain-r-test
           packages:
             - libssl1.0.0
             - bar
             - time
-            - gfortran
+            - g++-5
+            - gfortran-5
     - os: osx
       env: ARCH="x86_64"
       osx_image: xcode8
@@ -56,10 +64,19 @@ before_install:
     - make check-whitespace
     - if [ `uname` = "Linux" ]; then
         contrib/travis_fastfail.sh || exit 1;
+        mkdir -p $HOME/bin;
+        ln -s /usr/bin/gcc-5 $HOME/bin/gcc;
+        ln -s /usr/bin/g++-5 $HOME/bin/g++;
+        ln -s /usr/bin/gfortran-5 $HOME/bin/gfortran;
+        ln -s /usr/bin/gcc-5 $HOME/bin/x86_64-linux-gnu-gcc;
+        ln -s /usr/bin/g++-5 $HOME/bin/x86_64-linux-gnu-g++;
         gcc --version;
         BAR="bar -i 30";
-        BUILDOPTS="-j3 VERBOSE=1 FORCE_ASSERTIONS=1 LLVM_ASSERTIONS=1";
+        BUILDOPTS="-j5 VERBOSE=1 FORCE_ASSERTIONS=1 LLVM_ASSERTIONS=1";
         echo "override ARCH=$ARCH" >> Make.user;
+        sudo sh -c "echo 0 > /proc/sys/net/ipv6/conf/lo/disable_ipv6";
+        export JULIA_CPU_CORES=4;
+        export JULIA_TEST_MAXRSS_MB=1200;
         TESTSTORUN="all";
       elif [ `uname` = "Darwin" ]; then
         brew update;
@@ -81,6 +98,8 @@ before_install:
         export JULIA_MACOS_SPAWN="DYLD_FALLBACK_LIBRARY_PATH=\"$DYLD_FALLBACK_LIBRARY_PATH\" \$1";
         export BUILDOPTS="$BUILDOPTS spawn=\$(JULIA_MACOS_SPAWN)";
         make $BUILDOPTS -C contrib -f repackage_system_suitesparse4.make;
+        export JULIA_CPU_CORES=2;
+        export JULIA_TEST_MAXRSS_MB=600;
         TESTSTORUN="all --skip linalg/triangular subarray"; fi # TODO: re enable these if possible without timing out
     - git clone -q git://git.kitenet.net/moreutils
 script:
@@ -115,13 +134,12 @@ script:
       fi
     - cd .. && mv julia julia2
     # run tests
-    - /tmp/julia/bin/julia --precompiled=no -e 'true' &&
-        /tmp/julia/bin/julia-debug --precompiled=no -e 'true'
+    - /tmp/julia/bin/julia --sysimage-native-code=no -e 'true' &&
+        /tmp/julia/bin/julia-debug --sysimage-native-code=no -e 'true'
     - /tmp/julia/bin/julia -e 'versioninfo()'
     - pushd /tmp/julia/share/julia/test
-    - export JULIA_CPU_CORES=2 && export JULIA_TEST_MAXRSS_MB=600 &&
-        /tmp/julia/bin/julia --check-bounds=yes runtests.jl $TESTSTORUN &&
-        /tmp/julia/bin/julia --check-bounds=yes runtests.jl libgit2-online download pkg
+    - /tmp/julia/bin/julia --check-bounds=yes runtests.jl $TESTSTORUN &&
+      /tmp/julia/bin/julia --check-bounds=yes runtests.jl libgit2-online download pkg
     - popd
     # test that the embedding code works on our installation
     - mkdir /tmp/embedding-test &&

CONTRIBUTING.md

@@ -141,10 +141,6 @@ All docstrings are written inline above the methods or types they are associated
 4. check the output in `doc/_build/html/` to make sure the changes are correct;
 5. commit your changes and open a pull request.
 
-> **Note**
->
-> Currently there are a large number of docstrings found in `base/docs/helpdb/Base.jl`. When any of these docstrings are modified please move them out of this file and place them above the most appropriate definition in one of the `base/` source files.
-
 #### Adding a new docstring to `base/`
 
 The steps required to add a new docstring are listed below:

LICENSE.md

@@ -54,8 +54,6 @@ their own licenses:
 - [ARPACK](http://www.caam.rice.edu/software/ARPACK/RiceBSD.txt#LICENSE) [BSD-3]
 - [DSFMT](http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/LICENSE.txt) [BSD-3]
 - [OPENLIBM](https://github.com/JuliaLang/openlibm/blob/master/LICENSE.md) [MIT, BSD-2, ISC]
-- [OPENSPECFUN](https://github.com/JuliaLang/openspecfun) [MIT, public domain]
-- [FADDEEVA](http://ab-initio.mit.edu/Faddeeva) [MIT]
 - [GMP](http://gmplib.org/manual/Copying.html#Copying) [LGPL3+ or GPL2+]
 - [LIBGIT2](https://github.com/libgit2/libgit2/blob/development/COPYING) [GPL2+ with unlimited linking exception]
 - [CURL](https://curl.haxx.se/docs/copyright.html) [MIT/X derivative]

Make.inc

@@ -31,7 +31,6 @@ USE_SYSTEM_PCRE:=0
 USE_SYSTEM_LIBM:=0
 USE_SYSTEM_OPENLIBM:=0
 UNTRUSTED_SYSTEM_LIBM:=0
-USE_SYSTEM_OPENSPECFUN:=0
 USE_SYSTEM_DSFMT:=0
 USE_SYSTEM_BLAS:=0
 USE_SYSTEM_LAPACK:=0
@@ -1124,19 +1123,19 @@ endef
 endif
 
 define symlink_target
-CLEAN_TARGETS += clean-$(2)/$(1)
-clean-$$(abspath $(2)/$(1)):
+CLEAN_TARGETS += clean-$(2)/$(3)
+clean-$$(abspath $(2)/$(3)):
 ifeq ($(BUILD_OS), WINNT)
-	@-cmd //C rmdir $$(call mingw_to_dos,$(2)/$(1),cd $(2) &&)
+	@-cmd //C rmdir $$(call mingw_to_dos,$(2)/$(3),cd $(2) &&)
 else
-	@-rm $$(abspath $(2)/$(1))
+	@-rm $$(abspath $(2)/$(3))
 endif
-$$(subst $$(abspath $(JULIAHOME))/,,$$(abspath $(2)/$(1))): $$(abspath $(2)/$(1))
-$$(abspath $(2)/$(1)): | $$(abspath $(2))
+$$(subst $$(abspath $(JULIAHOME))/,,$$(abspath $(2)/$(3))): $$(abspath $(2)/$(3))
+$$(abspath $(2)/$(3)): | $$(abspath $(2))
 ifeq ($(BUILD_OS), WINNT)
-	@cmd //C mklink //J $$(call mingw_to_dos,$(2)/$(1),cd $(2) &&) $$(call mingw_to_dos,$(1),)
+	@cmd //C mklink //J $$(call mingw_to_dos,$(2)/$(3),cd $(2) &&) $$(call mingw_to_dos,$(1),)
 else ifneq (,$(findstring CYGWIN,$(BUILD_OS)))
-	@cmd /C mklink /J $$(call cygpath_w,$(2)/$(1)) $$(call cygpath_w,$(1))
+	@cmd /C mklink /J $$(call cygpath_w,$(2)/$(3)) $$(call cygpath_w,$(1))
 else ifdef JULIA_VAGRANT_BUILD
 	@cp -R $$(abspath $(1)) $$@
 else

Makefile

@@ -19,7 +19,7 @@ default: $(JULIA_BUILD_MODE) # contains either "debug" or "release"
 all: debug release
 
 # sort is used to remove potential duplicates
-DIRS := $(sort $(build_bindir) $(build_depsbindir) $(build_libdir) $(build_private_libdir) $(build_libexecdir) $(build_includedir) $(build_includedir)/julia $(build_sysconfdir)/julia $(build_datarootdir)/julia $(build_man1dir))
+DIRS := $(sort $(build_bindir) $(build_depsbindir) $(build_libdir) $(build_private_libdir) $(build_libexecdir) $(build_includedir) $(build_includedir)/julia $(build_sysconfdir)/julia $(build_datarootdir)/julia $(build_datarootdir)/julia/site $(build_man1dir))
 ifneq ($(BUILDROOT),$(JULIAHOME))
 BUILDDIRS := $(BUILDROOT) $(addprefix $(BUILDROOT)/,base src ui doc deps test test/perf examples examples/embedding)
 BUILDDIRMAKE := $(addsuffix /Makefile,$(BUILDDIRS))
@@ -49,7 +49,10 @@ configure:
 endif
 
 $(foreach dir,$(DIRS),$(eval $(call dir_target,$(dir))))
-$(foreach link,base test,$(eval $(call symlink_target,$(link),$(build_datarootdir)/julia)))
+$(foreach link,base test,$(eval $(call symlink_target,$(link),$(build_datarootdir)/julia,$(link))))
+
+build_defaultpkgdir = $(build_datarootdir)/julia/site/$(shell echo $(VERSDIR))
+$(eval $(call symlink_target,stdlib,$(build_datarootdir)/julia/site,$(shell echo $(VERSDIR))))
 
 julia_flisp.boot.inc.phony: julia-deps
 	@$(MAKE) $(QUIET_MAKE) -C $(BUILDROOT)/src julia_flisp.boot.inc.phony
@@ -81,7 +84,7 @@ ifndef JULIA_VAGRANT_BUILD
 endif
 endif
 
-julia-deps: | $(DIRS) $(build_datarootdir)/julia/base $(build_datarootdir)/julia/test
+julia-deps: | $(DIRS) $(build_datarootdir)/julia/base $(build_datarootdir)/julia/test $(build_defaultpkgdir)
 	@$(MAKE) $(QUIET_MAKE) -C $(BUILDROOT)/deps
 
 julia-base: julia-deps $(build_sysconfdir)/julia/juliarc.jl $(build_man1dir)/julia.1 $(build_datarootdir)/julia/julia-config.jl
@@ -218,9 +221,12 @@ COMMA:=,
 define sysimg_builder
 $$(build_private_libdir)/sys$1.o: $$(build_private_libdir)/inference.ji $$(JULIAHOME)/VERSION $$(BASE_SRCS)
 	@$$(call PRINT_JULIA, cd $$(JULIAHOME)/base && \
-	$$(call spawn,$3) $2 -C "$$(JULIA_CPU_TARGET)" --output-o $$(call cygpath_w,$$@) $$(JULIA_SYSIMG_BUILD_FLAGS) \
-		--startup-file=no --warn-overwrite=yes --sysimage $$(call cygpath_w,$$<) sysimg.jl $$(RELBUILDROOT) \
-		|| { echo '*** This error is usually fixed by running `make clean`. If the error persists$$(COMMA) try `make cleanall`. ***' && false; } )
+	if $$(call spawn,$3) $2 -C "$$(JULIA_CPU_TARGET)" --output-o $$(call cygpath_w,$$@).tmp $$(JULIA_SYSIMG_BUILD_FLAGS) \
+		--startup-file=no --warn-overwrite=yes --sysimage $$(call cygpath_w,$$<) sysimg.jl $$(RELBUILDROOT); then \
+		mv $$(call cygpath_w,$$@).tmp $$(call cygpath_w,$$@); \
+	else \
+		echo '*** This error is usually fixed by running `make clean`. If the error persists$$(COMMA) try `make cleanall`. ***' && false; \
+	fi )
 .SECONDARY: $(build_private_libdir)/sys$1.o
 endef
 ifneq ($(CPUID_SPECIFIC_BINARIES),0)
@@ -251,9 +257,6 @@ ifeq ($(USE_SYSTEM_LIBM),0)
 JL_PRIVATE_LIBS += openlibm
 endif
 endif
-ifeq ($(USE_SYSTEM_OPENSPECFUN),0)
-JL_PRIVATE_LIBS += openspecfun
-endif
 ifeq ($(USE_SYSTEM_DSFMT),0)
 JL_PRIVATE_LIBS += dSFMT
 endif
@@ -551,9 +554,9 @@ test: check-whitespace $(JULIA_BUILD_MODE)
 	@$(MAKE) $(QUIET_MAKE) -C $(BUILDROOT)/test default JULIA_BUILD_MODE=$(JULIA_BUILD_MODE)
 
 ifeq ($(JULIA_BUILD_MODE),release)
-JULIA_SYSIMG=$(build_private_libdir)/sys$(JULIA_LIBSUFFIX).$(SHLIB_EXT)
+JULIA_SYSIMG=$(build_private_libdir)/sys$(JULIA_LIBSUFFIX)$(CPUID_TAG).$(SHLIB_EXT)
 else
-JULIA_SYSIMG=$(build_private_libdir)/sys-$(JULIA_BUILD_MODE)$(JULIA_LIBSUFFIX).$(SHLIB_EXT)
+JULIA_SYSIMG=$(build_private_libdir)/sys-$(JULIA_BUILD_MODE)$(JULIA_LIBSUFFIX)$(CPUID_TAG).$(SHLIB_EXT)
 endif
 testall: check-whitespace $(JULIA_BUILD_MODE)
 	cp $(JULIA_SYSIMG) $(BUILDROOT)/local.$(SHLIB_EXT) && $(JULIA_EXECUTABLE) -J $(call cygpath_w,$(BUILDROOT)/local.$(SHLIB_EXT)) -e 'true' && rm $(BUILDROOT)/local.$(SHLIB_EXT)