Backports for 1.11.0-rc4/1.11.0 (#55586)

Backported PRs:
- [x] #55480 <!-- Fix push! for OffsetVectors, add tests for push! and
append! on AbstractVector -->
- [x] #55443 <!-- Add test for upper/lower/titlecase and fix call -->
- [x] #55524 <!-- Set `.jl` sources as read-only during installation -->
- [x] #55500 <!-- make jl_thread_suspend_and_get_state safe -->
- [x] #55506 <!-- Fix indexing in _mapreducedim for OffsetArrays -->
- [x] #55564 <!-- Empty out loaded_precompiles dict instead of asserting
it's empty. -->
- [x] #55567 <!-- Initialize threadpools correctly during sysimg build
-->
- [x] #55596 <!-- Fast bounds-check for CartesianIndex ranges -->
- [x] #55605 <!-- Reroute Symmetric/Hermitian + Diagonal through
triangular -->
- [x] #55640 <!-- win: move stack_overflow_warning to the backtrace
fiber -->
- [x] #55715 <!-- Add precompile signatures to Markdown to reduce
latency. -->
- [x] #55593 <!-- Fix invalidations for FileIO -->
- [x] #55555 <!-- Revert "Don't expose guard pages to malloc_stack API
consumers" -->
- [x] #55720 <!-- Fix `pkgdir` for extensions -->
- [x] #55729 <!-- Avoid confounding compilation side effects of
`@time_imports` -->
- [x] #55718 <!-- Fix `@time_imports` extension recognition -->
- [x] #55522 <!-- Fix tr for Symmetric/Hermitian block matrices -->

Contains multiple commits, manual intervention needed:
- [ ] #55509 <!-- Fix cong implementation to be properly random and not
just cycling. -->

Non-merged PRs with backport label:
- [ ] #55641 <!-- fall back to slower stat filesize if optimized
filesize fails -->
- [ ] #55534 <!-- Set stdlib sources as read-only during installation
-->
- [ ] #55499 <!-- propagate the terminal's `displaysize` to the
`IOContext` used by the REPL -->
- [ ] #55458 <!-- Allow for generically extracting unannotated string
-->
- [ ] #55457 <!-- Make AnnotateChar equality consider annotations -->
- [ ] #55453 <!-- Privatise the annotations API, for StyledStrings -->
- [ ] #55355 <!-- relocation: account for trailing path separator in
depot paths -->
- [ ] #55220 <!-- `isfile_casesensitive` fixes on Windows -->
- [ ] #55169 <!-- `propertynames` for SVD respects private argument -->
- [ ] #54457 <!-- Make `String(::Memory)` copy -->
- [ ] #53957 <!-- tweak how filtering is done for what packages should
be precompiled -->
- [ ] #51479 <!-- prevent code loading from lookin in the versioned
environment when building Julia -->
- [ ] #50813 <!-- More doctests for Sockets and capitalization fix -->
- [ ] #50157 <!-- improve docs for `@inbounds` and
`Base.@propagate_inbounds` -->
- [ ] #41244 <!-- Fix shell `cd` error when working dir has been deleted
-->

Author: KristofferC

Makefile

@@ -377,6 +377,11 @@ endif
 	cp -R -L $(JULIAHOME)/base/* $(DESTDIR)$(datarootdir)/julia/base
 	cp -R -L $(JULIAHOME)/test/* $(DESTDIR)$(datarootdir)/julia/test
 	cp -R -L $(build_datarootdir)/julia/* $(DESTDIR)$(datarootdir)/julia
+
+	# Set .jl sources as read-only to match package directories
+	find $(DESTDIR)$(datarootdir)/julia/base -type f -name \*.jl -exec chmod 0444 '{}' \;
+	find $(DESTDIR)$(datarootdir)/julia/test -type f -name \*.jl -exec chmod 0444 '{}' \;
+
 	# Copy documentation
 	cp -R -L $(BUILDROOT)/doc/_build/html $(DESTDIR)$(docdir)/
 	# Remove various files which should not be installed

base/Base.jl

@@ -603,7 +603,7 @@ function __init__()
     init_active_project()
     append!(empty!(_sysimage_modules), keys(loaded_modules))
     empty!(explicit_loaded_modules)
-    @assert isempty(loaded_precompiles)
+    empty!(loaded_precompiles) # If we load a packageimage when building the image this might not be empty
     for (mod, key) in module_keys
         loaded_precompiles[key => module_build_id(mod)] = mod
     end

base/abstractarray.jl

@@ -3504,24 +3504,25 @@ function push!(a::AbstractVector{T}, item) where T
     itemT = item isa T ? item : convert(T, item)::T
     new_length = length(a) + 1
     resize!(a, new_length)
-    a[new_length] = itemT
+    a[end] = itemT
     return a
 end
 
 # specialize and optimize the single argument case
 function push!(a::AbstractVector{Any}, @nospecialize x)
     new_length = length(a) + 1
     resize!(a, new_length)
-    a[new_length] = x
+    a[end] = x
     return a
 end
 function push!(a::AbstractVector{Any}, @nospecialize x...)
     @_terminates_locally_meta
     na = length(a)
     nx = length(x)
     resize!(a, na + nx)
+    e = lastindex(a) - nx
     for i = 1:nx
-        a[na+i] = x[i]
+        a[e+i] = x[i]
     end
     return a
 end

base/compiler/typelimits.jl

@@ -815,6 +815,7 @@ end
                     typenames[i] = Any.name
                     simplify[i] = false
                     types[j] = widen
+                    typenames[j] = ijname
                     break
                 end
             end

base/loading.jl

@@ -507,6 +507,8 @@ package root.
 To get the root directory of the package that implements the current module
 the form `pkgdir(@__MODULE__)` can be used.
 
+If an extension module is given, the root of the parent package is returned.
+
 ```julia-repl
 julia> pkgdir(Foo)
 "/path/to/Foo.jl"
@@ -524,7 +526,19 @@ function pkgdir(m::Module, paths::String...)
     rootmodule = moduleroot(m)
     path = pathof(rootmodule)
     path === nothing && return nothing
-    return joinpath(dirname(dirname(path)), paths...)
+    original = path
+    path, base = splitdir(dirname(path))
+    if base == "src"
+        # package source in `../src/Foo.jl`
+    elseif base == "ext"
+        # extension source in `../ext/FooExt.jl`
+    elseif basename(path) == "ext"
+        # extension source in `../ext/FooExt/FooExt.jl`
+        path = dirname(path)
+    else
+        error("Unexpected path structure for module source: $original")
+    end
+    return joinpath(path, paths...)
 end
 
 function get_pkgversion_from_path(path)
@@ -1152,7 +1166,7 @@ const TIMING_IMPORTS = Threads.Atomic{Int}(0)
 # these return either the array of modules loaded from the path / content given
 # or an Exception that describes why it couldn't be loaded
 # and it reconnects the Base.Docs.META
-function _include_from_serialized(pkg::PkgId, path::String, ocachepath::Union{Nothing, String}, depmods::Vector{Any}, ignore_native::Union{Nothing,Bool}=nothing)
+function _include_from_serialized(pkg::PkgId, path::String, ocachepath::Union{Nothing, String}, depmods::Vector{Any}, ignore_native::Union{Nothing,Bool}=nothing; register::Bool=true)
     if isnothing(ignore_native)
         if JLOptions().code_coverage == 0 && JLOptions().malloc_log == 0
             ignore_native = false
@@ -1201,23 +1215,11 @@ function _include_from_serialized(pkg::PkgId, path::String, ocachepath::Union{No
     for M in restored
         M = M::Module
         if parentmodule(M) === M && PkgId(M) == pkg
+            register && register_root_module(M)
             if timing_imports
-                elapsed = round((time_ns() - t_before) / 1e6, digits = 1)
+                elapsed_time = time_ns() - t_before
                 comp_time, recomp_time = cumulative_compile_time_ns() .- t_comp_before
-                print(lpad(elapsed, 9), " ms  ")
-                parentid = get(EXT_PRIMED, pkg, nothing)
-                if parentid !== nothing
-                    print(parentid.name, " → ")
-                end
-                print(pkg.name)
-                if comp_time > 0
-                    printstyled(" ", Ryu.writefixed(Float64(100 * comp_time / (elapsed * 1e6)), 2), "% compilation time", color = Base.info_color())
-                end
-                if recomp_time > 0
-                    perc = Float64(100 * recomp_time / comp_time)
-                    printstyled(" (", perc < 1 ? "<1" : Ryu.writefixed(perc, 0), "% recompilation)", color = Base.warn_color())
-                end
-                println()
+                print_time_imports_report(M, elapsed_time, comp_time, recomp_time)
             end
             return M
         end
@@ -1229,6 +1231,73 @@ function _include_from_serialized(pkg::PkgId, path::String, ocachepath::Union{No
     end
 end
 
+# printing functions for @time_imports
+# note that the time inputs are UInt64 on all platforms. Give default values here so that we don't have
+# confusing UInt64 types in generate_precompile.jl
+function print_time_imports_report(
+        mod::Module,
+        elapsed_time::UInt64=UInt64(1),
+        comp_time::UInt64=UInt64(1),
+        recomp_time::UInt64=UInt64(1)
+    )
+    print(lpad(round(elapsed_time / 1e6, digits=1), 9), " ms  ")
+    ext_parent = extension_parent_name(mod)
+    if ext_parent !== nothing
+        print(ext_parent::String, " → ")
+    end
+    print(string(mod))
+    if comp_time > 0
+        perc = Ryu.writefixed(Float64(100 * comp_time / (elapsed_time)), 2)
+        printstyled(" $perc% compilation time", color = Base.info_color())
+    end
+    if recomp_time > 0
+        perc = Float64(100 * recomp_time / comp_time)
+        perc_show = perc < 1 ? "<1" : Ryu.writefixed(perc, 0)
+        printstyled(" ($perc_show% recompilation)", color = Base.warn_color())
+    end
+    println()
+end
+function print_time_imports_report_init(
+        mod::Module, i::Int=1,
+        elapsed_time::UInt64=UInt64(1),
+        comp_time::UInt64=UInt64(1),
+        recomp_time::UInt64=UInt64(1)
+    )
+    connector = i > 1 ? "├" : "┌"
+    printstyled("               $connector ", color = :light_black)
+    print("$(round(elapsed_time / 1e6, digits=1)) ms $mod.__init__() ")
+    if comp_time > 0
+        perc = Ryu.writefixed(Float64(100 * (comp_time) / elapsed_time), 2)
+        printstyled("$perc% compilation time", color = Base.info_color())
+    end
+    if recomp_time > 0
+        perc = Float64(100 * recomp_time / comp_time)
+        printstyled(" ($(perc < 1 ? "<1" : Ryu.writefixed(perc, 0))% recompilation)", color = Base.warn_color())
+    end
+    println()
+end
+
+# if M is an extension, return the string name of the parent. Otherwise return nothing
+function extension_parent_name(M::Module)
+    rootmodule = moduleroot(M)
+    src_path = pathof(rootmodule)
+    src_path === nothing && return nothing
+    pkgdir_parts = splitpath(src_path)
+    ext_pos = findlast(==("ext"), pkgdir_parts)
+    if ext_pos !== nothing && ext_pos >= length(pkgdir_parts) - 2
+        parent_package_root = joinpath(pkgdir_parts[1:ext_pos-1]...)
+        parent_package_project_file = locate_project_file(parent_package_root)
+        if parent_package_project_file isa String
+            d = parsed_toml(parent_package_project_file)
+            name = get(d, "name", nothing)
+            if name !== nothing
+                return name
+            end
+        end
+    end
+    return nothing
+end
+
 function register_restored_modules(sv::SimpleVector, pkg::PkgId, path::String)
     # This function is also used by PkgCacheInspector.jl
     restored = sv[1]::Vector{Any}
@@ -1265,31 +1334,18 @@ function run_module_init(mod::Module, i::Int=1)
     # `i` informs ordering for the `@time_imports` report formatting
     if TIMING_IMPORTS[] == 0
         ccall(:jl_init_restored_module, Cvoid, (Any,), mod)
-    else
-        if isdefined(mod, :__init__)
-            connector = i > 1 ? "├" : "┌"
-            printstyled("               $connector ", color = :light_black)
-
-            elapsedtime = time_ns()
-            cumulative_compile_timing(true)
-            compile_elapsedtimes = cumulative_compile_time_ns()
+    elseif isdefined(mod, :__init__)
+        elapsed_time = time_ns()
+        cumulative_compile_timing(true)
+        compile_elapsedtimes = cumulative_compile_time_ns()
 
-            ccall(:jl_init_restored_module, Cvoid, (Any,), mod)
+        ccall(:jl_init_restored_module, Cvoid, (Any,), mod)
 
-            elapsedtime = (time_ns() - elapsedtime) / 1e6
-            cumulative_compile_timing(false);
-            comp_time, recomp_time = (cumulative_compile_time_ns() .- compile_elapsedtimes) ./ 1e6
+        elapsed_time = time_ns() - elapsed_time
+        cumulative_compile_timing(false);
+        comp_time, recomp_time = cumulative_compile_time_ns() .- compile_elapsedtimes
 
-            print("$(round(elapsedtime, digits=1)) ms $mod.__init__() ")
-            if comp_time > 0
-                printstyled(Ryu.writefixed(Float64(100 * comp_time / elapsedtime), 2), "% compilation time", color = Base.info_color())
-            end
-            if recomp_time > 0
-                perc = Float64(100 * recomp_time / comp_time)
-                printstyled(" ($(perc < 1 ? "<1" : Ryu.writefixed(perc, 0))% recompilation)", color = Base.warn_color())
-            end
-            println()
-        end
+        print_time_imports_report_init(mod, i, elapsed_time, comp_time, recomp_time)
     end
 end
 
@@ -1403,7 +1459,7 @@ function _insert_extension_triggers(parent::PkgId, extensions::Dict{String, Any}
         triggers = triggers::Union{String, Vector{String}}
         triggers isa String && (triggers = [triggers])
         id = PkgId(uuid5(parent.uuid::UUID, ext), ext)
-        if id in keys(EXT_PRIMED) || haskey(Base.loaded_modules, id)
+        if haskey(EXT_PRIMED, id) || haskey(Base.loaded_modules, id)
             continue  # extension is already primed or loaded, don't add it again
         end
         EXT_PRIMED[id] = parent
@@ -1833,8 +1889,7 @@ function _tryrequire_from_serialized(pkg::PkgId, path::String, ocachepath::Union
         depmods[i] = dep
     end
     # then load the file
-    loaded = _include_from_serialized(pkg, path, ocachepath, depmods, ignore_native)
-    loaded isa Module && register_root_module(loaded)
+    loaded = _include_from_serialized(pkg, path, ocachepath, depmods, ignore_native; register = true)
     return loaded
 end
 
@@ -1901,8 +1956,7 @@ end
                     if dep === nothing
                         try
                             set_pkgorigin_version_path(modkey, modpath)
-                            dep = _include_from_serialized(modkey, modcachepath, modocachepath, modstaledeps)
-                            dep isa Module && stalecheck && register_root_module(dep)
+                            dep = _include_from_serialized(modkey, modcachepath, modocachepath, modstaledeps; register = stalecheck)
                         finally
                             end_loading(modkey, dep)
                         end
@@ -1918,9 +1972,8 @@ end
             end
             restored = get(loaded_precompiles, pkg => newbuild_id, nothing)
             if !isa(restored, Module)
-                restored = _include_from_serialized(pkg, path_to_try, ocachefile, staledeps)
+                restored = _include_from_serialized(pkg, path_to_try, ocachefile, staledeps; register = stalecheck)
             end
-            isa(restored, Module) && stalecheck && register_root_module(restored)
             isa(restored, Module) && return restored
             @debug "Deserialization checks failed while attempting to load cache from $path_to_try" exception=restored
             @label check_next_path

base/multidimensional.jl

@@ -693,6 +693,8 @@ using .IteratorsMD
 end
 @inline checkindex(::Type{Bool}, inds::Tuple, I::CartesianIndex) =
     checkbounds_indices(Bool, inds, I.I)
+@inline checkindex(::Type{Bool}, inds::Tuple, i::AbstractRange{<:CartesianIndex}) =
+    isempty(i) | (checkindex(Bool, inds, first(i)) & checkindex(Bool, inds, last(i)))
 
 # Indexing into Array with mixtures of Integers and CartesianIndices is
 # extremely performance-sensitive. While the abstract fallbacks support this,

base/reducedim.jl

@@ -261,8 +261,9 @@ function _mapreducedim!(f, op, R::AbstractArray, A::AbstractArrayOrBroadcasted)
         # use mapreduce_impl, which is probably better tuned to achieve higher performance
         nslices = div(length(A), lsiz)
         ibase = first(LinearIndices(A))-1
-        for i = 1:nslices
-            @inbounds R[i] = op(R[i], mapreduce_impl(f, op, A, ibase+1, ibase+lsiz))
+        for i in eachindex(R)
+            r = op(@inbounds(R[i]), mapreduce_impl(f, op, A, ibase+1, ibase+lsiz))
+            @inbounds R[i] = r
             ibase += lsiz
         end
         return R

base/strings/annotated.jl

@@ -384,7 +384,7 @@ a vector of region–annotation tuples.
 In accordance with the semantics documented in [`AnnotatedString`](@ref), the
 order of annotations returned matches the order in which they were applied.
 
-See also: `annotate!`.
+See also: [`annotate!`](@ref).
 """
 annotations(s::AnnotatedString) = s.annotations
 

base/strings/io.jl

@@ -365,7 +365,8 @@ function _join_preserve_annotations(iterator, args...)
         # in nature, we extract an `AnnotatedString`, otherwise we just extract
         # a plain `String` from `io`.
         if isconcretetype(et) || !isempty(io.annotations)
-            read(seekstart(io), AnnotatedString{String})
+            seekstart(io)
+            read(io, AnnotatedString{String})
         else
             String(take!(io.io))
         end

base/strings/unicode.jl

@@ -5,7 +5,8 @@ module Unicode
 
 import Base: show, ==, hash, string, Symbol, isless, length, eltype,
              convert, isvalid, ismalformed, isoverlong, iterate,
-             AnnotatedString, AnnotatedChar, annotated_chartransform
+             AnnotatedString, AnnotatedChar, annotated_chartransform,
+             annotations
 
 # whether codepoints are valid Unicode scalar values, i.e. 0-0xd7ff, 0xe000-0x10ffff