From 0da9578148ddd237470eb588943a29e9100778a3 Mon Sep 17 00:00:00 2001
From: Elliot Saba <staticfloat@gmail.com>
Date: Mon, 19 Aug 2024 12:10:29 -0700
Subject: [PATCH 01/22] Set `.jl` sources as read-only during installation
 (#55524)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This sets all `.jl` files in `$(prefix)/base` and `$(prefix)/test` to
have `0444` permissions, to better match how `Pkg` installs packages
(and sets them to be read-only).

Fixes https://github.com/JuliaLang/juliaup/issues/865

---------

Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>
(cherry picked from commit 62e7705845f9dbf0c22b291c3d63e3cc6af57df4)
---
 Makefile | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/Makefile b/Makefile
index 57d5cde328e02..ec13f23bbb2cf 100644
--- a/Makefile
+++ b/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

From e3657193498736a0e5d1543c42ea2efab75b6647 Mon Sep 17 00:00:00 2001
From: Jameson Nash <vtjnash@gmail.com>
Date: Mon, 19 Aug 2024 21:57:48 -0400
Subject: [PATCH 02/22] make jl_thread_suspend_and_get_state safe (#55500)

Fixes async safety, thread safety, FreeBSD safety.

(cherry picked from commit d4bd540d0f30605ef184af79f2aaaff9aa351a54)
---
 src/signals-unix.c | 109 +++++++++++++++++++++++----------------------
 1 file changed, 55 insertions(+), 54 deletions(-)

diff --git a/src/signals-unix.c b/src/signals-unix.c
index 8b79e11863e1f..5732fd1e9c91d 100644
--- a/src/signals-unix.c
+++ b/src/signals-unix.c
@@ -292,6 +292,8 @@ int exc_reg_is_write_fault(uintptr_t esr) {
 #if defined(HAVE_MACH)
 #include "signals-mach.c"
 #else
+#include <poll.h>
+#include <sys/eventfd.h>
 
 int jl_lock_stackwalk(void)
 {
@@ -404,17 +406,13 @@ JL_NO_ASAN static void segv_handler(int sig, siginfo_t *info, void *context)
     }
 }
 
-#if !defined(JL_DISABLE_LIBUNWIND)
-static bt_context_t *signal_context;
-pthread_mutex_t in_signal_lock;
-static pthread_cond_t exit_signal_cond;
-static pthread_cond_t signal_caught_cond;
+pthread_mutex_t in_signal_lock; // shared with jl_delete_thread
+static bt_context_t *signal_context; // protected by in_signal_lock
+static int exit_signal_cond = -1;
+static int signal_caught_cond = -1;
 
 int jl_thread_suspend_and_get_state(int tid, int timeout, bt_context_t *ctx)
 {
-    struct timespec ts;
-    clock_gettime(CLOCK_REALTIME, &ts);
-    ts.tv_sec += timeout;
     pthread_mutex_lock(&in_signal_lock);
     jl_ptls_t ptls2 = jl_atomic_load_relaxed(&jl_all_tls_states)[tid];
     jl_task_t *ct2 = ptls2 ? jl_atomic_load_relaxed(&ptls2->current_task) : NULL;
@@ -423,48 +421,51 @@ int jl_thread_suspend_and_get_state(int tid, int timeout, bt_context_t *ctx)
         pthread_mutex_unlock(&in_signal_lock);
         return 0;
     }
-    jl_atomic_store_release(&ptls2->signal_request, 1);
-    pthread_kill(ptls2->system_id, SIGUSR2);
-    // wait for thread to acknowledge
-    int err = pthread_cond_timedwait(&signal_caught_cond, &in_signal_lock, &ts);
-    if (err == ETIMEDOUT) {
-        sig_atomic_t request = 1;
+    sig_atomic_t request = 0;
+    if (!jl_atomic_cmpswap(&ptls2->signal_request, &request, 1)) {
+        // something is wrong, or there is already a usr2 in flight elsewhere
+        pthread_mutex_unlock(&in_signal_lock);
+        return 0;
+    }
+    request = 1;
+    int err = pthread_kill(ptls2->system_id, SIGUSR2);
+    // wait for thread to acknowledge or timeout
+    struct pollfd event = {signal_caught_cond, POLLIN, 0};
+    if (err == 0) {
+        do {
+            err = poll(&event, 1, timeout * 1000);
+        } while (err == -1 && errno == EINTR);
+    }
+    if ((event.revents & POLLIN) == 0) {
+        // not ready after timeout: try to cancel this request
         if (jl_atomic_cmpswap(&ptls2->signal_request, &request, 0)) {
             pthread_mutex_unlock(&in_signal_lock);
             return 0;
         }
-        // Request is either now 0 (meaning the other thread is waiting for
-        //   exit_signal_cond already),
-        // Or it is now -1 (meaning the other thread
-        //   is waiting for in_signal_lock, and we need to release that lock
-        //   here for a bit, until the other thread has a chance to get to the
-        //   exit_signal_cond)
-        if (request == -1) {
-            err = pthread_cond_wait(&signal_caught_cond, &in_signal_lock);
-            assert(!err);
-        }
     }
+    eventfd_t got;
+    do {
+        err = read(signal_caught_cond, &got, sizeof(eventfd_t));
+    } while (err == -1 && errno == EINTR);
+    if (err != sizeof(eventfd_t)) abort();
+    assert(got == 1); (void) got;
     // Now the other thread is waiting on exit_signal_cond (verify that here by
     // checking it is 0, and add an acquire barrier for good measure)
-    int request = jl_atomic_load_acquire(&ptls2->signal_request);
+    request = jl_atomic_load_acquire(&ptls2->signal_request);
     assert(request == 0); (void) request;
-    jl_atomic_store_release(&ptls2->signal_request, 1); // prepare to resume normally
+    jl_atomic_store_release(&ptls2->signal_request, 4); // prepare to resume normally, but later code may change this
     *ctx = *signal_context;
     return 1;
 }
 
 void jl_thread_resume(int tid)
 {
-    jl_ptls_t ptls2 = jl_atomic_load_relaxed(&jl_all_tls_states)[tid];
-    pthread_cond_broadcast(&exit_signal_cond);
-    pthread_cond_wait(&signal_caught_cond, &in_signal_lock); // wait for thread to acknowledge (so that signal_request doesn't get mixed up)
-    // The other thread is waiting to leave exit_signal_cond (verify that here by
-    // checking it is 0, and add an acquire barrier for good measure)
-    int request = jl_atomic_load_acquire(&ptls2->signal_request);
-    assert(request == 0); (void) request;
+    int err;
+    eventfd_t got = 1;
+    err = write(exit_signal_cond, &got, sizeof(eventfd_t));
+    if (err != sizeof(eventfd_t)) abort();
     pthread_mutex_unlock(&in_signal_lock);
 }
-#endif
 
 // Throw jl_interrupt_exception if the master thread is in a signal async region
 // or if SIGINT happens too often.
@@ -473,9 +474,11 @@ static void jl_try_deliver_sigint(void)
     jl_ptls_t ptls2 = jl_atomic_load_relaxed(&jl_all_tls_states)[0];
     jl_safepoint_enable_sigint();
     jl_wake_libuv();
+    pthread_mutex_lock(&in_signal_lock);
     jl_atomic_store_release(&ptls2->signal_request, 2);
     // This also makes sure `sleep` is aborted.
     pthread_kill(ptls2->system_id, SIGUSR2);
+    pthread_mutex_unlock(&in_signal_lock);
 }
 
 // Write only by signal handling thread, read only by main thread
@@ -508,12 +511,12 @@ static void jl_exit_thread0(int signo, jl_bt_element_t *bt_data, size_t bt_size)
 }
 
 // request:
-// -1: beginning processing [invalid outside here]
 //  0: nothing [not from here]
-//  1: get state
+//  1: get state & wait for request
 //  2: throw sigint if `!defer_signal && io_wait` or if force throw threshold
 //     is reached
 //  3: raise `thread0_exit_signo` and try to exit
+//  4: no-op
 void usr2_handler(int sig, siginfo_t *info, void *ctx)
 {
     jl_task_t *ct = jl_get_current_task();
@@ -524,25 +527,21 @@ void usr2_handler(int sig, siginfo_t *info, void *ctx)
         return;
     int errno_save = errno;
     // acknowledge that we saw the signal_request
-    sig_atomic_t request = jl_atomic_exchange(&ptls->signal_request, -1);
-#if !defined(JL_DISABLE_LIBUNWIND)
+    sig_atomic_t request = jl_atomic_exchange(&ptls->signal_request, 0);
     if (request == 1) {
-        pthread_mutex_lock(&in_signal_lock);
         signal_context = jl_to_bt_context(ctx);
-        // acknowledge that we set the signal_caught_cond broadcast
+        int err;
+        eventfd_t got = 1;
+        err = write(signal_caught_cond, &got, sizeof(eventfd_t));
+        if (err != sizeof(eventfd_t)) abort();
+        do {
+            err = read(exit_signal_cond, &got, sizeof(eventfd_t));
+        } while (err == -1 && errno == EINTR);
+        if (err != sizeof(eventfd_t)) abort();
+        assert(got == 1);
         request = jl_atomic_exchange(&ptls->signal_request, 0);
-        assert(request == -1); (void) request;
-        pthread_cond_broadcast(&signal_caught_cond);
-        pthread_cond_wait(&exit_signal_cond, &in_signal_lock);
-        request = jl_atomic_exchange(&ptls->signal_request, 0);
-        assert(request == 1 || request == 3);
-        // acknowledge that we got the resume signal
-        pthread_cond_broadcast(&signal_caught_cond);
-        pthread_mutex_unlock(&in_signal_lock);
+        assert(request == 2 || request == 3 || request == 4);
     }
-    else
-#endif
-    jl_atomic_exchange(&ptls->signal_request, 0); // returns -1
     if (request == 2) {
         int force = jl_check_force_sigint();
         if (force || (!ptls->defer_signal && ptls->io_wait)) {
@@ -987,10 +986,12 @@ void restore_signals(void)
     jl_sigsetset(&sset);
     pthread_sigmask(SIG_SETMASK, &sset, 0);
 
-#if !defined(HAVE_MACH) && !defined(JL_DISABLE_LIBUNWIND)
+#if !defined(HAVE_MACH)
+    exit_signal_cond = eventfd(0, EFD_CLOEXEC);
+    signal_caught_cond = eventfd(0, EFD_CLOEXEC);
     if (pthread_mutex_init(&in_signal_lock, NULL) != 0 ||
-        pthread_cond_init(&exit_signal_cond, NULL) != 0 ||
-        pthread_cond_init(&signal_caught_cond, NULL) != 0) {
+            exit_signal_cond == -1 ||
+            signal_caught_cond == -1) {
         jl_error("SIGUSR pthread init failed");
     }
 #endif

From 803520ee849c8402a17a1525d6e996ec65224aba Mon Sep 17 00:00:00 2001
From: Jishnu Bhattacharya <jishnub.github@gmail.com>
Date: Fri, 23 Aug 2024 12:55:46 +0530
Subject: [PATCH 03/22] Fix indexing in _mapreducedim for OffsetArrays (#55506)

The destination array was being indexed incorrectly if it had offset
indices. This led to the following on nightly:
```julia
julia> using OffsetArrays

julia> r = 5:100;

julia> a = OffsetVector(r, 2);

julia> sum(a, dims=1)
1-element OffsetArray(::Vector{Int64}, 3:3) with eltype Int64 with indices 3:3:
 0

julia> sum(a)
5040
```
The indexing was marked `@inbounds`, so this was not throwing an error.
This PR also follows #55329 and only marks the indexing operations as
`@inbounds`, omitting the function calls.

---------

Co-authored-by: Matt Bauman <mbauman@juliahub.com>
(cherry picked from commit 3d20a9210a59097b46ed2cbdcd1e87435873bcfa)
---
 base/reducedim.jl   | 5 +++--
 test/offsetarray.jl | 7 +++++++
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/base/reducedim.jl b/base/reducedim.jl
index 19d8f0a5af77c..2f51837a66050 100644
--- a/base/reducedim.jl
+++ b/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
diff --git a/test/offsetarray.jl b/test/offsetarray.jl
index c50f38c382385..5f0c19d7593f5 100644
--- a/test/offsetarray.jl
+++ b/test/offsetarray.jl
@@ -878,3 +878,10 @@ end
     v = view([1,2,3,4], :)
     @test v[Base.IdentityUnitRange(2:3)] == OffsetArray(2:3, 2:3)
 end
+
+@testset "mapreduce with OffsetRanges" begin
+    r = 5:100
+    a = OffsetArray(r, 2)
+    b = sum(a, dims=1)
+    @test b[begin] == sum(r)
+end

From 808203f43fa2b3d97ca62dedc32c13cadf01b861 Mon Sep 17 00:00:00 2001
From: Gabriel Baraldi <baraldigabriel@gmail.com>
Date: Sun, 25 Aug 2024 10:21:58 -0300
Subject: [PATCH 04/22] Empty out loaded_precompiles dict instead of asserting
 it's empty. (#55564)

This dict will contain things if we load a package image during
precompilation

(cherry picked from commit 0c8641aacb53e6f4c7f21dd08e35873a2801a8f8)
---
 base/Base.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/base/Base.jl b/base/Base.jl
index 21c9a101758a0..0aa191206e3df 100644
--- a/base/Base.jl
+++ b/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

From 598a4de169af8385a5ce85fec23bcc058eba5d20 Mon Sep 17 00:00:00 2001
From: DilumAluthgeBot <43731525+DilumAluthgeBot@users.noreply.github.com>
Date: Wed, 28 Aug 2024 13:16:39 -0400
Subject: [PATCH 05/22] =?UTF-8?q?=F0=9F=A4=96=20[backports-release-1.11]?=
 =?UTF-8?q?=20Bump=20the=20Downloads=20stdlib=20from=20a9d274f=20to=201061?=
 =?UTF-8?q?ecc=20(#55615)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Stdlib: Downloads
URL: https://github.com/JuliaLang/Downloads.jl.git
Stdlib branch: master
Julia branch: backports-release-1.11
Old commit: a9d274f
New commit: 1061ecc
Julia version: 1.11.0-rc2
Downloads version: 1.6.0(It's okay that it doesn't match)
Bump invoked by: @IanButterworth
Powered by:
[BumpStdlibs.jl](https://github.com/JuliaLang/BumpStdlibs.jl)

Diff:
https://github.com/JuliaLang/Downloads.jl/compare/a9d274ff6588cc5dbfa90e908ee34c2408bab84a...1061ecc377a053fce0df94e1a19e5260f7c030f5

```
$ git log --oneline a9d274f..1061ecc
1061ecc Fix setting atexit. Fixes trailing download tasks during precompilation (#257)
b871386 Add debug information to `setopt` commands (#248)
51e5321 fix: use invokelatest for easy_hook, avoid race (#241)
05f9ec2 make precompile workload relocatable (#236)
2dd891a Hardcode doc edit backlink (#232)
```

Co-authored-by: Dilum Aluthge <dilum@aluthge.com>
---
 .../md5                                                         | 1 +
 .../sha512                                                      | 1 +
 .../md5                                                         | 1 -
 .../sha512                                                      | 1 -
 stdlib/Downloads.version                                        | 2 +-
 5 files changed, 3 insertions(+), 3 deletions(-)
 create mode 100644 deps/checksums/Downloads-1061ecc377a053fce0df94e1a19e5260f7c030f5.tar.gz/md5
 create mode 100644 deps/checksums/Downloads-1061ecc377a053fce0df94e1a19e5260f7c030f5.tar.gz/sha512
 delete mode 100644 deps/checksums/Downloads-a9d274ff6588cc5dbfa90e908ee34c2408bab84a.tar.gz/md5
 delete mode 100644 deps/checksums/Downloads-a9d274ff6588cc5dbfa90e908ee34c2408bab84a.tar.gz/sha512

diff --git a/deps/checksums/Downloads-1061ecc377a053fce0df94e1a19e5260f7c030f5.tar.gz/md5 b/deps/checksums/Downloads-1061ecc377a053fce0df94e1a19e5260f7c030f5.tar.gz/md5
new file mode 100644
index 0000000000000..f42bbedb6d415
--- /dev/null
+++ b/deps/checksums/Downloads-1061ecc377a053fce0df94e1a19e5260f7c030f5.tar.gz/md5
@@ -0,0 +1 @@
+70878dd96911d6960537dfee2a820d98
diff --git a/deps/checksums/Downloads-1061ecc377a053fce0df94e1a19e5260f7c030f5.tar.gz/sha512 b/deps/checksums/Downloads-1061ecc377a053fce0df94e1a19e5260f7c030f5.tar.gz/sha512
new file mode 100644
index 0000000000000..83164cad9a89d
--- /dev/null
+++ b/deps/checksums/Downloads-1061ecc377a053fce0df94e1a19e5260f7c030f5.tar.gz/sha512
@@ -0,0 +1 @@
+87d2bdc6c85cbbce5302aab8ffe92fc542c9c71a396844fcc04c0416be059b00298b4816ab5e5491dbf865660a3a6152f1c245875a1ec75fb49b4c7ba0d303d8
diff --git a/deps/checksums/Downloads-a9d274ff6588cc5dbfa90e908ee34c2408bab84a.tar.gz/md5 b/deps/checksums/Downloads-a9d274ff6588cc5dbfa90e908ee34c2408bab84a.tar.gz/md5
deleted file mode 100644
index fc3bce951cafb..0000000000000
--- a/deps/checksums/Downloads-a9d274ff6588cc5dbfa90e908ee34c2408bab84a.tar.gz/md5
+++ /dev/null
@@ -1 +0,0 @@
-97bb33510fadec7f4cc4c718c739e9a0
diff --git a/deps/checksums/Downloads-a9d274ff6588cc5dbfa90e908ee34c2408bab84a.tar.gz/sha512 b/deps/checksums/Downloads-a9d274ff6588cc5dbfa90e908ee34c2408bab84a.tar.gz/sha512
deleted file mode 100644
index bf2821e8252b0..0000000000000
--- a/deps/checksums/Downloads-a9d274ff6588cc5dbfa90e908ee34c2408bab84a.tar.gz/sha512
+++ /dev/null
@@ -1 +0,0 @@
-a362aaf762f42deebb8632a7a7980cd22b2777e8c4dc629e418580269e24a64217ad846d61acad70438cfdc190e47ba2ff7716edd4e04d8d10c1d765efce604d
diff --git a/stdlib/Downloads.version b/stdlib/Downloads.version
index 7805348a4b2f5..cb041d86d7f66 100644
--- a/stdlib/Downloads.version
+++ b/stdlib/Downloads.version
@@ -1,4 +1,4 @@
 DOWNLOADS_BRANCH = master
-DOWNLOADS_SHA1 = a9d274ff6588cc5dbfa90e908ee34c2408bab84a
+DOWNLOADS_SHA1 = 1061ecc377a053fce0df94e1a19e5260f7c030f5
 DOWNLOADS_GIT_URL := https://github.com/JuliaLang/Downloads.jl.git
 DOWNLOADS_TAR_URL = https://api.github.com/repos/JuliaLang/Downloads.jl/tarball/$1

From 890ac86f29dd08ec1bc5daf5c74248f8186c95bb Mon Sep 17 00:00:00 2001
From: Mark Kittisopikul <mkitti@users.noreply.github.com>
Date: Fri, 16 Aug 2024 03:33:22 -0400
Subject: [PATCH 06/22] Fix push! for OffsetVectors, add tests for push! and
 append! on AbstractVector (#55480)

Per
https://github.com/JuliaLang/julia/pull/55470#discussion_r1714000529,
the `push!(::AbstractArray, ...)` array implementation assumed one-based
indexing and did not account for an `OffsetVector`
scenario.

Here we add tests for `push!(::AbstractArray, ...)` and
`append(::AbstractArray, ...)` including using `@invoke` to test the
effect on `OffsetVector`.

cc: @fredrikekre
(cherry picked from commit 5230d27de950165475892acfabded59713c8cd3e)
---
 base/abstractarray.jl |  7 ++++---
 test/abstractarray.jl | 18 +++++++++++++++++-
 test/offsetarray.jl   | 29 +++++++++++++++++++++++++++++
 3 files changed, 50 insertions(+), 4 deletions(-)

diff --git a/base/abstractarray.jl b/base/abstractarray.jl
index 2d281b487c437..ad70b973ab10b 100644
--- a/base/abstractarray.jl
+++ b/base/abstractarray.jl
@@ -3504,7 +3504,7 @@ 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
 
@@ -3512,7 +3512,7 @@ end
 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...)
@@ -3520,8 +3520,9 @@ function push!(a::AbstractVector{Any}, @nospecialize x...)
     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
diff --git a/test/abstractarray.jl b/test/abstractarray.jl
index 88cffbcf2947d..8244d3fc791f5 100644
--- a/test/abstractarray.jl
+++ b/test/abstractarray.jl
@@ -1424,14 +1424,30 @@ using .Main.OffsetArrays
 end
 
 @testset "Check push!($a, $args...)" for
-    a in (["foo", "Bar"], SimpleArray(["foo", "Bar"]), OffsetVector(["foo", "Bar"], 0:1)),
+    a in (["foo", "Bar"], SimpleArray(["foo", "Bar"]), SimpleArray{Any}(["foo", "Bar"]), OffsetVector(["foo", "Bar"], 0:1)),
     args in (("eenie",), ("eenie", "minie"), ("eenie", "minie", "mo"))
         orig = copy(a)
         push!(a, args...)
         @test length(a) == length(orig) + length(args)
+        @test a[axes(orig,1)] == orig
         @test all(a[end-length(args)+1:end] .== args)
 end
 
+@testset "Check append!($a, $args)" for
+    a in (["foo", "Bar"], SimpleArray(["foo", "Bar"]), SimpleArray{Any}(["foo", "Bar"]), OffsetVector(["foo", "Bar"], 0:1)),
+    args in (("eenie",), ("eenie", "minie"), ("eenie", "minie", "mo"))
+        orig = copy(a)
+        append!(a, args)
+        @test length(a) == length(orig) + length(args)
+        @test a[axes(orig,1)] == orig
+        @test all(a[end-length(args)+1:end] .== args)
+end
+
+@testset "Check sizehint!($a)" for
+    a in (["foo", "Bar"], SimpleArray(["foo", "Bar"]), SimpleArray{Any}(["foo", "Bar"]), OffsetVector(["foo", "Bar"], 0:1))
+        @test sizehint!(a, 10) === a
+end
+
 @testset "splatting into hvcat" begin
     t = (1, 2)
     @test [t...; 3 4] == [1 2; 3 4]
diff --git a/test/offsetarray.jl b/test/offsetarray.jl
index 5f0c19d7593f5..fb5855dfbaa0d 100644
--- a/test/offsetarray.jl
+++ b/test/offsetarray.jl
@@ -383,6 +383,18 @@ v2 = copy(v)
 @test v2[end-1] == 2
 @test v2[end] == 1
 
+# push!(v::AbstractVector, x...)
+v2 = copy(v)
+@test @invoke(push!(v2::AbstractVector, 3)) === v2
+@test v2[axes(v,1)] == v
+@test v2[end] == 3
+@test v2[begin] == v[begin] == v[-2]
+v2 = copy(v)
+@test @invoke(push!(v2::AbstractVector, 5, 6)) == v2
+@test v2[axes(v,1)] == v
+@test v2[end-1] == 5
+@test v2[end] == 6
+
 # append! from array
 v2 = copy(v)
 @test append!(v2, [2, 1]) === v2
@@ -399,6 +411,23 @@ v2 = copy(v)
 @test v2[axes(v, 1)] == v
 @test v2[lastindex(v)+1:end] == [2, 1]
 
+# append!(::AbstractVector, ...)
+# append! from array
+v2 = copy(v)
+@test @invoke(append!(v2::AbstractVector, [2, 1]::Any)) === v2
+@test v2[axes(v, 1)] == v
+@test v2[lastindex(v)+1:end] == [2, 1]
+# append! from HasLength iterator
+v2 = copy(v)
+@test @invoke(append!(v2::AbstractVector, (v for v in [2, 1])::Any)) === v2
+@test v2[axes(v, 1)] == v
+@test v2[lastindex(v)+1:end] == [2, 1]
+# append! from SizeUnknown iterator
+v2 = copy(v)
+@test @invoke(append!(v2::AbstractVector, (v for v in [2, 1] if true)::Any)) === v2
+@test v2[axes(v, 1)] == v
+@test v2[lastindex(v)+1:end] == [2, 1]
+
 # other functions
 v = OffsetArray(v0, (-3,))
 @test lastindex(v) == 1

From d6fca1558127bad162df8e4f0e63d65b573c3255 Mon Sep 17 00:00:00 2001
From: Gabriel Baraldi <baraldigabriel@gmail.com>
Date: Tue, 27 Aug 2024 15:00:55 -0300
Subject: [PATCH 07/22] Initialize threadpools correctly during sysimg build
 (#55567)

I made a mistake with which threadpool was which.

(cherry picked from commit d5bbcc5aaec8033de1dd5b4b0de730ab40575469)
---
 src/init.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/init.c b/src/init.c
index 2c1ad618948f8..a5c9a6b19f94d 100644
--- a/src/init.c
+++ b/src/init.c
@@ -883,8 +883,8 @@ static NOINLINE void _finish_julia_init(JL_IMAGE_SEARCH rel, jl_ptls_t ptls, jl_
         jl_n_markthreads = 0;
         jl_n_sweepthreads = 0;
         jl_n_gcthreads = 0;
-        jl_n_threads_per_pool[0] = 1;
-        jl_n_threads_per_pool[1] = 0;
+        jl_n_threads_per_pool[0] = 0; // Interactive threadpool
+        jl_n_threads_per_pool[1] = 1; // Default threadpool
     } else {
         post_image_load_hooks();
     }

From 561e5c8c8b2a8a200551d889ec7e9b3aa1bf6487 Mon Sep 17 00:00:00 2001
From: Jishnu Bhattacharya <jishnub.github@gmail.com>
Date: Wed, 28 Aug 2024 14:05:58 +0530
Subject: [PATCH 08/22] Fast bounds-check for CartesianIndex ranges (#55596)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

`StepRangeLen{<:CartesianIndex}` indices have been supported since
v1.11, but bounds-checking for such indices currently falls back to
iterating over the entire range. This PR adds a quick `checkindex` for
such ranges.

The performance improvement as a consequence:
```julia
julia> D = Diagonal(1:10_000);

julia> @btime checkbounds($D, diagind($D, IndexCartesian()));
  6.697 μs (0 allocations: 0 bytes) # nightly, O(n)
  4.044 ns (0 allocations: 0 bytes) # This PR, O(1)
```

(cherry picked from commit 644029282cfeafcb3b80d999b0054cdaa9278e3d)
---
 base/multidimensional.jl              | 2 ++
 stdlib/LinearAlgebra/test/diagonal.jl | 5 +++++
 2 files changed, 7 insertions(+)

diff --git a/base/multidimensional.jl b/base/multidimensional.jl
index 519ac06e6e7ec..b6c93fa318d78 100644
--- a/base/multidimensional.jl
+++ b/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,
diff --git a/stdlib/LinearAlgebra/test/diagonal.jl b/stdlib/LinearAlgebra/test/diagonal.jl
index c20c63b5b3477..fd4ebfb714a37 100644
--- a/stdlib/LinearAlgebra/test/diagonal.jl
+++ b/stdlib/LinearAlgebra/test/diagonal.jl
@@ -1312,4 +1312,9 @@ end
     end
 end
 
+@testset "bounds-check with CartesianIndex ranges" begin
+    D = Diagonal(1:typemax(Int))
+    @test checkbounds(Bool, D, diagind(D, IndexCartesian()))
+end
+
 end # module TestDiagonal

From dde7c107871e775a0d2a4f5ef7f200269fa226ea Mon Sep 17 00:00:00 2001
From: Jameson Nash <vtjnash@gmail.com>
Date: Tue, 3 Sep 2024 12:24:01 -0400
Subject: [PATCH 09/22] win: move stack_overflow_warning to the backtrace fiber
 (#55640)

There is not enough stack space remaining after a stack overflow on
Windows to allocate the 4k page used by `write` to call the WriteFile
syscall. This causes it to hard-crash. But we can simply run this on the
altstack implementation, where there is plenty of space.

(cherry picked from commit eebc1e4e083b9b597bef328a5bd8eeda9ec52c1f)
---
 src/signals-win.c | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/signals-win.c b/src/signals-win.c
index a2980a0c063d9..2b01310964ddb 100644
--- a/src/signals-win.c
+++ b/src/signals-win.c
@@ -109,6 +109,8 @@ static jl_ptls_t stkerror_ptls;
 static int have_backtrace_fiber;
 static void JL_NORETURN start_backtrace_fiber(void)
 {
+    // print the warning (this mysteriously needs a lot of stack for the WriteFile syscall)
+    stack_overflow_warning();
     // collect the backtrace
     stkerror_ptls->bt_size =
         rec_backtrace_ctx(stkerror_ptls->bt_data, JL_MAX_BT_SIZE, stkerror_ctx,

From 972d618bc222b97af5dee5e61b6c2b36417c9716 Mon Sep 17 00:00:00 2001
From: Katharine Hyatt <kshyatt@users.noreply.github.com>
Date: Mon, 19 Aug 2024 11:38:52 -0400
Subject: [PATCH 10/22] Add test for upper/lower/titlecase and fix missing
 import (#55443)

(cherry picked from commit 39eaa3cfc1a861cf898d89fbe320ffa858f41939)
---
 base/strings/annotated.jl | 2 +-
 base/strings/unicode.jl   | 3 ++-
 test/strings/annotated.jl | 3 +++
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/base/strings/annotated.jl b/base/strings/annotated.jl
index 69b04202edbf6..ef1ea28f42738 100644
--- a/base/strings/annotated.jl
+++ b/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
 
diff --git a/base/strings/unicode.jl b/base/strings/unicode.jl
index a3b06063b98ac..2e142be901b0b 100644
--- a/base/strings/unicode.jl
+++ b/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
 
diff --git a/test/strings/annotated.jl b/test/strings/annotated.jl
index 62bf9a0c91c00..9e24ae46fd206 100644
--- a/test/strings/annotated.jl
+++ b/test/strings/annotated.jl
@@ -66,6 +66,9 @@ end
 @testset "AnnotatedChar" begin
     chr = Base.AnnotatedChar('c')
     @test chr == Base.AnnotatedChar(chr.char, Pair{Symbol, Any}[])
+    @test uppercase(chr) == Base.AnnotatedChar('C')
+    @test titlecase(chr) == Base.AnnotatedChar('C')
+    @test lowercase(Base.AnnotatedChar('C')) == chr
     str = Base.AnnotatedString("hmm", [(1:1, :attr => "h0h0"),
                                (1:2, :attr => "h0m1"),
                                (2:3, :attr => "m1m2")])

From e7ca87b325d8146f8870316832220163a1cc7ad5 Mon Sep 17 00:00:00 2001
From: KristofferC <kristoffer.carlsson@juliacomputing.com>
Date: Mon, 9 Sep 2024 13:07:08 +0200
Subject: [PATCH 11/22] Revert "Don't expose guard pages to malloc_stack API
 consumers (#54591)"

This reverts commit 5dfd57d25c189f6d5558dac9499b45f8bb9b271d.
---
 src/gc-stacks.c | 30 +-----------------------------
 1 file changed, 1 insertion(+), 29 deletions(-)

diff --git a/src/gc-stacks.c b/src/gc-stacks.c
index 3f40e2fc15d81..82094035349b3 100644
--- a/src/gc-stacks.c
+++ b/src/gc-stacks.c
@@ -22,22 +22,13 @@
 // number of stacks to always keep available per pool
 #define MIN_STACK_MAPPINGS_PER_POOL 5
 
-#if defined(_OS_WINDOWS_) || (!defined(_OS_OPENBSD_) && !defined(JL_HAVE_UCONTEXT) && !defined(JL_HAVE_SIGALTSTACK))
-#define JL_USE_GUARD_PAGE   1
 const size_t jl_guard_size = (4096 * 8);
-#else
-const size_t jl_guard_size = 0;
-#endif
-
 static _Atomic(uint32_t) num_stack_mappings = 0;
 
 #ifdef _OS_WINDOWS_
 #define MAP_FAILED NULL
 static void *malloc_stack(size_t bufsz) JL_NOTSAFEPOINT
 {
-    size_t guard_size = LLT_ALIGN(jl_guard_size, jl_page_size);
-    bufsz += guard_size;
-
     void *stk = VirtualAlloc(NULL, bufsz, MEM_RESERVE | MEM_COMMIT, PAGE_READWRITE);
     if (stk == NULL)
         return MAP_FAILED;
@@ -46,7 +37,6 @@ static void *malloc_stack(size_t bufsz) JL_NOTSAFEPOINT
         VirtualFree(stk, 0, MEM_RELEASE);
         return MAP_FAILED;
     }
-    stk = (char *)stk + guard_size;
 
     jl_atomic_fetch_add(&num_stack_mappings, 1);
     return stk;
@@ -55,12 +45,6 @@ static void *malloc_stack(size_t bufsz) JL_NOTSAFEPOINT
 
 static void free_stack(void *stkbuf, size_t bufsz)
 {
-#ifdef JL_USE_GUARD_PAGE
-    size_t guard_size = LLT_ALIGN(jl_guard_size, jl_page_size);
-    bufsz += guard_size;
-    stkbuf = (char *)stkbuf - guard_size;
-#endif
-
     VirtualFree(stkbuf, 0, MEM_RELEASE);
     jl_atomic_fetch_add(&num_stack_mappings, -1);
 }
@@ -69,22 +53,16 @@ static void free_stack(void *stkbuf, size_t bufsz)
 
 static void *malloc_stack(size_t bufsz) JL_NOTSAFEPOINT
 {
-#ifdef JL_USE_GUARD_PAGE
-    size_t guard_size = LLT_ALIGN(jl_guard_size, jl_page_size);
-    bufsz += guard_size;
-#endif
-
     void* stk = mmap(0, bufsz, PROT_READ | PROT_WRITE, MAP_PRIVATE | MAP_ANONYMOUS, -1, 0);
     if (stk == MAP_FAILED)
         return MAP_FAILED;
 
-#ifdef JL_USE_GUARD_PAGE
+#if !defined(JL_HAVE_UCONTEXT) && !defined(JL_HAVE_SIGALTSTACK)
     // set up a guard page to detect stack overflow
     if (mprotect(stk, jl_guard_size, PROT_NONE) == -1) {
         munmap(stk, bufsz);
         return MAP_FAILED;
     }
-    stk = (char *)stk + guard_size;
 #endif
     jl_atomic_fetch_add(&num_stack_mappings, 1);
     return stk;
@@ -92,12 +70,6 @@ static void *malloc_stack(size_t bufsz) JL_NOTSAFEPOINT
 
 static void free_stack(void *stkbuf, size_t bufsz)
 {
-#ifdef JL_USE_GUARD_PAGE
-    size_t guard_size = LLT_ALIGN(jl_guard_size, jl_page_size);
-    bufsz += guard_size;
-    stkbuf = (char *)stkbuf - guard_size;
-#endif
-
     munmap(stkbuf, bufsz);
     jl_atomic_fetch_add(&num_stack_mappings, -1);
 }

From 287847936f9c952c6cdbf87fa5ecbbbbd4d1f605 Mon Sep 17 00:00:00 2001
From: Jishnu Bhattacharya <jishnub.github@gmail.com>
Date: Mon, 2 Sep 2024 20:12:39 +0530
Subject: [PATCH 12/22] Reroute Symmetric/Hermitian + Diagonal through
 triangular (#55605)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This should fix the `Diagonal`-related issue from
https://github.com/JuliaLang/julia/issues/55590, although the
`SymTridiagonal` one still remains.
```julia
julia> using LinearAlgebra

julia> a = Matrix{BigFloat}(undef, 2,2)
2×2 Matrix{BigFloat}:
 #undef  #undef
 #undef  #undef

julia> a[1] = 1; a[3] = 1; a[4] = 1
1

julia> a = Hermitian(a)
2×2 Hermitian{BigFloat, Matrix{BigFloat}}:
 1.0  1.0
 1.0  1.0

julia> b = Symmetric(a)
2×2 Symmetric{BigFloat, Matrix{BigFloat}}:
 1.0  1.0
 1.0  1.0

julia> c = Diagonal([1,1])
2×2 Diagonal{Int64, Vector{Int64}}:
 1  ⋅
 ⋅  1

julia> a+c
2×2 Hermitian{BigFloat, Matrix{BigFloat}}:
 2.0  1.0
 1.0  2.0

julia> b+c
2×2 Symmetric{BigFloat, Matrix{BigFloat}}:
 2.0  1.0
 1.0  2.0
```

(cherry picked from commit 39f2ad1e941fd092b906d60e8d23c004e8ee5b7e)
---
 stdlib/LinearAlgebra/src/diagonal.jl | 15 ---------------
 stdlib/LinearAlgebra/src/special.jl  | 19 +++++++++++++++++++
 stdlib/LinearAlgebra/test/special.jl | 13 +++++++++++++
 3 files changed, 32 insertions(+), 15 deletions(-)

diff --git a/stdlib/LinearAlgebra/src/diagonal.jl b/stdlib/LinearAlgebra/src/diagonal.jl
index d27da450205f7..bea8183546d90 100644
--- a/stdlib/LinearAlgebra/src/diagonal.jl
+++ b/stdlib/LinearAlgebra/src/diagonal.jl
@@ -250,21 +250,6 @@ end
 (+)(Da::Diagonal, Db::Diagonal) = Diagonal(Da.diag + Db.diag)
 (-)(Da::Diagonal, Db::Diagonal) = Diagonal(Da.diag - Db.diag)
 
-for f in (:+, :-)
-    @eval function $f(D::Diagonal{<:Number}, S::Symmetric)
-        return Symmetric($f(D, S.data), sym_uplo(S.uplo))
-    end
-    @eval function $f(S::Symmetric, D::Diagonal{<:Number})
-        return Symmetric($f(S.data, D), sym_uplo(S.uplo))
-    end
-    @eval function $f(D::Diagonal{<:Real}, H::Hermitian)
-        return Hermitian($f(D, H.data), sym_uplo(H.uplo))
-    end
-    @eval function $f(H::Hermitian, D::Diagonal{<:Real})
-        return Hermitian($f(H.data, D), sym_uplo(H.uplo))
-    end
-end
-
 (*)(x::Number, D::Diagonal) = Diagonal(x * D.diag)
 (*)(D::Diagonal, x::Number) = Diagonal(D.diag * x)
 (/)(D::Diagonal, x::Number) = Diagonal(D.diag / x)
diff --git a/stdlib/LinearAlgebra/src/special.jl b/stdlib/LinearAlgebra/src/special.jl
index 1363708fb515f..2a3b6bf2a8e00 100644
--- a/stdlib/LinearAlgebra/src/special.jl
+++ b/stdlib/LinearAlgebra/src/special.jl
@@ -264,6 +264,25 @@ function (-)(A::UniformScaling, B::Diagonal)
     Diagonal(Ref(A) .- B.diag)
 end
 
+for f in (:+, :-)
+    @eval function $f(D::Diagonal{<:Number}, S::Symmetric)
+        uplo = sym_uplo(S.uplo)
+        return Symmetric(parentof_applytri($f, Symmetric(D, uplo), S), uplo)
+    end
+    @eval function $f(S::Symmetric, D::Diagonal{<:Number})
+        uplo = sym_uplo(S.uplo)
+        return Symmetric(parentof_applytri($f, S, Symmetric(D, uplo)), uplo)
+    end
+    @eval function $f(D::Diagonal{<:Real}, H::Hermitian)
+        uplo = sym_uplo(H.uplo)
+        return Hermitian(parentof_applytri($f, Hermitian(D, uplo), H), uplo)
+    end
+    @eval function $f(H::Hermitian, D::Diagonal{<:Real})
+        uplo = sym_uplo(H.uplo)
+        return Hermitian(parentof_applytri($f, H, Hermitian(D, uplo)), uplo)
+    end
+end
+
 ## Diagonal construction from UniformScaling
 Diagonal{T}(s::UniformScaling, m::Integer) where {T} = Diagonal{T}(fill(T(s.λ), m))
 Diagonal(s::UniformScaling, m::Integer) = Diagonal{eltype(s)}(s, m)
diff --git a/stdlib/LinearAlgebra/test/special.jl b/stdlib/LinearAlgebra/test/special.jl
index 7e96af369e310..148ccd85efeb1 100644
--- a/stdlib/LinearAlgebra/test/special.jl
+++ b/stdlib/LinearAlgebra/test/special.jl
@@ -536,4 +536,17 @@ end
     @test v * S isa Matrix
 end
 
+@testset "Partly filled Hermitian and Diagonal algebra" begin
+    D = Diagonal([1,2])
+    for S in (Symmetric, Hermitian), uplo in (:U, :L)
+        M = Matrix{BigInt}(undef, 2, 2)
+        M[1,1] = M[2,2] = M[1+(uplo == :L), 1 + (uplo == :U)] = 3
+        H = S(M, uplo)
+        HM = Matrix(H)
+        @test H + D == D + H == HM + D
+        @test H - D == HM - D
+        @test D - H == D - HM
+    end
+end
+
 end # module TestSpecial

From 26440bd4467c900c08a4fef97211037fdb839407 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?P=C3=A1ll=20Haraldsson?= <Pall.Haraldsson@gmail.com>
Date: Mon, 9 Sep 2024 17:57:18 +0000
Subject: [PATCH 13/22] Add precompile signatures to Markdown to reduce
 latency. (#55715)

Fixes #55706 that is seemingly a 4472x regression, not just 16x (was my
first guess, based on CondaPkg, also fixes or greatly mitigates
https://github.com/JuliaPy/CondaPkg.jl/issues/145), and large part of 3x
regression for PythonCall.

---------

Co-authored-by: Kristoffer Carlsson <kcarlsson89@gmail.com>
(cherry picked from commit 1463c9991c4a75730e4d6822313180ca323241c0)
---
 stdlib/Markdown/src/Markdown.jl | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/stdlib/Markdown/src/Markdown.jl b/stdlib/Markdown/src/Markdown.jl
index 93d8dbc39fc59..e8c64deb3d593 100644
--- a/stdlib/Markdown/src/Markdown.jl
+++ b/stdlib/Markdown/src/Markdown.jl
@@ -98,4 +98,25 @@ import Base.Docs: catdoc
 
 catdoc(md::MD...) = MD(md...)
 
+if Base.generating_output()
+    # workload to reduce latency
+    md"""
+    # H1
+    ## H2
+    ### H3
+    **bold text**
+    *italicized text*
+    > blockquote
+    1. First item
+    2. Second item
+    3. Third item
+    - First item
+    - Second item
+    - Third item
+    `code`
+    Horizontal Rule
+    ---
+    """
+end
+
 end

From b702d7611bc98bcc3d08475a01322fb4564d4b1a Mon Sep 17 00:00:00 2001
From: Nathan Zimmerberg <39104088+nhz2@users.noreply.github.com>
Date: Mon, 9 Sep 2024 14:23:38 -0400
Subject: [PATCH 14/22] Fix invalidations for FileIO (#55593)

Fixes https://github.com/JuliaIO/FileIO.jl/issues/396

(cherry picked from commit 68feddc7c89b7f328eb72e336c7dbe51ac47b626)
---
 base/strings/io.jl | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/base/strings/io.jl b/base/strings/io.jl
index 97cdedac3db78..4e413c0ebd78c 100644
--- a/base/strings/io.jl
+++ b/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

From 6270b903719ce4a236825debee9b63422b2cae0e Mon Sep 17 00:00:00 2001
From: Ian Butterworth <i.r.butterworth@gmail.com>
Date: Tue, 10 Sep 2024 07:33:56 -0400
Subject: [PATCH 15/22] Fix `@time_imports` extension recognition (#55718)

(cherry picked from commit d2807927656efe2bfbfe4402f83e2ea417306db2)
---
 base/loading.jl | 41 ++++++++++++++++++++++++++++++-----------
 1 file changed, 30 insertions(+), 11 deletions(-)

diff --git a/base/loading.jl b/base/loading.jl
index 5614c3603e540..6436f15a3ac16 100644
--- a/base/loading.jl
+++ b/base/loading.jl
@@ -1152,7 +1152,7 @@ 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
@@ -1201,13 +1201,14 @@ 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)
                 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, " → ")
+                ext_parent = extension_parent_name(M)
+                if ext_parent !== nothing
+                    print(ext_parent::String, " → ")
                 end
                 print(pkg.name)
                 if comp_time > 0
@@ -1229,6 +1230,27 @@ function _include_from_serialized(pkg::PkgId, path::String, ocachepath::Union{No
     end
 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}
@@ -1403,7 +1425,7 @@ 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 +1855,7 @@ 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 +1922,7 @@ 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 +1938,8 @@ 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

From b86812d127e9477b7580bf3d85befc04de95fe75 Mon Sep 17 00:00:00 2001
From: Ian Butterworth <i.r.butterworth@gmail.com>
Date: Mon, 9 Sep 2024 21:01:08 -0400
Subject: [PATCH 16/22] Fix `pkgdir` for extensions (#55720)

Fixes https://github.com/JuliaLang/julia/issues/55719

---------

Co-authored-by: Max Horn <241512+fingolfin@users.noreply.github.com>
(cherry picked from commit 99b8868ff563eded17376b3f90ffc1637222f2c6)
---
 base/loading.jl | 16 +++++++++++++++-
 test/loading.jl | 17 +++++++++++++++--
 2 files changed, 30 insertions(+), 3 deletions(-)

diff --git a/base/loading.jl b/base/loading.jl
index 6436f15a3ac16..43ffb2cf52ca2 100644
--- a/base/loading.jl
+++ b/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)
diff --git a/test/loading.jl b/test/loading.jl
index 9207294a205b5..71d0b07b64376 100644
--- a/test/loading.jl
+++ b/test/loading.jl
@@ -1034,6 +1034,16 @@ end
 end
 
 @testset "Extensions" begin
+    test_ext = """
+    function test_ext(parent::Module, ext::Symbol)
+        _ext = Base.get_extension(parent, ext)
+        _ext isa Module || error("expected extension \$ext to be loaded")
+        _pkgdir = pkgdir(_ext)
+        _pkgdir == pkgdir(parent) != nothing || error("unexpected extension \$ext pkgdir path: \$_pkgdir")
+        _pkgversion = pkgversion(_ext)
+        _pkgversion == pkgversion(parent) || error("unexpected extension \$ext version: \$_pkgversion")
+    end
+    """
     depot_path = mktempdir()
     try
         proj = joinpath(@__DIR__, "project", "Extensions", "HasDepWithExtensions.jl")
@@ -1044,6 +1054,7 @@ end
             cmd = """
             $load_distr
             begin
+                $ew $test_ext
                 $ew push!(empty!(DEPOT_PATH), $(repr(depot_path)))
                 using HasExtensions
                 $ew using HasExtensions
@@ -1051,6 +1062,7 @@ end
                 $ew HasExtensions.ext_loaded && error("ext_loaded set")
                 using HasDepWithExtensions
                 $ew using HasDepWithExtensions
+                $ew test_ext(HasExtensions, :Extension)
                 $ew Base.get_extension(HasExtensions, :Extension).extvar == 1 || error("extvar in Extension not set")
                 $ew HasExtensions.ext_loaded || error("ext_loaded not set")
                 $ew HasExtensions.ext_folder_loaded && error("ext_folder_loaded set")
@@ -1100,11 +1112,12 @@ end
 
         test_ext_proj = """
         begin
+            $test_ext
             using HasExtensions
             using ExtDep
-            Base.get_extension(HasExtensions, :Extension) isa Module || error("expected extension to load")
+            test_ext(HasExtensions, :Extension)
             using ExtDep2
-            Base.get_extension(HasExtensions, :ExtensionFolder) isa Module || error("expected extension to load")
+            test_ext(HasExtensions, :ExtensionFolder)
         end
         """
         for compile in (`--compiled-modules=no`, ``)

From f09de94afb0c574f84274c746624df2ed840847d Mon Sep 17 00:00:00 2001
From: KristofferC <kristoffer.carlsson@juliacomputing.com>
Date: Wed, 11 Sep 2024 14:16:55 +0200
Subject: [PATCH 17/22] Revert "Reroute Symmetric/Hermitian + Diagonal through
 triangular (#55605)"

This reverts commit 287847936f9c952c6cdbf87fa5ecbbbbd4d1f605.
---
 stdlib/LinearAlgebra/src/diagonal.jl | 15 +++++++++++++++
 stdlib/LinearAlgebra/src/special.jl  | 19 -------------------
 stdlib/LinearAlgebra/test/special.jl | 13 -------------
 3 files changed, 15 insertions(+), 32 deletions(-)

diff --git a/stdlib/LinearAlgebra/src/diagonal.jl b/stdlib/LinearAlgebra/src/diagonal.jl
index bea8183546d90..d27da450205f7 100644
--- a/stdlib/LinearAlgebra/src/diagonal.jl
+++ b/stdlib/LinearAlgebra/src/diagonal.jl
@@ -250,6 +250,21 @@ end
 (+)(Da::Diagonal, Db::Diagonal) = Diagonal(Da.diag + Db.diag)
 (-)(Da::Diagonal, Db::Diagonal) = Diagonal(Da.diag - Db.diag)
 
+for f in (:+, :-)
+    @eval function $f(D::Diagonal{<:Number}, S::Symmetric)
+        return Symmetric($f(D, S.data), sym_uplo(S.uplo))
+    end
+    @eval function $f(S::Symmetric, D::Diagonal{<:Number})
+        return Symmetric($f(S.data, D), sym_uplo(S.uplo))
+    end
+    @eval function $f(D::Diagonal{<:Real}, H::Hermitian)
+        return Hermitian($f(D, H.data), sym_uplo(H.uplo))
+    end
+    @eval function $f(H::Hermitian, D::Diagonal{<:Real})
+        return Hermitian($f(H.data, D), sym_uplo(H.uplo))
+    end
+end
+
 (*)(x::Number, D::Diagonal) = Diagonal(x * D.diag)
 (*)(D::Diagonal, x::Number) = Diagonal(D.diag * x)
 (/)(D::Diagonal, x::Number) = Diagonal(D.diag / x)
diff --git a/stdlib/LinearAlgebra/src/special.jl b/stdlib/LinearAlgebra/src/special.jl
index 2a3b6bf2a8e00..1363708fb515f 100644
--- a/stdlib/LinearAlgebra/src/special.jl
+++ b/stdlib/LinearAlgebra/src/special.jl
@@ -264,25 +264,6 @@ function (-)(A::UniformScaling, B::Diagonal)
     Diagonal(Ref(A) .- B.diag)
 end
 
-for f in (:+, :-)
-    @eval function $f(D::Diagonal{<:Number}, S::Symmetric)
-        uplo = sym_uplo(S.uplo)
-        return Symmetric(parentof_applytri($f, Symmetric(D, uplo), S), uplo)
-    end
-    @eval function $f(S::Symmetric, D::Diagonal{<:Number})
-        uplo = sym_uplo(S.uplo)
-        return Symmetric(parentof_applytri($f, S, Symmetric(D, uplo)), uplo)
-    end
-    @eval function $f(D::Diagonal{<:Real}, H::Hermitian)
-        uplo = sym_uplo(H.uplo)
-        return Hermitian(parentof_applytri($f, Hermitian(D, uplo), H), uplo)
-    end
-    @eval function $f(H::Hermitian, D::Diagonal{<:Real})
-        uplo = sym_uplo(H.uplo)
-        return Hermitian(parentof_applytri($f, H, Hermitian(D, uplo)), uplo)
-    end
-end
-
 ## Diagonal construction from UniformScaling
 Diagonal{T}(s::UniformScaling, m::Integer) where {T} = Diagonal{T}(fill(T(s.λ), m))
 Diagonal(s::UniformScaling, m::Integer) = Diagonal{eltype(s)}(s, m)
diff --git a/stdlib/LinearAlgebra/test/special.jl b/stdlib/LinearAlgebra/test/special.jl
index 148ccd85efeb1..7e96af369e310 100644
--- a/stdlib/LinearAlgebra/test/special.jl
+++ b/stdlib/LinearAlgebra/test/special.jl
@@ -536,17 +536,4 @@ end
     @test v * S isa Matrix
 end
 
-@testset "Partly filled Hermitian and Diagonal algebra" begin
-    D = Diagonal([1,2])
-    for S in (Symmetric, Hermitian), uplo in (:U, :L)
-        M = Matrix{BigInt}(undef, 2, 2)
-        M[1,1] = M[2,2] = M[1+(uplo == :L), 1 + (uplo == :U)] = 3
-        H = S(M, uplo)
-        HM = Matrix(H)
-        @test H + D == D + H == HM + D
-        @test H - D == HM - D
-        @test D - H == D - HM
-    end
-end
-
 end # module TestSpecial

From 4ab4722b6ee18009ea7f2fce4a63711a1efcd148 Mon Sep 17 00:00:00 2001
From: Jishnu Bhattacharya <jishnub.github@gmail.com>
Date: Thu, 12 Sep 2024 15:12:07 +0530
Subject: [PATCH 18/22] Reland "Reroute Symmetric/Hermitian + Diagonal through
 triangular"

This backports the following commits:
commit 9690961c426ce2640d7db6c89952e69f87873a93
Author: Jishnu Bhattacharya <jishnub.github@gmail.com>
Date:   Mon Apr 29 21:43:31 2024 +0530

    Add upper/lowertriangular functions and use in applytri (#53573)

    We may use the fact that a `Diagonal` is already triangular to avoid
    adding a wrapper.

    Fixes the specific example in
    https://github.com/JuliaLang/julia/issues/53564, although not the
    broader issue. This is because it changes the operation from a
    `UpperTriangular + UpperTriangular` to a `UpperTriangular + Diagonal`,
    which uses broadcasting. The latter operation may also allow one to
    define more efficient methods.

commit 77821cdddb968eeabf31ccb6b214ccf59a604c68
Author: Jishnu Bhattacharya <jishnub.github@gmail.com>
Date:   Wed Aug 28 00:53:31 2024 +0530

    Remove Diagonal-triangular specialization

commit 621fb2e739a04207df63857700aca3562b41b5eb
Author: Jishnu Bhattacharya <jishnub.github@gmail.com>
Date:   Wed Aug 28 00:50:49 2024 +0530

    Restrict broadcasting to strided-diag Diagonal

commit 58eb2045ddb5dbbfdb759c06239ca54751e73d71
Author: Jishnu Bhattacharya <jishnub.github@gmail.com>
Date:   Wed Aug 28 00:44:47 2024 +0530

    Add tests for partly filled parent

commit 5aa6080a580bfbc9453e94a06f3e379e4517b316
Author: Jishnu Bhattacharya <jishnub.github@gmail.com>
Date:   Tue Aug 27 20:42:07 2024 +0530

    Reroute Symmetric/Hermitian + Diagonal through triangular
---
 stdlib/LinearAlgebra/src/diagonal.jl    | 18 +++---------------
 stdlib/LinearAlgebra/src/special.jl     | 19 +++++++++++++++++++
 stdlib/LinearAlgebra/src/symmetric.jl   | 12 ++++++------
 stdlib/LinearAlgebra/src/triangular.jl  |  6 ++++++
 stdlib/LinearAlgebra/test/diagonal.jl   |  6 ++++++
 stdlib/LinearAlgebra/test/special.jl    | 13 +++++++++++++
 stdlib/LinearAlgebra/test/symmetric.jl  | 25 +++++++++++++++++++++++++
 stdlib/LinearAlgebra/test/triangular.jl |  8 ++++++++
 8 files changed, 86 insertions(+), 21 deletions(-)

diff --git a/stdlib/LinearAlgebra/src/diagonal.jl b/stdlib/LinearAlgebra/src/diagonal.jl
index d27da450205f7..830332db0dbb1 100644
--- a/stdlib/LinearAlgebra/src/diagonal.jl
+++ b/stdlib/LinearAlgebra/src/diagonal.jl
@@ -250,21 +250,6 @@ end
 (+)(Da::Diagonal, Db::Diagonal) = Diagonal(Da.diag + Db.diag)
 (-)(Da::Diagonal, Db::Diagonal) = Diagonal(Da.diag - Db.diag)
 
-for f in (:+, :-)
-    @eval function $f(D::Diagonal{<:Number}, S::Symmetric)
-        return Symmetric($f(D, S.data), sym_uplo(S.uplo))
-    end
-    @eval function $f(S::Symmetric, D::Diagonal{<:Number})
-        return Symmetric($f(S.data, D), sym_uplo(S.uplo))
-    end
-    @eval function $f(D::Diagonal{<:Real}, H::Hermitian)
-        return Hermitian($f(D, H.data), sym_uplo(H.uplo))
-    end
-    @eval function $f(H::Hermitian, D::Diagonal{<:Real})
-        return Hermitian($f(H.data, D), sym_uplo(H.uplo))
-    end
-end
-
 (*)(x::Number, D::Diagonal) = Diagonal(x * D.diag)
 (*)(D::Diagonal, x::Number) = Diagonal(D.diag * x)
 (/)(D::Diagonal, x::Number) = Diagonal(D.diag / x)
@@ -991,3 +976,6 @@ end
 function Base.muladd(A::Diagonal, B::Diagonal, z::Diagonal)
     Diagonal(A.diag .* B.diag .+ z.diag)
 end
+
+uppertriangular(D::Diagonal) = D
+lowertriangular(D::Diagonal) = D
diff --git a/stdlib/LinearAlgebra/src/special.jl b/stdlib/LinearAlgebra/src/special.jl
index 1363708fb515f..2a3b6bf2a8e00 100644
--- a/stdlib/LinearAlgebra/src/special.jl
+++ b/stdlib/LinearAlgebra/src/special.jl
@@ -264,6 +264,25 @@ function (-)(A::UniformScaling, B::Diagonal)
     Diagonal(Ref(A) .- B.diag)
 end
 
+for f in (:+, :-)
+    @eval function $f(D::Diagonal{<:Number}, S::Symmetric)
+        uplo = sym_uplo(S.uplo)
+        return Symmetric(parentof_applytri($f, Symmetric(D, uplo), S), uplo)
+    end
+    @eval function $f(S::Symmetric, D::Diagonal{<:Number})
+        uplo = sym_uplo(S.uplo)
+        return Symmetric(parentof_applytri($f, S, Symmetric(D, uplo)), uplo)
+    end
+    @eval function $f(D::Diagonal{<:Real}, H::Hermitian)
+        uplo = sym_uplo(H.uplo)
+        return Hermitian(parentof_applytri($f, Hermitian(D, uplo), H), uplo)
+    end
+    @eval function $f(H::Hermitian, D::Diagonal{<:Real})
+        uplo = sym_uplo(H.uplo)
+        return Hermitian(parentof_applytri($f, H, Hermitian(D, uplo)), uplo)
+    end
+end
+
 ## Diagonal construction from UniformScaling
 Diagonal{T}(s::UniformScaling, m::Integer) where {T} = Diagonal{T}(fill(T(s.λ), m))
 Diagonal(s::UniformScaling, m::Integer) = Diagonal{eltype(s)}(s, m)
diff --git a/stdlib/LinearAlgebra/src/symmetric.jl b/stdlib/LinearAlgebra/src/symmetric.jl
index 6f778629b51b7..8cc07566c109e 100644
--- a/stdlib/LinearAlgebra/src/symmetric.jl
+++ b/stdlib/LinearAlgebra/src/symmetric.jl
@@ -277,21 +277,21 @@ diag(A::Hermitian) = hermitian.(diag(parent(A)), sym_uplo(A.uplo))
 
 function applytri(f, A::HermOrSym)
     if A.uplo == 'U'
-        f(UpperTriangular(A.data))
+        f(uppertriangular(A.data))
     else
-        f(LowerTriangular(A.data))
+        f(lowertriangular(A.data))
     end
 end
 
 function applytri(f, A::HermOrSym, B::HermOrSym)
     if A.uplo == B.uplo == 'U'
-        f(UpperTriangular(A.data), UpperTriangular(B.data))
+        f(uppertriangular(A.data), uppertriangular(B.data))
     elseif A.uplo == B.uplo == 'L'
-        f(LowerTriangular(A.data), LowerTriangular(B.data))
+        f(lowertriangular(A.data), lowertriangular(B.data))
     elseif A.uplo == 'U'
-        f(UpperTriangular(A.data), UpperTriangular(_conjugation(B)(B.data)))
+        f(uppertriangular(A.data), uppertriangular(_conjugation(B)(B.data)))
     else # A.uplo == 'L'
-        f(UpperTriangular(_conjugation(A)(A.data)), UpperTriangular(B.data))
+        f(uppertriangular(_conjugation(A)(A.data)), uppertriangular(B.data))
     end
 end
 parentof_applytri(f, args...) = applytri(parent ∘ f, args...)
diff --git a/stdlib/LinearAlgebra/src/triangular.jl b/stdlib/LinearAlgebra/src/triangular.jl
index 0cd5a49a0956d..fb9f6b2df9121 100644
--- a/stdlib/LinearAlgebra/src/triangular.jl
+++ b/stdlib/LinearAlgebra/src/triangular.jl
@@ -153,6 +153,12 @@ const UpperOrUnitUpperTriangular{T,S} = Union{UpperTriangular{T,S}, UnitUpperTri
 const LowerOrUnitLowerTriangular{T,S} = Union{LowerTriangular{T,S}, UnitLowerTriangular{T,S}}
 const UpperOrLowerTriangular{T,S} = Union{UpperOrUnitUpperTriangular{T,S}, LowerOrUnitLowerTriangular{T,S}}
 
+uppertriangular(M) = UpperTriangular(M)
+lowertriangular(M) = LowerTriangular(M)
+
+uppertriangular(U::UpperOrUnitUpperTriangular) = U
+lowertriangular(U::LowerOrUnitLowerTriangular) = U
+
 imag(A::UpperTriangular) = UpperTriangular(imag(A.data))
 imag(A::LowerTriangular) = LowerTriangular(imag(A.data))
 imag(A::UpperTriangular{<:Any,<:StridedMaybeAdjOrTransMat}) = imag.(A)
diff --git a/stdlib/LinearAlgebra/test/diagonal.jl b/stdlib/LinearAlgebra/test/diagonal.jl
index fd4ebfb714a37..7049dd784faa8 100644
--- a/stdlib/LinearAlgebra/test/diagonal.jl
+++ b/stdlib/LinearAlgebra/test/diagonal.jl
@@ -1277,6 +1277,12 @@ end
     @test c == Diagonal([2,2,2,2])
 end
 
+@testset "uppertriangular/lowertriangular" begin
+    D = Diagonal([1,2])
+    @test LinearAlgebra.uppertriangular(D) === D
+    @test LinearAlgebra.lowertriangular(D) === D
+end
+
 @testset "mul/div with an adjoint vector" begin
     A = [1.0;;]
     x = [1.0]
diff --git a/stdlib/LinearAlgebra/test/special.jl b/stdlib/LinearAlgebra/test/special.jl
index 7e96af369e310..148ccd85efeb1 100644
--- a/stdlib/LinearAlgebra/test/special.jl
+++ b/stdlib/LinearAlgebra/test/special.jl
@@ -536,4 +536,17 @@ end
     @test v * S isa Matrix
 end
 
+@testset "Partly filled Hermitian and Diagonal algebra" begin
+    D = Diagonal([1,2])
+    for S in (Symmetric, Hermitian), uplo in (:U, :L)
+        M = Matrix{BigInt}(undef, 2, 2)
+        M[1,1] = M[2,2] = M[1+(uplo == :L), 1 + (uplo == :U)] = 3
+        H = S(M, uplo)
+        HM = Matrix(H)
+        @test H + D == D + H == HM + D
+        @test H - D == HM - D
+        @test D - H == D - HM
+    end
+end
+
 end # module TestSpecial
diff --git a/stdlib/LinearAlgebra/test/symmetric.jl b/stdlib/LinearAlgebra/test/symmetric.jl
index 23556c6548742..25522042dcf2b 100644
--- a/stdlib/LinearAlgebra/test/symmetric.jl
+++ b/stdlib/LinearAlgebra/test/symmetric.jl
@@ -507,6 +507,31 @@ end
             @test Su - Sl == -(Sl - Su) == MSu - MSl
         end
     end
+    @testset "non-strided" begin
+        @testset "diagonal" begin
+            for ST1 in (Symmetric, Hermitian), uplo1 in (:L, :U)
+                m = ST1(Matrix{BigFloat}(undef,2,2), uplo1)
+                m.data[1,1] = 1
+                m.data[2,2] = 3
+                m.data[1+(uplo1==:L), 1+(uplo1==:U)] = 2
+                A = Array(m)
+                for ST2 in (Symmetric, Hermitian), uplo2 in (:L, :U)
+                    id = ST2(I(2), uplo2)
+                    @test m + id == id + m == A + id
+                end
+            end
+        end
+        @testset "unit triangular" begin
+            for ST1 in (Symmetric, Hermitian), uplo1 in (:L, :U)
+                H1 = ST1(UnitUpperTriangular(big.(rand(Int8,4,4))), uplo1)
+                M1 = Matrix(H1)
+                for ST2 in (Symmetric, Hermitian), uplo2 in (:L, :U)
+                    H2 = ST2(UnitUpperTriangular(big.(rand(Int8,4,4))), uplo2)
+                    @test H1 + H2 == M1 + Matrix(H2)
+                end
+            end
+        end
+    end
 end
 
 # bug identified in PR #52318: dot products of quaternionic Hermitian matrices,
diff --git a/stdlib/LinearAlgebra/test/triangular.jl b/stdlib/LinearAlgebra/test/triangular.jl
index 98334639c11e9..f37bf05650452 100644
--- a/stdlib/LinearAlgebra/test/triangular.jl
+++ b/stdlib/LinearAlgebra/test/triangular.jl
@@ -996,6 +996,14 @@ end
     end
 end
 
+@testset "uppertriangular/lowertriangular" begin
+    M = rand(2,2)
+    @test LinearAlgebra.uppertriangular(M) === UpperTriangular(M)
+    @test LinearAlgebra.lowertriangular(M) === LowerTriangular(M)
+    @test LinearAlgebra.uppertriangular(UnitUpperTriangular(M)) === UnitUpperTriangular(M)
+    @test LinearAlgebra.lowertriangular(UnitLowerTriangular(M)) === UnitLowerTriangular(M)
+end
+
 @testset "arithmetic with partly uninitialized matrices" begin
     @testset "$(typeof(A))" for A in (Matrix{BigFloat}(undef,2,2), Matrix{Complex{BigFloat}}(undef,2,2)')
         A[2,1] = eltype(A) <: Complex ? 4 + 3im : 4

From 65c1ecbc2ab875afa780c4cccab488284b09d4af Mon Sep 17 00:00:00 2001
From: Kristoffer Carlsson <kcarlsson89@gmail.com>
Date: Thu, 12 Sep 2024 11:23:53 +0200
Subject: [PATCH 19/22] bump to latest Pkg 1.11

---
 .../Pkg-2ff691035e9b2780cbd2fcb8dd30b640d85edde2.tar.gz/md5     | 1 -
 .../Pkg-2ff691035e9b2780cbd2fcb8dd30b640d85edde2.tar.gz/sha512  | 1 -
 .../Pkg-69938284d6804dd30a24577397f52dfdedbd37e1.tar.gz/md5     | 1 +
 .../Pkg-69938284d6804dd30a24577397f52dfdedbd37e1.tar.gz/sha512  | 1 +
 stdlib/Pkg.version                                              | 2 +-
 5 files changed, 3 insertions(+), 3 deletions(-)
 delete mode 100644 deps/checksums/Pkg-2ff691035e9b2780cbd2fcb8dd30b640d85edde2.tar.gz/md5
 delete mode 100644 deps/checksums/Pkg-2ff691035e9b2780cbd2fcb8dd30b640d85edde2.tar.gz/sha512
 create mode 100644 deps/checksums/Pkg-69938284d6804dd30a24577397f52dfdedbd37e1.tar.gz/md5
 create mode 100644 deps/checksums/Pkg-69938284d6804dd30a24577397f52dfdedbd37e1.tar.gz/sha512

diff --git a/deps/checksums/Pkg-2ff691035e9b2780cbd2fcb8dd30b640d85edde2.tar.gz/md5 b/deps/checksums/Pkg-2ff691035e9b2780cbd2fcb8dd30b640d85edde2.tar.gz/md5
deleted file mode 100644
index fe1a6a5d418b4..0000000000000
--- a/deps/checksums/Pkg-2ff691035e9b2780cbd2fcb8dd30b640d85edde2.tar.gz/md5
+++ /dev/null
@@ -1 +0,0 @@
-6f6793bcb797bfd2c48f52c631ce9479
diff --git a/deps/checksums/Pkg-2ff691035e9b2780cbd2fcb8dd30b640d85edde2.tar.gz/sha512 b/deps/checksums/Pkg-2ff691035e9b2780cbd2fcb8dd30b640d85edde2.tar.gz/sha512
deleted file mode 100644
index ea7ace0f5e812..0000000000000
--- a/deps/checksums/Pkg-2ff691035e9b2780cbd2fcb8dd30b640d85edde2.tar.gz/sha512
+++ /dev/null
@@ -1 +0,0 @@
-70a9e47694082ab3f999891e03a932d1d43f9a700de1c7943d943f11c98d0893dafa9ed19f585dfe1af9aa053c5db1efde4af55c26b824632afa057ecb97f07a
diff --git a/deps/checksums/Pkg-69938284d6804dd30a24577397f52dfdedbd37e1.tar.gz/md5 b/deps/checksums/Pkg-69938284d6804dd30a24577397f52dfdedbd37e1.tar.gz/md5
new file mode 100644
index 0000000000000..12ef870b31933
--- /dev/null
+++ b/deps/checksums/Pkg-69938284d6804dd30a24577397f52dfdedbd37e1.tar.gz/md5
@@ -0,0 +1 @@
+248ce4c4b85394431e71b6f555f82216
diff --git a/deps/checksums/Pkg-69938284d6804dd30a24577397f52dfdedbd37e1.tar.gz/sha512 b/deps/checksums/Pkg-69938284d6804dd30a24577397f52dfdedbd37e1.tar.gz/sha512
new file mode 100644
index 0000000000000..b51345f090447
--- /dev/null
+++ b/deps/checksums/Pkg-69938284d6804dd30a24577397f52dfdedbd37e1.tar.gz/sha512
@@ -0,0 +1 @@
+84f193d72062199f2791ba7f7c2b6eb547e1a97569ae20cbb3557bc291715dd0cf55b2e121c4829b4572929e97255fd53b9210a168a7fde36f09ae6cf76c7f40
diff --git a/stdlib/Pkg.version b/stdlib/Pkg.version
index 9c627070566a9..5729fc9f7c69d 100644
--- a/stdlib/Pkg.version
+++ b/stdlib/Pkg.version
@@ -1,4 +1,4 @@
 PKG_BRANCH = release-1.11
-PKG_SHA1 = 2ff691035e9b2780cbd2fcb8dd30b640d85edde2
+PKG_SHA1 = 69938284d6804dd30a24577397f52dfdedbd37e1
 PKG_GIT_URL := https://github.com/JuliaLang/Pkg.jl.git
 PKG_TAR_URL = https://api.github.com/repos/JuliaLang/Pkg.jl/tarball/$1

From 50c1ea848579ddc99e3c3633b85669988c2c89f2 Mon Sep 17 00:00:00 2001
From: Ian Butterworth <i.r.butterworth@gmail.com>
Date: Wed, 11 Sep 2024 11:50:05 -0400
Subject: [PATCH 20/22] Precompile the `@time_imports` printing so it doesn't
 confuse reports (#55729)

Makes functions for the report printing that can be precompiled into the
sysimage.

(cherry picked from commit 255162c7197e973d0427cc11d1e0117cdd76a1bf)
---
 base/loading.jl                | 94 +++++++++++++++++++++-------------
 contrib/generate_precompile.jl |  9 ++++
 2 files changed, 66 insertions(+), 37 deletions(-)

diff --git a/base/loading.jl b/base/loading.jl
index 43ffb2cf52ca2..0262ace997a09 100644
--- a/base/loading.jl
+++ b/base/loading.jl
@@ -1217,22 +1217,9 @@ function _include_from_serialized(pkg::PkgId, path::String, ocachepath::Union{No
         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  ")
-                ext_parent = extension_parent_name(M)
-                if ext_parent !== nothing
-                    print(ext_parent::String, " → ")
-                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
@@ -1244,6 +1231,52 @@ 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)
@@ -1301,31 +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
 
diff --git a/contrib/generate_precompile.jl b/contrib/generate_precompile.jl
index 92dde676244e4..e4eeeed577686 100644
--- a/contrib/generate_precompile.jl
+++ b/contrib/generate_precompile.jl
@@ -41,6 +41,8 @@ precompile(Base.__require_prelocked, (Base.PkgId, Nothing))
 precompile(Base._require, (Base.PkgId, Nothing))
 precompile(Base.indexed_iterate, (Pair{Symbol, Union{Nothing, String}}, Int))
 precompile(Base.indexed_iterate, (Pair{Symbol, Union{Nothing, String}}, Int, Int))
+precompile(Tuple{typeof(Base.Threads.atomic_add!), Base.Threads.Atomic{Int}, Int})
+precompile(Tuple{typeof(Base.Threads.atomic_sub!), Base.Threads.Atomic{Int}, Int})
 
 # Pkg loading
 precompile(Tuple{typeof(Base.Filesystem.normpath), String, String, Vararg{String}})
@@ -163,6 +165,8 @@ for match = Base._methods(+, (Int, Int), -1, Base.get_world_counter())
     push!(Expr[], Expr(:return, false))
     vcat(String[], String[])
     k, v = (:hello => nothing)
+    Base.print_time_imports_report(Base)
+    Base.print_time_imports_report_init(Base)
 
     # Preferences uses these
     get(Dict{String,Any}(), "missing", nothing)
@@ -174,6 +178,11 @@ for match = Base._methods(+, (Int, Int), -1, Base.get_world_counter())
     # interactive statup uses this
     write(IOBuffer(), "")
 
+    # not critical, but helps hide unrelated compilation from @time when using --trace-compile
+    foo() = rand(2,2) * rand(2,2)
+    @time foo()
+    @time foo()
+
     break   # only actually need to do this once
 end
 """

From a29fae6b6e83d155a38255671898857b22b20955 Mon Sep 17 00:00:00 2001
From: Kristoffer Carlsson <kcarlsson89@gmail.com>
Date: Mon, 16 Sep 2024 15:05:54 +0200
Subject: [PATCH 21/22] Revert "win: move stack_overflow_warning to the
 backtrace fiber (#55640)"

This reverts commit dde7c107871e775a0d2a4f5ef7f200269fa226ea.
---
 src/signals-win.c | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/signals-win.c b/src/signals-win.c
index 2b01310964ddb..a2980a0c063d9 100644
--- a/src/signals-win.c
+++ b/src/signals-win.c
@@ -109,8 +109,6 @@ static jl_ptls_t stkerror_ptls;
 static int have_backtrace_fiber;
 static void JL_NORETURN start_backtrace_fiber(void)
 {
-    // print the warning (this mysteriously needs a lot of stack for the WriteFile syscall)
-    stack_overflow_warning();
     // collect the backtrace
     stkerror_ptls->bt_size =
         rec_backtrace_ctx(stkerror_ptls->bt_data, JL_MAX_BT_SIZE, stkerror_ctx,

From 1c516dc002cca734c6afd621e765bb97c5b49e86 Mon Sep 17 00:00:00 2001
From: Gabriel Baraldi <baraldigabriel@gmail.com>
Date: Mon, 16 Sep 2024 15:58:40 -0300
Subject: [PATCH 22/22] Fix hang in tmerge_types_slow (#55757)

Fixes https://github.com/JuliaLang/julia/issues/55751

Co-authored-by: Jameson Nash <jameson@juliacomputing.com>
(cherry picked from commit 753296e89ddc484e54937ce7195a3f152fd5a14a)
---
 base/compiler/typelimits.jl |  1 +
 test/compiler/inference.jl  | 11 +++++++++++
 2 files changed, 12 insertions(+)

diff --git a/base/compiler/typelimits.jl b/base/compiler/typelimits.jl
index 318ac0b5c27e5..e5133f9aca0bf 100644
--- a/base/compiler/typelimits.jl
+++ b/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
diff --git a/test/compiler/inference.jl b/test/compiler/inference.jl
index f203d411a4424..a849ddbf982a8 100644
--- a/test/compiler/inference.jl
+++ b/test/compiler/inference.jl
@@ -5671,3 +5671,14 @@ end
 
 # fieldcount on `Tuple` should constant fold, even though `.fields` not const
 @test fully_eliminated(Base.fieldcount, Tuple{Type{Tuple{Nothing, Int, Int}}})
+
+# Issue https://github.com/JuliaLang/julia/issues/55751
+
+abstract type AbstractGrid55751{T, N} <: AbstractArray{T, N} end
+struct Grid55751{T, N, AT} <: AbstractGrid55751{T, N}
+    axes::AT
+end
+
+t155751 = Union{AbstractArray{UInt8, 4}, Array{Float32, 4}, Grid55751{Float32, 3, _A} where _A}
+t255751 = Array{Float32, 3}
+@test Core.Compiler.tmerge_types_slow(t155751,t255751) == AbstractArray # shouldn't hang