biology/py-goatools: Fix some dependency issues
Patch out obsolete py-setuptools_scm_git_archive dependency
Basic run-testing performed
New maintainer: patrick at crandol.com
Patches have been submitted to upstream
PR: 300072
Reported by: patrick at crandol.com
[AMDGPU] Price under-aligned memory operations
Without unaligned access for the address space, an access aligned below
4 bytes is split into pieces of its alignment. LDS accesses aligned to 4
use 8-byte pieces, and take a 12-byte piece only when aligned to 16 or
when unaligned DS access is enabled.
[AMDGPU] Price memory operations by the number of memory instructions
Price a load or store as the number of memory instructions it is split
into.
Constant and buffer "fat" pointers are left alone (for now).
[OpenMP][omptest] Run the ompTest unit tests on the AMDGPU clang-flang bot
ompTest ships unit tests that register as check-ompt-omptest, but
LIBOMPTEST_BUILD_UNITTESTS defaults to OFF, so no buildbot builds or runs
them. Its install rules are likewise never exercised.
Enable both on the openmp-offload-amdgpu-clang-flang bot, which already runs
check-openmp and installs.
Assisted-by: Claude Opus 5 <noreply at anthropic.com>
[OpenMP][omptest] Install the package config at a target-independent path
Make it predictable where the installed cmake config lands in presence
of LLVM_ENABLE_PER_TARGET_RUNTIME_DIR.
Install it under lib${LLVM_LIBDIR_SUFFIX}/cmake, which does not depend
on the target. The library itself stays next to libomp; the generated files
resolve their prefix relative to the config, so nothing else changes.
Assisted-by: Claude Opus 5 <noreply at anthropic.com>
[OpenMP][omptest] Export the standalone build mode to library users
OmptTester.h picks its test-case implementation from
OPENMP_LIBOMPTEST_BUILD_STANDALONE, but the definition was PRIVATE and never
reached users of an installed ompTest: they pulled in the GoogleTest variant
against a standalone libomptest and failed to link.
Make it PUBLIC so the exported target carries it, and consumers select the
header matching the library without having to know how it was built.
Assisted-by: Claude Opus 5 <noreply at anthropic.com>
[OpenMP][omptest] Fix target dependency on runtimes GTest
Linking default_gtest PUBLIC puts it into omptest's link interface, so
install(EXPORT) fails with "requires target runtimes_gtest that is not in any
export set".
Only GTest's include directories and compile definitions are needed, and only
while building, so attach those behind BUILD_INTERFACE. Embedding the GTest
objects is unchanged.
pf: fix pf_krule_item memory leak during counters:match_fail
If pf_counters_inc() did not increment the counters because the rule
failed to apply it potentially failed to free match rules (which were
not bound to a state already).
Do so.
While here explicitly hand match_rules over from the pf_test_ctx to the
state so we never list them in two places.
Sponsored by: Rubicon Communications, LLC ("Netgate")
pf: remove armv7-specific counter code
The armv7 specific counter code is less useful now that armv7 is
basically end-of-life.
This removes a lot of armv7-specific code.
Sponsored by: Rubicon Communications, LLC ("Netgate")
pf: have DIOCXBEGIN/DIOCXROLLBACK/DIOCXCOMMIT use the new functions
The netlink begin/rollback/commit code has separate functions for this.
Deduplicate the code and just use those functions.
Sponsored by: Rubicon Communications, LLC ("Netgate")
markdown-editor: Add markdown-editor-2.10.0
Markdown-editor is a lightweight, native WYSIWYG Markdown editor written in
C++ with Qt6 (no Electron). It supports TeX formulas, Mermaid/PlantUML
diagrams, document tabs, spell checking, export to PDF, HTML, LaTeX, ODT,
DOCX and EPUB, and provides its user interface in nine languages.
tests: Expect the legacy arch name in altabi on all OSes.
pkg_arch_to_legacy() translates the arch the same way regardless of OS,
so on aarch64 Linux "pkg config altabi" reports linux:<ver>:aarch64:64.
The native test only applied that translation on FreeBSD and failed on
aarch64 Linux. x86_64, the only Linux arch CI covers, is not translated,
which is why this went unnoticed.
Compute the expected altabi after the per-OS handling instead.
Co-Authored-By: Claude Opus 5.5 <noreply at anthropic.com>
tests: Run the fingerprint tests on Linux.
They were skipped there because dash, the /bin/sh on Debian and Ubuntu,
rejected the "read -t" in the signing script. With the script now
portable they pass on Ubuntu 24.04.
Co-Authored-By: Claude Opus 5.5 <noreply at anthropic.com>
tests: Check that the fingerprint tests' repository was accepted.
The fingerprint tests only checked that pkg update extracted the
signature, not that the repository was accepted, so a signature that
failed to verify went unnoticed. Add a check_loaded helper that checks
with rquery that the catalogue was actually loaded, and use it in every
fingerprint test.
Co-Authored-By: Claude Opus 5.5 <noreply at anthropic.com>
Answer whether a file has a POSIX ACL from statx
filesystem.stat and filesystem.listdir learn whether a file has an ACL
by listing its xattrs, unless ZFS reports the NFSv4 ACL trivial in
stx_zfsflags, which it does on NFSv4 ACL datasets alone. So every file
of a POSIX ACL dataset costs a listxattr. The TrueNAS kernel now
answers STATX_ACL from the ACLs the inode caches, with
STATX_ATTR_ACL_ACCESS for an access ACL and STATX_ATTR_ACL_DEFAULT for
a default one.
STATX_DEFAULT_MASK asks STATX_ACL, and zfs_acl_is_trivial becomes
statx_acl_is_trivial, which takes the two bits where the kernel
answered and the trivial flag of ZFS otherwise, so a file with no ACL
needs no listxattr on either acltype. It needs truenas_pyos with
STATX_ACL, whose iter_filesystem_contents asks it for each entry.
A unit test sets an access ACL on a file and a default ACL on a folder
in the temporary folder, which keeps POSIX ACLs on tmpfs, checks the
answer for each, and checks that listdir lists the xattrs of the two
with an ACL alone. It needs a kernel with the change.
