gnu: coreutils: Skip another test on the Hurd.

This test fails after 9051aa1bd14559f37ae378105d00fc2d2ec4bbca.
Previously it got skipped because the mtab file was not found.

* gnu/packages/base.scm (coreutils): Skip 'cp/parent-perm-race' test on Hurd systems.

Change-Id: I5c33cf585878b802a66bb763d5e94eca6a82a6ca
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: hurd: Update to 0.9.git20251029.

* gnu/packages/commencement.scm (hurd-headers-boot0): Update to
0.9.git20251029.
* gnu/packages/hurd.scm (hurd-headers): Same.
[#:configure-flags]: Disable check for mach_port_set_ktype.

Change-Id: Ic6c98a679c32de3493b058a54d15691aa3397194
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: hurd: Update to 0.9.git20250801.

* gnu/packages/commencement.scm (hurd-headers-boot0): Update to
0.9.git20250801.
* gnu/packages/hurd.scm (hurd-headers): Same.
(hurd): Remove hurd-socket-activation.patch.
* gnu/packages/patches/hurd-socket-activation.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Deregister it.
* gnu/packages/patches/hurd-rumpdisk-no-hd.patch: Update patch.

Change-Id: I88f94a940c49a4d938e1e21e13df9815204d5d22
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: gnumach: Fix division by zero trap on x86_64.

* gnu/packages/patches/gnumach-div0.patch: New patch
* gnu/packages/hurd.scm (gnumach): Add it.
* gnu/local.mk (dist_patch_DATA): Register patch.

Change-Id: If2c096209a23619cafd55855e519674076c6a043
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: gnumach: Update to 1.8+git20250731.

* gnu/packages/commencement.scm (gnumach-headers-boot0): Update to 1.8+git20250731.
* gnu/packages/hurd.scm (gnumach-headers): Same.

Change-Id: I7387c5f20c06c9857782c0b48e8387f9c779e872
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

daemon: Use starts_with() and ends_with() instead of string() or hasSuffix()

* nix/libstore/build.cc (DerivationGoal::tryBuildHook): Use starts_with instead
of string()
* nix/libstore/builtins.cc (lookupBuiltinBuilder): Same.
* nix/libstore/builtins.hh (isBuiltin): Same and fix indentation of the file.
* nix/libstore/derivations.cc (DerivationOutput::parseHashInfo, isDerivation):
Same and clean header files.
* nix/libstore/gc.cc (addPermRoot, LocalStore::isActiveTempFile): Same.
* nix/libstore/globals.cc: Same.
* nix/libstore/local-store.cc: Same.
* nix/libstore/misc.cc: Same.
* nix/libstore/store-api.cc (checkStoreName): Same.
* nix/libutil/affinity.cc: Same.
* nix/libutil/archive.cc: Same.
* nix/libutil/spawn.cc: Same.
* nix/libutil/util.{cc, hh} (hasSuffix): Removed.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: tensorflow-lite: Update to 2.15.1.

* gnu/packages/machine-learning.scm (tensorflow-lite): Update to 2.15.1.

Change-Id: Ideb7605cb2cb6ddae7f53f5f6841522969ffbe83

gnu: tensorflow-lite: Adjust style.

* gnu/packages/machine-learning.scm (tensorflow-lite): Tweak whitespaces.
[native-inputs]: Remove labels.
Replace auto-generated git repository tarballs to git-fetch.

Change-Id: I5993c5accffff5b5831643ac2e221f26c899e0eb

gnu: tensorflow-lite: Fix package.

Fixes some breakages since the last python-team merge.

* gnu/packages/machine-learning.scm (tensorflow-lite) [arguments]
<#:configure-flags>: Access OpenCL headers through mesa-headers.
<#:phases>: Adapt phase 'build-python to process <#:configure-flags> properly,
in particular -DCMAKE_C_FLAGS and -DCMAKE_CXX_FLAGS.
[native-inputs]: Add python-setuptools and python-wrapper.
Remove python-wheel.
[inputs]: Replace python-wrapper by python.
Remove opencl-clhpp and opencl-headers, their content is already provided
through mesa-headers.

Change-Id: I77c287141238081e4df0c8df48f374d8d6aa5a82
Signed-off-by: Hilton Chain <hako@ultrarare.space>

profiles: package->manifest-entry: Filter packages.

The new Rust packaging model moves sources to inputs and there'll be
possiblity to have sources in propagated-inputs as well.

* guix/profiles.scm (package->manifest-entry): Filter packages.
* tests/profiles.scm ("package->manifest-entry, origin in propagated inputs"):
New test.

Change-Id: Id5b9ceb693a35760289b04cd9b8f208b4cbf2e35

gnu: Add ngs-bits.

* gnu/packages/bioinformatics.scm (ngs-bits): New variable.

Change-Id: I501cc8246aad6876c520d897ab6b9195b449db2a

gnu: Add python-modbedtools.

Change-Id: Ia35e2e1640e44766960b28f74786f8371878990e

gnu: Add python-weblogo.

* gnu/packages/bioinformatics.scm (python-weblogo): New variable.

Change-Id: Ib91f8d04d0df79eeb6039388e7ae6084fa245ad6

gnu: ncdu: Update to 2.9.2.

* gnu/packages/ncdu.scm (ncdu): Update to 2.9.2.

Change-Id: If09fa95b3c863b3032ba0e4ecd432dbba69b71ba

gnu: usbguard: Update to 1.1.4.

* gnu/packages/hardware.scm (usbguard): Update to 1.1.4.

Change-Id: I5fd8404f951c1e3aabc08c84381f3830f77989da

gnu: pacemaker: Update to 2.1.10.

* gnu/packages/high-availability.scm (pacemaker): Update to 2.1.10.

Change-Id: I5b3d035c6643ad61bedc94d6fe2eb985f78f3981

gnu: nats-server: Update to 2.12.1.

* gnu/packages/high-availability.scm (nats-server): Update to 2.12.1.
[inputs]: Add go-github-com-antithesishq-antithesis-sdk-go and
go-github-com-google-go-tpm.

Change-Id: I511c4c3543fdf4a7826631a41a272a6adf9577aa

gnu: Add go-github-com-antithesishq-antithesis-sdk-go.

* gnu/packages/golang-web.scm (go-github-com-antithesishq-antithesis-sdk-go): New variable.

Change-Id: I5f459eb2fe9b512695465c8362f1504fab85948a

gnu: go-github-com-nats-io-nats-go: Update to 1.47.0.

* gnu/packages/golang-xyz.scm (go-github-com-nats-io-nats-go): Update to 1.47.0.
[propagated-inputs]: Remove go-golang-org-x-text and go-google-golang-org-protobuf.
[native-inputs]: Remove go-github-com-nats-io-jwt-v2; add
go-google-golang-org-protobuf.

Change-Id: I1ca847e765844bc0eff9f940a088e0463834af42

gnu: go-github-com-nats-io-nkeys: Update to 0.4.11.

* gnu/packages/golang-crypto.scm (go-github-com-nats-io-nkeys): Update to 0.4.11.

Change-Id: Id3f7b20df87e0c15b68338116904229f8ffa2310