gnu: nemo: Update to 6.4.5.

* gnu/packages/cinnamon.scm (nemo): Update to 6.4.5.
[inputs]: Add json-glib.

Signed-off-by: Danny Milosavljevic <dannym@friendly-machines.com>

gnu: dpkg: Update to 1.22.21.

Fixes CVE-2025-6297.

* gnu/packages/debian.scm (dpkg): Update to 1.22.21.

Signed-off-by: Danny Milosavljevic <dannym@friendly-machines.com>

gnu: clamav: Update to 1.4.3.

Fixes CVE-2025-20234, CVE-2025-20260.

* gnu/packages/antivirus.scm (clamav): Update to 1.4.3.

Signed-off-by: Danny Milosavljevic <dannym@friendly-machines.com>

build-system/tree-sitter: Build with -std=c11.

* guix/build/tree-sitter-build-system.scm (install): Switch to
building with -std=c11.

Fixes: guix/guix#2215
Change-Id: I04f3ede07aeaaa9cf95272611d6346295f603b69
Signed-off-by: Danny Milosavljevic <dannym@friendly-machines.com>

gnu: go-connectrpc-com-connect: Enable tests.

* gnu/packages/golang-web.scm (go-connectrpc-com-connect) [source]
<snippet>: Delete submodules with their own go.mod.
[arguments] <tests?>: Run short unit tests.
<test-flags>: Skip some problematic tests.

Change-Id: If5019334ab41b37b1428c92be2ba15cb41723689

gnu: go-connectrpc-com-connect: Move to golang-web.

* gnu/packages/golang-xyz.scm (go-connectrpc-com-connect): Move from
here ...
* gnu/packages/golang-web.scm: ... to here.

* gnu/packages/ci.scm: Add golang-web module.

Change-Id: Ia255d3bfbe3e7da1202b2d40caa40fd63f4ecc65

gnu: Add python-whereismyip.

* gnu/packages/python-xyz.scm (python-whereismyip): New variable.

Change-Id: I7da706fb5c6e0ac3788397926f25b844a3b2d550
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-musical-scales: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-musical-scales):
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Remove python-wheel; add python-setuptools-next.
[home-page]: Fix URL.

Change-Id: Id77d49aa4e75f54aacb09b1ddc94e01eeccb6490
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-clrprint: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-clrprint):
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools-next.

Change-Id: I8f6f06925f84ef892f7c25d553d8f249ab1a856b
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-titlecase: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-titlecase):
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools-next.
[arguments] <phases>: Use custom 'check.

Change-Id: I0c52c3f815d0c7a44eed92b4cc9c5dbf25be23d0
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Remove python-colormath.

* gnu/packages/python-xyz.scm (python-colormath): Delete variable.
(python-colormath2): Do not inherit and adopt all missing fields from
python-colormath.
[native-inputs]: Remove python-setuptools, and python-wheel; add
python-setuptools-next, and python-pytest.

Change-Id: Ied54dda89d2078150fd4d832974f74cef980a1da
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: parallel: Update to 20250822.

* gnu/packages/parallel.scm (parallel): Update to 20250822.

Change-Id: I3ffd3f418df8a15f30083fa8e6cf16b9b554339e
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: shepherd: Update to 1.0.7.

* gnu/packages/admin.scm (shepherd-1.0): Update to 1.0.7.

Change-Id: I61474e237b6ca68baa9c60c19608664236dd47d9

gnu: zfs: Update to 2.3.4.

* gnu/packages/file-systems.scm (zfs): Update to 2.3.4.

Change-Id: I822df0d197552a0785ba20421772029db24ea918
Signed-off-by: Danny Milosavljevic <dannym@friendly-machines.com>

gnu: waybar-cpu-histogram: Update to 1.0.1.

* gnu/packages/wm.scm (waybar-cpu-histogram): Update to 1.0.1.

Change-Id: I06f39bdc5518e7465dfa7fbd703414027eb6beef
Signed-off-by: Danny Milosavljevic <dannym@friendly-machines.com>

gnu: Add rocm-hip-cpu.

* gnu/packages/rocm.scm (rocm-hip-cpu): New variable.

Change-Id: I0b459ab0fe4b2e7f6835b906d178488fcb702a99
Signed-off-by: Danny Milosavljevic <dannym@friendly-machines.com>

gnu: sentencepiece: Update to 0.2.1.

* gnu/packages/machine-learning.scm (sentencepiece): Update to 0.2.1.
[source]: Switch to git-fetch.

Change-Id: Ic5d8caa05355e2a87be0bbbb1ca16a62bcd6ce14
Signed-off-by: Danny Milosavljevic <dannym@friendly-machines.com>

gnu: python-sentencepiece: Inherit from sentencepiece.

* gnu/packages/machine-learning.scm (python-sentencepiece): Inherit from sentencepiece.
[arguments]: Add chdir #:phase.
[native-inputs]: Add protobuf.
[home-page]: Remove.
[license]: Remove.

Change-Id: I1072520b6786ded284cc28043fcfb356f748767e
Signed-off-by: Danny Milosavljevic <dannym@friendly-machines.com>

gnu: openmm: Update to 8.3.1.

* gnu/packages/machine-learning.scm (openmm): Update to 8.3.1.

Change-Id: Iccb86d75fd931959da1e004e6d9715dcc35e936d
Signed-off-by: Danny Milosavljevic <dannym@friendly-machines.com>

gnu: libsvm: Update to 3.36.

* gnu/packages/machine-learning.scm (libsvm)[source]: Switch to git-fetch.
[arguments]: Use G-Expressions.
<#:phases>{install}: Simplify.
* gnu/packages/machine-learning.scm (python-libsvm)[build-system]: Switch to
pyproject-build-system.
<#:phases>: Add chdir.
[native-inputs]: Add python-setuptools, python-wheel.
[propagated-inputs]: Add libsvm, python-scipy.
* gnu/packages/bioinformatics.scm (seek)[arguments]:
Adapt #:configure-flags accordingly.

Change-Id: Icf9f1081f037fb2fcda999a0c22e20d75d63c8c0
Signed-off-by: Danny Milosavljevic <dannym@friendly-machines.com>