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Commit Graph

185216 Commits

Author SHA1 Message Date
Ricardo Wurmus
158098977f gnu: python-cell2cell: Update to 0.8.4.
* gnu/packages/bioinformatics.scm (python-cell2cell): Update to 0.8.4.

Change-Id: I0210208e0d61f46a707e352d45c9246c473200d0
2026-03-12 14:51:11 +01:00
Ricardo Wurmus
38917f00de gnu: python-gseapy: Update to 1.1.12.
* gnu/packages/bioinformatics.scm (python-gseapy): Update to 1.1.12.
* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
python-gseapy.

Change-Id: Ia912e4cb5aac93cb2aa523baccd9cc5bfbff6a6a
2026-03-12 14:51:11 +01:00
Cayetano Santos
eaed801e32 gnu: nextpnr: Update to 0.10.
* gnu/packages/patches/nextpnr-imgui.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Unregister it.
* gnu/packages/electronics.scm (nextpnr): Update to 0.10.
[sources]<#:snippet>: Keep ’imgui and ’qtimgui.
<#:patches>: Delete.
[inputs]: Replace pybind11-2 by pybind11; delete qtimgui.
[arguments]: Add ’fix-test #:phase.
* gnu/packages/electronics.scm (nextpnr-cli)[inputs]: Restore.

Merges guix/guix!6057

Change-Id: I2beb8629967b20309051a7ab8c67528742d080cc
2026-03-12 14:13:54 +01:00
Cayetano Santos
8be660ea5e gnu: apycula: Update to 0.31.
* gnu/packages/electronics.scm (apycula): Update to 0.31.
[inputs]: Remove python-crc.
[propagated-inputs]: Add python-cattrs, python-crcmod, python-numpy,
python-msgpack, and python-msgspec.
[native-inputs]: Add python-setuptools-scm.

Merges guix/guix!6057

Change-Id: Ie5c8950a2632a168ed4686f744c06704495f5ddf
2026-03-12 14:11:30 +01:00
Cayetano Santos
7ca9795c58 gnu: prjpeppercorn: Update to 1.12.
* gnu/packages/electronics.scm (prjpeppercorn): Update to 1.12.
[inputs]: Remove boost-1.88; add boost.

Merges guix/guix!6057

Change-Id: I337b0861c2628267db77db7ad2f8533973a3e5ca
2026-03-12 14:11:23 +01:00
Cayetano Santos
41bcf04f85 gnu: prjtrellis: Update dependencies.
* gnu/packages/electronics.scm (prjtrellis)[inputs]: Replace boost-1.88
by boost; replace pybind11-2 by pybind11.

Merges guix/guix!6057

Change-Id: I345cd8d5e652f014c9becffa0d4cec0365a9d4ba
2026-03-12 14:11:16 +01:00
crai0
46b660ac0b gnu: Add cocogitto.
* gnu/packages/rust-apps.scm (cocogitto): New variable.
* gnu/packages/rust-crates.scm: Add crates for cocogitto.

Change-Id: I022acd6727e22adeff0df011e7d56c4653217b4f
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2026-03-12 14:59:05 +02:00
Spencer King
51ca2c0da1 gnu: Add deacon.
* gnu/packages/bioinformatics.scm (deacon): New variable.
* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Add entry for
deacon.

Change-Id: I148a0bdc56abf5dbe68a8cdf81f6fe2944645f4d
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2026-03-12 14:10:13 +02:00
Sharlatan Hellseher
391200d054 gnu: go-1.25: Update to 1.25.8 [security-fixes].
go1.25.8 (released 2026-03-05) includes security fixes to the
html/template, net/url, and os packages, as well as bug fixes to the go
command, the compiler, and the os package.

See: <https://github.com/golang/go/compare/go1.25.7...go1.25.8>,
<https://www.openwall.com/lists/oss-security/2026/03/06/1>

Containes fixes for:
CVE-2026-27142: URLs in meta content attribute actions are not escaped
                in html/template.
CVE-2026-25679: Incorrect parsing of IPv6 host literals in net/url.
CVE-2026-27139: FileInfo can escape from a Root in os.

* gnu/packages/golang.scm (go-1.25): Update to 1.25.8.

Change-Id: I01a80a78f20075fe6c05c46f97dfe35f770a99a0
2026-03-12 11:18:05 +00:00
Sharlatan Hellseher
ac0efb2c97 gnu: go-1.26: Update to 1.26.1 [security-fixes].
go1.26.1 (released 2026-03-05) includes security fixes to the
crypto/x509, html/template, net/url, and os packages, as well as bug
fixes to the go command, the go fix command, the compiler, and the os
and reflect packages.

See: <https://github.com/golang/go/compare/go1.26.0...go1.26.1>,
<https://www.openwall.com/lists/oss-security/2026/03/06/1>

Containes fixes for:
CVE-2026-27137: Incorrect enforcement of email constraints in
                crypto/x509.
CVE-2026-27138: Panic in name constraint checking for malformed
                certificates in crypto/x509.
CVE-2026-27142: URLs in meta content attribute actions are not escaped
                in html/template.
CVE-2026-25679: Incorrect parsing of IPv6 host literals in net/url.
CVE-2026-27139: FileInfo can escape from a Root in os.

* gnu/packages/golang.scm (go-1.26): Update to 1.26.1.

Change-Id: I1c014a334407d9ca927d9e403c8c7e92cad8fe1d
2026-03-12 11:17:56 +00:00
Efraim Flashner
952a8d75d8 gnu: git-cliff: Install manpage and shell completions.
* gnu/packages/version-control.scm (git-cliff)[arguments]: Add a phase
to generate and install the manpage and the shell completions.

Change-Id: Ib548fed6cd03f21c0dade2d773fcf8146638dc5b
2026-03-12 12:56:53 +02:00
Aaron Covrig
17f966389b gnu: Add git-cliff.
* gnu/packages/version-control.scm (git-cliff): New variable.
* gnu/packages/rust-crates.scm: Add dependencies for git-cliff.

Change-Id: I9369a4e2a94b46a0d8085f502159f5a87e671002
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2026-03-12 12:42:45 +02:00
Steve George
a1125cec7b gnu: jujutsu: Update to 0.39.0.
* gnu/packages/rust-apps.scm (jujutsu): Update to 0.39.0.
  [arguments]<cargo-test-flags>: skip test_push_updates_with_options.

Change-Id: I8d9dfa16856a67263167a3ef63def9e722f9176c
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2026-03-12 12:08:28 +02:00
Efraim Flashner
362fe5e09c gnu: rust-hashify-0.2.7.b787649: Make regular cargo source.
* gnu/packages/rust-crates.scm (rust-hashify-0.2.7.b787649): Rename to
rust-hashify-0.2.7.b787649-for-pimsync, use git-fetch.
(lookup-cargo-inputs): Adjust accordingly.
* gnu/packages/rust-sources.scm (rust-hashify-0.2.7.b787649): Remove
variable.

Change-Id: Ia2c68a8df078a35abf6b60ebdc526a2a006b0999
2026-03-12 12:04:00 +02:00
Cayetano Santos
cbfed3a6a5 gnu: openfpgaloader: Update to 1.1.1.
* gnu/packages/flashing-tools.scm (openfpgaloader): Update to 1.1.1.
[arguments]: Update ’install-rules #:phase.

Change-Id: Ia291e91534141f7c4eed6234d46a906debcaf7b9
2026-03-12 10:11:41 +01:00
Efraim Flashner
1eed2746e4 gnu: dmd-bootstrap: Use gdb/pinned.
* gnu/packages/dlang.scm (dmd-bootstrap)[native-inputs]: Replace gdb
with gdb/pinned.

Change-Id: I64c1ea0fbe6cfd994cfa504c256c7ece8d756eb1
2026-03-12 10:38:19 +02:00
Liliana Marie Prikler
0adf301971 gnu: lager: Update to 0.1.3.
* gnu/packages/cpp.scm (lager): Update to 0.1.3.
2026-03-12 08:57:23 +01:00
Liliana Marie Prikler
dfb1b7d18d gnu: zug: Update to 0.1.2.
* gnu/packages/cpp.scm (zug): Update to 0.1.2.
2026-03-12 08:57:23 +01:00
Liliana Marie Prikler
dc597e30fe gnu: immer: Update to 0.9.1.
* gnu/packages/cpp.scm (immer): Update to 0.9.1.
[#:configure-flags]: Drop “-DDISABLE_WERROR=ON”.
2026-03-12 08:57:23 +01:00
Sergey Trofimov
df01541cde gnu: emacs-telega: Update to 0.8.601.
* gnu/packages/emacs-xyz.scm (emacs-telega): Update to 0.8.601.
[propagated-inputs]: Remove emacs-company which is optional.
[native-inputs]: Delete empty list.

Change-Id: I77245943014043b4278e094192ca02b11f8b3e6c
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:23 +01:00
Noé Lopez
171b21a8f7 gnu: Remove guile-gnome.
* gnu/packages/gtk.scm (guile-gnome): Remove.

Closes <https://issues.guix.gnu.org/34499>.
Closes guix/guix#6300.

Change-Id: I16314205d939ced3803c390cf3853db26b2f6051
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:23 +01:00
Jonas Meeuws
54d5bf9a38 gnu: d-demangler: Update synopsis and description.
gnu/packages/dlang.scm (d-demangler) [synopsis, description]: Remove mention
of a non-existent command.  Refer to the package as a library.  Note that this
only wraps D's ‘std.demangle’.

Change-Id: I8fe98d4bb031f8f50468a4c1a5b907d3ff24de0c
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:23 +01:00
Jonas Meeuws
b923081da0 gnu: d-demangler: Reformat.
* gnu/packages/dlang.scm (d-demangler): Reformat.

Change-Id: I910f786afbc1fe4819ca9b1081a89553213bde2f
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:23 +01:00
Jonas Meeuws
f1d06ca5f7 gnu: dmd: Reformat.
* gnu/packages/dlang.scm (dmd-bootstrap, dmd): Reformat.

Change-Id: I93ac5dff7a57138343e46b57f8d18121fec4cc20
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:23 +01:00
Jonas Meeuws
fc67e0bb2f gnu: dmd: Reinstate tests.
* gnu/packages/dlang.scm (dmd-bootstrap)
[#:phases]: Add ‘patch-tests’.
[native-inputs]: Add gdb.

* gnu/packages/dlang.scm (dmd)
[arguments]: Strip ‘#:tests?’.

Change-Id: I2208f9a74749c366fc32f7c885d1773955d041a8
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:23 +01:00
Jonas Meeuws
6000c99766 gnu: dmd: Update to 2.111.0.
* gnu/packages/dlang.scm (dmd-bootstrap): Update to 2.111.0.
[#:make-flags]: Remove deprecated “-f posix.mak”.
[#:phases]<patch-git-ls-tree>: Apply ‘substitute*’ to “Makefile” instead of
the deprecated “posix.mak”.
[supported-systems]: Add aarch64-linux (experimental).

Change-Id: Ia9be09edfe7790e8e0989b2ce473dd65e66f4cb7
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:23 +01:00
Jonas Meeuws
0cb07b2acd gnu: dmd: Improve packaging.
* gnu/packages/dlang.scm (dmd-bootstrap)
[#:make-flags]: Remove unneeded “DFLAGS=-L--allow-multiple-definition”.
[#:modules]: Move here from dmd.  Add (srfi srfi-26).
[#:phases]: Add ‘patch-git-ls-tree’, ‘patch-paths-in-phobos‘.
Remove ‘copy-phobos-source-and-chdir’ in favor of custom ‘unpack’.
Remove ‘adjust-phobos-install-dirs’, ‘install-druntime’, ‘install-includes’,
‘install-dmd’, ‘refine-install-layout’, ‘patch-dmd.conf’ in favor of custom
‘install’.
<unpack>: Replace with a copy of the gnu phase, but unpack the 2 sources to
“source/dmd” and “source/phobos”.
<build>: Replace.  Run gnu ‘build’ in dmd subdir.
<build-phobos>: New phase.  Run gnu ‘build’ in phobos subdir.
<check>: Replace.  Run gnu ‘check’ in dmd subdir.
<check-phobos>: New phase.  Run gnu ‘check’ in phobos subdir.
<install>: Replace with custom install script, that gets everything right the
first time.  Shared libraries get installed to “lib/lib“, static libraries to
“out/lib”.  Include files are installed to “out/include/d/dmd” to avoid
conflicts with other compilers.
<install-license-files>: Replace.  Run gnu ‘install-license-files’ in the dmd
subdir.
[inputs]: Add bash-minimal (for std.process).

* gnu/packages/dlang.scm (dmd)
[#:modules]: Move to dmd-bootstrap.
[#:make-flags]: Don't delete “DFLAGS=-L--allow-multiple-definition” as it no
longer exists.
[#:phases]<rewrite-references-to-bootstrap>: Rebase the ‘add-after’ on the
‘install’ phase.  Simplify discovery of the executable.
[native-inputs]: Substitute replacing gdmd with dmd-bootstrap for remove and
append.
[outputs]: Add “lib” (for “.so” files) and “debug”.

Change-Id: If0d5e1a2e4a45a26252b886aaa0ac91d9814e4fe
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:22 +01:00
Jonas Meeuws
0a716ce224 gnu: dmd: Disable no-op tests.
* gnu/packages/dlang.scm (dmd)[arguments]: Don't reinstate tests.  Add a
comment explaining the reasoning.

Change-Id: I8ad8d6cd63b7f5b148ae448d6b4521398837208c
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:22 +01:00
Jonas Meeuws
1183614bbe gnu: Reorganize dlang.scm.
* gnu/packages/dlang.scm: Add additional section comments.
[d-tools]: Move down.

Change-Id: Ic0ac1ded1e7171d78a75d18bb2ff85e9ee50b303
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:22 +01:00
Jonas Meeuws
b7d24094ac gnu: gdmd: Update to 0.26.0.
Change-Id: I3435e05606629e908a0ceba9c11a1438e4a2e9b9
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:22 +01:00
Jonas Meeuws
9ae76a34d7 gnu: gdmd: Alias to gdmd-14.
* gnu/packages/gcc.scm (gdmd): Redefine as an alias to gdmd-14.  Avoids
ambiguous package specification warnings and executing make-gdmd twice.

Change-Id: I45455d4b3f547d8d77bc46a553102eebf727b45e
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:22 +01:00
Jonas Meeuws
734f27f40b gnu: Add gdmd-15.
* gnu/packages/gcc.scm (gdmd-15): New variable.

Change-Id: Ie0ca533fc682e8b253d6ec1704d983defd9af210
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:22 +01:00
Jonas Meeuws
da9924996d gnu: Add gdmd-14.
* gnu/packages/gcc.scm (gdmd-14): New variable.

Change-Id: Ia48a712e6a467ba19b6e076a4e4e02c348562264
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:22 +01:00
Jonas Meeuws
ae5e8e6f38 gnu: Add gdmd-13.
* gnu/packages/gcc.scm (gdmd-13): New variable.

Change-Id: Icfb019980c92044bd2ed4a2e1457702a67db206c
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:22 +01:00
Jonas Meeuws
78a99ae8df gnu: Add gdmd-12.
* gnu/packages/gcc.scm (gdmd-12): New variable.

Change-Id: I5e67d746d44200ba3eb98a4329be0cac3f996ac1
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:22 +01:00
Jonas Meeuws
8741d3ac63 gnu: Add gdmd-11.
* gnu/packages/gcc.scm (gdmd-11): New variable.

Change-Id: Ic42eead141efc199c867ac80d44b1e083cc76bd3
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:22 +01:00
Jonas Meeuws
4415dfd7d1 gnu: Add gdmd-10.
* gnu/packages/gcc.scm (gdmd-10): New variable.

Change-Id: I2473a0078934dcde937395c5dba0fb62c703725d
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:22 +01:00
Jonas Meeuws
36a763ebcc gnu: Add gdmd-9.
* gnu/packages/gcc.scm (gdmd-9): New variable.

Change-Id: I9e10f6ff88122761baa3c751e8cfbe6c7708c168
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:22 +01:00
Jonas Meeuws
7026105c94 gnu: gdmd: Base version on the wrapped gdc version.
* gnu/packages/gcc.scm (make-gdmd): New private procedure.
(gdmd): Implement in terms of make-gdmd.

Change-Id: I3fc2ce8af7ca3489a8f3bf4d607b530083a900b1
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:22 +01:00
Jonas Meeuws
79f19d37da gnu: gdmd: Reformat.
* gnu/packages/gcc.scm (gdmd): Reformat.

Change-Id: I107ae3bf5ab982dccdaf5450bd7ed3937da3b192
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:21 +01:00
Jonas Meeuws
02fea8e954 gnu: gdmd: Update to 0.25.0.
* gnu/packages/gcc.scm (gdmd): Update to 0.25.0.
[source]: Prefix git tag with “script-”.

Change-Id: Icab7bb068d87e3813b15d1c360fb593ee5eac716
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:21 +01:00
Jonas Meeuws
4c5cce5c44 gnu: gdmd: Move to gcc.
* gnu/packages/dlang.scm (gdmd): Move from here ...
* gnu/packages/gcc.scm: ... to here.

Change-Id: I43fa2f66f812edc6c74442c7d911fe902265f5e0
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:21 +01:00
Jonas Meeuws
7d203df47b gnu: Add gdc-15.
* gnu/packages/gcc.scm (gdc-15): New public variable.

Change-Id: Ib8e2d6ca8bab3c0412b7d59b7acd40e075f61d74
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:21 +01:00
Jonas Meeuws
f4aa217a16 gnu: Add gdc-13.
* gnu/packages/gcc.scm (gdc-13): New public variable.

Change-Id: If7ac081ece1185da1004adf90027e412ae471ae8
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:21 +01:00
Jonas Meeuws
97091b854f gnu: Add gdc-12.
* gnu/packages/gcc.scm (gdc-12): New public variable.

Change-Id: Ic5711bc318aeb766763e3dfc6f1da81a340b8c7b
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:21 +01:00
Jonas Meeuws
5310af43cd gnu: Add gdc-10.
* gnu/packages/gcc.scm (gdc-10): New public variable.

Change-Id: I74e8ed8c635e2f80af5b5504e4d2de97aed188a5
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:21 +01:00
Jonas Meeuws
d06610cb8a gnu: Add gdc-9.
* gnu/packages/gcc.scm (gdc-9): New public variable.

Change-Id: I059397ce7ee398c1ed8b6cfcc1d294916c64203a
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:21 +01:00
Jonas Meeuws
5b8d122129 gnu: gdc: Add intermediary gdc-14 variable.
* gnu/packages/gcc.scm (gdc-14): New variable, renamed from gdc.
(gdc): Redefine as an alias for gdc-14.

Change-Id: Ic2f4252fb75da703c9048b74c66026eda249023b
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:21 +01:00
Jonas Meeuws
298ed1adc6 gnu: gdc: Support GCC 9 through 15 with cleaner packaging.
* gnu/packages/gcc.scm (make-gdc): New variable.  This procedure returns a
package based on the previous gdc-11 and gdc definitions.
[#:modules]: Add (ice-9 ftw).
[#:configure-flags]: Add “--disable-c++tools” and “--disable-plugin”.
Add “--disable-libcc1”, “--disable-libatomic” (since version 11),
“--disable-libcc1”, “--disable-libgomp”, “--disable-libitm”,
“--disable-libquadmath”, “--disable-libsanitizer”, “--disable-libssp”, and
“--disable-libstdcxx” (until version 15).
[#:phases]: Add ‘gdc-cleanup-install’.
[inputs]: Add gcc:lib.
[synopsis]: Override the one inherited from gcc.
[description]: Override the one inherited from gcc.  Append a frontend version
note if such version was provided as argument.
[home-page]: Override the one inherited from gcc.
(gdc-11): Implement in terms of make-gdc.  Make public.
(gdc): Implement in terms of make-gdc, with gdc-11 as bootstrap-gdc
argument.  Make public.

Change-Id: I44d351f8c97427a6bbd1821f9547ae680a154b06
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2026-03-12 08:57:20 +01:00
jgart
e7771eb39d gnu: lilypond: Downgrade to 2.24.4.
* gnu/packages/music.scm (lilypond): Downgrade to 2.24.4.

This package should track the stable release of LilyPond.

Change-Id: I3a4ae814a719961039a8b7180e8dbd4d8ecc5012
2026-03-12 13:18:13 +05:30