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145570 commits

Author SHA1 Message Date
Ludovic Courtès
58a8d3b180
tests: Adjust ‘guix build -P1’ test to new packages.
Fixes a bug introduced in 794e079437
whereby the grep patterns used in this test would also match
/gnu/store/…-rust-libgit2-sys-0.17.0+1.8.1.drv, thus getting 5 matches
instead of 4.

* tests/guix-build.sh: Refine grep patterns for ‘guix build -P1’ test.

Reported-by: Janneke Nieuwenhuizen <janneke@gnu.org>
Change-Id: Iae35e6ee44b8eca0ef66c1d8ab7f9ff65a59d8d0
2024-12-02 23:18:52 +01:00
Ricardo Wurmus
d97a67d41d
gnu: homer: Install config.txt.
* gnu/packages/bioinformatics.scm (homer)[native-inputs]: Add config.txt.
[arguments]: Update 'configure phase to place config.txt in expected location;
patch configuration code to optionally load a user's configuration file.

Change-Id: Ib05c828e751c6568524bbef45997a42fade4545a
2024-12-02 13:41:08 +01:00
Ricardo Wurmus
af774e2780
gnu: homer: Install homer executable.
* gnu/packages/bioinformatics.scm (homer)[arguments]: Update 'install phase to
also install "homer" to the bin directory.

Change-Id: Ia2d23fce493f9c10cc43ac126cd83956b4b9bb05
2024-12-02 13:41:08 +01:00
Efraim Flashner
541abedc0a
Merge remote-tracking branch 'origin/rust-team'
Change-Id: I6d5c28252f060eeb69eb02fd281e7268bb885b29
2024-12-02 14:13:39 +02:00
Efraim Flashner
b764dbc319
gnu: zstd: Fix cross-building to mingw32.
* gnu/packages/compression.scm (zstd)[arguments]: Adjust the custom
'adjust-library-locations phase to have separate logic for targeting
mingw32.  Adjust the make-flags to add some extra flags when targeting
mingw32.

Change-Id: Ifd32a6bd9157af93c7338dacc96467e2756b9314
2024-12-02 13:54:08 +02:00
Efraim Flashner
767bfcb45c
gnu: redis: Add comment about upcoming license change.
* gnu/packages/databases.scm (redis): Add a note with the package to be
aware of the upcoming non-free license change.

Change-Id: I60ef9bce81b6650d88f567e98c5bcf543a13082e
2024-12-02 13:54:04 +02:00
Greg Hogan
522732d5c1
packages: 'package-input-rewriting/spec' optionally replace hidden.
Commit eee95b5a87 changed package
rewriting to ignore hidden packages. This patch permits the previous use
by adding an option to rewrite hidden packages.

* guix/packages.scm (package-input-rewriting/spec)[rewrite]: When P is
hidden, return it as-is unless #:replace-hidden? has been enabled.
* tests/packages.scm ("package-input-rewriting/spec, replace hidden
package"): New test.
* doc/guix.texi (Defining Package Variants): Update.

Change-Id: I0a7988cac70e0c6b88b0fe6e27c1036fa723e030
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-12-02 12:00:52 +01:00
Arne Babenhauserheide
62f8399e6a
pack: Add ‘--file=FILE’ with the same meaning as for ‘guix build’.
* guix/scripts/pack.scm (%options): add --file=FILE, but no
  shorthand (that’s already taken for format).
* doc/guix.texi (Invoking guix pack): Document it.

Change-Id: I87797fccdf218ead3b7f471a84034e8a8d566245
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-12-02 11:57:13 +01:00
Ludovic Courtès
fb41002935
maint: Run ‘etc/upgrade-manifest.scm’ in a UTF-8 locale.
* etc/upgrade-manifest.scm: Add calls to ‘setlocale’ to force a UTF-8
locale.

Change-Id: Ia567a1e08124d9eab7fb32f3363681a8f37431b1
2024-12-02 11:55:09 +01:00
Ricardo Wurmus
2756c660fb
gnu: python-pairtools: Update to 1.1.0-fix.
* gnu/packages/bioinformatics.scm (python-pairtools): Update to 1.1.0-fix.
[build-system]: Use pyproject-build-system.
[arguments]: Add phase 'patch-setup.py.
[native-inputs]: Add python-pytest-cov, python-setuptools, and python-wheel.

Change-Id: Ifa3c12de228420d8fdd7b0053bb9da80b9b3efe4
2024-12-02 10:49:06 +01:00
Ricardo Wurmus
207c69e40d
gnu: Add macs-3.
* gnu/packages/bioinformatics.scm (macs-3): New variable.

Change-Id: I4bc417e90a1e9d6d28226ea4f66ddc035826c2c4
2024-12-02 10:28:59 +01:00
Ricardo Wurmus
1f047996b8
gnu: python-hmmlearn: Update to 0.3.3.
* gnu/packages/machine-learning.scm (python-hmmlearn): Update to 0.3.3.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add phases 'set-core-count and
'build-extensions.
[propagated-inputs]: Remove pybind11 and python-setuptools-scm.
[native-inputs]: Add pybind11, python-setuptools-scm, and util-linux.
[properties]: Add hints for the updater.

Change-Id: I1acb69c74ae9c4a508fe28cdaf834d258e7778ff
2024-12-02 10:28:59 +01:00
Ricardo Wurmus
ed1266ea8c
import/crate: Fix typo.
guix/import/crate.scm (lookup-crate): Fix typo in docstring.

Change-Id: I5492387b93b27ab42999d5984fa7f02e8bee11e2
2024-12-02 10:28:59 +01:00
Ricardo Wurmus
30c2403a85
gnu: Add python-cykhash.
* gnu/packages/python-xyz.scm (python-cykhash): New variable.

Change-Id: I7f46da1f53b10957c102ca21e74f144955676730
2024-12-02 10:28:59 +01:00
Thanos Apollo
ca3a79ccee
gnu: emacs-gnosis: Update to 0.4.8.
* gnu/packages/emacs-xyz.scm (emacs-gnosis): Update to 0.4.8.
[home-page]: Add ending slash.
[synopsis]: Remove ending period.
[description]: Use two spaces after sentence.

Change-Id: Ie80016fc190e66695b7a8ea8e3fded7854ebc872
Signed-off-by: Hilton Chain <hako@ultrarare.space>
2024-12-02 07:49:50 +08:00
Ian Eure
41fd9cfc65
gnu: librewolf: Update to 133.0-1 [security fixes].
New upstream version.  Fixes CVEs:

CVE-2024-11691: Out-of-bounds write in Apple GPU drivers via WebGL
CVE-2024-11700: Potential Tapjacking Exploit for Intent Confirmation
                on Android
CVE-2024-11692: Select list elements could be shown over another site
CVE-2024-11701: Misleading Address Bar State During Navigation
                Interruption
CVE-2024-11702: Inadequate Clipboard Protection in Private Browsing
                Mode on Android
CVE-2024-11693: Download Protections were bypassed by .library-ms
                files on Windows
CVE-2024-11694: CSP Bypass and XSS Exposure via Web Compatibility
                Shims
CVE-2024-11695: URL Bar Spoofing via Manipulated Punycode and
                Whitespace Characters
CVE-2024-11703: Password access without authentication via PIN bypass
                on Android
CVE-2024-11696: Unhandled Exception in Add-on Signature Verification
CVE-2024-11697: Improper Keypress Handling in Executable File
                Confirmation Dialog
CVE-2024-11704: Potential Double-Free Vulnerability in PKCS#7
                Decryption Handling
CVE-2024-11698: Fullscreen Lock-Up When Modal Dialog Interrupts
                Transition on macOS
CVE-2024-11705: Null Pointer Dereference in NSC_DeriveKey
CVE-2024-11706: Null Pointer Dereference in PKCS#12 Utility
CVE-2024-11708: Data race with PlaybackParams
CVE-2024-11699: Memory safety bugs fixed in Firefox 133, Firefox ESR
                128.5, and Thunderbird 128.5

* gnu/packages/librewolf.scm (librewolf): Update to 133.0-1.

Change-Id: I611505daf4d4f0940405190471f443d99102c2b9
Signed-off-by: Hilton Chain <hako@ultrarare.space>
2024-12-02 07:42:22 +08:00
Ian Eure
395abb86a6
gnu: nss-rapid: Update to 3.107.
* gnu/packages/nss.scm (nss-rapid): Update to 3.107.

Change-Id: I05c6e9c6633ed222d26b76ae5def35179f31f317
Signed-off-by: Hilton Chain <hako@ultrarare.space>
2024-12-02 07:42:22 +08:00
Hilton Chain
b91b992ed0
gnu: redis: Update to 7.2.6.
* gnu/packages/databases.scm (redis): Update to 7.2.6.
[arguments]<#:phases>: Update failing tests.

Change-Id: Ife107541697fda4f0928497560871f8ffb07d445
2024-12-02 07:42:20 +08:00
Ludovic Courtès
858dd7e721
etc: Add upgrade manifest.
* guix/scripts/build.scm (dependents): Export.
* etc/upgrade-manifest.scm: New file.
* Makefile.am (EXTRA_DIST): Add it.

Change-Id: I1b2a2ebd09e559c68da9f25772bf33caacb4c031
2024-12-01 20:14:16 +01:00
Ludovic Courtès
3dfb757a45
transformations: Add #:authenticate? to ‘package-with-upstream-version’.
* guix/transformations.scm (upstream-source-without-signatures): New
procedures.
(package-with-upstream-version): Add #:authenticate? and honor it.

Change-Id: Ib86feb765f57bc1b129e813780abc605c43ed97b
2024-12-01 20:14:16 +01:00
Ludovic Courtès
dbce5c2d47
transformations: ‘package-with-upstream-version’ can preserve patches.
* guix/transformations.scm (upstream-fetch): New procedure.
(package-with-upstream-version): Add #:preserve-patches? and honor it.

Change-Id: Ib56b84957d8bdad2eebe2551e2a6e477506fc55e
2024-12-01 20:14:16 +01:00
Ludovic Courtès
c6050cce28
guix build: Validate that the file passed to ‘-m’ returns a manifest.
* guix/scripts/build.scm (options->things-to-build)[ensure-manifest]:
New procedure.
Use it.

Change-Id: If64c483d7079f441a296d5bd4e06e67f44cbb7bf
2024-12-01 20:14:16 +01:00
Ludovic Courtès
5d6691d33e
gnu-maintenance: ‘generic-html’ update honors <base href="…">.
This fixes updates of ‘curl’: <https://curl.se/download/> includes
<base href="…"> in its head and ignoring it would lead to incorrect
download URLs.

* guix/gnu-maintenance.scm (html-links): Keep track of <base href="…">
in ‘loop’.  Rewrite relative links at the end.

Change-Id: I989da78df3431034c9a584f8e10cad87ae6dc920
2024-12-01 20:14:16 +01:00
Ludovic Courtès
db59509931
gnu: git-minimal: Add ‘upstream-name’ property.
* gnu/packages/version-control.scm (git-minimal)[properties]: Add
‘upstream-name’.

Change-Id: I2d2516003b7f686852a3531859d06ca7f4e4820d
2024-12-01 20:14:16 +01:00
Ludovic Courtès
79be44fb51
gnu: gnutls: Change release monitoring URL.
* gnu/packages/tls.scm (gnutls)[properties]: Change release monitoring
URL.  Add ‘upstream-name’.

Change-Id: If6ee941246b130914ddf7ca11c074a9547b9d739
2024-12-01 20:14:16 +01:00
Ludovic Courtès
2227a6b084
gnu: Update updater properties for GnuPG-related packages.
* gnu/packages/gnupg.scm (libgpg-error)[properties]: Remove.
(libgcrypt)[properties]: Remove.
(libassuan)[properties]: Remove.
(libksba)[properties]: Remove.
(npth)[properties]: Remove.
(gnupg)[properties]: Remove.
(gpgme)[properties]: Remove.
(pinentry-tty)[properties]: Change for ‘generic-html’.
(gpa)[properties]: Remove.

Change-Id: I1eb9d6ad5bb3ecbfbef3d44dbae281a3de7ebac7
2024-12-01 20:14:15 +01:00
Ludovic Courtès
e85cce3431
gnu-maintenance: ‘gnu-ftp’ updater excludes GnuPG-hosted packages.
Since ftp://ftp.gnupg.org no longer exists, another updater should be
used for packages with code fetched from mirror://gnupg.

* guix/gnu-maintenance.scm (gnupg-hosted?): New procedure.
(%gnu-ftp-updater): Exclude packages that match ‘gnupg-hosted?’.
* guix/download.scm (%mirrors): Remove ftp://ftp.gnupg.org.

Change-Id: I653877ad843da60281d3a234acc85743bee64856
2024-12-01 20:14:15 +01:00
Ludovic Courtès
da9c3195ed
import: gnome: Keep going upon HTTP errors.
* guix/import/gnome.scm (import-gnome-release): Do not re-raise
condition C, emit a warning instead.

Change-Id: I9a7c337a17d1f7ed4677398e7b0f383befca7d74
2024-12-01 20:14:15 +01:00
Ludovic Courtès
6b14eb3402
guix build: Add ‘--dependents’.
* guix/scripts/build.scm (show-help, %options): Add ‘--dependents’.
(dependents): New procedure.
(options->things-to-build): Add ‘store’ parameter; honor ‘dependents’
option.
[for-type]: Handle ‘dependents’ type.
(options->derivations): Update call to ‘options->things-to-build’.
* tests/guix-build.sh: Add test.
* doc/guix.texi (Additional Build Options): Document ‘--dependents’.
(Invoking guix refresh): Cross-reference it.
* doc/contributing.texi (Submitting Patches): Mention it.

Change-Id: I00b6d5831e1f1d35dc8b84a82605391d5a8f417c
2024-12-01 20:14:15 +01:00
Ludovic Courtès
4b5dae8def
packages: Factorize ‘all-packages’.
* gnu/packages.scm (all-packages): New procedure.
* etc/source-manifest.scm (all-packages): Remove.
* guix/scripts/graph.scm (all-packages): Remove.
* guix/scripts/refresh.scm (all-packages): Remove.
* guix/scripts/weather.scm (all-packages): Remove.

Change-Id: I6072952c4b877b541037ce86402cfb7744eeb0a0
2024-12-01 20:14:15 +01:00
Ludovic Courtès
a633422371
guix build: Add ‘--development’ option.
* guix/scripts/build.scm (show-help, %options): Add ‘-D’.
(options->things-to-build): Change ‘append-map’ to a loop.  Honor ‘-D’.
* tests/guix-build.sh: Add test.
* doc/guix.texi (Additional Build Options): Document it.

Reviewed-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Change-Id: I99227aadfe861e43c001a4872292bd687b37f5d4
2024-12-01 20:14:15 +01:00
Ludovic Courtès
bc3c89a475
gnu-maintenance: Savannah/Xorg updaters no longer abort on network errors.
Previously these updaters would fail upon networking error, causing the
whole process to abort:

  $ guix refresh coreutils libgcrypt
  guix refresh: error: connect*: Connection refused

* guix/gnu-maintenance.scm (import-release*, import-xorg-release): Wrap
in ‘false-if-networking-error’.

Change-Id: I8d309bf8662e2d46460585b4a1b7da0a4f2e8907
2024-12-01 20:14:15 +01:00
Ludovic Courtès
2c5f6787fd
gnu-maintenance: ‘import-html-release’ doesn’t abort upon HTTP 404.
Previously, updaters using ‘import-html-release’ would throw to 'quit
when the HTML page isn’t found, aborting the whole process:

  $ guix refresh coreutils libchop
  guix refresh: error: https://de.freedif.org/savannah//libchop/: HTTP download failed: 404 ("Not Found")

* guix/gnu-maintenance.scm (url->links): Guard against ‘http-get-error?’
and return the empty list when it is raised.

Reviewed-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Change-Id: I419ff96ddb424aa8c74d6bab3d66a5e85355c3dc
2024-12-01 20:14:14 +01:00
Ludovic Courtès
8ee03e30bd
transformations: Export ‘package-with-upstream-version’.
* guix/transformations.scm (package-with-upstream-version): Export.

Change-Id: I8e09e69e9c32bffc329c97ef1c0258f750181b11
2024-12-01 20:14:14 +01:00
Efraim Flashner
85743578bc
gnu: ucx: Enable building on riscv64-linux.
* gnu/packages/fabric-management.scm (ucx)[supported-systems]: Add
riscv64-linux.

Change-Id: I84d506c3ebfd8d4d237a6545ba125f4a037fa821
2024-12-01 19:58:10 +02:00
Efraim Flashner
d767459ba3
gnu: ucx: Fix building on powerpc64le-linux.
* gnu/packages/fabric-management.scm (ucx)[source]: Add snippet to add
missing include file.

Change-Id: I65a0d6e57a2728013030f3f344305744fa913390
2024-12-01 19:57:10 +02:00
Herman Rimm
2348283dab
bootloader: u-boot: Add procedure to share installer code.
* gnu/bootloader/u-boot.scm (make-u-boot-installer): Add procedure.
(install-u-boot-ts7970-q-2g-1000mhz-c-u-boot,
install-qemu-riscv64-u-boot): Remove variables.
(install-starfive-visionfive2-uEnv.txt,
u-boot-ts7970-q-2g-1000mhz-c-bootloader,
u-boot-qemu-riscv64-bootloader): Use make-u-boot-installer.

Change-Id: I0b0b507925a7c8ca608f7307d442d9588862ae91
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-12-01 17:56:00 +01:00
Herman Rimm
ca748392ce
bootloader: grub: Add procedure to share EFI installer code.
* gnu/bootloader/grub.scm (make-grub-efi-bootloader): Add procedure.
(install-grub-efi, install-grub-efi32): Remove variables.
(install-grub-efi-removable): Deprecate variable.

Change-Id: Ie10b506bb1088179d459ddafe3229fd730ac45aa
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-12-01 17:55:56 +01:00
Ludovic Courtès
15647355e5
gnu: openmpi@5: Update to 5.0.6.
* gnu/packages/mpi.scm (openmpi-5): Update to 5.0.6.

Change-Id: I1aed5f0e76d64a215c4a13f445628ec206e31acf
2024-12-01 17:48:20 +01:00
Ludovic Courtès
db1d75b9fd
gnu: rdma-core: Update to 54.0.
* gnu/packages/linux.scm (rdma-core): Update to 54.0.

Change-Id: I7f10ec57a1cad585abb08bdc30bd9e2aaafe7624
2024-12-01 17:48:15 +01:00
Ludovic Courtès
8ba6651d39
gnu: ucx: Update to 1.17.0.
* gnu/packages/fabric-management.scm (ucx): Update to 1.17.0.
* gnu/packages/patches/ucx-tcp-iface-ioctl.patch: Rebase.

Change-Id: I2089de93da88f4f81c4b233eb03abae1f41dfe7f
2024-12-01 17:48:11 +01:00
Ludovic Courtès
c25fd8eeb1
Revert "gnu: ucx: Update to 1.17.0."
This reverts commit 7c36577cde, which
broke unit tests running in the chroot build environment.

For instance, tests of ‘hdf5-parallel-openmpi’ would fail with:

  Testing ../../src/h5diff/ph5diff -c 1_vds.h5 2_vds.h5                 *FAILED*
  ====Expected result (expect_sorted) differs from actual result (actual_sorted)
      *** expect_sorted	2024-12-01 16:41:03.795879595 +0000
      --- actual_sorted	2024-12-01 16:41:03.791879542 +0000
      ***************
      *** 1,3 ****
      --- 1,15 ----
	Not comparable: </vds_dset> has rank 3, dimensions [5x18x8], max dimensions [18446744073709551615x18x8]
	Warning: </vds_dset> or </vds_dset> is a virtual dataset
      + [1733071262.437780] [localhost:33263:0]       tcp_iface.c:893  UCX  ERROR scandir(/sys/class/net) failed: No such file or directory
      + [1733071262.468994] [localhost:33247:0]       tcp_iface.c:893  UCX  ERROR scandir(/sys/class/net) failed: No such file or directory
      + [1733071262.479911] [localhost:33242:0]       tcp_iface.c:893  UCX  ERROR scandir(/sys/class/net) failed: No such file or directory

Change-Id: I9c08d3c5375a2abd7d78344dfbef9b407828d1e0
2024-12-01 17:46:43 +01:00
Jonathan Brielmaier
4f6e9c7de1
gnu: icedove: Update to 115.16.3.
* gnu/packages/gnuzilla.scm (icedove): Update to 115.16.3.

Change-Id: I076e670a5442a910ac6d5aeb7ed8f64236442062
2024-12-01 14:12:33 +01:00
Efraim Flashner
1bcf1a0146
gnu: openmpi-5: Don't force building with ucx.
* gnu/packages/mpi.scm (openmpi-5)[inputs]: Use inherited inputs to only
add ucx when it is supported.
[arguments]: Only add configure-flag for ucx when it is included as an
input.

Change-Id: I4a5fc86999ffbafdb99bd68c170fc7a1fa6a33a5
2024-12-01 14:55:08 +02:00
Efraim Flashner
7c36577cde
gnu: ucx: Update to 1.17.0.
* gnu/packages/mpi.scm (ucx): Update to 1.17.0.
[source]: Remove patch.  Add snippet to add missing header.
[supported-systems]: Add riscv64-linux.
* gnu/packages/patches/ucx-tcp-iface-ioctl.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Change-Id: I56db18f32ec0baa8439a31a1781763f318e8726e
2024-12-01 14:55:08 +02:00
Efraim Flashner
0aae7c333d
gnu: libfabric: Check for transitive supported packages.
* gnu/packages/linux.scm (libfabric)[inputs]: Adjust if-supported
function to check the package-transitive-supported-systems.

Change-Id: I47d14b08906753d20f6f2a7ab4068a9e84319350
2024-12-01 14:55:08 +02:00
Efraim Flashner
2790f7b437
gnu: cassini-headers: Limit supported systems.
* gnu/packages/linux.scm (cassini-headers)[supported-systems]: New field.

Change-Id: I44efa95de527099774abb57da78410c627fdc968
2024-12-01 14:55:04 +02:00
Josep Bigorra
d08c219b4a
gnu: Add scenefx.
* gnu/packages/wm.scm (scenefx): New variable.

Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
Change-Id: Ia91747cbec59226a83a020b5fedbfd99886c35df
2024-12-01 19:04:50 +08:00
Lynn Leichtle
af13915b28
gnu: cataclysm-dda: Update to 0-H.
* gnu/packages/games.scm (cataclysm-dda): Update to 0.H.

Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>
Change-Id: I8f3776b1bbb4ead2d409b2e1a3c4c98537126f12
2024-12-01 19:04:26 +08:00
Zheng Junjie
ff3c9fd5e3
gnu: plasma-nm: Add missing inputs.
* gnu/packages/kde-plasma.scm (plasma-nm)[inputs]: Add
mobile-broadband-provider-info.
[arguments]: Stop replace 'check phase.

Change-Id: I82b220694e26b48f190c1c5d6609da39e955cc30
2024-12-01 18:15:07 +08:00