gnu: r-glmgampoi: Update to 1.14.2.

* gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.14.2.

Change-Id: Id7265b49246e75d23086dc159da9b4f69a756a7d

gnu: r-trajectoryutils: Update to 1.10.1.

* gnu/packages/bioconductor.scm (r-trajectoryutils): Update to 1.10.1.

Change-Id: I18a94851cd139951c2987054c22f01809d2479b3

gnu: r-rcas: Update to 1.28.3.

* gnu/packages/bioconductor.scm (r-rcas): Update to 1.28.3.
[propagated-inputs]: Remove r-ggseqlogo and pandoc; add r-seqlogo.

Change-Id: I8be7d8fc4278c8ec2db6932935f70292a4f47049

gnu: r-genomeinfodb: Update to 1.38.6.

* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.38.6.

Change-Id: I57a53d4a73e9b4ce36d97092dab0789d6509484f

gnu: r-dittoseq: Update to 1.14.2.

* gnu/packages/bioconductor.scm (r-dittoseq): Update to 1.14.2.

Change-Id: I8930f72b47ff92b3b798d9a45fc0598bec1ba53e

gnu: r-bsgenome: Update to 1.70.2.

* gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.70.2.

Change-Id: I45ba28279e0b843bcd635c2e30fb696e85195ce7

gnu: r-animalcules: Update to 1.18.3.

* gnu/packages/bioconductor.scm (r-animalcules): Update to 1.18.3.

Change-Id: I4f8d5897af796afbce269748c6a5676db72e4baf

gnu: r-curatedtcgadata: Update to 1.24.1.

* gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.24.1.

Change-Id: I42ae64544b53d6ddd72b948af4093ef4dd31a9c6

gnu: r-rhdf5lib: Update to 1.24.2.

* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.24.2.
[propagated-inputs]: Remove r-biocstyle and r-stringr.
[native-inputs]: Remove r-rmarkdown.

Change-Id: I76b1601397bc69651c0b788404c6b0c67d830830

gnu: parallel: Update to 20240122.

* gnu/packages/parallel.scm (parallel): Update to 20240122.

Change-Id: I4e416cbad5b6f4267a9aab7996c9156a861e3ad1
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: parinfer-rust: Add phase to install editor plugins.

* gnu/packages/text-editors.scm (rust-parinfer)[arguments]: Install the
bundled Vim and Kakoune plugins.

Change-Id: I881315481ec08c59576c4530ae72b877c399fc66
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add python-gguf.

* gnu/packages/machine-learning.scm (python-gguf): New variable.

Change-Id: Icf6138486cccc5b4c3141424baccf17c4edb3449
Signed-off-by: Andreas Enge <andreas@enge.fr>

services: Add ‘virtual-build-machine’ service.

* gnu/services/virtualization.scm (<virtual-build-machine>): New record type.
(%build-vm-ssh-port, %build-vm-secrets-port, %x86-64-intel-cpu-models):
New variables.
(qemu-cpu-model-for-date, virtual-build-machine-ssh-port)
(virtual-build-machine-secrets-port): New procedures.
(%minimal-vm-syslog-config, %virtual-build-machine-operating-system):
New variables.
(virtual-build-machine-default-image):
(virtual-build-machine-account-name)
(virtual-build-machine-accounts)
(build-vm-shepherd-services)
(initialize-build-vm-substitutes)
(build-vm-activation)
(virtual-build-machine-offloading-ssh-key)
(virtual-build-machine-activation)
(virtual-build-machine-secret-root)
(check-vm-availability)
(build-vm-guix-extension): New procedures.
(initialize-hurd-vm-substitutes): Remove.
(hurd-vm-activation): Rewrite in terms of ‘build-vm-activation’.
* gnu/system/vm.scm (linux-image-startup-command): New procedure.
(operating-system-for-image): Export.
* gnu/tests/virtualization.scm (run-command-over-ssh): New procedure,
extracted from…
(run-childhurd-test): … here.
[test]: Adjust accordingly.
(%build-vm-os): New variable.
(run-build-vm-test): New procedure.
(%test-build-vm): New variable.
* doc/guix.texi (Virtualization Services)[Virtual Build Machines]: New
section.
(Build Environment Setup): Add cross-reference.

Change-Id: I0a47652a583062314020325aedb654f11cb2499c

marionette: Add #:peek? to ‘wait-for-tcp-port?’.

* gnu/build/marionette.scm (wait-for-tcp-port): Add #:peek? parameter
and honor it.

Change-Id: Ie7515a5223299390ab8af6fe5aa3cf63ba5c8078

vm: Add ‘cpu-count’ field to <virtual-machine>.

* gnu/system/vm.scm (<virtual-machine>)[cpu-count]: New field.
(virtual-machine-compiler): Honor it.

Change-Id: I907a89365f32ac7a9981c4ae5f59cf6eb199c3cc

vm: Export <virtual-machine> accessors.

* gnu/system/vm.scm: Export.

Change-Id: If65d96f4052d070af5baee26f3dd9b233b8480f4

vm: Add ‘date’ field to <virtual-machine>.

* gnu/system/vm.scm (<virtual-machine>)[date]: New field.
(virtual-machine-compiler): Honor it.

Change-Id: Idab1c152466d57cbc6784c031a99fdfd37080bcb

services: secret-service: Make the endpoint configurable.

Until now, the secret service had a hard-coded TCP endpoint on port
1004.  This change lets users specify arbitrary socket addresses.

* gnu/build/secret-service.scm (socket-address->string): New procedure,
taken from Shepherd.
(secret-service-send-secrets): Replace ‘port’ by ‘address’ and adjust
accordingly.
(secret-service-receive-secrets): Likewise.
* gnu/services/virtualization.scm (secret-service-shepherd-services):
Likewise.
(secret-service-operating-system): Add optional ‘address’ parameter and
honor it.  Adjust ‘start’ method accordingly.

Change-Id: I87a9514f1c170dca756ce76083d7182c6ebf6578

gnu: openmolar-1: Update to release 1.1.6-g81838c8 and partial runtime fix.

Fixes <https://issues.guix.gnu.org/29365>.

WebKit was removed from Qt5 in favor of WebEngine; upstream addressed
this in their last stable release, in 2018.  The package still fails at
runtime: this commit lays the ground for further fixes.

* gnu/packages/medical.scm (openmolar-1): Update to release 1.1.6-g81838c8.
[arguments]: Extend 'patch-/usr phase to source file localsettings.py.
[inputs]: Add python-pyqtwebengine.
[propagated-inputs]: Add qtwebengine-5.

Change-Id: Ia4e4c052397201c26834dec2358ca5c20beb581d
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add python-scikit-opt.

* gnu/packages/python-science.scm (python-scikit-opt): New variable.

Change-Id: I47d6b35d9658a37a242b4db61d293fa7efd33802
Signed-off-by: Ludovic Courtès <ludo@gnu.org>