gnu: python-scanpy: Disable one more test.

* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Disable one
failing test.

Change-Id: If262b33a3e2c6789c0ce4b8a91f26a8a48054632

gnu: cutecom: Fix the license.

* gnu/packages/engineering.scm (cutecom) [license]: Set to gpl3+.

Change-Id: Ifc2c1581b8adad42d5452728ca66c53efc901139

gnu: python-unyt: Update to 3.0.3, fix build.

* gnu/packages/python-science.scm (python-unyt): Update to 3.0.3. Fix
build.

Change-Id: Ic894ddfa982b9d41b40fc7e18149de099dd705f6

gnu: packages/golang-xyz: Simplify some difinitions.

This changes utilize default go-build-system options to skip build and
test the whole project recursively.

* gnu/packages/golang-xyz.scm (go-github-com-syndtr-goleveldb,
go-github-com-jdkato-twine) [arguments]: <test-flags>: Move skip test
logic here.
<skip-build?>: No go files in project's root.
<phases>: Use default 'check, preserve 'build.

* gnu/packages/golang-xyz.scm: (go-github-com-muesli-reflow,
go-github-com-matttproud-golang-protobuf-extensions-v2,
go-github-com-liyue201-gostl, go-github-com-lithammer-fuzzysearch,
go-github-com-google-gnostic-models,
go-github-com-burntsushi-graphics-go)
[arguments]: <skip-build?>: No go files in project's root.
<phases>: Preserve 'build.

Change-Id: I02840169f6f572c947a725f0a03491f0769fd807

gnu: go-github-com-opencontainers-runtime-spec: Enable tests.

* gnu/packages/golang-xyz.scm (go-github-com-opencontainers-runtime-spec)
[arguments] <skip-tests?>: No go files in project's root.
<phases>: Preserve 'build and 'check.
[native-inputs]: Add go-github-com-xeipuuv-gojsonschema.

Change-Id: Ic170a7de808577ae7c783f8fc29cf9e7d92c37b6

gnu: Add cutecom.

* gnu/packages/engineering.scm (cutecom): New variable.

Change-Id: Ib560ba855074514e9e2df1884b49722218b1a410

gnu: Add python-scikit-misc.

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

Change-Id: I8fb3c46fe8a927e5d2fbd3222a423330e771379e

profiles: emacs-subdirs: Avoid building circular lists.

This is a follow-up to e9b13294700de7082ee23aa6e1c17b4a8c8828ec.  If
the EMACSNATIVELOADPATH environment variable (by mistake) has duplicated
paths, Emacs fails to start up with a message along the lines of

  List contains a loop:
  ("$HOME/.guix-profile/lib/emacs/native-site-lisp" […] . #2)

To prevent this issue in the face of possibly duplicated search path elements,
use non-destructive methods where possible.

* guix/profiles.scm (emacs-subdirs): Use 'append' rather than 'nconc'.

Change-Id: If646b806f24666b5247850d30d2819c7482c130b
Fixes: Emacs "List contains a loop" <https://issues.guix.gnu.org/75709>
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

gnu: git: Update to 2.48.1. [security fixes]

Fixes the CVE-2024-50349 and CVE-2024-52006.

* gnu/packages/version-control.scm (git-minimal): Update to 2.48.1.
[#:phases]<patch-tests>: Purge purged tests in meson.build.
(git)[#:phases]<build-subtree>: Update to also generate asciidoc.conf.
<install-man-pages>: Update hash.

Change-Id: I6616e95822ded252a9bec1312702016985cb9de7
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

grafts: Allow file-like objects in the ‘replacement’ field of <graft>.

This is a followup to and simplification of
3331d675fbf5287e8cbe12af48fb2de14f1ad8bc.

* guix/grafts.scm (graft-derivation/shallow)[mapping]: Wrap origin and
replacement in ‘with-parameters’.
(cumulative-grafts)[finalize-graft]: Remove, and remove its sole user.
* guix/packages.scm (input-graft, input-cross-graft): Add ‘replacement’
straight into the ‘replacement’ field of <graft>.
* tests/packages.scm ("package-grafts, indirect grafts")
("package-grafts, indirect grafts, propagated inputs")
("package-grafts, same replacement twice")
("package-grafts, dependency on several outputs")
("replacement also grafted"): Adjust accordingly.

Suggested-by: David Elsing <david.elsing@posteo.net>
Change-Id: I286fceae53df9d3051137bbca5f944d51d0c92f3

gexp: ‘with-parameters’ accepts plain store items in its body.

* guix/gexp.scm (compile-parameterized): Return ‘obj’ as-is when it’s
not a struct.
* tests/gexp.scm ("with-parameters + store item"): New test.

Change-Id: I5b5348b98bce923d07f6fa39b2f0948723011db8

gnu: Add xmlpatch.

* gnu/packages/xml.scm (xmlpatch): New variable.

Change-Id: I557f2dfbaadfef11c8ca592bb03ec829782fcb4e
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: lapack: Update to 3.12.0.

* gnu/packages/maths.scm (lapack): Update to 3.12.0 and switch to
‘git-fetch’.
[inputs]: Remove labels.

Change-Id: I3ae813f55ddd3229b9924853cdb8c31c4e420112
Co-authored-by: Andy Tai <atai@atai.org>

gnu: ccwl: Update to 0.4.0.

* gnu/packages/bioinformatics.scm (ccwl): Update to 0.4.0.

Change-Id: I6726438f3a2ec9bb01971f14a22e4123abc01793

gnu: font-intel-one-mono: Update to 1.4.0.

* gnu/packages/fonts.scm (font-intel-one-mono): Update to 1.4.0.

Change-Id: Idf6801e94230327d4172f15591db2f8a62c064e1
Signed-off-by: 宋文武 <iyzsong@member.fsf.org>

gnu: Add xfce4-i3-workspaces-plugin.

* gnu/packages/xfce.scm (xfce4-i3-workspaces-plugin): New variable.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
Change-Id: Iab03c16391290963db5f834f7b4d72f02d270f41

gnu: Add i3ipc-glib.

* gnu/packages/wm.scm (i3ipc-glib): New variable.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
Change-Id: I7a7e882752de4a833ebf082fbe4967dac13840dd

gnu: python-fenics-dijitso: Fix build.

* gnu/packages/simulation.scm (python-fenics-dijitso): Improve style,
fix build, use G-Expressions.
[phases] {check}: Respect tests? flag.
[native-inputs]: Add python-pytest-cov.

Change-Id: I4032735228d36366a7014b48e9d21606628c56a6

gnu: python-deepdish: Fix indentation.

* gnu/packages/python-science.scm (python-deepdish): Fix indentation.

Change-Id: Idf8a0b5cdb9e371cb5d1f5f51f993da6209342d5

gnu: python-deepdish: Update to 0.3.7-0.3f2dff7, fix build.

* gnu/packages/python-science.scm (python-deepdish): Update to 0.3.7-0.3f2dff7.
[source]: Swap to git checkout containing fixes for NumPy.
[native-inputs]: Add python-pytest.

Change-Id: Icbc8c0895bcac0bdfede65ac7b6006186c684a70