gnu: python-debugpy: Update to 1.8.9.

* gnu/packages/python-xyz.scm (python-debugpy): Update to 1.8.9.

Change-Id: I323570fc007af04fa8c9c59571cc3cc79833da04

gnu: python-pydevd: Update to 3.2.3.

* gnu/packages/python-xyz.scm (python-pydevd): Update to 3.2.3.

Change-Id: Ibb1bb9880b2c456f27bf373259a0e604a62b9515

gnu: Update otpclient to 4.0.2

Requires updating `libcotp` to 3.1.0, that introduced a new way for
testing that requires `criterium`, a package we don't have and that has
dependencies that we don't have either.

As the tests in `libcotp` are not an exhaustive testsuite and
`otpclient` is its only dependent package, tests are disabled for the
moment.

* gnu/packages/authentication.scm (libcotp): Update to 3.1.0
[arguments] Disable tests.
* gnu/packages/password-utils.scm (otpclient): Update to 4.0.2

Change-Id: Ie6d37b5efe59397d4979c7490b94f1c871c27d6d

gnu: Fix java-jaxen.

java-jaxen was missing the dom4j and xom sub-packages. This was caused by
java-jaxen-bootstrap deleting the respective directories (which is okay) and
java-javen not removing the phase that does this.

Solve this by removing the #:phases argument for java-jaxen and thus make guix
use the default phases.

* gnu/packages/java-xml.scm (java-jaxen)[arguments]: Remove #:phases.
, making

gnu: go-github-com-cyphar-filepath-securejoin: Fix url.

Fix url incorrectly changed in 9399db35c2105157407fd4a59aeb0cacc58a0c54.

* gnu/packages/golang-xyz.scm (go-github-com-cyphar-filepath-securejoin)
[origin]: Fix url.

Change-Id: Ibac24d11efdd6414bdeb8be2cd2184e21d7f8676
Signed-off-by: Ekaitz Zarraga <ekaitz@elenq.tech>

gnu: eisl: Update to 5.38.

* gnu/packages/lisp.scm (eisl): Update to 5.38.

Change-Id: I115706d2b06bed71a24cf2c1ab1f5c1bf2e88284

gnu: gqrx: Update to 2.17.6.

* gnu/packages/radio.scm (gqrx): Update to 2.17.6.

Change-Id: Ief1ec50d0e64fa325dc2f270612a978105c05f3a

gnu: Add cl-simple-matrix.

* gnu/packages/lisp-xyz.scm (cl-simple-matrix, ecl-simple-matrix,
  sbcl-simple-matrix): New variables.

Change-Id: I79499aae2c8c7dc0ba2d1193104f2f3dd1d3621c

gnu: make-rust-sysroot: Adjust for newer cross-gcc.

* gnu/packages/rust.scm (make-rust-sysroot/implementation)
[native-inputs]: Add gcc-14.

Change-Id: If9bc74bfe2e236accc39dc09e03b28dee62e332d

gnu: make-rust-sysroot: Simplify native-inputs.

* gnu/packages/rust.scm (make-rust-sysroot/implementation)
[native-inputs]: Combine the different modify-input branches into one.

Change-Id: Ia7df5d1566099f9934a76b2660f46a55547c88b9

gnu: make-rust-sysroot: Accept other mingw targets.

* gnu/packages/rust.scm (make-rust-sysroot/implementation)[arguments]:
Adjust the custom 'patch-for-mingw phase to generate the name of the
mingw input package based on the target architecture.
[inputs, native-inputs]: Use make-mingw-w64 to choose the mingw package
for the target.

Change-Id: I48638095a504675753e65fdb6f0286c31cebde66

gnu: glibc-dynamic-linker: Match all mingw systems.

* gnu/packages/bootstrap.scm (glibc-dynamic-linker): Match any system
which ends in '-mingw'.

Change-Id: I057e3d0abfc37f4b2b8784f444bbaf865c67ce3e

Partial revert "gnu: bootstrap: %bootstrap-gcc: Also wrap g++ for the 64bit Hurd."

This partially reverts commit 877b925df16740f9419d165d39cb7f191a86d5d1.

This part accidentally triggered a world rebuild for non-x86 architectures.

Change-Id: Iabc5422bb0e2bb37816ad437994af94d04830cb0

Partial revert "gnu: bootstrap: %bootstrap-glibc: Also fix libm.so."

This partially reverts commit 204fe1b1f05f4438d1cf72c568b45696e55e54c9.

This part accidentally triggered a world rebuild for non-x86 architectures.

Change-Id: I921984ef5eff58792ffc17b64675db6a8e79695c

Partial revert "gnu: make-bootstrap: Update gcc-static to gcc-14, for the 64bit Hurd."

This partially reverts commit ec8a5ec15f898e864705e5a5c834532e3fa8d0a4.

This part accidentally triggered a world rebuild for non-x86 architectures.

Change-Id: Id2f9bcbcda8dc86ea407e9a7857a854dc1a742b5

gnu: Add r-ggupset.

* gnu/packages/cran.scm (r-ggupset): New variable.

Change-Id: I044fff58b66dbb56e6b7fb1ebcb5353e7ab3d1f7

gnu: Add skewer.

* gnu/packages/bioinformatics.scm (skewer): New variable.

Change-Id: Ieeb95ed7449b91ea853d73ecca05e5436121df6a

gnu: packages/python-science: Update copyright header.

* gnu/packages/python-science.scm: Update copyright header for Antero
Mejr <antero@mailbox.org> .

Change-Id: I4153d51d74f7de1629d5a7851346021b77e7352d

gnu: Add python-scikit-surprise.

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

Change-Id: I9b5e13f0c985f34bb0bd759e76ebd27221a340a4
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: ikiwiki: Fix build by disabling a test.

* gnu/packages/web.scm (ikiwiki)[arguments]: In stage "pre-check", disable
failing "t/t.po" test.

Change-Id: I4fc1240512b4d3df3ece837521116aee5746e181