gnu: openpmix: Simplify.

* gnu/packages/parallel.scm (openpmix)[source]: Use ‘modules’ field and adjust
‘snippet’ accordingly.
[arguments]: Remove now-useless configure flag.

Change-Id: I2ec33232021485a019a8f86818e2f540963d4338
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: openpmix: Update to 6.0.0.

* gnu/packages/parallel.scm (openpmix): Update to 6.0.0.
(openpmix-4): New variable.
(slurm-minimal)[inputs]: Change ‘openpmix’ to ‘openpmix-4’.
(slurm-minimal-25.05)[inputs]: New field.

Change-Id: I043ef4545524e6757f47194e2c7f8793ccedf1b4
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: diod: Update to 1.1.0

* gnu/packages/plan9.scm (diod): Update to 1.1.0.
[source]<origin>: Add file-name.
[arguments]<#:phases>: Add 'patch-tests' phase.

Change-Id: I4f3ef885f3570589589034c8c24c29a648c6f66f
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #5425

gnu: wofi: Update to 1.5.3

* gnu/packages/xdisorg.scm (wofi): Update to 1.5.3.

Change-Id: I5b06f32e70fd7a8b92fca03495e00adc53af19d6
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #5435

gnu: flexbar: Update to 3.5.0.

* gnu/packages/bioinformatics.scm (flexbar): Update to 3.5.0.
[arguments]: Use G-Expressions.

Change-Id: If8a61ea506d30eebf29ae1116d7950fce497cb19

gnu: flatpak-kcm: Enable wayland.

* gnu/packages/kde-plasma.scm (flatpak-kcm)[inputs]: Add wayland.

Change-Id: Ib276309549ea87eaf91e86906866f3a5c96d6f7f

gnu: flatpak: Enable wayland security.

* gnu/packages/package-management.scm (flatpak)[arguments]<#:configure-flags>:
Add -Dwayland_security_context=enabled.
[inputs]: Add wayland.
[native-inputs]: Add wayland, wayland-protocols.

Change-Id: Idd2b28536750af6bf5d050c989a293f301ce1142

gnu: Remove embree-2.

* gnu/packages/graphics.scm (embree-2): Delete variable.

Change-Id: I1de940ac7e4e8dabafcb3dfad7edc1780c6205d4

gnu: ericw-tools: Update to 0.18.2-rc1.

* gnu/packages/game-development.scm (ericw-tools): Update to 0.18.2-rc1.
[inputs]: Remove embree-2; add embree.

Change-Id: Idbc5aa38adf1e39f538989612c0620097cf5434d

gnu: Fix source-url for some java packages.

For the apache updater to find the updates, the path-part of the source-url
must start with a single slash.

* gnu/packages/java.scm (java-apache-ivy,
  java-httpcomponents-httpcore)[source]: Fix url.

gnu: Add upstream-name to some java packages.

This will make the apache updater work.

* gnu/packages/java.scm Jjava-commons-bcel, java-commons-bsf,
  java-commons-dbcp, java-commons-jcs, java-commons-logging-minimal,
  java-commons-pool, java-httpcomponents-httpclient): [properies]: New field.

gnu: onetbb: Update to 2022.3.0.

* gnu/packages/oneapi.scm (onetbb): Update to 2022.3.0.

Change-Id: If883a90957fc3e01eb62bfc72c9d1359ba029e94

gnu: Add emacs-helm-comint.

* gnu/packages/emacs-xyz.scm (emacs-helm-comint): New variable.

Merges guix/guix#5290

Change-Id: I38fc5d3ec8eedb12f878125a99dedbc2ae742eeb

gnu: emacs-xyz: Add emacs-nftables-mode.

* gnu/packages/emacs-xyz (emacs-nftables-mode): New variable.

Merges guix/guix#5484

Change-Id: I4ec20df10c5ed902fd995aea8738c6c4afd76470
Modified-by: Cayetano Santos <csantosb@inventati.org>
Signed-off-by: Cayetano Santos <csantosb@inventati.org>

gnu: luanti: Update luanti-paths patch, per upstream comments.

* gnu/packages/patches/luanti-paths.patch: Update and add upstream-status
reference.

Change-Id: Id98ed5b20d24560f9a9b2b3aff03294e385fd468

gnu: emacs-lua-mode: 20221027-2.2f6b8d7.

* gnu/packages/emacs-xyz.scm (emacs-lua-mode): Update to 20221027-2.2f6b8d7.

Change-Id: Ic1bf4aee70e6ca95a17a50ea93bfc956cccaf037

gnu: hh-suite: Adjust for GCC@14.

* gnu/packages/bioinformatics.scm (hh-suite)[arguments]: New phase.

Change-Id: Ic1c6078febbffe6a81393c8a114ac4b41d269cda

gnu: phyml: Add font required by documentation.

* gnu/packages/bioinformatics.scm (phyml):
[native-inputs]: Add texlive-ec.
[arguments]<phases>: Replace /homeless-shelter by /tmp.

Change-Id: I2a1d1fb343d2dd333846093fece511fe8af1cd6e

gnu: velvet: Adjust for GCC@14 and documentation building.

* gnu/packages/bioinformatics.scm (velvet)
[arguments]:<make-flags>: Add incompatible-pointer-types.
<phases>: Allow TeXlive to create font.
[native-inputs]: Add texlive-ec.

Fixes: guix/guix#5471
Change-Id: I0d44b763a77a64c900f09efdea30d8a89d3b2496
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: spindle: Fix missing dependency.

* gnu/packages/admin.scm (spindle)[inputs]: Add zlib.

Change-Id: If5b088f957a282921d931f52f5baf68ef34c0d24
Signed-off-by: Andreas Enge <andreas@enge.fr>