gnu: guile-hoot: Update to 0.6.0.

* gnu/packages/guile-xyz.scm (guile-hoot): Update to 0.6.0.

Change-Id: Ib0394fa75b798240f3378fa40803e55a4b5afcb2

gnu: Add python-pot.

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

Change-Id: I2a844a41031ce80d46a3ffe03ead9652d5a87348

gnu: Add python-pymanopt.

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

Change-Id: Id10413a0f2f76a8a3ac9e6fee22005a92625323c

gnu: python-sphinx-click: Update to 6.0.0.

* gnu/packages/sphinx.scm (python-sphinx-click): Update to 6.0.0.
[arguments]: Add phase 'fix-build-system; remove custom 'check phase.
[native-inputs]: Remove python-pbr; add python-setuptools.

Change-Id: I0796ee373f9172686753d5d32d274917828d3b41

gnu: Add python-geomloss.

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

Change-Id: Id54d81c8c942c69151a7667983073a28419170d0

gnu: python-jupyter-sphinx: Update to 0.5.3.

* gnu/packages/sphinx.scm (python-jupyter-sphinx): Update to 0.5.3.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add phase 'ignore-warnings.
[native-inputs]: Add python-hatchling and python-ipykernel.

Change-Id: I94979e034fa45da898aed0dd37bcea4f37a5a5f8

gnu: opensmtpd: Fix fix for queuing of offline messages.

The substituted path in smtpd.h was not used due to an #ifndef.  The correct
place to patch it seems to be mk/pathnames.  This sadly triggers a bootstrap,
so we need to add autoconf and automake to the native-inputs.

* gnu/packages/mail.scm (opensmtpd)[arguments]<#:phases>
{'patch-test-FHS-file-names}: Patch in mk/pathnames instead.
[native-inputs]: Add autoconf and automake.

Change-Id: I1d569b8aaae839d6fd4871ccb97c116e6930f1c9
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: gnuradio: Update to 3.10.11.0.

* gnu/packages/radio.scm (gnuradio): Update to 3.10.11.0.

Change-Id: I4d8b83effcadd831f1cfc769bfcfb90d4a1439f5
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: gpa: Update to 0.11.0.

* gnu/packages/gnupg.scm (gpa): Update to 0.11.0.
  [inputs]: Replace gtk+-2 by gtk+.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
Change-Id: I4ca1165b6753dbed922049f2f2839a5be5abd6da

gnu: Add cl-trivial-battery.

* gnu/packages/lisp-xyz.scp (cl-trivial-battery, ecl-trivial-battery,
  sbcl-trivial-battery): New variables.

Change-Id: Icdcf77738ba71e4705410aadedd6fe6f7babf1e1
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: sbcl-alexandria: Add info manual.

* gnu/packages/lisp-xyz.scm (sbcl-alexandria)[native-inputs]: Add texinfo.
  [arguments]: Add 'build-doc' phase.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
Change-Id: Ib8e6a5f4a0a20bf9c78a65bb15bb63e7a0d66ad5

gnu: js8call: Remove ruby-asciidoctor.

* gnu/packages/radio.scm (js8call)[native-inputs]: Remove
ruby-asciidoctor.

Change-Id: Id551c21e3e54d360abc28269f9f07dc424ba07e8

gnu: jtdx: Enable building on more systems.

* gnu/packages/radio.scm (jtdx)[native-inputs]: Only add
ruby-asciidoctor on supported systems.
[arguments]: When building without ruby-asciidoctor add a configure-flag
to skip building the documentation.

Change-Id: Ie167c703ac92743b201573d1a883ae2ff6ccd879

gnu: open-adventure: Enable building on more systems.

* gnu/packages/games.scm (open-adventure)[arguments]: Adjust or remove
some phases when building without ruby-asciidoctor.
[native-inputs]: Only add ruby-asciidoctor on supported systems.

Change-Id: I573a488721557442769f4e8b9e68ea1e70d4fbf0

gnu: chrony: Enable building on more systems.

* gnu/packages/ntp.scm (chrony)[arguments]: Add a phase to enable
building without ruby-asciidoctor.
[native-inputs]: Only add ruby-asciidoctor on supported systems.

Change-Id: I812cea438cb8c2b1f74d7674baa70b9159151c8f

gnu: btrbk: Enable building on more systems.

* gnu/packages/backup.scm (btrbk)[arguments]: Add some phases to enable
building without ruby-asciidoctor.
[native-inputs]: Only add ruby-asciidoctor on supported systems.

Change-Id: I86b5b1b307d3a226cae0231d85519ebb96a29f8c

gnu: hdf-java: Update to 1.10.9.

The version string does not seem like an upgrade, but it is.  hdf-java used to
be released separately up to version 3.3.2.  It is now part of the hdf5
sources.

* gnu/packages/maths.scm (hdf-java): Update to 1.10.9.
[source]: Fetch hdf5 sources from git.
[arguments]: Adjust configure flags; add phase 'unbundle; remove phase
'build-examples.
[native-inputs]: Drop labels.
[inputs]: Replace hdf5-1.8 with hdf5; drop labels.

Change-Id: I30ef41aa9255d6d4eb49f5382a6fe5a62080e6fa

gnu: Add r-phytools.

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

Change-Id: Ie4fa9f40febf3b114a3da38b9cdf668e8ac415ca
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

gnu: nvc: Update to 1.15.1.

* gnu/packages/fpga.scm (nvc): Update to 1.15.1.
[native-inputs]: Remove gnu-gettext; add gettext-minimal.

Change-Id: Ic71084121b1bdb2f3c37f863edd305c16d2d7ea6

gnu: nvc: Improve package style.

* gnu/packages/fpga.scm (nvc)[source]: Use git-file-name. Remove .git to fix
the redirection.
[arguments]: Use G-expressions.

Change-Id: I44115f13503ae5b3f82cc50cb2fc31168ea3a714