gnu: Remove htslib-for-samtools-1.2.

* gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2):
Delete variable.

Change-Id: I62c8525d27321acd7fea32e25623e5cbd7e74c33

gnu: Remove samtools-1.2.

* gnu/packages/bioinformatics.scm (samtools-1.2): Delete variable.

Change-Id: I38effe41c32349b5b72754da07fe6696d2f21669

gnu: ghc-xml-conduit, ghc-pcg-random: Correct deprecated input.

* gnu/packages/haskell-xyz.scm (ghc-xml-conduit, ghc-pcg-random)[inputs]:
Replace ghc-cabal-doctest by cabal-doctest.

Change-Id: I2e763313c500567928864da520eeff6b3616f825

gnu: neovim: Correct deprecated input.

* gnu/packages/vim.scm (neovim)[inputs]: Remove msgpack; add msgpack-c.

Change-Id: I6a022c48d2a1914af9b871cf943037e1b23d2c75

gnu: rtorrent: Update to 0.16.1.

* gnu/packages/bittorrent.scm (rtorrent): Update to 0.16.1.
[native-inputs]: Add autoconf, automake, and libtool.

Change-Id: Ide9681d533d54c4c6e4843d6972cd5fae956d3d5
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: libtorrent: Update to 0.16.1.

* gnu/packages/bittorrent.scm (libtorrent): Update to 0.16.1.
[source]: Switch to git-fetch.
[inputs]: Add curl.
[native-inputs]: Add autoconf, automake, and libtool.

Change-Id: I4406a50980656e236863bf932cb2ad69b8a2e3a7
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: pluma: Add missing inputs and improve build steps

* gnu/packages/mate.scm (pluma): Use gexps.
[inputs]: Remove enchant-1.6; add enchant, python-pygobject, python-wrapper,
python-pycairo, and python-six.
[native-inputs]: Add perl.

Change-Id: Iada5d8863281c704d00d15d644eca150f4fe80bd

Add missing perl input

Change-Id: Idc5461ce5a97483d4c017b21b909bedcc67a75d5
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: gitolite: Update to 3.6.14.

* gnu/packages/version-control.scm (gitolite): Update to 3.6.14.

Change-Id: I9b0ddc36798d3e5a984ba5bad803d54941066efe
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: Add python-capablerobot-usbhub.

This was previously removed due to dropping python-pyyaml-5, though currently
builds fine with the default python-pyyaml and python-click. See:

https://codeberg.org/guix/guix/issues/1390

* gnu/packages/libusb.scm (python-capablerobot-usbhub): New variable.

gnu: lcrq: Update to 0.3.1.

* gnu/packages/networking.scm (lcrq): Update to 0.3.1.

inferior: cached-channel-instances: Optimize caching for (partially) locked channels.

This makes it possible to skip the guix derivation calculation phase for
channels.scm that aren't fully locked (specifically with missing channel
dependencies).

* guix/inferior.scm (cached-channel-instance): Return cached early after
calculating latest-channel-instances.

Change-Id: Ie77c1903c7a79b082e440046092fd697fd941afc
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

inferior: cached-channel-instance: Recalculate key after fetching channels.

Fixes #3454.

Because the channels in the incoming argument do not have to include all
dependencies, it is possible a cache entry with wrong key is created.

Recalculate the key after obtaining all dependencies of channels
through latest-channel-instances.

* guix/inferior.scm (cached-channel-instance): Recalculate cached file
location from latest-channel-instances commits before caching.

Change-Id: I37da107520bf5abd89c92a5ce6d3e2fc399454c3
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

services: unbound: Remove dns from provision.

Fixes <https://issues.guix.gnu.org/76301>.

The ‘dns’ provision collides with that of Knot.

* gnu/services/dns.scm (unbound-shepherd-service): Remove dns from provision.

Change-Id: Ice774a9a338416e865dbc4d26a8f37243f084a35
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: niftilib: Rename package to nifticlib.

* gnu/packages/image.scm (niftilib): Define in terms of
'deprecated-package'.
(nifticlib): New variable, formerly known as "niftilib".
* gnu/packages/medical.scm (xmedcon)[inputs]: Replace niftilib with
nifticlib.

Change-Id: I5c8e12191202a97e3fb7202e428fd60627f49a2e
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: niftilib: Update to 3.0.1.

* gnu/packages/image.scm (niftlib): Update to 3.0.1.
[source, home-page]: Switch to https://github.com/NIFTI-Imaging/nifti_clib.
[source]: Switch to git-fetch.
[build-system, arguments]: Switch to cmake-build-system.
[arguments]: Use G-expression.
[inputs]: Add expat.
[native-inputs]: Add test data.  Add help2man when not cross-compiling.
[synopsis]: Update it.
[description]: Update it.

Change-Id: Iae16d2205044378558731b9236cb40368b1f9171
Co-authored-by: Ghislain Vaillant <ghislain.vaillant@inria.fr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

system: Set ‘HISTSIZE’ in default bashrc.

This provides more appropriate defaults for today.  This change affects
/etc/bashrc, /etc/skel/.bashrc, along with ~/.bashrc for Home users.

* gnu/system/shadow.scm (%default-bashrc): Set ‘HISTSIZE’.

Change-Id: I4ffa7ad75c6f39f3f36d5a15ce420eae52e241e5

home: services: bash: Support setting shell variables.

* gnu/home/services.scm (shell-variable-definitions): New procedure.
* gnu/home/services/shells.scm (serialize-shell-variables): New procedure.
(home-bash-configuration)[variables]: New field.
(add-bash-configuration): Honor it.
(home-bash-extension)[variables]: New field.
(home-bash-extensions): Handle ‘variables’.
* doc/guix.texi (Shells Home Services): Update.  Change ‘PS1’ example to use
‘variables’, not ‘environment-variables’.
* doc/he-config-bare-bones.scm: Use ‘variables’ instead of ‘bash-profile’.

Change-Id: I29083d6313d10b1eb9d91eccacfb33efefe60d58

doc: Refer to the Deprecation Policy from “Creating a Channel”.

* doc/guix.texi (Creating a Channel): Reword warning to refer to the
deprecation policy.

Change-Id: I6c1cd8dfac557634c2963f13f17903f16acbe720

doc: Recommend ‘define-deprecated-package’ in the Deprecation Policy.

* doc/contributing.texi (Deprecation Policy): Document and recommend
‘define-deprecated-package’.

Change-Id: I530310f5216f09025525d91f690bb3885fe2cfb4

gnu: Use ‘define-deprecated-package’ for deprecated packages.

Use ‘define-deprecated-package’ instead of (define x (deprecated-package …))
throughout gnu/packages/*.scm.

Change-Id: I4e176da9ac660327489dab256ca4d12c4e78fe8d