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

gnu: ruby: Avoid use of deprecated ‘ruby-concurrent’.

* gnu/packages/rails.scm (ruby-activesupport)[propagated-inputs]: Use
‘ruby-concurrent-ruby’ instead of ‘ruby-concurrent’.
(ruby-sprockets)[propagated-inputs]: Likewise.

Change-Id: Ib6222cad61f09d404bc303736426fbb19cbe2e73

packages: Add ‘define-deprecated-package’.

* gnu/packages/tex.scm (define-deprecated-package): Move to…
* guix/packages.scm (define-deprecated-package): … here.  Add extra clause to
handle the case where the package name differs from the variable name.

Change-Id: Ie28e6c37a38dfb05e0b7a2530f14c8b07ef3df8b

gnu: libngspice and ngspice: Move to electronics.

* gnu/packages/engineering.scm (libngspice, ngspice): Move from here ...
* gnu/packages/electronics.scm: ... to here.

Change-Id: I41b4611c1e878c5cfdd38f0ed6c13625476119bd
Signed-off-by: Gabriel Wicki <gabriel@erlikon.ch>

gnu: capypdf: Update to 0.18.0.

* gnu/packages/pdf.scm (capypdf): Update to 0.18.0.

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

gnu: Remove glibc-2.32.

* gnu/packages/base.scm (glibc-2.32): Delete variable.
* gnu/packages/patches/glibc-2.31-hurd-clock_gettime_monotonic.patch,
gnu/packages/patches/glibc-skip-c++.patch: Remove files.
* gnu/local.mk (dist_patch_DATA): Unregister files. Order glibc patches.

Fixes: guix/guix#3572
Change-Id: I8df841580c64ce0964817700a1f66da41fd5aab4

gnu: Remove glibc-locales-2.32.

* gnu/packages/base.scm (glibc-locales-2.32): Delete variable.

Change-Id: Ib8721e7a49e2374167b56a54d9bd8f6db982d22e

gnu: Remove glibc-2.31.

* gnu/packages/base.scm (glibc-2.31): Delete variable.

Change-Id: I60a58cb4acef54b01e287036b47a54308d1f54fe

gnu: Remove glibc-locales-2.31.

* gnu/packages/base.scm (glibc-locales-2.31): Delete variable.

Change-Id: Ifa8f0f3471b065bbd1be27c169a43de48f2d6201

gnu: Remove glibc-2.30.

* gnu/packages/base.scm (glibc-2.30): Delete variable.
* gnu/packages/patches/glibc-2.29-supported-locales.patch,
gnu/packages/patches/glibc-CVE-2019-19126.patch,
gnu/packages/patches/glibc-CVE-2019-7309.patch,
gnu/packages/patches/glibc-CVE-2019-9169.patch: Remove files.
* gnu/local.mk (dist_patch_DATA): Unregister files.

Change-Id: Iaf2ad2ccd938780f6f90ad846d81635b07e485f5

gnu: Remove glibc-locales-2.30.

* gnu/packages/base.scm (glibc-locales-2.30): Delete variable.

Change-Id: I7369eb63a46e3462fd990392b6da12f8c15e6db6

gnu: glibc-locales: Remove unused patch.

* gnu/packages/patches/glibc-locales-2.28.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Unregister file.
* gnu/packages/base.scm (make-glibc-locales): Remove unused branch of
conditional.

Change-Id: I853cbd0f8724a57d15af3fbb1aed3bdf1ef78e0e

gnu: xpra: Update to 6.3.4.

* gnu/packages/xorg.scm (xpra): Update to 6.3.4.

Change-Id: Idc6a2a24e1daa0d76f1aae282eb7283322d66030
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: netperf: Update to 2.7.0-2.afc51ff.

* gnu/packages/networking.scm (netperf): Update to 2.7.0-2.afc51ff.
This fixes the build with current gcc.
[arguments]<#:configure-flags>: Extend CFLAGS.

Change-Id: I473d5c9773e47bc87530453ec8cc46570a2498f2
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: python-trio-websocket: Move to python-web.

* gnu/packages/python-xyz.scm (python-trio-websocket): Move from here ...
* gnu/packages/python-web.scm: ... to here.

Change-Id: Ifffadaa04808a64dc443b912a8bccfd4c7dcb8dd