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Paul A. Patience 797f3de592
gnu: gnuplot: Update to 5.4.4. 
* gnu/packages/maths.scm (gnuplot): Update to 5.4.4.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-08-02 20:50:01 +03:00
Paul A. Patience a53bc40036
gnu: gnuplot: Use G-expressions. 
* gnu/packages/maths.scm (gnuplot)[arguments]: Use G-expressions.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-08-02 20:49:56 +03:00
Paul A. Patience 44c7098809
gnu: gnuplot: Remove input labels. 
* gnu/packages/maths.scm (gnuplot)[inputs]: Move below native-inputs and
sort.
[native-inputs]: Remove labels.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-08-02 20:49:50 +03:00
Efraim Flashner 29c51c6525
gnu: wcalc: Remove pre-generated files. 
* gnu/packages/maths.scm (wcalc)[source]: Add snippet to remove files
generated by bison and flex.
[native-inputs]: Add bison, flex.
 2022-08-02 19:47:50 +03:00
Efraim Flashner e1fb703e3e
gnu: nano: Update to 6.4. 
* gnu/packages/nano.scm (nano): Update to 6.4.
 2022-08-02 19:09:22 +03:00
Efraim Flashner 51a6dd170b
gnu: parallel: Add bash-minimal. 
* gnu/packages/parallel.scm (parallel)[inputs]: Add bash-minimal.
 2022-08-02 19:04:36 +03:00
Efraim Flashner 6f52d3aec1
gnu: parallel: Update to 20220722. 
* gnu/packages/parallel.scm (parallel): Update to 20220722.
 2022-08-02 18:55:26 +03:00
Ricardo Wurmus d5ba31c19a
gnu: Add r-rcppalgos. 
* gnu/packages/cran.scm (r-rcppalgos): New variable.
 2022-08-02 15:12:10 +02:00
Ricardo Wurmus 20f9473532
gnu: Add r-phylotools. 
* gnu/packages/cran.scm (r-phylotools): New variable.
 2022-08-02 15:12:01 +02:00
Ricardo Wurmus 03858a7908
gnu: Add python-scanorama. 
* gnu/packages/bioinformatics.scm (python-scanorama): New variable.
 2022-08-02 14:37:38 +02:00
Ricardo Wurmus c69c2c1c4d
gnu: python-intervaltree: Update to 3.1.0. 
* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.1.0.
 2022-08-02 14:37:38 +02:00
Ricardo Wurmus 4bc130dcc0
gnu: Add python-geosketch. 
* gnu/packages/python-science.scm (python-geosketch): New variable.
 2022-08-02 14:37:38 +02:00
Ricardo Wurmus d4b0dc047f
gnu: Add python-fbpca. 
* gnu/packages/python-science.scm (python-fbpca): New variable.
 2022-08-02 14:37:38 +02:00
Guillaume Le Vaillant d4b7aae9f4
gnu: monero-gui: Update to 0.18.0.0. 
* gnu/packages/finance.scm (monero-gui): Update to 0.18.0.0.
  [inputs]: remove labels.
  [arguments]: Use gexps.
 2022-08-02 12:32:46 +02:00
Guillaume Le Vaillant e7bac8584b
gnu: monero: Update to 0.18.0.0. 
* gnu/packages/finance.scm (monero): Update to 0.18.0.0.
  [source]: Update snippet.
  [arguments]: Use gexps.
 2022-08-02 12:32:46 +02:00
Nicolas Goaziou b4d9493ceb
gnu: scummvm: Update to 2.6.0. 
* gnu/packages/emulators.scm (scummvm): Update to 2.6.0.
 2022-08-02 11:53:59 +02:00
Nicolas Goaziou fde477442e
gnu: emacs-clojure-mode: Update to 5.15.1. 
* gnu/packages/emacs-xyz.scm (emacs-clojure-mode): Update to 5.15.1.
 2022-08-02 11:53:59 +02:00
Andrew Tropin 9355d46329
home: Add explicit dependency on env to activation script. 
* gnu/home/services.scm (compute-activation-script): Add explicit dependency
on env to activation script.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2022-08-02 16:53:29 +08:00
Michael Rohleder ead27209b5
gnu: strawberry: Update to 1.0.7. 
* gnu/packages/music.scm (strawberry): Update to 1.0.7.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2022-08-02 16:21:29 +08:00
Peter Polidoro a1f7d98a9c
gnu: kicad: Update to 6.0.7. 
* gnu/packages/engineering.scm (kicad): Update to 6.0.7.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2022-08-02 14:13:49 +08:00
Mădălin Ionel Patrașcu af207dd46d
gnu: Add r-infercnv. 
* gnu/packages/bioconductor.scm (r-infercnv): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-08-01 23:53:23 +02:00
Mădălin Ionel Patrașcu 5baa37b56c
gnu: Add r-phyclust. 
* gnu/packages/cran.scm (r-phyclust): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-08-01 23:53:23 +02:00
Efraim Flashner 1085514a18
gnu: node-lts: Build with icu4c-71. 
* gnu/packages/node.scm (node-lts)[inputs]: Replace icu4c-70 with
icu4c-71.
[native-inputs]: Same.
 2022-08-02 00:45:41 +03:00
Maxim Cournoyer 4637de6a41
gnu: Add qtlottie. 
* gnu/packages/qt.scm (qtlottie): New variable.
 2022-08-01 17:21:01 -04:00
Maxim Cournoyer f5cc7d03a7
gnu: telephony: Add a Jami test for a partially defined jami-account. 
* gnu/tests/telephony.scm (%dummy-jami-account-partial): New variable.
(make-jami-os): Add a PARTIAL? argument and use it to select the jami-account
variant to use.
(%jami-os-provisioning-partial): New variable.
(run-jami-test): Add a PARTIAL? argument, and use it to select operating
system variant.  Skip allowed-contacts and moderators test when PARTIAL? is
true.
(%test-jami-provisioning-partial): New test.
 2022-08-01 12:49:44 -04:00
Maxim Cournoyer a2b89a3319
services: configuration: Step back from *unspecified*. 
Fixes <https://issues.guix.gnu.org/56799>.

This partially reverts 8cb1a49a39.

Rationale: *unspecified* cannot be serialized thus used as a G-Expression
input, which is problematic/inconvenient when using deeply nested records.  As
an example, jami-service-type was broken when using partially defined
<jami-account> records.

* gnu/services/configuration.scm (define-maybe-helper): Check against the
'unset symbol.
(normalize-field-type+def): Adjust value to 'unset.
(define-configuration-helper): Use 'unset as the default value thunk.
* gnu/services/file-sharing.scm (serialize-maybe-string): Check against the
'unset symbol.
(serialize-maybe-file-object): Likewise.
* gnu/services/messaging.scm (define-all-configurations): Use 'unset as
value.
(raw-content?): Check against 'unset symbol.
(prosody-configuration)[http-max-content-size]: Default to 'unset.
[http-external-url]: Likewise.
[mod-muc]: Likewise.
[raw-content]: Likewise.
* gnu/services/networking.scm (opendht-configuration): Adjust documentation.
* gnu/services/telephony.scm (jami-shepherd-services): Replace *undefined*
with the 'unset symbol.
* tests/services/configuration.scm ("maybe type, no default"): Check against
the 'unset symbol.
* doc/guix.texi: Regenerate the opendht-configuration,
openvpn-client-configuration and openvpn-server-configuration documentation.
 2022-08-01 12:49:35 -04:00
Maxim Cournoyer 4905b5b839
build-system: qt: Ensure a default value is provided for #:qtbase. 
* guix/build-system/qt.scm (qt-build)[qtbase]: Specify a default value.  Lower
it using ungexp-native.
(qt-cross-build): Likewise.

Reported-by: Maxime Devos <maximedevos@telenet.be> and others.
 2022-08-01 12:48:37 -04:00
Ricardo Wurmus f1b9ae8c20
gnu: python-bbknn: Update to 1.5.1. 
* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.5.1.
[propagated-inputs]: Add python-pandas.
 2022-08-01 17:46:21 +02:00
muradm d7e7494bc4
gnu: Add fail2ban. 
* gnu/packages/admin.scm (fail2ban): New variable.
* gnu/packages/patches/fail2ban-0.11.2_CVE-2021-32749.patch,
gnu/packages/patches/fail2ban-0.11.2_fix-setuptools-drop-2to3.patch,
gnu/packages/patches/fail2ban-0.11.2_fix-test-suite.patch,
gnu/packages/patches/fail2ban-paths-guix-conf.patch,
gnu/packages/patches/fail2ban-python310-server-action.patch,
gnu/packages/patches/fail2ban-python310-server-actions.patch,
gnu/packages/patches/fail2ban-python310-server-jails.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 17:20:27 +02:00
Paul A. Patience 18d998ffdb
gnu: trilinos-for-dealii-openmpi: Use G-expressions. 
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[arguments]: Use
G-expressions.
<#:phases>: Remove trailing boolean.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 17:20:27 +02:00
Paul A. Patience 32bcadc98c
gnu: trilinos-for-dealii-openmpi: Remove input labels. 
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[native-inputs,
inputs, propagated-inputs]: Remove labels.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 17:20:26 +02:00
Paul A. Patience a42730183a
gnu: dealii: Update to 9.4.0. 
* gnu/packages/maths.scm (dealii): Update to 9.4.0.
[propagated-inputs]: Replace sundials-5 with sundials.
(dealii-openmpi)[propagated-inputs]: Replace sundials-openmpi-5 with
sundials-openmpi.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 17:20:26 +02:00
Paul A. Patience 6a15bd031f
gnu: dealii: Use G-expressions. 
* gnu/packages/maths.scm (dealii)[snippet, arguments]: Use
G-expressions.
(dealii-openmpi)[arguments]: Same.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 17:20:26 +02:00
Paul A. Patience bbf5e033d4
gnu: trilinos-for-dealii-openmpi: Fix build. 
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[native-inputs]:
Add gcc-7 to fix the failing build with newer versions of gcc.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 17:20:26 +02:00
Mădălin Ionel Patrașcu c6800aa31e
gnu: Add r-muscat. 
* gnu/packages/bioconductor.scm (r-muscat): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-08-01 16:08:11 +02:00
muradm 7e3234cb70
gnu: mu: Update to 1.8.7. 
* gnu/packages/mail.scm (mu): Update to 1.8.7.
[source]: Fetch from git.
[build-system]: Use meson-build-system.
[native-inputs]: Remove glib:bin and tzdata; add gnupg and texinfo; use new
style.
[inputs]: Remove guile.
[arguments]: Remove obsolete 'patch-configure, 'fix-ffi, and
'check-tz-setup phases.  Rename 'patch-bin-sh-in-tests
to 'patch-bin-references and update it.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-08-01 16:03:21 +02:00
Maxim Cournoyer c454cf6343
gnu: qutebrowser: Fix indentation. 
* gnu/packages/web-browsers.scm (qutebrowser): Fix indentation.
 2022-08-01 09:32:28 -04:00
Maxim Cournoyer aea756ea33
gnu: qutebrowser: Fix build. 
Fixes <https://issues.guix.gnu.org/56864>, which is a regression introduced
with a0beb297a3.

* gnu/packages/web-browsers.scm (qutebrowser)
[phases]{wrap-qt-process-path}: Do not use the (no longer valid)
"qtwebengine-5" label; instead, locate QtWebEngineProcess via
'search-input-file'.

Reported-by: Jack Hill <jackhill@jackhill.us>
 2022-08-01 09:32:28 -04:00
Mădălin Ionel Patrașcu 8d7a721400
gnu: Add r-millefy. 
* gnu/packages/bioinformatics.scm (r-millefy): New variable.
 2022-08-01 15:14:47 +02:00
Marcel van der Boom b8df15b748
gnu: exiv2: Fix test failure on ppc64le and aarch64. 
ppc64 and aarch64 do not raise exception and thus output and exit code
for test is different.

See:

  https://github.com/Exiv2/exiv2/issues/365 and
  https://github.com/Exiv2/exiv2/issues/933

* gnu/packages/image.scm (exiv2)[arguments]: Add 'adjust-tests' phase.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:09 +02:00
Philip McGrath d7ab54cdb1
gnu: Add python-biblib. 
* gnu/packages/python-xyz.scm (python-biblib): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:09 +02:00
Maya dd3cf14402
services: opensmtpd: Make commands setgid to "smtpq" by default. 
This is a patch that fixes "<executable name>: this program must be setgid smtpq".

* gnu/services/mail.scm (<opensmtpd-configuration>)[setgid-commands?]: New field.
(opensmtpd-set-gids): New procedure.
(opensmtpd-service-type)[extensions]: Add SETUID-PROGRAM-SERVICE-TYPE extension.
* doc/guix.texi (Mail Services): Document it.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:08 +02:00
Danial Behzadi 432ea6446d
gnu: tractor: Update to 3.14. 
* gnu/packages/tor.scm (tractor): Update to 3.14.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:08 +02:00
Paul A. Patience d1b60cb65b
gnu: Add comma after “i.e.” in descriptions. 
* gnu/packages/bioconductor.scm (r-anota)[description]: Add comma after
“i.e.”.
* gnu/packages/code.scm (xenon)[description]: Same.
* gnu/packages/cran.scm (r-crosstalk)[description]: Same.
* gnu/packages/python-xyz.scm (python-radon)[description]: Same.
* gnu/packages/statistics.scm (r-logspline)[description]: Same.
* gnu/packages/suckless.scm (tabbed)[description]: Same.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:08 +02:00
Paul A. Patience e0de48f0e4
gnu: hdf5-1.8: Add missing comma to linker flag. 
* gnu/packages/maths.scm (hdf5-1.8)[arguments]<#:phases>: Add missing
comma to linker flag.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:08 +02:00
Z572 dee64d4776
gnu: guile-lens: Fix build. 
* gnu/packages/guile-xyz.scm (guile-lens)
[phases]{run-hall}: replace "dist" to "build-system".

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:08 +02:00
Denis 'GNUtoo' Carikli 49000523d2
gnu: xdot: Build with librsvg-for-system. 
* gnu/packages/graphviz.scm (xdot)[inputs]: Replace librsvg with
  librsvg-for-system.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:07 +02:00
Denis 'GNUtoo' Carikli 4f57da7668
gnu: Add cardpeek. 
* gnu/packages/security-token.scm (cardpeek): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:07 +02:00
Sharlatan Hellseher d790ec21e8
gnu: python-sep: Update to 1.2.1 
* gnu/packages/astronomy.scm: (python-sep): Update to 1.2.1.
  Inherit from libsep

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:07 +02:00
Sharlatan Hellseher 6ad9a094c1
gnu: Add libsep 
* gnu/packages/astronomy.scm: (libsep): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:07 +02:00