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This is a follow-up to commit 370cb92eaa089af19c08d9a7b4f5a96ac5b27716 .
* gnu/packages/graphviz.scm: Drop imported modules.
(graphviz-2.38): Remove package.
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* gnu/packages/code.scm (lcov): Update to 1.16.
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* gnu/packages/perl-compression.scm (perl-io-compress): Update to 2.204.
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* gnu/packages/perl-compression.scm (perl-compress-raw-bzip2): Update to
2.204.
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* gnu/packages/perl-compression.scm (perl-compress-raw-zlib): Update to
2.204.
[arguments]: Remove.
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* gnu/packages/tls.scm (gnutls)[arguments]: Adjust powerpc-linux phase
'increase-test-timeout to not be embedded inside another phase.
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* gnu/packages/mpd.scm (mpdevil)[native-inputs]: Add gettext-minimal.
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* gnu/packages/fcitx.scm (presage)[arguments]: Adjust configure-flags to
use c++-14 cor CFLAGS and CXXFLAGS.
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* gnu/packages/mail.scm (libpst)[arguments]: Add a phase to detect newer
versions of python3.
[native-inputs]: Add autoconf, automake, gettext-minimal, libool.
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* gnu/packages/perl.scm (perl-data-dumper): Update to 2.183.
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"setup.py install is deprecated. Use build and pip and other standards-based
tools." It then falls back to attempting to install packages via pip.
* gnu/packages/bioinformatics.scm (cwltool)[build-system]: Use
pyproject-build-system.
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The python-build-system fails with "setuptools.installer is
deprecated. Requirements should be satisfied by a PEP 517 installer." This,
in turn, causes all Python packages to be ignored and "pip install" to be
invoked for them.
* gnu/packages/bioinformatics.scm (python-schema-salad)[build-system]: Use
pyproject-build-system.
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* gnu/packages/syndication.scm (gfeeds)[inputs]: Add gettext-minimal.
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* gnu/packages/syndication.scm (syndication-domination): Update to
1.0-1-7592032.
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* gnu/packages/gnome.scm (evolution): Update to 3.46.4.
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* gnu/packages/gnome.scm (evolution-data-server): Update to 3.46.4.
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* gnu/packages/bioinformatics.scm (adapterremoval): Update to 2.3.3.
[arguments]: Simplify.
[inputs]: Reformat.
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* gnu/packages/ocaml.scm (ocaml-lwt)[properties]: New field.
(ocaml4.07-lwt): New variable.
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* gnu/packages/tls.scm (perl-crypt-openssl-rsa): Update to 0.33.
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* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Fix operators in
'compatibility phase.
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* gnu/packages/bioinformatics.scm (hisat)[native-inputs]: Add gcc-10.
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* gnu/packages/bioinformatics.scm (kallisto): Update to 0.48.0.
[arguments]: Remove trailing #T from build phase.
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* gnu/packages/bioinformatics.scm (bpp-core)[native-inputs]: Add gcc-10.
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* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.9.
[source]: Update snippet.
[inputs]: Add curl, pybind11, and wfa2-lib.
[arguments]: Adjust and reformat.
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* gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.2.
[source]: Simplify snippet.
[inputs]: Add curl.
[arguments]: Simplify and reformat.
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* gnu/packages/bioinformatics.scm (wfa2-lib): New variable.
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* gnu/packages/patches/biber-adapt-perl-5.36.patch: Backport patch from
upstream's 760e6e4ec08a3097f7e6136331541a7b8c1c9df7.
* gnu/packages/tex.scm (biber): Use it.
* gnu/local.mk (dist_patch_DATA): Register it.
Signed-off-by: Andreas Enge <andreas@enge.fr>
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* gnu/packages/gcc.scm (gcc-configure-flags-for-triplet): Disable gcov when
targetting mingw.
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/machine-learning.scm (nerd-dictation)[inputs]: Remove.
(nerd-dictation-gexp): New procedure.
(nerd-dictation/xdotool, nerd-dictation/sox-xdotool)
(nerd-dictation/sox-ydotool, nerd-dictation/sox-wtype): New variables
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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Due to (now renamed) 'hidden-service' record type not being exported, the only
way Onion services (formely hidden services) could have worked is through the
now deprecated 'tor-hidden-service' procedure.
This commit updates the Tor service documentation, corrects some inconsistently
named accessors in <tor-configuration> record-type, renames and refactors
tor-hidden-service-configuration to tor-onion-service-configuration using
define-configuration and also exports it, allowing Onion services to be
configured directly within a <tor-configuration> record.
Lastly, it also deprecates the 'tor-hidden-service' procedure.
* doc/guix.texi (Networking Services): Substitute mentions of “Hidden services”
with “Onion Services”. Add a Tor Onion service configuration example.
Document <tor-onion-service-configuration>. Remove mention of
'tor-hidden-service' procedure.
* gnu/services/networking.scm: Export tor-configuration-tor,
tor-configuration-config-file, tor-configuration-hidden-services,
tor-configuration-socks-socket-type, tor-configuration-control-socket-path,
tor-onion-service-configuration, tor-onion-service-configuration?,
tor-onion-service-configuration-name, tor-onion-service-configuration-mapping.
(<tor-configuration>)[control-socket?]: Rename accessor.
(<hidden-service>): Replace with …
(<tor-onion-service-configuration>): … this.
(tor-configuration->torrc): Update record-type name.
(tor-activation): Ditto.
(tor-hidden-service-type): Remove variable.
(tor-hidden-service): Deprecate procedure.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/haskell.scm (ghc-8.10)[arguments]: Add new phase
'skip-failing-tests-i686-cuirass.
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This keeps Python from complaining: "ZIP does not support timestamps before
1980".
* gnu/packages/bioinformatics.scm (lofreq)[arguments]: Add build phase
'set-source-file-times-to-1980.
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* gnu/packages/bioinformatics.scm (lofreq)[inputs]: Drop package labels.
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* gnu/packages/bioinformatics.scm (ivar): Update to 1.4.2.
[arguments]: Remove -Werror flag.
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* gnu/packages/embedded.scm (propeller-gcc-4)[native-inputs]: Use
MODIFY-INPUTS and drop package label.
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* gnu/packages/embedded.scm (propeller-gcc-4)[arguments]: Use G-expression
because the parent GCC package uses them too.
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* gnu/packages/curl.scm (trurl): Replace non-existant input curl-7.84.0 by
curl, which is version 7.85.0.
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Includes fix for python-cryptography>=39 disallowing SHA-1 signatures,
which caused the testsuite to fail.
* gnu/packages/ssh.scm (python-asyncssh): Update to 2.13.1.
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* gnu/packages/terminals.scm (alacritty)[arguments]: Add a phase to add
an absolute reference to xdg-open.
[inputs]: Add xdg-utils.
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* gnu/packages/emacs-xyz.scm (emacs-eshell-syntax-highlighting): Update to 0.5.
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* gnu/packages/games.scm (nethack): Update to 3.6.7.
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* gnu/packages/curl.scm (trurl): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
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* gnu/packages/emacs-xyz.scm (emacs-auctex): Update to 13.2.0.
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* gnu/packages/emacs-xyz.scm (emacs-xonsh-mode): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
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* gnu/packages/python-xyz.scm (python-importlib-resources): Update to 5.12.0.
[build-system]: Use pyproject-build-system.
[arguments]: Add phase to avoid "pip install".
[native-inputs]: Remove python-toml; add python-flake8, python-pytest,
python-pytest-black, python-pytest-checkdocs, python-pytest-cov,
python-pytest-enabler, python-pytest-flake8, python-pytest-mypy, and
python-setuptools-57.
[propagated-inputs]: Add python-zipp.
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* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-79.6a4e827.
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* gnu/packages/music.scm (schismtracker): Update to 20221201.
[source]: Convert snippet to gexp.
[arguments]: Convert to gexp, add configure flags for FLAC and Wayland
support.
[inputs]: Remove libx11, libxext, and sdl; add flac and sdl2.
Signed-off-by: Christopher Baines <mail@cbaines.net>
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* gnu/packages/python-xyz.scm (python-anyio): Upgrade to 3.6.2.
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Not compatible with python-trio 0.8.
This reverts commit 27a4bfbd07022ebabc352a419c7588fcfc881d88.
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