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Author SHA1 Message Date
Cayetano Santos
486aa1df18 gnu: mygnuhealth: Upgrade dependency on python-pyside. 
* gnu/packages/medical.scm (mygnuhealth)[native-inputs]: Remove
python-pyside-2; add python-pyside-6.

Change-Id: Ifcaa63d33b9877332833be8d62ce00e61c873339
 2026-03-26 08:28:22 +01:00
Ludovic Courtès
1ae20f03f4 gnu: Reference the inherited inputs values. 
This commit was made by running this command:

  sed -e's/modify-inputs (package-\([a-z-]*\)inputs [a-zA-Z0-9-]\+)/modify-inputs \1inputs/g' -i gnu/packages/*.scm

… and then reverting individual hunks where the change would trigger unbound
variable warnings or other issues (such as ‘native-inputs’ is bound in the
body of the ‘inputs’ field, but it refers to the ‘native-inputs’ thunk defined
just above).

Change-Id: I6d94819f2809313fa1fbefc61897502ee7d66fab
 2026-03-20 13:27:16 +01:00
Ludovic Courtès
2a50c9598b gnu: Reference the inherited ‘arguments’ value. 
This commit was made by running this command:

  sed -e's/substitute-keyword-arguments (package-arguments [a-zA-Z0-9-]\+)/substitute-keyword-arguments arguments/g' -i gnu/packages/*.scm

… and then:

  1. reverting changes from ‘gnu/packages/rust.scm’ and
     ‘gnu/packages/java.scm’ since they would incur derivation changes and/or
     breakage;
  2. reverting the change for ‘gcc-final’ in ‘gnu/packages/commencement.scm’;
  3. reverting the change for ‘onnx-optimizer’, ‘openquest’, and ‘certbot’,
     which use ‘substitute-keyword-arguments’ for arguments that are not
     inherited (and thus ‘arguments’ would be unbound);
  4. reverting the change for ‘insight-toolkit-legacy’ and ‘wine64-staging’
     which make bogus assumptions about inherited arguments.

Change-Id: I122a7cf517b6b63cae38944b5d33ade4b1f5a89c
 2026-03-20 13:27:15 +01:00
Jake Forster
07992d2593 gnu: orthanc-postgresql: Update to 10.0. 
* gnu/packages/medical.scm (orthan-postgresql): Update to 10.0.

Change-Id: I60c0a418bf336f6ec6ec30ffeee5f7060b2f7676
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-03-13 15:22:13 +00:00
Jake Forster
f799b7fc1e gnu: orthanc: Update to 1.12.10. 
* gnu/packages/medical.scm (orthanc): Update to 1.12.10.
[arguments]<#:phases>{remove-localtime-requirement}: Update substitution.
[inputs]: Replace boost-1.83 with boost.

Change-Id: I08f72fe6fe3f9dde590b791d5ed03684d081fea6
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-03-13 15:22:13 +00:00
Jake Forster
73f87c741d gnu: xmedcon: Update to 0.26.1. 
* gnu/packages/medical.scm (xmedcon): Update to 0.26.1.

Change-Id: I7260ef89b825afc6ee9a8b89023e7c98809322c7
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-03-04 12:03:56 +01:00
Greg Hogan
1aebfc74f1 gnu: boost: Update to 1.89.0. 
* gnu/packages/boost.scm (boost-for-source-highlight): Rename this ...
(boost-1.83): ... to this.
(boost-numpy): Inherit from boost-1.83.
* gnu/packages/pretty-print.scm (source-highlight): Update accordingly.

* gnu/packages/boost.scm (boost): Update to 1.89.0.
[source]: Remove patches.

* gnu/packages/boost.scm (mdds)
[propagated-inputs]: Replace boost with boost-1.83.

* gnu/packages/astronomy.scm (aoflagger),
* gnu/packages/embedded.scm (cc-tool),
* gnu/packages/games.scm (0ad, vcmi),
* gnu/packages/image.scm (gpick),
* gnu/packages/maths.scm (highfive),
* gnu/packages/plotutils.scm (asymptote)
[native-inputs]: Replace boost with boost-1.83.

* gnu/packages/audio.scm (guitarix, supercollider),
* gnu/packages/bioconductor.scm (r-mzr),
* gnu/packages/bioinformatics.scm (ataqv, bless, express, isolator,
metabat, r-velocytom, rsem, sailfish, salmon),
* gnu/packages/bittorrent.scm (libtorrent-rasterbar),
* gnu/packages/code.scm (sourcetrail),
* gnu/packages/compression.scm (innoextract),
* gnu/packages/cpp.scm (lager),
* gnu/packages/crypto.scm (cryfs),
* gnu/packages/electronics.scm (nextpnr, prjpeppercorn, prjtrellis,
pulseview),
* gnu/packages/emulators.scm (mupen64plus-video-glide64mk2),
* gnu/packages/engineering.scm (cadabra2, freecad, libigl,
openscad, prusa-slicer),
* gnu/packages/file-systems.scm (snapper),
* gnu/packages/finance.scm (ledger),
* gnu/packages/game-development.scm (dds),
* gnu/packages/games.scm (colobot, fifengine, knightsgame, leela-zero,
pokerth, supertux, wesnoth, wesnoth-server),
* gnu/packages/geo.scm (gplates),
* gnu/packages/gnucash.scm (gnucash),
* gnu/packages/graph.scm (python-graph-tool),
* gnu/packages/graphics.scma (openshadinglanguage),
* gnu/packages/i2p.scm (i2pd),
* gnu/packages/image-viewers.scm (luminance-hdr),
* gnu/packages/kde-graphics.scm (krita),
* gnu/packages/mail.scm (astroid),
* gnu/packages/medical.scm (orthanc, orthanc-mysql,
orthanc-postgresql),
* gnu/packages/messaging.scm (libphonenumber),
* gnu/packages/mpd.scm (ncmpcpp),
* gnu/packages/networking.scm (kismet),
* gnu/packages/opencog.scm (cogutil),
* gnu/packages/photo.scm (hugin),
* gnu/packages/poedit.scm (poedit),
* gnu/packages/radio.scm (gnuradio),
* gnu/packages/rdf.scm (lucene++),
* gnu/packages/serialization.scm (avro-cpp),
* gnu/packages/simulation.scm (fenics-dolfin),
* gnu/packages/version-control.scm (gource),
* gnu/packages/video.scm (aegisub, mkvtoolnix),
* gnu/packages/web.scm (websocketpp)
[inputs]: Replace boost with boost-1.83.

* gnu/packages/libreoffice.scm (libcmis): Update to 0.6.2-00a85bf6.
(librevenge): Update to 0.0.5.
[arguments]<#:configure-flags>: Remove reference to boost system
component for which the compatibility stub has been removed.
* gnu/packages/serialization.scm (msgpack-cxx): Update to 7.0.0.

Change-Id: I247f3eaecde3de3fe227586b840f0312b4797ee1
 2025-11-28 12:26:24 +00:00
Andreas Enge
3e933e9492 gnu: Remove openmolar-1. 
* gnu/packages/medical.scm (openmolar-1): Delete variable.

Fixes: guix/guix#3762
Change-Id: I44512fc468dc1ce11976f84576d3885c36571ce9
 2025-11-24 11:03:40 +01:00
Jake Forster
6c9ce6b900 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>
 2025-10-23 19:35:07 +02:00
Jake Forster
4c92edde11 gnu: Add xmedcon-minimal. 
* gnu/packages/medical.scm (xmedcon-minimal): New variable.

Change-Id: Ie817bd1c994d8978d4f07f16fce9a6d103aa9423
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-10-03 23:15:24 +01:00
Nicolas Graves
b972e487a5 gnu: mygnuhealth: Switch to pyproject. 
* gnu/packages/medical.scm (mygnuhealth):
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests>: Disable them.
<#:imported-modules, #:modules>: Refresh them.
<#:phases>: Run guix style.
[native-inputs]: Add python-setuptools.

Change-Id: Ieec8cbd7c1c87f1482a8dc8049fcb8ad1aae4f9e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-09-28 19:23:53 +01:00
Jake Forster
16c93b80d9 gnu: Add xmedcon. 
* gnu/packages/medical.scm (xmedcon): New variable.

Change-Id: I5f89083b3725054db4bd54faa2570dded71a6d03
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-08-12 16:45:42 +01:00
Sharlatan Hellseher
9efddd7dae gnu: orthanc-mysql: Fix searching of mysql.h. 
Fixes guix/guix#1386

* gnu/packages/medical.scm (orthanc-mysql): [phases]
  {fix-mysql-include-path}: Swap to SEARCH-INPUT-DIRECTORY, see
  guix/guix#1385.

Change-Id: I879001041733c03bd1e5dd8659c0e3c67fc8b6ee
 2025-07-19 20:45:35 +01:00
Jake Forster
b79adccf44 gnu: Add orthanc-mariadb. 
* gnu/packages/medical.scm (orthanc-mariadb): New variable.

Change-Id: I672c8ef886dbe341d69ad16da569956ddad74f96
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-30 10:37:58 +01:00
Jake Forster
65c5c2bd40 gnu: Add orthanc-mysql. 
* gnu/packages/medical.scm (orthanc-mysql): New variable.

Change-Id: I66da128f49a04449609019058912c82db49b7c68
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-30 10:37:52 +01:00
Jake Forster
54b33b33dc gnu: Add orthanc-postgresql. 
* gnu/packages/medical.scm (orthanc-postgresql): New variable.

Change-Id: I27412daf588f4bb9d0ae35101c2586d2d3b7728b
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-30 10:37:39 +01:00
Jake Forster
2305201d58 gnu: Add orthanc. 
* gnu/packages/medical.scm (orthanc): New variable.

Change-Id: I52e73a1545ddf68ff3ce2b90fcf2da9d492a9fb1
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2025-06-23 14:47:08 +02:00
Jake Forster
7d7551f9a5 gnu: Use license: prefix in (gnu packages medical). 
* gnu/packages/medical.scm: Import (guix licenses) with the license:
prefix.  Adjust all license fields.

Change-Id: Icebc104412924d5dfbd98ffd2046744c94f644d3
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2025-06-23 14:47:08 +02:00
Nicolas Graves
f8cedfb8c0 gnu: openmolar: Fix build. 
* gnu/packages/medical.scm (openmolar): Fix build.
[build-system]: Switch to pyproject-build-system.
[arguments]{use-setuptools?}: Drop it.
{phases}: Add phase 'set-acceptable-version.
[native-inputs]: Add python-setuptools, python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:26 +02:00
Ryan Desfosses
382a8feae0 gnu: mygnuhealth: Update to 2.2.1. 
* gnu/packages/medical.scm (mygnuhealth): Update to 2.2.1

Change-Id: Ifeaead2c6ee715b94706267c1d5b1dcd0e98e84e
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-12-25 23:51:09 +01:00
Marco Rimoldi
11d5b505e5 gnu: openmolar-1: Update to release 1.1.6-g81838c8 and partial runtime fix. 
Fixes <https://issues.guix.gnu.org/29365>.

WebKit was removed from Qt5 in favor of WebEngine; upstream addressed
this in their last stable release, in 2018.  The package still fails at
runtime: this commit lays the ground for further fixes.

* gnu/packages/medical.scm (openmolar-1): Update to release 1.1.6-g81838c8.
[arguments]: Extend 'patch-/usr phase to source file localsettings.py.
[inputs]: Add python-pyqtwebengine.
[propagated-inputs]: Add qtwebengine-5.

Change-Id: Ia4e4c052397201c26834dec2358ca5c20beb581d
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-02-10 22:54:05 +01:00
Petr Hodina
ac6e5d5b80 gnu: Add mygnuhealth. 
* gnu/packages/medical.scm (mygnuhealth): New variable.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Co-authored-by: Morgan Smith <Morgan.J.Smith@outlook.com>
Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-03-20 23:46:16 -04:00
Ludovic Courtès
8394619bac gnu: Simplify package inputs. 
This commit was obtained by running:

  ./pre-inst-env guix style

without any additional argument.
 2021-12-13 17:48:25 +01:00
Ricardo Wurmus
44d10b1f72 gnu: Separate Python core packages from the rest. 
* gnu/packages/python.scm: Move hundreds of package definitions from here...
* gnu/packages/python-xyz.scm: ...to this new module.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/ada.scm,
gnu/packages/admin.scm,
gnu/packages/android.scm,
gnu/packages/audio.scm,
gnu/packages/backup.scm,
gnu/packages/benchmark.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/bittorrent.scm,
gnu/packages/calendar.scm,
gnu/packages/check.scm,
gnu/packages/chemistry.scm,
gnu/packages/cluster.scm,
gnu/packages/compression.scm,
gnu/packages/connman.scm,
gnu/packages/crypto.scm,
gnu/packages/cups.scm,
gnu/packages/databases.scm,
gnu/packages/dav.scm,
gnu/packages/direct-connect.scm,
gnu/packages/disk.scm,
gnu/packages/django.scm,
gnu/packages/dlang.scm,
gnu/packages/docker.scm,
gnu/packages/ebook.scm,
gnu/packages/elf.scm,
gnu/packages/emacs.scm,
gnu/packages/emulators.scm,
gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm,
gnu/packages/finance.scm,
gnu/packages/fltk.scm,
gnu/packages/fontutils.scm,
gnu/packages/freedesktop.scm,
gnu/packages/game-development.scm,
gnu/packages/games.scm,
gnu/packages/geo.scm,
gnu/packages/gl.scm,
gnu/packages/glib.scm,
gnu/packages/gnome.scm,
gnu/packages/gnupg.scm,
gnu/packages/gnuzilla.scm,
gnu/packages/graph.scm,
gnu/packages/graphics.scm,
gnu/packages/graphviz.scm,
gnu/packages/gtk.scm,
gnu/packages/ham-radio.scm,
gnu/packages/image-processing.scm,
gnu/packages/image-viewers.scm,
gnu/packages/image.scm,
gnu/packages/irc.scm,
gnu/packages/jrnl.scm,
gnu/packages/julia.scm,
gnu/packages/kde-frameworks.scm,
gnu/packages/key-mon.scm,
gnu/packages/libffi.scm,
gnu/packages/libreoffice.scm,
gnu/packages/libusb.scm,
gnu/packages/lirc.scm,
gnu/packages/logging.scm,
gnu/packages/machine-learning.scm,
gnu/packages/mail.scm,
gnu/packages/mate.scm,
gnu/packages/maths.scm,
gnu/packages/medical.scm,
gnu/packages/messaging.scm,
gnu/packages/monitoring.scm,
gnu/packages/mp3.scm,
gnu/packages/mpd.scm,
gnu/packages/music.scm,
gnu/packages/networking.scm,
gnu/packages/nutrition.scm,
gnu/packages/openldap.scm,
gnu/packages/openstack.scm,
gnu/packages/package-management.scm,
gnu/packages/password-utils.scm,
gnu/packages/patchutils.scm,
gnu/packages/pdf.scm,
gnu/packages/photo.scm,
gnu/packages/polkit.scm,
gnu/packages/protobuf.scm,
gnu/packages/python-crypto.scm,
gnu/packages/python-web.scm,
gnu/packages/qt.scm,
gnu/packages/rdf.scm,
gnu/packages/ruby.scm,
gnu/packages/search.scm,
gnu/packages/selinux.scm,
gnu/packages/serialization.scm,
gnu/packages/shells.scm,
gnu/packages/simulation.scm,
gnu/packages/ssh.scm,
gnu/packages/statistics.scm,
gnu/packages/storage.scm,
gnu/packages/sync.scm,
gnu/packages/terminals.scm,
gnu/packages/textutils.scm,
gnu/packages/time.scm,
gnu/packages/tls.scm,
gnu/packages/tor.scm,
gnu/packages/tryton.scm,
gnu/packages/version-control.scm,
gnu/packages/video.scm,
gnu/packages/virtualization.scm,
gnu/packages/vpn.scm,
gnu/packages/web-browsers.scm,
gnu/packages/web.scm,
gnu/packages/wicd.scm,
gnu/packages/xdisorg.scm,
gnu/packages/xorg.scm: Update module references.
 2019-01-15 14:46:44 +01:00
Ricardo Wurmus
a8714bf680 gnu: Move database packages from python.scm to databases.scm. 
* gnu/packages/python.scm (python-ccm, python2-ccm, python2-pysqlite,
python-sqlalchemy, python2-sqlalchemy, python-sqlalchemy-utils,
python2-sqlalchemy-utils, python-alembic, python2-alembic,
python-pickleshare, python2-pickleshare, python-apsw, python2-apsw,
python2-neo4j-driver, python2-py2neo, python-psycopg2, python2-psycopg2,
python-sadisplay, python2-sadisplay, python-mysqlclient,
python2-mysqlclient, python-hiredis, python2-hiredis, python-fakeredis,
python2-fakeredis, python-redis, python2-redis, python-rq, python2-rq,
python-trollius-redis, python2-trollius-redis, python-sqlparse,
python2-sqlparse, python-sql, python2-sql): Move from here...
* gnu/packages/databases.scm: ...to here.
* gnu/packages/tryton.scm,
gnu/packages/python-web.scm,
gnu/packages/nutrition.scm,
gnu/packages/medical.scm: Adjust accordingly.
 2017-11-17 22:36:27 +01:00
Ricardo Wurmus
a68a83f015 gnu: Add openmolar. 
* gnu/packages/medical.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

Co-authored-by: Quiliro <quiliro@fsfla.org>
 2017-07-22 23:48:58 +02:00