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guix/gnu/packages/medical.scm
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

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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017 Quiliro <quiliro@fsfla.org>
;;; Copyright © 2022 Petr Hodina <phodina@protonmail.com>
;;; Copyright © 2025 Jake Forster <jakecameron.forster@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages medical)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system pyproject)
#:use-module (guix build-system python)
#:use-module (guix build-system qt)
#:use-module (guix download)
#:use-module (guix gexp)
#:use-module (guix git-download)
#:use-module (guix hg-download)
#:use-module (guix packages)
#:use-module (guix utils)
#:use-module (gnu packages base)
#:use-module (gnu packages bash) ; wrap-program
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages curl)
#:use-module (gnu packages databases)
#:use-module (gnu packages documentation)
#:use-module (gnu packages glib)
#:use-module (gnu packages gtk)
#:use-module (gnu packages image)
#:use-module (gnu packages image-processing)
#:use-module (gnu packages kde-frameworks) ; kirigami
#:use-module (gnu packages linux)
#:use-module (gnu packages lua)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages qt)
#:use-module (gnu packages serialization)
#:use-module (gnu packages sqlite)
#:use-module (gnu packages tls)
#:use-module (gnu packages web)
#:use-module (gnu packages xml))
(define-public mygnuhealth
(package
(name "mygnuhealth")
(version "2.2.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "MyGNUHealth" version))
(sha256
(base32 "1jcrriccqzb4jx7zayhiqmpvi3cvfy3bbf9zr3m83878f94yww8j"))))
(build-system pyproject-build-system)
(arguments
(list
#:tests? #f ; no tests.
#:imported-modules
`(,@%pyproject-build-system-modules
,@%qt-build-system-modules)
#:modules
`(((guix build qt-build-system) #:prefix qt:)
(guix build pyproject-build-system)
(guix build utils))
#:phases
#~(modify-phases %standard-phases
(add-after 'install 'qt-wrap
(assoc-ref qt:%standard-phases 'qt-wrap))
(add-before 'check 'env-setup
(lambda _
(mkdir-p "/tmp/mygh/")
(setenv "HOME" "/tmp"))))))
(native-inputs (list python-pyside-2 python-setuptools))
(inputs (list bash-minimal
kirigami-5
python
python-bcrypt
python-matplotlib
python-requests
python-tinydb
qtbase-5
qtdeclarative-5
qtgraphicaleffects
qtquickcontrols-5
qtquickcontrols2-5
qtsvg-5))
(home-page "https://www.gnuhealth.org")
(synopsis "The GNU Health Personal Health Record")
(description
"This package provides GNUHealth Personal Health Record
application for desktop and mobile devices that integrates with the GNU
Health Federation.")
(license license:gpl3+)))
(define-public orthanc
(package
(name "orthanc")
(version "1.12.7")
(source
(origin
(method hg-fetch)
(uri (hg-reference (url "https://orthanc.uclouvain.be/hg/orthanc")
(changeset "a30cc2fa7250")))
(file-name (hg-file-name name version))
(sha256
(base32 "1n8v0dh17g9ihny8cpq63qd6ai5l95i5h3sz9vwzfnd7q3qh0rb9"))))
(build-system cmake-build-system)
(arguments
(list
#:configure-flags
#~(list (string-append "-DDCMTK_DICTIONARY_DIR="
#$(this-package-input "dcmtk") "/share/dcmtk-"
#$(package-version (this-package-input "dcmtk")))
;; Building Connectivity Checks plugin requires the network.
"-DBUILD_CONNECTIVITY_CHECKS=OFF"
;; Disable 4 tests that require the network.
"-DUNIT_TESTS_WITH_HTTP_CONNEXIONS=OFF")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
;; The OrthancServer/ subdirectory contains the root
;; CMakeLists.txt file.
(chdir "OrthancServer")))
(add-after 'unpack 'remove-localtime-requirement
(lambda _
;; /etc/localtime is not present in the build container;
;; don't let that stop the build.
(substitute* "OrthancFramework/Sources/Toolbox.cpp"
(("if \\(!SystemToolbox::IsExistingFile\\(LOCALTIME\\)\\)")
"if (false)"))))
;; There is no test target; simply run the binary.
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "./UnitTests")))))))
(native-inputs (list doxygen
glibc-utf8-locales ;for one test
googletest
python))
(inputs (list boost-1.83
civetweb
curl
dcmtk
jsoncpp
libjpeg-turbo
libpng
lua
openssl
protobuf
pugixml
`(,util-linux "lib") ;for uuid.h
sqlite
unzip))
(home-page "https://orthanc-server.com")
(synopsis
"Standalone @acronym{DICOM, Digital Imaging and Communications in
Medicine} server")
(description
"Orthanc is a standalone @acronym{DICOM, Digital Imaging and
Communications in Medicine} server with a RESTful API and plugin
mechanism for extending its functionality.")
(license license:gpl3+)))
(define-public orthanc-postgresql
;; No tags provided.
(let ((changeset "ddc98844d931")
(revision "0"))
(package
(name "orthanc-postgresql")
(version (git-version "7.2" revision changeset))
(source
(origin
(method hg-fetch)
(uri (hg-reference
(url "https://orthanc.uclouvain.be/hg/orthanc-databases")
(changeset changeset)))
(file-name (hg-file-name name version))
(sha256
(base32 "1zv2lrj0f3fahmdyiwyj70ayv5ysa3cj33i58fbk7hy2zclrkjzf"))))
(build-system cmake-build-system)
(arguments
(list
#:configure-flags
#~(list
;; Don't try to download the Orthanc source code.
"-DORTHANC_FRAMEWORK_SOURCE=path"
(string-append "-DORTHANC_FRAMEWORK_ROOT="
#$(package-source (this-package-input "orthanc"))
"/OrthancFramework/Sources"))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
;; The PostgreSQL/ subdirectory contains the root
;; CMakeLists.txt file.
(chdir "PostgreSQL")))
;; There is no test target; simply run the binary.
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
;; The tests rely on a PostgreSQL test server
;; being available.
(let ((pgdata "/tmp/pgdata")
(host "/tmp")
(port "5432")
;; This username is hard-coded in tests.
(username "postgres")
(password "")
(database "orthanctest"))
(invoke "initdb" pgdata)
(invoke "pg_ctl" "-D" pgdata
"-o" (string-append "-k " host)
"start")
(invoke "createdb" "-h" host database)
(invoke "createuser" "-h" host username)
;; The tests include managing Large Objects.
(invoke "psql" "-h" host "-d" database "-c"
(string-append "ALTER ROLE " username
" WITH SUPERUSER;"))
(invoke "./UnitTests" host port username password
database))))))))
(native-inputs
(list googletest
python))
(inputs
(list boost-1.83
jsoncpp
openssl
orthanc
postgresql
protobuf
unzip
(list util-linux "lib") ; <uuid.h>
zlib))
(home-page "https://orthanc-server.com")
(synopsis "PostgreSQL plugins for Orthanc")
(description
"This package provides plugins to use PostgreSQL as the database
backend of an Orthanc @acronym{DICOM, Digital Imaging and Communications in
Medicine} server instead of SQLite.")
(license license:agpl3+))))
(define-public orthanc-mysql
;; No tags provided.
(let ((changeset "a6300ccf6683")
(revision "0"))
(package
(name "orthanc-mysql")
(version (git-version "5.2" revision changeset))
(source
(origin
(method hg-fetch)
(uri (hg-reference
(url "https://orthanc.uclouvain.be/hg/orthanc-databases")
(changeset changeset)))
(file-name (hg-file-name name version))
(sha256
(base32 "0hi3bawj117lk7lrxpa6h7vq4hx9jwqb3m5pwn3726hnf4kmp4jc"))))
(build-system cmake-build-system)
(arguments
(list
#:configure-flags
#~(list
;; Don't try to download the Orthanc source code.
"-DORTHANC_FRAMEWORK_SOURCE=path"
(string-append "-DORTHANC_FRAMEWORK_ROOT="
#$(package-source (this-package-input "orthanc"))
"/OrthancFramework/Sources"))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
;; The MySQL/ subdirectory contains the root CMakeLists.txt
;; file.
(chdir "MySQL")))
(add-after 'unpack 'fix-mysql-include-path
(lambda* (#:key inputs #:allow-other-keys)
;; Help it find mysql.h, either from mysql in this package or
;; from mariadb:dev in orthanc-mariadb.
(substitute* "Resources/CMake/MariaDBConfiguration.cmake"
(("/usr/include/mysql")
(search-input-directory inputs "include/mysql")))))
;; There is no test target; simply run the binary.
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
;; The tests rely on a MySQL or MariaDB test server
;; being available.
(let ((datadir "/tmp/mysql")
(socket "/tmp/mysql/mysqld.sock")
(username "root")
(password "")
(database "orthanctest"))
(invoke "mysqld" "--initialize-insecure"
(string-append "--datadir=" datadir))
(spawn "mysqld"
(list
"mysqld"
;; Respect '--datadir'.
"--no-defaults"
(string-append "--datadir=" datadir)
(string-append "--socket=" socket)
;; For one test.
"--max_allowed_packet=32m"))
(sleep 1)
(invoke "mysql"
(string-append "--socket=" socket)
"-u" username
"-e" "CREATE DATABASE orthanctest;")
(invoke "./UnitTests" socket username password
database))))))))
(native-inputs
(list googletest
python))
(inputs
(list boost-1.83
curl
jsoncpp
mysql
openssl
orthanc
protobuf
unzip
(list util-linux "lib") ; <uuid.h>
zlib))
(home-page "https://orthanc-server.com")
(synopsis "MySQL plugins for Orthanc")
(description
"This package provides plugins to use MySQL or MariaDB as the database
backend of an Orthanc @acronym{DICOM, Digital Imaging and Communications in
Medicine} server instead of SQLite.")
(license license:agpl3+))))
;; Provide this variant without MySQL to save MariaDB users ~340 MiB
;; of disk space.
(define-public orthanc-mariadb
(package/inherit orthanc-mysql
(name "orthanc-mariadb")
(arguments
(substitute-keyword-arguments (package-arguments orthanc-mysql)
((#:phases phases)
#~(modify-phases #$phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
;; The tests rely on a MySQL or MariaDB test server
;; being available.
(let ((datadir "/tmp/mysql")
(socket "/tmp/mysql/mysqld.sock")
(username "root")
(password "")
(database "orthanctest"))
(invoke "mariadb-install-db"
(string-append "--datadir=" datadir)
"--auth-root-authentication-method=normal")
(spawn "mysqld"
(list
"mysqld"
;; Respect '--datadir'.
"--no-defaults"
(string-append "--datadir=" datadir)
(string-append "--socket=" socket)
;; For one test.
"--max-allowed-packet=32m"))
(sleep 1)
(invoke "mysql"
(string-append "--socket=" socket)
"-u" username
"-e" "CREATE DATABASE orthanctest;")
(invoke "./UnitTests" socket username password
database)))))))))
(native-inputs (modify-inputs (package-native-inputs orthanc-mysql)
(prepend mariadb))) ;for tests
(inputs (modify-inputs (package-inputs orthanc-mysql)
(delete "mysql")
(prepend `(,mariadb "dev")
`(,mariadb "lib"))))
(synopsis "MariaDB plugins for Orthanc")))
(define-public xmedcon
(package
(name "xmedcon")
(version "0.25.3")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "git://git.code.sf.net/p/xmedcon/code")
(commit (string-append "Version-"
(string-replace-substring version "." "_")))))
(file-name (git-file-name name version))
(sha256
(base32 "1rvh1i967s87d8vpm5fgz07c9vnvwbh3cdphwp806jcvw93y90kw"))))
(build-system gnu-build-system)
(arguments
(list
#:configure-flags
#~(list "--disable-static"
(string-append "--with-nifti-prefix="
#$(this-package-input "nifticlib")))))
(inputs (list glib gtk+ libpng nifticlib))
(native-inputs (list pkg-config))
(home-page "https://xmedcon.sourceforge.io")
(synopsis "Medical image conversion utility")
(description
"@acronym{(X)MedCon, Medical Image Conversion} can be used to convert
between different file formats used in medical imaging. The supported formats
are @acronym{ACR, American College of Radiology}-@acronym{NEMA, National
Electrical Manufacturers Association} 2.0, Analyze (@acronym{SPM, Statistical
Parametric Mapping}), Concorde/μPET, @acronym{DICOM, Digital Imaging and
Communications in Medicine} 3.0, CTI ECAT 6/7, @acronym{NIfTI, Neuroimaging
Informatics Technology Initiative}-1, Interfile 3.3, @acronym{PNG, Portable
Network Graphics}, and @acronym{GIF, Graphics Interchange Format}87a/89a.
This package includes a command-line utility (@code{medcon}) and a GTK+ based
GUI application (@code{xmedcon}).")
(license license:lgpl2.0+)))
(define-public xmedcon-minimal
(package/inherit xmedcon
(name "xmedcon-minimal")
(arguments
(substitute-keyword-arguments (package-arguments xmedcon)
((#:configure-flags flags #~'())
#~(append (list "--disable-glib" "--disable-gui") #$flags))))
(inputs (modify-inputs (package-inputs xmedcon)
(delete "glib" "gtk+")))
(synopsis "Medical image conversion utility (variant with CLI only)")))
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