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Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 29 Mar 2025 09:30:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77287 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77287@debbugs.gnu.org Cc: rekado@elephly.net, Andreas Enge Received: via spool by 77287-submit@debbugs.gnu.org id=B77287.174324058018763 (code B ref 77287); Sat, 29 Mar 2025 09:30:08 +0000 Received: (at 77287) by debbugs.gnu.org; 29 Mar 2025 09:29:40 +0000 Received: from localhost ([127.0.0.1]:56864 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tySVX-0004sU-F0 for submit@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:39 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:60028) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tySVA-0004qj-0w for 77287@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:16 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id C03022BB; Sat, 29 Mar 2025 10:29:09 +0100 (CET) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id 2Fsd1uT6NB-V; Sat, 29 Mar 2025 10:29:09 +0100 (CET) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 669F935B; Sat, 29 Mar 2025 10:29:07 +0100 (CET) From: Andreas Enge Date: Sat, 29 Mar 2025 10:21:30 +0100 Message-ID: X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: C03022BB X-Spamd-Result: default: False [-6.32 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-2.72)[-0.905]; FORGED_RECIPIENTS(2.00)[m:andreas@enge.fr,s:andreas.enge@aquilenet.fr]; MID_CONTAINS_FROM(1.00)[]; R_MISSING_CHARSET(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; FROM_HAS_DN(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: ------ X-Rspamd-Server: hera X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches TODO: So far this is only for testing purposes. * gnu/packages/image-processing.scm (itk-snap): Delete variable. Change-Id: Iccdc5c60987fec57ee11ca190b43effb19675165 --- gnu/packages/image-processing.scm | 131 ------------------------------ 1 file changed, 131 deletions(-) diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index 4ddb01f450..a89874fc06 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -1386,137 +1386,6 @@ (define-public insight-toolkit-4.12 ;; error: ISO C++17 does not allow dynamic exception specifications #~(cons* "-DCMAKE_CXX_FLAGS=-std=c++14" #$cf)))))) -(define-public itk-snap - (package - (name "itk-snap") - (version "3.8.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://git.code.sf.net/p/itk-snap/src") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q")) - (patches (search-patches "itk-snap-alt-glibc-compat.patch")))) - (build-system cmake-build-system) - (arguments - `(#:configure-flags - (list "-DSNAP_VERSION_GIT_SHA1=release" - "-DSNAP_VERSION_GIT_BRANCH=release" - "-DSNAP_VERSION_GIT_TIMESTAMP=0" - "-DSNAP_PACKAGE_QT_PLUGINS=OFF" - "-DCMAKE_POSITION_INDEPENDENT_CODE=ON") - #:phases - (modify-phases %standard-phases - ;; During the installation phase all libraries provided by all - ;; dependencies will be copied to the lib directory. That's insane, - ;; so we disable this. - (add-after 'unpack 'do-not-copy-dependencies - (lambda _ - (substitute* "CMakeLists.txt" - (("install_qt5_executable\ -\\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)") - "")))) - (add-after 'unpack 'disable-gui-tests - (lambda _ - ;; The GUI tests just time out. - (substitute* "CMakeLists.txt" - ((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\ -|RandomForest|RandomForestBailOut)") - "")))) - (add-after 'unpack 'make-reproducible - (lambda _ - (substitute* "CMakeLists.txt" - (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)") - "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")")))) - (add-after 'unpack 'prepare-submodules - (lambda* (#:key inputs #:allow-other-keys) - (rmdir "Submodules/c3d") - (copy-recursively (assoc-ref inputs "c3d-src") - "Submodules/c3d") - (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx" - "Submodules/c3d/adapters/ApplyMetric.cxx") - (("vcl_") "std::")) - (rmdir "Submodules/greedy") - (symlink (assoc-ref inputs "greedy-src") - "Submodules/greedy"))) - (add-after 'unpack 'fix-includes - (lambda _ - (substitute* "GUI/Model/RegistrationModel.cxx" - (("") - "")))) - (add-before 'check 'prepare-tests - (lambda _ - ;; Needed by at least one test. - (setenv "HOME" "/tmp"))) - (add-after 'install 'wrap-executable - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (wrap-program (string-append out "/bin/itksnap") - `("QT_PLUGIN_PATH" ":" prefix - ,(map (lambda (label) - (string-append (assoc-ref inputs label) - "/lib/qt5/plugins")) - '("qtbase" "qtdeclarative-5")))))))))) - (inputs - (list bash-minimal - curl - fftw - fftwf - glu - hdf5 - mesa-opencl - ;; This package does not build with either insight-toolkit 5.0.0 - ;; and not with 4.13. It really needs to be 4.12. - insight-toolkit-4.12 - vtk-7 - qtbase-5 - qtdeclarative-5 - vxl-1 - zlib)) - (native-inputs - `(("googletest" ,googletest) - ("qttools-5" ,qttools-5) - ("pkg-config" ,pkg-config) - ("c3d-src" - ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3") - (revision "1") - (version (git-version "0" revision commit))) - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/pyushkevich/c3d") - (commit commit))) - (file-name (git-file-name "c3d" version)) - (sha256 - (base32 - "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3"))))) - ;; We are using an arbitrary commit from 2017 because the latest - ;; version breaks the build... - ("greedy-src" - ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3") - (revision "1") - (version (git-version "0" revision commit))) - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/pyushkevich/greedy") - (commit commit))) - (file-name (git-file-name "greedy" version)) - (sha256 - (base32 - "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab"))))))) - (home-page "https://sourceforge.net/p/itk-snap/") - (synopsis "Medical image segmentation") - (description "ITK-SNAP is a tool for segmenting anatomical structures in -medical images. It provides an automatic active contour segmentation -pipeline, along with supporting a manual segmentation toolbox. ITK-SNAP has a -full-featured UI aimed at clinical researchers.") - ;; This includes the submodules greedy and c3d. - (license license:gpl3+))) - (define-public metapixel ;; Follow stable branch. (let ((commit "98ee9daa093b6c334941242e63f90b1c2876eb4f"))