Package: guix-patches;
Reported by: David Elsing <david.elsing <at> posteo.net>
Date: Mon, 3 Oct 2022 00:06:02 UTC
Severity: normal
Tags: patch
Done: Liliana Marie Prikler <liliana.prikler <at> gmail.com>
Bug is archived. No further changes may be made.
View this message in rfc822 format
From: Liliana Marie Prikler <liliana.prikler <at> gmail.com> To: David Elsing <david.elsing <at> posteo.net>, 58261 <at> debbugs.gnu.org Subject: [bug#58261] [PATCH v2 13/13] gnu: Add rdkit. Date: Sun, 09 Oct 2022 14:12:31 +0200
Am Freitag, dem 07.10.2022 um 15:22 +0000 schrieb David Elsing:
> * gnu/packages/chemistry.scm (rdkit): New variable.
> ---
> gnu/packages/chemistry.scm | 178
> ++++++++++++++++++
> .../rdkit-cmake-external-dependencies.patch | 102 ++++++++++
> 2 files changed, 280 insertions(+)
> create mode 100644 gnu/packages/patches/rdkit-cmake-external-
> dependencies.patch
>
> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
> index 43953238cd..4b34a38797 100644
> --- a/gnu/packages/chemistry.scm
> +++ b/gnu/packages/chemistry.scm
> @@ -34,6 +34,7 @@ (define-module (gnu packages chemistry)
> #:use-module (gnu packages algebra)
> #:use-module (gnu packages autotools)
> #:use-module (gnu packages backup)
> + #:use-module (gnu packages base)
> #:use-module (gnu packages bison)
> #:use-module (gnu packages boost)
> #:use-module (gnu packages check)
> @@ -41,10 +42,12 @@ (define-module (gnu packages chemistry)
> #:use-module (gnu packages cpp)
> #:use-module (gnu packages documentation)
> #:use-module (gnu packages flex)
> + #:use-module (gnu packages fonts)
> #:use-module (gnu packages fontutils)
> #:use-module (gnu packages gcc)
> #:use-module (gnu packages gl)
> #:use-module (gnu packages graphviz)
> + #:use-module (gnu packages gtk)
> #:use-module (gnu packages gv)
> #:use-module (gnu packages image)
> #:use-module (gnu packages maths)
> @@ -56,6 +59,7 @@ (define-module (gnu packages chemistry)
> #:use-module (gnu packages qt)
> #:use-module (gnu packages serialization)
> #:use-module (gnu packages sphinx)
> + #:use-module (gnu packages sqlite)
> #:use-module (gnu packages stb)
> #:use-module (gnu packages tex)
> #:use-module (gnu packages web)
> @@ -1101,3 +1105,177 @@ (define-public ringdecomposerlib
> unique ring families, relevant cycles, the smallest set of smallest
> rings and
> other ring topology descriptions.")
> (license license:bsd-3)))
> +
> +(define-public rdkit
> + (package
> + (name "rdkit")
> + (version "2022.03.5")
> + (source (origin
> + (method git-fetch)
> + (uri (git-reference
> + (url "https://github.com/rdkit/rdkit")
> + (commit
> + (string-append
> + "Release_" (string-replace-substring version
> "." "_")))))
> + (file-name (git-file-name name version))
> + (sha256
> + (base32
> +
> "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
> + (patches
> + (search-patches "rdkit-cmake-external-
> dependencies.patch"))
> + (modules '((guix build utils)))
> + (snippet
> + #~(begin
> + ;; Remove pickle files (only used in tests),
> + ;; as they are compiled programs
> + (for-each
> + (lambda (name)
> + (display (string-append name "\n"))
> + (delete-file name))
> + (find-files "." "\\.pkl(\\.gz)?$"))
> + ;; Remove SQLite data files (can be generated)
> + (delete-file "Data/RDData.sqlt")
> + (delete-file "Data/RDTests.sqlt")))))
> + (build-system cmake-build-system)
> + (arguments
> + (list
> + #:imported-modules (append %cmake-build-system-modules
> + '((guix build python-build-
> system)))
> + #:modules '((guix build cmake-build-system)
> + (guix build utils)
> + ((guix build python-build-system)
> + #:select (add-installed-pythonpath)))
> + #:configure-flags
> + #~(list
> + "-DRDK_BUILD_AVALON_SUPPORT=ON"
> + "-DRDK_BUILD_CAIRO_SUPPORT=ON"
> + "-DRDK_BUILD_CPP_TESTS=ON"
> + "-DRDK_BUILD_FREESASA_SUPPORT=ON"
> + "-DRDK_BUILD_INCHI_SUPPORT=ON"
> + "-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
Are any of these implied or do they have to be explicitly enabled?
> + (string-append "-DCATCH_DIR="
> + #$(this-package-native-input "catch2")
> + "/include/catch2")
> + "-DRDK_INSTALL_DEV_COMPONENT=ON"
> + "-DRDK_INSTALL_INTREE=OFF"
> + "-DRDK_INSTALL_STATIC_LIBS=OFF"
> + (string-append
> + "-DRDK_OPTIMIZE_POPCNT="
> + #$(let ((system (or (%current-target-system)
> + (%current-system))))
> + (cond
> + ((string-prefix? "x86_64" system) "ON")
> + ((string-prefix? "i686" system) "ON")
> + (else "OFF"))))
> + "-DRDK_USE_BOOST_IOSTREAMS=ON"
> + "-DRDK_USE_FLEXBISON=ON")
> + #:phases
> + #~(modify-phases %standard-phases
> + (add-after 'unpack 'copy-external-dependencies
> + (lambda _
> + (symlink
> + (string-append
> + #$(this-package-input "font-comic-neue")
> + "/share/fonts/truetype/ComicNeue-Regular.ttf")
> + "Data/Fonts/ComicNeue-Regular.ttf")))
Try (search-input-file) instead.
> + (add-after 'copy-external-dependencies 'patch-source
> + (lambda _
> + (substitute* "External/AvalonTools/CMakeLists.txt"
> + (("^if\\(NOT RDK_BUILD" orig)
> + (string-append "if(0)\n" orig))
> + (("include_directories.*AVALON_SRC_PATH.*")
> + (string-append "endif()\ninclude_directories("
> + #$avalontoolkit
> "/include/avalontoolkit)\n"))
> + (("LINK_LIBRARIES avalon_clib")
> + (string-append
> + "LINK_LIBRARIES -L" #$avalontoolkit "/lib -
> lavalontoolkit")))
> + (let ((port
> + (open-file "External/RingFamilies/dummy.cpp"
> "w")))
> + (display "" port)
> + (close port))
> + (let ((port
> + (open-file
> "External/RingFamilies/CMakeLists.txt" "w")))
> + (display (string-append
> + "rdkit_library(RingDecomposerLib dummy.cpp
> SHARED"
> + " LINK_LIBRARIES -lRingDecomposerLib)\n"
> + "set(RDK_URF_LIBS RingDecomposerLib CACHE
> STRING \"\" FORCE)\n")
> + port)
> + (close port))
> + (substitute*
> "Code/GraphMol/MolInterchange/CMakeLists.txt"
> + (("if\\(NOT" orig)
> + (string-append "if(0)\n" orig))
> + (("^include_directories.*") "endif()\n"))
> + (substitute* "External/YAeHMOP/EHTTools.cpp"
> + (("<yaehmop/tightbind/bind.h>")
> "<yaehmop/bind.h>"))))
I think you might want to unbundle these with a patch.
> + (add-after 'unpack 'fix-inchi-include
> + (lambda _
> + (substitute* "Code/cmake/Modules/FindInchi.cmake"
> + (("inchi_api.h.*\\)") "inchi/inchi_api.h)")
> + (("INCHI_LIBRARY NAMES.*\\)")
> + "INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)")
> + (("find_library" prev)
> + (string-append
> + "list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n"
> + prev)))
> + (substitute* "External/INCHI-API/inchi.cpp"
> + (("<inchi_api.h>") "<inchi/inchi_api.h>"))))
> + (add-before 'build 'enable-bytecode-determinism
> + (lambda _
> + (setenv "PYTHONHASHSEED" "0")
> + (setenv "PYTHONDONTWRITEBYTECODE" "1")))
> + (add-after 'install 'pre-check
> + (lambda* (#:key inputs outputs #:allow-other-keys)
> + (with-directory-excursion "../source"
> + (invoke "sqlite3" "Data/RDData.sqlt"
> + ".read rdkit/Dbase/test_data/RDData.sqlite")
> + (invoke "sqlite3" "Data/RDTests.sqlt"
> + ".read
> rdkit/Dbase/test_data/RDTests.sqlite")
> + (setenv "RDBASE" (canonicalize-path ".")))
> + (add-installed-pythonpath inputs outputs)))
> + (delete 'check)
> + (add-after 'pre-check 'check
> + (lambda* (#:key tests? parallel-tests? #:allow-other-
> keys)
> + (when tests?
> + (let ((job-count (number->string
> + (if parallel-tests? (parallel-job-
> count) 1))))
> + (invoke
> + "ctest" "-j" job-count
> + "-E" (string-append
> + "(" (string-join
> + '(;; need pickled data
> + "(pyDiscreteValueVect"
> "pySparseIntVect"
> + "graphmoltestPickler"
> "pyPartialCharges"
> + "substructLibraryTest" "pyFeatures"
> + "pythonTestDirML"
> "pythonTestDirChem"
> + ;; Catching Python exception fails
> + "pyRanker)") "|") ")")))))))))
I think you have two layers of brackets now – delete the inner ones.
> + (native-inputs
> + (list bison
> + boost
> + catch2
> + eigen
> + flex
> + freesasa
> + pkg-config
> + rapidjson
> + tar))
> + (inputs
> + (list avalontoolkit
> + cairo
> + coordgenlibs
> + font-comic-neue
> + freetype
> + inchi
> + maeparser
> + python
> + ringdecomposerlib
> + sqlite
> + yaehmop))
> + (propagated-inputs
> + (list python-numpy python-cairocffi python-pillow))
> + (home-page "https://rdkit.org/")
> + (synopsis "Collection of cheminformatics software")
> + (description "RDKit is a C++ and Python library for
> cheminformatics, which
> +includes (among other things) the analysis and modification of
> molecules in 2D
> +and 3D and descriptor generation for machine learning.")
> + (license license:bsd-3)))
> diff --git a/gnu/packages/patches/rdkit-cmake-external-
> dependencies.patch b/gnu/packages/patches/rdkit-cmake-external-
> dependencies.patch
> new file mode 100644
> index 0000000000..5b73864f51
> --- /dev/null
> +++ b/gnu/packages/patches/rdkit-cmake-external-dependencies.patch
> @@ -0,0 +1,102 @@
> +diff -ur a/External/FreeSASA/CMakeLists.txt
> b/External/FreeSASA/CMakeLists.txt
> +--- a/External/FreeSASA/CMakeLists.txt
> ++++ b/External/FreeSASA/CMakeLists.txt
> +@@ -10,7 +10,7 @@
> + endif()
> + endif()
> +
> +-if(needDownload)
> ++if(FALSE)
> + # don't actually use the md5 here
> + set(FREESASA_VERSION "2.0.3")
> + set(FREESASA_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa-
> ${FREESASA_VERSION}")
> +@@ -66,24 +66,24 @@
> + endif()
> +
> + set (freesasa_h ${FREESASA_SRC_DIR}/src/freesasa.h)
> +-file(READ ${freesasa_h} freesasa_h_data)
> ++#file(READ ${freesasa_h} freesasa_h_data)
> + string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include
> <RDGeneral/export.h>" freesasa_h_data "${freesasa_h_data}")
> + string(REGEX REPLACE
> "([^R][^D][^K][^I][^T][^_][^F][^R][^E][^E][^S][^A][^S][^A][^_][^C][^L
> ][^I][^B][^_][^E][^X][^P][^O][^R][^T][^ ])(extern const)"
> "\\1RDKIT_FREESASA_CLIB_EXPORT \\2" freesasa_h_data
> "${freesasa_h_data}")
> +-file(WRITE ${freesasa_h} "${freesasa_h_data}")
> ++#file(WRITE ${freesasa_h} "${freesasa_h_data}")
> +
> + add_definitions(-DUSE_THREADS=0)
> + add_definitions(-DUSE_JSON=0)
> + add_definitions(-DUSE_XML=0)
> +-rdkit_library(freesasa_clib ${freesasa_clib_srcs})
> +-target_compile_definitions(freesasa_clib PRIVATE
> RDKIT_FREESASALIB_BUILD)
> ++#rdkit_library(freesasa_clib ${freesasa_clib_srcs})
> ++#target_compile_definitions(freesasa_clib PRIVATE
> RDKIT_FREESASALIB_BUILD)
> +
> + if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
> + set_target_properties(freesasa_clib PROPERTIES
> WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
> + endif()
> +-include_directories("${FREESASA_SRC_DIR}/src")
> ++#include_directories("${FREESASA_SRC_DIR}/src")
> +
> + rdkit_library(FreeSASALib RDFreeSASA.cpp SHARED
> +- LINK_LIBRARIES freesasa_clib GraphMol )
> ++ LINK_LIBRARIES -lfreesasa GraphMol )
> + target_compile_definitions(FreeSASALib PRIVATE
> RDKIT_FREESASALIB_BUILD)
> +
> + rdkit_headers(RDFreeSASA.h DEST GraphMol)
> +diff -ur a/External/YAeHMOP/CMakeLists.txt
> b/External/YAeHMOP/CMakeLists.txt
> +--- a/External/YAeHMOP/CMakeLists.txt
> ++++ b/External/YAeHMOP/CMakeLists.txt
> +@@ -18,32 +18,32 @@
> +
> + include_directories( ${RDKit_ExternalDir}/YAeHMOP )
> +
> +-ExternalProject_Add(yaehmop_project
> +- GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git
> +- GIT_TAG master
> +- UPDATE_COMMAND ""
> +- PATCH_COMMAND ""
> +- PREFIX ${CMAKE_CURRENT_SOURCE_DIR}
> +- SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop"
> +- SOURCE_SUBDIR "tightbind"
> +- CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -
> DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -
> DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -
> DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
> +- TEST_COMMAND "")
> +-
> +-include_directories(${PROJECT_BINARY_DIR}/include)
> +-link_directories(${PROJECT_BINARY_DIR}/lib)
> +-link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-
> build)
> +-
> +-set(EHT_PARAM_FILE
> ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
> +-install(FILES ${EHT_PARAM_FILE}
> +- DESTINATION ${RDKit_ShareDir}/Data
> +- COMPONENT data)
> ++#ExternalProject_Add(yaehmop_project
> ++# GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git
> ++# GIT_TAG master
> ++# UPDATE_COMMAND ""
> ++# PATCH_COMMAND ""
> ++# PREFIX ${CMAKE_CURRENT_SOURCE_DIR}
> ++# SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop"
> ++# SOURCE_SUBDIR "tightbind"
> ++# CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -
> DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -
> DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -
> DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
> ++# TEST_COMMAND "")
> ++
> ++#include_directories(${PROJECT_BINARY_DIR}/include)
> ++#link_directories(${PROJECT_BINARY_DIR}/lib)
> ++#link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-
> build)
> ++
> ++#set(EHT_PARAM_FILE
> ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
> ++#install(FILES ${EHT_PARAM_FILE}
> ++# DESTINATION ${RDKit_ShareDir}/Data
> ++# COMPONENT data)
> +
> +-message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include")
> +-message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib
> ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build")
> ++#message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include")
> ++#message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib
> ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build")
> +
> +-rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht
> GraphMol )
> ++rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES -
> lyaehmop_eht GraphMol )
> + target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD)
> +-add_dependencies(EHTLib yaehmop_project)
> ++#add_dependencies(EHTLib yaehmop_project)
> + rdkit_headers(EHTTools.h DEST GraphMol)
> + rdkit_catch_test(testEHTLib1 test1.cpp
> + LINK_LIBRARIES EHTLib FileParsers SmilesParse )
Cheers
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