Subject: [bug#58261] [PATCH v2 13/13] gnu: Add rdkit.

From: David Elsing <[email-masked]>
Date: Thu, 13 Oct 2022 21:01:52 +0000

Liliana Marie Prikler <[email-masked]> writes:

> 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)?$"))
>> +                   ;; Remove SQLite data files (can be generated)
>> +                   (delete-file "Data/RDData.sqlt")
>> +                   (delete-file "Data/RDTests.sqlt")))))
>> +    (build-system cmake-build-system)
>> +    (arguments
>> +     (list
>> +      #:imported-modules (append %cmake-build-system-modules
>> +                                 '((guix build python-build-
>> system)))
>> +      #:modules '((guix build cmake-build-system)
>> +                  (guix build utils)
>> +                  ((guix build python-build-system)
>> +                   #:select (add-installed-pythonpath)))
>> +      #:configure-flags
>> +      #~(list
>> +         "-DRDK_BUILD_AVALON_SUPPORT=ON"
>> +         "-DRDK_BUILD_CAIRO_SUPPORT=ON"
>> +         "-DRDK_BUILD_CPP_TESTS=ON"
>> +         "-DRDK_BUILD_FREESASA_SUPPORT=ON"
>> +         "-DRDK_BUILD_INCHI_SUPPORT=ON"
>> +         "-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
> Are any of these implied or do they have to be explicitly enabled?
Oops, I overlooked some, now only flags changing the default are specified.
>> +         (string-append "-DCATCH_DIR="
>> +                        #$(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.
Is the patch ok?
>> +          (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.
Oh thanks!
>> +    (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