[bug#68790,9/9] gnu: rdkit: Update to 2023.09.4.

Message ID	20240128230215.1389-9-david.elsing@posteo.net
State	New
Headers	show Return-Path: <guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org> Subject: [bug#68790] [PATCH 9/9] gnu: rdkit: Update to 2023.09.4. Resent-From: David Elsing <david.elsing@posteo.net> Original-Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org> Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 28 Jan 2024 23:04:03 +0000 Resent-Message-ID: <handler.68790.B68790.170648298917532@debbugs.gnu.org> Resent-Sender: help-debbugs@gnu.org To: 68790@debbugs.gnu.org Cc: David Elsing <david.elsing@posteo.net> From: David Elsing <david.elsing@posteo.net> Date: Sun, 28 Jan 2024 23:02:02 +0000 Message-ID: <20240128230215.1389-9-david.elsing@posteo.net> In-Reply-To: <20240128225919.795-2-david.elsing@posteo.net> References: <20240128225919.795-2-david.elsing@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Precedence: list 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
Series	Update rdkit and its dependencies \| expand [bug#68790,0/9] Update rdkit and its dependencies [bug#68790,1/9] gnu: tinydir: Update to 1.2.6. [bug#68790,2/9] gnu: fast-float: Update to 6.0.0. [bug#68790,3/9] gnu: gemmi: Update to 0.6.4. [bug#68790,4/9] gnu: maeparser: Update to 1.3.1. [bug#68790,5/9] gnu: coordgenlibs: Update to 3.0.2. [bug#68790,6/9] gnu: yaehmop: Update to 2023.03.1. [bug#68790,7/9] gnu: avalon-toolkit: Update to 2.0.5a. [bug#68790,8/9] gnu: freesasa: Fix memerr tests. [bug#68790,9/9] gnu: rdkit: Update to 2023.09.4.

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 98141737ac..bd27bfad7a 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -1073,7 +1073,7 @@ (define-public ringdecomposerlib (define-public rdkit (package (name "rdkit") - (version "2022.03.5") + (version "2023.09.4") (source (origin (method git-fetch) (uri (git-reference @@ -1084,7 +1084,7 @@ (define-public rdkit (file-name (git-file-name name version)) (sha256 (base32 - "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9")) + "1lgcgijlzzwpfxndsdlx13npdfk7hcii11zg25cvpmzhbpn6vyn8")) (patches (search-patches "rdkit-unbundle-external-dependencies.patch")) (modules '((guix build utils))) @@ -1183,7 +1183,10 @@ (define-public rdkit "substructLibraryTest" "pyFeatures" "pythonTestDirML" "pythonTestDirChem" ;; Catching Python exception fails - "pyRanker") "|") + "pyRanker" + ;; Flaky test depending on floating point rounding + "testConrec" + ) "|") ")"))))))))) (inputs (list avalon-toolkit @@ -1200,7 +1203,7 @@ (define-public rdkit (native-inputs (list bison boost - catch2 + catch2-3 eigen flex freesasa @@ -1214,4 +1217,8 @@ (define-public rdkit (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.") + ;; For 32 bit systems, there is a bug in Boost.Python: + ;; https://github.com/boostorg/python/issues/312. Additionally, several + ;; other test fail. + (supported-systems %64bit-supported-systems) (license license:bsd-3))) diff --git a/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch b/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch index 8ee0611d3b..e22ff57ee0 100644 --- a/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch +++ b/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch @@ -58,99 +58,82 @@ diff --git a/External/AvalonTools/CMakeLists.txt b/External/AvalonTools/CMakeLis index 3e31195fc..314ba35b5 100644 --- a/External/AvalonTools/CMakeLists.txt +++ b/External/AvalonTools/CMakeLists.txt -@@ -2,107 +2,14 @@ if(NOT RDK_BUILD_AVALON_SUPPORT) +@@ -2,90 +2,8 @@ if(NOT RDK_BUILD_AVALON_SUPPORT) return() endif(NOT RDK_BUILD_AVALON_SUPPORT) +-set(AVALON_VERSION "2.0.5-pre.3") -if(NOT DEFINED AVALONTOOLS_DIR) -- set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/SourceDistribution") -- set(fileToPatch "${CMAKE_CURRENT_SOURCE_DIR}/SourceDistribution/common/reaccsio.c") +- set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/ava-formake-AvalonToolkit_${AVALON_VERSION}") +- set(fileToCheck "${AVALONTOOLS_DIR}/src/main/C/common/reaccsio.c") - set(needDownload "TRUE") -- if(EXISTS "${fileToPatch}") -- file(READ "${fileToPatch}" buffer) -- if("${buffer}" MATCHES "//MyFree\$\\(char \\*\$tempdir\\);") -- set(needDownload "FALSE") -- endif() +- if(EXISTS "${fileToCheck}") +- set(needDownload "FALSE") - endif() -else() - string(REGEX REPLACE "\\\\" "/" AVALONTOOLS_DIR ${AVALONTOOLS_DIR}) - set(needDownload "FALSE") -endif() - --set(AVALON_SRC_PATH ${AVALONTOOLS_DIR}/common) +-set(AVALON_SRC_PATH "${AVALONTOOLS_DIR}/src/main/C") +-set(AVALON_COMMON_PATH "${AVALON_SRC_PATH}/common") +-set(AVALON_INCLUDE_PATH "${AVALON_SRC_PATH}/include") +-set(AVALON_PROGRAMS_PATH "${AVALON_SRC_PATH}/programs") - -if(needDownload) - if(NOT DEFINED AVALONTOOLS_URL) -- set(AVALONTOOLS_URL "https://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar") +- set(AVALONTOOLS_URL "https://github.com/rdkit/ava-formake/archive/refs/tags/AvalonToolkit_${AVALON_VERSION}.tar.gz") - endif() - if(NOT DEFINED AVALONTOOLS_MD5SUM) -- set(AVALONTOOLS_MD5SUM "092a94f421873f038aa67d4a6cc8cb54") +- set(AVALONTOOLS_MD5SUM "7a20c25a7e79f3344e0f9f49afa03351") - endif() - if(NOT DEFINED AVALONTOOLS_BASE) - string(REGEX REPLACE "^.*/" "" AVALONTOOLS_BASE "${AVALONTOOLS_URL}") - endif() - downloadAndCheckMD5(${AVALONTOOLS_URL} "${CMAKE_CURRENT_SOURCE_DIR}/${AVALONTOOLS_BASE}" ${AVALONTOOLS_MD5SUM}) -- execute_process(COMMAND ${CMAKE_COMMAND} -E tar xf -- ${CMAKE_CURRENT_SOURCE_DIR}/AvalonToolkit_1.2.0.source.tar +- execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf +- ${CMAKE_CURRENT_SOURCE_DIR}/AvalonToolkit_${AVALON_VERSION}.tar.gz - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) -- # apply patch to AvalonTools -- configure_file("${fileToPatch}" "${fileToPatch}.orig" COPYONLY) -- file(READ "${fileToPatch}" buffer) -- string(REGEX REPLACE "MyFree\$\\(char \\*\$tempdir\\);" -- "//MyFree((char *)tempdir);" buffer "${buffer}") -- file(WRITE "${fileToPatch}" "${buffer}") --endif() - - if (MSVC) - add_definitions("/D_CRT_SECURE_NO_WARNINGS") - add_compile_options(/wd4224 /wd4101 /wd4018 /wd4996 /wd4244 /wd4305 /wd4013 /wd4146 /wd4334 /wd4715 /wd4715 /nologo) - endif(MSVC) - --set(avalon_clib_srcs ${AVALON_SRC_PATH}/layout.c -- ${AVALON_SRC_PATH}/symboltable.c -- ${AVALON_SRC_PATH}/patclean.c -- ${AVALON_SRC_PATH}/utilities.c -- ${AVALON_SRC_PATH}/symbol_lists.c -- ${AVALON_SRC_PATH}/stereo.c -- ${AVALON_SRC_PATH}/set.c -- ${AVALON_SRC_PATH}/perceive.c -- ${AVALON_SRC_PATH}/local.c -- ${AVALON_SRC_PATH}/graph.c -- ${AVALON_SRC_PATH}/geometry.c -- ${AVALON_SRC_PATH}/forio.c -- ${AVALON_SRC_PATH}/depictutil.c -- ${AVALON_SRC_PATH}/denormal.c -- ${AVALON_SRC_PATH}/casutils.c -- ${AVALON_SRC_PATH}/ssmatch.c -- ${AVALON_SRC_PATH}/rtutils.c -- ${AVALON_SRC_PATH}/smi2mol.c -- ${AVALON_SRC_PATH}/didepict.c -- ${AVALON_SRC_PATH}/pattern.c -- ${AVALON_SRC_PATH}/canonizer.c -- ${AVALON_SRC_PATH}/aacheck.c -- ${AVALON_SRC_PATH}/fixcharges.c -- ${AVALON_SRC_PATH}/struchk.c -- ${AVALON_SRC_PATH}/reaccsio.c -- ${AVALON_SRC_PATH}/hashcode.c -- ) -- --# we need this to ensure that builds continue --# to work on linux systems with older versions --# of glibc when we're building with gcc-4.1. --# Without this flag, we'll endup requiring --# glibc 2.7. --if(CMAKE_SYSTEM_NAME STREQUAL "Linux") -- add_definitions(-D_GNU_SOURCE=1) -endif() - --if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang") -- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-return-type -Wno-implicit-function-declaration -Wno-absolute-value -Wno-parentheses -Wno-logical-op-parentheses -Wno-dangling-else -Wno-format") +-if(CMAKE_C_COMPILER_ID STREQUAL "GNU") +- add_compile_options(-Wno-format-security -Wformat=0 -Wstringop-overflow=0 -Wformat-overflow=0 -Wno-unused-result ) -endif() --if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU") -- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-unused-result -Wformat-overflow=0 -Wformat=0 -Wno-format-security -Wno-implicit-function-declaration") +-if(CMAKE_C_COMPILER_ID STREQUAL "Clang") +- add_compile_options(-Wno-absolute-value -Wno-return-type -Wno-tautological-overlap-compare) -endif() +-if (MSVC) +- add_definitions("/D_CRT_SECURE_NO_WARNINGS") +- add_compile_options(/wd4018 /wd4101 /wd4146 /wd4334 /wd4477 /wd4715 /wd4716 /wd4996 /nologo) +-endif(MSVC) - -- +-set(avalon_clib_srcs ${AVALON_COMMON_PATH}/layout.c +- ${AVALON_COMMON_PATH}/symboltable.c +- ${AVALON_COMMON_PATH}/patclean.c +- ${AVALON_COMMON_PATH}/utilities.c +- ${AVALON_COMMON_PATH}/symbol_lists.c +- ${AVALON_COMMON_PATH}/stereo.c +- ${AVALON_COMMON_PATH}/set.c +- ${AVALON_COMMON_PATH}/perceive.c +- ${AVALON_COMMON_PATH}/local.c +- ${AVALON_COMMON_PATH}/graph.c +- ${AVALON_COMMON_PATH}/geometry.c +- ${AVALON_COMMON_PATH}/forio.c +- ${AVALON_COMMON_PATH}/depictutil.c +- ${AVALON_COMMON_PATH}/denormal.c +- ${AVALON_COMMON_PATH}/casutils.c +- ${AVALON_COMMON_PATH}/ssmatch.c +- ${AVALON_COMMON_PATH}/rtutils.c +- ${AVALON_COMMON_PATH}/smi2mol.c +- ${AVALON_COMMON_PATH}/didepict.c +- ${AVALON_COMMON_PATH}/pattern.c +- ${AVALON_COMMON_PATH}/canonizer.c +- ${AVALON_COMMON_PATH}/aacheck.c +- ${AVALON_COMMON_PATH}/fixcharges.c +- ${AVALON_PROGRAMS_PATH}/struchk.c +- ${AVALON_COMMON_PATH}/reaccsio.c +- ${AVALON_COMMON_PATH}/hashcode.c +- ) - -rdkit_library(avalon_clib ${avalon_clib_srcs}) -target_compile_definitions(avalon_clib PRIVATE RDKIT_AVALONLIB_BUILD) @@ -159,11 +142,11 @@ index 3e31195fc..314ba35b5 100644 -endif() - -include_directories(${CMAKE_CURRENT_SOURCE_DIR}) --include_directories(${AVALON_SRC_PATH}) +-include_directories(${AVALON_INCLUDE_PATH}) - rdkit_library(AvalonLib AvalonTools.cpp SHARED - LINK_LIBRARIES avalon_clib SubstructMatch FileParsers SmilesParse GraphMol DataStructs ) -+ LINK_LIBRARIES -lavalontoolkit SubstructMatch FileParsers SmilesParse GraphMol DataStructs ) ++ LINK_LIBRARIES -lavalon4rdkit SubstructMatch FileParsers SmilesParse GraphMol DataStructs ) target_compile_definitions(AvalonLib PRIVATE RDKIT_AVALONLIB_BUILD) rdkit_headers(AvalonTools.h DEST GraphMol) rdkit_test(testAvalonLib1 test1.cpp @@ -278,7 +261,7 @@ diff --git a/External/RingFamilies/CMakeLists.txt b/External/RingFamilies/CMakeL index 08dd1fe04..66ecd5834 100644 --- a/External/RingFamilies/CMakeLists.txt +++ b/External/RingFamilies/CMakeLists.txt -@@ -1,47 +1,6 @@ +@@ -1,47 +1,7 @@ -add_custom_target(ringdecomposerlib_support ALL) - if(NOT RDK_USE_URF) @@ -324,10 +307,9 @@ index 08dd1fe04..66ecd5834 100644 -rdkit_headers(${URFLIB_DIR}/RingDecomposerLib.h DEST "") - - --set(RDK_URF_LIBS RingDecomposerLib -- CACHE STRING "the libraries for the URF calculation" FORCE) +rdkit_library(RingDecomposerLib dummy.cpp SHARED LINK_LIBRARIES -lRingDecomposerLib) -+set(RDK_URF_LIBS RingDecomposerLib CACHE STRING "" FORCE) + set(RDK_URF_LIBS RingDecomposerLib + CACHE STRING "the libraries for the URF calculation" FORCE) diff --git a/External/RingFamilies/dummy.cpp b/External/RingFamilies/dummy.cpp new file mode 100644 index 000000000..e69de29bb @@ -335,40 +317,60 @@ diff --git a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt index f1027b3bd..8bee2f910 100644 --- a/External/YAeHMOP/CMakeLists.txt +++ b/External/YAeHMOP/CMakeLists.txt -@@ -18,32 +18,8 @@ endif() +@@ -4,52 +4,7 @@ endif(NOT RDK_BUILD_YAEHMOP_SUPPORT) - include_directories( ${RDKit_ExternalDir}/YAeHMOP ) + add_definitions(-DRDK_BUILD_YAEHMOP_SUPPORT) --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) +-if(NOT DEFINED YAEHMOP_DIR) +- set(YAEHMOP_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop") +-endif() +- +-if(NOT EXISTS "${YAEHMOP_DIR}/tightbind/bind.h") +- set(RELEASE_NO "2023.03.1") +- set(MD5 "e6450f13e02c54d024233b993c3c7ff6") +- downloadAndCheckMD5("https://github.com/greglandrum/yaehmop/archive/refs/tags/v${RELEASE_NO}.tar.gz" +- "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz" ${MD5}) +- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf +- ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz +- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +- +- file(RENAME "yaehmop-${RELEASE_NO}" "${YAEHMOP_DIR}") +-else() +- message("-- Found YAeHMOP source in ${YAEHMOP_DIR}") +-endif() +- +-set(yaehmop_INCLUDE_DIRS ${YAEHMOP_DIR}/.. +- CACHE STRING "yaehmop Include File" FORCE) +-include_directories(${yaehmop_INCLUDE_DIRS}) +- +-if(CMAKE_COMPILER_IS_GNUCXX AND NOT CYGWIN) +- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC") +-endif() +-if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang") +- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC") +-endif() +- +-# bring in the eHT code, but skip the targets (we'll get yaehmop_eht anyway because it's a dependency) +-add_subdirectory(yaehmop/tightbind EXCLUDE_FROM_ALL True) +- +-# set install dir for the yaehmop library: +-INSTALL(TARGETS yaehmop_eht EXPORT rdkit-targets +- DESTINATION ${RDKit_LibDir}/${RDKLIB_DEST} +- COMPONENT runtime ) +- +- +- - -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") -- -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) rdkit_headers(EHTTools.h DEST GraphMol) rdkit_catch_test(testEHTLib1 test1.cpp - LINK_LIBRARIES EHTLib FileParsers SmilesParse ) diff --git a/External/YAeHMOP/EHTTools.cpp b/External/YAeHMOP/EHTTools.cpp index 7a229f51f..71033dc5c 100644 --- a/External/YAeHMOP/EHTTools.cpp @@ -382,3 +384,23 @@ index 7a229f51f..71033dc5c 100644 } namespace RDKit { +@@ -160,4 +160,4 @@ bool runMol(const ROMol &mol, EHTResults &results, int confId, + } + + } // end of namespace EHTTools +-} // end of namespace RDKit +\ No newline at end of file ++} // end of namespace RDKit +diff --git a/External/YAeHMOP/Wrap/CMakeLists.txt b/External/YAeHMOP/Wrap/CMakeLists.txt +index 759a9f360..114d24532 100644 +--- a/External/YAeHMOP/Wrap/CMakeLists.txt ++++ b/External/YAeHMOP/Wrap/CMakeLists.txt +@@ -4,6 +4,8 @@ rdkit_python_extension(rdEHTTools + DEST Chem + LINK_LIBRARIES + EHTLib ) ++ ++target_include_directories(rdEHTTools PRIVATE ${RDKit_ExternalDir}/YAeHMOP) + + add_pytest(pyEHTTools + ${CMAKE_CURRENT_SOURCE_DIR}/testEHTTools.py)

[bug#68790,9/9] gnu: rdkit: Update to 2023.09.4.

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