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gnu: rdkit: Update to 2023.09.4. 

* gnu/packages/chemistry.scm (rdkit): Update to 2023.09.4.
[arguments]: Skip testConrec test in check phase.
[native-inputs]: Replace catch2 with catch2-3.
* gnu/packages/patches/rdkit-unbundle-external-dependencies.patch: Adjust
patch.
[supported-systems]: New field.

Signed-off-by: Christopher Baines <mail@cbaines.net>
master
David Elsing 2024-01-28 23:02:02 +00:00 committed by Christopher Baines
parent cc772e7f31
commit e5bfc462dd
No known key found for this signature in database
GPG Key ID: 5E28A33B0B84F577
2 changed files with 128 additions and 99 deletions
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15
gnu/packages/chemistry.scm
View File

@ -1073,7 +1073,7 @@ other ring topology descriptions.")
(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 @@ other ring topology descriptions.")
(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 @@ other ring topology descriptions.")
"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 @@ other ring topology descriptions.")
(native-inputs
(list bison
boost
catch2
catch2-3
eigen
flex
freesasa
@ -1214,4 +1217,8 @@ other ring topology descriptions.")
(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)))

212
gnu/packages/patches/rdkit-unbundle-external-dependencies.patch
View File

@ -58,100 +58,83 @@ 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
-
-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_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
- ${AVALON_COMMON_PATH}/hashcode.c
- )
-
-# we need this to ensure that builds continue
-# to work on linux systems with older versions
-# of glibc when we're building with gcc-4.1.
-# Without this flag, we'll endup requiring
-# glibc 2.7.
-if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
- add_definitions(-D_GNU_SOURCE=1)
-endif()
-
-if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-return-type -Wno-implicit-function-declaration -Wno-absolute-value -Wno-parentheses -Wno-logical-op-parentheses -Wno-dangling-else -Wno-format")
-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")
-endif()
-
-
-
-rdkit_library(avalon_clib ${avalon_clib_srcs})
-target_compile_definitions(avalon_clib PRIVATE RDKIT_AVALONLIB_BUILD)
-if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
@ -159,11 +142,11 @@ index 3e31195fc..314ba35b5 100644
-endif()
-
-include_directories(${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=${CMAKE_BUILD_TYPE}
- TEST_COMMAND "")
-if(NOT DEFINED YAEHMOP_DIR)
- set(YAEHMOP_DIR "${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 )
-
-
-
-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")
-
-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)