diff options
Diffstat (limited to 'pkgs/development/python-modules/rdkit/default.nix')
| -rw-r--r-- | pkgs/development/python-modules/rdkit/default.nix | 140 |
1 files changed, 68 insertions, 72 deletions
diff --git a/pkgs/development/python-modules/rdkit/default.nix b/pkgs/development/python-modules/rdkit/default.nix index 2d5af44a068d..ec98f19c271f 100644 --- a/pkgs/development/python-modules/rdkit/default.nix +++ b/pkgs/development/python-modules/rdkit/default.nix @@ -1,22 +1,23 @@ -{ lib -, stdenv -, buildPythonPackage -, fetchFromGitHub -, cmake -, comic-neue -, boost -, catch2_3 -, inchi -, cairo -, eigen -, python -, rapidjson -, maeparser -, coordgenlibs -, numpy -, pandas -, pillow -, memorymappingHook +{ + lib, + stdenv, + buildPythonPackage, + fetchFromGitHub, + cmake, + comic-neue, + boost, + catch2_3, + inchi, + cairo, + eigen, + python, + rapidjson, + maeparser, + coordgenlibs, + numpy, + pandas, + pillow, + memorymappingHook, }: let external = { @@ -29,8 +30,8 @@ let yaehmop = fetchFromGitHub { owner = "greglandrum"; repo = "yaehmop"; - rev = "v2023.03.1"; - hash = "sha256-K9//cDN69U4sLETfIZq9NUaBE3RXOReH53qfiCzutqM="; + rev = "v2024.03.1"; + hash = "sha256-rhR7Ev+9Fk/Ks7R2x2SjWu1L/48a4zHDHUBohx1Dw/M="; }; freesasa = fetchFromGitHub { owner = "mittinatten"; @@ -38,11 +39,18 @@ let rev = "2.0.3"; hash = "sha256-7E+imvfDAJFnXQRWb5hNaSu+Xrf9NXeIKc9fl+o3yHQ="; }; + pubchem-align3d = fetchFromGitHub { + owner = "ncbi"; + repo = "pubchem-align3d"; + rev = "daefab3dd0c90ca56da9d3d5e375fe4d651e6be3"; + hash = "sha256-tQB4wqza9rlSoy4Uj9bA99ddawjxGyN9G7DYbcv/Qdo="; + }; }; + boost' = boost.override { enableNumpy = true; }; in buildPythonPackage rec { pname = "rdkit"; - version = "2023.09.5"; + version = "2024.09.1"; pyproject = false; src = @@ -50,10 +58,10 @@ buildPythonPackage rec { versionTag = lib.replaceStrings [ "." ] [ "_" ] version; in fetchFromGitHub { - owner = pname; - repo = pname; + owner = "rdkit"; + repo = "rdkit"; rev = "Release_${versionTag}"; - hash = "sha256-ZYNAHNBHQPx8rBJSvEWFEpdSpYyXcoqJ+nBA7tpHwQs="; + hash = "sha256-UsyPlAJ8FISblF8szEmRqWansunIhW/gbEBZx13YM+A="; }; unpackPhase = '' @@ -73,23 +81,24 @@ buildPythonPackage rec { chmod +w External/FreeSASA/freesasa/src cp External/FreeSASA/freesasa2.c External/FreeSASA/freesasa/src + ln -s ${external.pubchem-align3d} External/pubchem_shape/pubchem-align3d ln -s ${rapidjson} External/rapidjson-1.1.0 ln -s ${comic-neue}/share/fonts/truetype/ComicNeue-Regular.ttf Data/Fonts/ ''; - nativeBuildInputs = [ - cmake - ]; + nativeBuildInputs = [ cmake ]; buildInputs = [ - boost + boost' cairo catch2_3 - ] ++ lib.optionals (stdenv.system == "x86_64-darwin") [ - memorymappingHook - ]; + coordgenlibs + eigen + inchi + maeparser + ] ++ lib.optionals (stdenv.system == "x86_64-darwin") [ memorymappingHook ]; - propagatedBuildInputs = [ + dependencies = [ numpy pandas pillow @@ -97,45 +106,29 @@ buildPythonPackage rec { hardeningDisable = [ "format" ]; # required by yaehmop - dontUseSetuptoolsBuild = true; - dontUsePipInstall = true; - dontUseSetuptoolsCheck = true; - - preConfigure = '' - # Since we can't expand with bash in cmakeFlags - cmakeFlags="$cmakeFlags -DPYTHON_NUMPY_INCLUDE_PATH=$(${python}/bin/python -c 'import numpy; print(numpy.get_include())')" - cmakeFlags="$cmakeFlags -DFREESASA_DIR=$PWD/External/FreeSASA/freesasa" - cmakeFlags="$cmakeFlags -DFREESASA_SRC_DIR=$PWD/External/FreeSASA/freesasa" - cmakeFlags="$cmakeFlags -DAVALONTOOLS_DIR=$PWD/External/AvalonTools/avalon" - ''; - cmakeFlags = [ - "-DINCHI_LIBRARY=${inchi}/lib/libinchi.so" - "-DINCHI_LIBRARIES=${inchi}/lib/libinchi.so" - "-DINCHI_INCLUDE_DIR=${inchi}/include/inchi" - "-DEIGEN3_INCLUDE_DIR=${eigen}/include/eigen3" - "-DRDK_INSTALL_INTREE=OFF" - "-DRDK_INSTALL_STATIC_LIBS=OFF" - "-DRDK_BUILD_INCHI_SUPPORT=ON" - "-DRDK_BUILD_AVALON_SUPPORT=ON" - "-DRDK_BUILD_FREESASA_SUPPORT=ON" - "-DRDK_BUILD_YAEHMOP_SUPPORT=ON" - "-DRDK_BUILD_MAEPARSER_SUPPORT=ON" - "-DMAEPARSER_DIR=${maeparser}" - "-DRDK_BUILD_COORDGEN_SUPPORT=ON" - "-DCOORDGEN_DIR=${coordgenlibs}" - "-DRDK_USE_URF=OFF" - "-DRDK_USE_FLEXBISON=OFF" - "-DRDK_BUILD_CAIRO_SUPPORT=ON" - "-DRDK_BUILD_THREADSAFE_SSS=ON" - "-DRDK_TEST_MULTITHREADED=ON" - "-DRDK_BUILD_CPP_TESTS=ON" - "-DRDK_TEST_MULTITHREADED=ON" - "-DPYTHON_EXECUTABLE=${python}/bin/python" - "-DBOOST_ROOT=${boost}" - "-DBoost_NO_SYSTEM_PATHS=ON" - "-DBoost_NO_BOOST_CMAKE=TRUE" - "-DCMAKE_SKIP_BUILD_RPATH=ON" # fails to find libs in pythonImportsCheckPhase otherwise + (lib.cmakeBool "Boost_NO_BOOST_CMAKE" true) + (lib.cmakeBool "Boost_NO_SYSTEM_PATHS" true) + (lib.cmakeBool "CMAKE_SKIP_BUILD_RPATH" true) # fails to find libs in pythonImportsCheckPhase otherwise + (lib.cmakeBool "RDK_BUILD_AVALON_SUPPORT" true) + (lib.cmakeBool "RDK_BUILD_CAIRO_SUPPORT" true) + (lib.cmakeBool "RDK_BUILD_COORDGEN_SUPPORT" true) + (lib.cmakeBool "RDK_BUILD_CPP_TESTS" true) + (lib.cmakeBool "RDK_BUILD_FREESASA_SUPPORT" true) + (lib.cmakeBool "RDK_BUILD_INCHI_SUPPORT" true) + (lib.cmakeBool "RDK_BUILD_MAEPARSER_SUPPORT" true) + (lib.cmakeBool "RDK_BUILD_THREADSAFE_SSS" true) + (lib.cmakeBool "RDK_BUILD_YAEHMOP_SUPPORT" true) + (lib.cmakeBool "RDK_INSTALL_INTREE" false) + (lib.cmakeBool "RDK_INSTALL_STATIC_LIBS" false) + (lib.cmakeBool "RDK_TEST_MULTITHREADED" true) + (lib.cmakeBool "RDK_TEST_MULTITHREADED" true) + (lib.cmakeBool "RDK_USE_FLEXBISON" false) + (lib.cmakeBool "RDK_USE_URF" false) + (lib.cmakeFeature "AVALONTOOLS_DIR" "avalon") + (lib.cmakeFeature "FREESASA_SRC_DIR" "freesasa") + (lib.cmakeFeature "INCHI_INCLUDE_DIR" "${inchi}/include/inchi") + (lib.cmakeFeature "PUBCHEMSHAPE_DIR" "External/pubchem_shape/pubchem-align3d") ]; checkPhase = '' @@ -153,7 +146,10 @@ buildPythonPackage rec { meta = with lib; { description = "Open source toolkit for cheminformatics"; - maintainers = with maintainers; [ rmcgibbo natsukium ]; + maintainers = with maintainers; [ + rmcgibbo + natsukium + ]; license = licenses.bsd3; homepage = "https://www.rdkit.org"; changelog = "https://github.com/rdkit/rdkit/releases/tag/${src.rev}"; |