commit e4902f2eb0c2e03a02bc2eb4df7f5585d5c54b95 · pyrox.dev/nixpkgs

+30 -35
pkgs/development/python-modules/rdkit/default.nix
···

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       { lib

     

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       , buildPythonPackage

     

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       , fetchFromGitHub

     

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       -
       , fetchzip

     

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       , cmake

     

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       +
       , comic-neue

     

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       , boost

     

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       , catch2

     

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       , inchi

     
···

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       , numpy

     

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       , pandas

     

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       , pillow

     

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       , git

     

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       }:

     

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       let

     

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         external = {

     

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       -
           avalon = fetchzip {

     

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             url = "http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar";

     

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       -
             sha256 = "0nhxfxckb5a5qs0g148f55yarhncqjgjzcvdskkv9rxi2nrs7160";

     

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       -
             stripRoot = false;

     

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           avalon = fetchFromGitHub {

     

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             owner = "rohdebe1";

     

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             repo = "ava-formake";

     

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             rev = "AvalonToolkit_2.0.2";

     

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       +
             hash = "sha256-YI39OknHiSyArNGqRKrSVzEJnFc1xJ0W3UcTZrTKeME=";

     

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           };

     

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           yaehmop = fetchFromGitHub {

     

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             owner = "greglandrum";

     

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             repo = "yaehmop";

     

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       -
             rev = "cfb5aeebbdf5ae93c4f4eeb14c7a507dea54ae9e";

     

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       -
             sha256 = "sha256-QMnc5RyHlY3giw9QmrkGntiA+Srs7OhCIKs9GGo5DfQ=";

     

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       +
             rev = "v2022.09.1";

     

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       +
             hash = "sha256-QMnc5RyHlY3giw9QmrkGntiA+Srs7OhCIKs9GGo5DfQ=";

     

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           };

     

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           freesasa = fetchFromGitHub {

     

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             owner = "mittinatten";

     

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             repo = "freesasa";

     

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             rev = "2.1.1";

     

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       -
             sha256 = "sha256-fUJvLDTVhpBWl9MavZwp0kAO5Df1QuHEKqe20CXNfcg=";

     

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       +
             rev = "2.0.3";

     

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       +
             hash = "sha256-7E+imvfDAJFnXQRWb5hNaSu+Xrf9NXeIKc9fl+o3yHQ=";

     

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           };

     

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         };

     

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       in

     

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       buildPythonPackage rec {

     

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         pname = "rdkit";

     

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       -
         version = "2022.03.5";

     

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       +
         version = "2022.09.1";

     

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         format = "other";

     

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         src =

     
···

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             owner = pname;

     

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             repo = pname;

     

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             rev = "Release_${versionTag}";

     

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       -
             sha256 = "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9";

     

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       +
             hash = "sha256-AaawjCv3/ShByOKU0c37/hjuyfD7NhFC8UngDoG7C0s=";

     

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           };

     

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         unpackPhase = ''

     

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           mkdir -p source/External/AvalonTools/avalon source/External/YAeHMOP/yaehmop source/External/FreeSASA/freesasa

     

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           cp -r ${src}/* source

     

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           cp -r ${external.avalon}/SourceDistribution/* source/External/AvalonTools/avalon

     

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           cp -r ${external.yaehmop}/* source/External/YAeHMOP/yaehmop

     

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           cp -r ${external.freesasa}/* source/External/FreeSASA/freesasa

     

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           cp -r $src/* .

     

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           find . -type d -exec chmod +w {} +

     

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       +
       

     

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           mkdir External/AvalonTools/avalon

     

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           ln -s ${external.avalon}/* External/AvalonTools/avalon

     

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       +
       

     

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           mkdir External/YAeHMOP/yaehmop

     

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           ln -s ${external.yaehmop}/* External/YAeHMOP/yaehmop

     

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       +
       

     

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           mkdir -p External/FreeSASA/freesasa

     

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           cp -r ${external.freesasa}/* External/FreeSASA/freesasa

     

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           chmod +w External/FreeSASA/freesasa/src

     

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           cp External/FreeSASA/freesasa2.c External/FreeSASA/freesasa/src

     

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           find source -type d -exec chmod 755 {} +

     

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           cp source/External/FreeSASA/freesasa2.c source/External/FreeSASA/freesasa/src

     

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           ln -s ${rapidjson} source/External/rapidjson-1.1.0

     

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           ln -s ${rapidjson} External/rapidjson-1.1.0

     

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           ln -s ${comic-neue}/share/fonts/truetype/ComicNeue-Regular.ttf Data/Fonts/

     

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         '';

     

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       -
       

     

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         sourceRoot = "source";

     

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         nativeBuildInputs = [

     

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           cmake

     

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           git # required by freesasa

     

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         ];

     

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         buildInputs = [

     

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           boost

     

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           catch2

     

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           inchi

     

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           eigen

     

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           cairo

     

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           rapidjson

     

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         ];

     

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         propagatedBuildInputs = [

     
···

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         dontUseSetuptoolsCheck = true;

     

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         preConfigure = ''

     

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           # Don't want this contacting the git remote during the build

     

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           substituteInPlace External/YAeHMOP/CMakeLists.txt --replace \

     

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             'GIT_TAG master' 'DOWNLOAD_COMMAND true'

     

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           # Since we can't expand with bash in cmakeFlags

     

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           cmakeFlags="$cmakeFlags -DPYTHON_NUMPY_INCLUDE_PATH=$(${python}/bin/python -c 'import numpy; print(numpy.get_include())')"

     

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           cmakeFlags="$cmakeFlags -DFREESASA_DIR=$PWD/External/FreeSASA/freesasa"

     
···

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           "-DEIGEN3_INCLUDE_DIR=${eigen}/include/eigen3"

     

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           "-DRDK_INSTALL_INTREE=OFF"

     

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           "-DRDK_INSTALL_STATIC_LIBS=OFF"

     

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           "-DRDK_INSTALL_COMIC_FONTS=OFF"

     

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           "-DRDK_BUILD_INCHI_SUPPORT=ON"

     

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           "-DRDK_BUILD_AVALON_SUPPORT=ON"

     

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           "-DRDK_BUILD_FREESASA_SUPPORT=ON"

     
···

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         '';

     

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         pythonImportsCheck = [

     

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            "rdkit"

     

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            "rdkit.Chem"

     

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            "rdkit.Chem.AllChem"

     

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           "rdkit"

     

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           "rdkit.Chem"

     

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           "rdkit.Chem.AllChem"

     

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         ];

     

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         meta = with lib; {