Unverified Commit af13f1dd authored by Matt Wittmann's avatar Matt Wittmann
Browse files

python3Packages.rdkit: 2022.03.5 -> 2022.09.1

parent 6b72268e

pkgs/development/python-modules/rdkit/default.nix

+31 −36
Original line number Diff line number Diff line 
{ lib

, buildPythonPackage

, fetchFromGitHub

, fetchzip

, cmake

, comic-neue

, boost

, catch2

, inchi
@@ -15,32 +15,32 @@ 
, numpy

, pandas

, pillow

, git

}:

let

  external = {

    avalon = fetchzip {

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

      sha256 = "0nhxfxckb5a5qs0g148f55yarhncqjgjzcvdskkv9rxi2nrs7160";

      stripRoot = false;

    avalon = fetchFromGitHub {

      owner = "rohdebe1";

      repo = "ava-formake";

      rev = "AvalonToolkit_2.0.2";

      hash = "sha256-YI39OknHiSyArNGqRKrSVzEJnFc1xJ0W3UcTZrTKeME=";

    };

    yaehmop = fetchFromGitHub {

      owner = "greglandrum";

      repo = "yaehmop";

      rev = "cfb5aeebbdf5ae93c4f4eeb14c7a507dea54ae9e";

      sha256 = "sha256-QMnc5RyHlY3giw9QmrkGntiA+Srs7OhCIKs9GGo5DfQ=";

      rev = "v2022.09.1";

      hash = "sha256-QMnc5RyHlY3giw9QmrkGntiA+Srs7OhCIKs9GGo5DfQ=";

    };

    freesasa = fetchFromGitHub {

      owner = "mittinatten";

      repo = "freesasa";

      rev = "2.1.1";

      sha256 = "sha256-fUJvLDTVhpBWl9MavZwp0kAO5Df1QuHEKqe20CXNfcg=";

      rev = "2.0.3";

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

    };

  };

in

buildPythonPackage rec {

  pname = "rdkit";

  version = "2022.03.5";

  version = "2022.09.1";

  format = "other";



  src =
@@ -51,35 +51,35 @@ buildPythonPackage rec { 
      owner = pname;

      repo = pname;

      rev = "Release_${versionTag}";

      sha256 = "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9";

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

    };



  unpackPhase = ''

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

    cp -r ${src}/* source

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

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

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



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

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

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

  '';

    cp -r $src/* .

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



    mkdir External/AvalonTools/avalon

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



    mkdir External/YAeHMOP/yaehmop

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



  sourceRoot = "source";

    mkdir -p External/FreeSASA/freesasa

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

    chmod +w External/FreeSASA/freesasa/src

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



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

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

  '';



  nativeBuildInputs = [

    cmake

    git # required by freesasa

  ];



  buildInputs = [

    boost

    catch2

    inchi

    eigen

    cairo

    rapidjson

  ];



  propagatedBuildInputs = [
@@ -95,10 +95,6 @@ buildPythonPackage rec { 
  dontUseSetuptoolsCheck = true;



  preConfigure = ''

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

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

      'GIT_TAG master' 'DOWNLOAD_COMMAND true'



    # 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"
@@ -114,7 +110,6 @@ buildPythonPackage rec { 
    "-DEIGEN3_INCLUDE_DIR=${eigen}/include/eigen3"

    "-DRDK_INSTALL_INTREE=OFF"

    "-DRDK_INSTALL_STATIC_LIBS=OFF"

    "-DRDK_INSTALL_COMIC_FONTS=OFF"

    "-DRDK_BUILD_INCHI_SUPPORT=ON"

    "-DRDK_BUILD_AVALON_SUPPORT=ON"

    "-DRDK_BUILD_FREESASA_SUPPORT=ON"