Commit 436d2122 authored by Gaetan Lepage's avatar Gaetan Lepage
Browse files

python3Packages.rdkit: 2024.09.1 -> 2025.03.1

parent 27142e13

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

+73 −19
Original line number Diff line number Diff line 
{

  lib,

  stdenv,

  buildPythonPackage,

  fetchFromGitHub,

  fetchzip,

  applyPatches,

  replaceVars,

  cmake,

  comic-neue,

  boost,

  catch2_3,

  inchi,

  cairo,

  eigen,

  python,
@@ -26,12 +27,28 @@ let 
      rev = "AvalonToolkit_2.0.5-pre.3";

      hash = "sha256-2MuFZgRIHXnkV7Nc1da4fa7wDx57VHUtwLthrmjk+5o=";

    };

    yaehmop = fetchFromGitHub {

    chemdraw = fetchFromGitHub {

      owner = "Glysade";

      repo = "chemdraw";

      tag = "v1.0.10";

      hash = "sha256-ee2Oxvo2d7Yb59lN0zkrbFqy/3rOvVLo6qdS+f23wVQ=";

    };

    yaehmop = applyPatches {

      src = fetchFromGitHub {

        owner = "greglandrum";

        repo = "yaehmop";

      rev = "v2024.03.1";

        rev = "v2025.03.1";

        hash = "sha256-rhR7Ev+9Fk/Ks7R2x2SjWu1L/48a4zHDHUBohx1Dw/M=";

      };



      # Compatibility with CMake < 3.5 has been removed from CMake.

      postPatch = ''

        substituteInPlace tightbind/CMakeLists.txt \

          --replace-fail \

            "cmake_minimum_required(VERSION 3.0)" \

            "cmake_minimum_required(VERSION 3.5)"

      '';

    };

    freesasa = fetchFromGitHub {

      owner = "mittinatten";

      repo = "freesasa";
@@ -44,12 +61,23 @@ let 
      rev = "daefab3dd0c90ca56da9d3d5e375fe4d651e6be3";

      hash = "sha256-tQB4wqza9rlSoy4Uj9bA99ddawjxGyN9G7DYbcv/Qdo=";

    };

    better_enums = fetchFromGitHub {

      owner = "aantron";

      repo = "better-enums";

      tag = "0.11.3";

      hash = "sha256-UYldCOkRTySc78oEOJzgoY9h2lB386W/D5Rz3KjVCO8=";

    };

    # We cannot use the inchi from nixpkgs as the version is too old

    inchi = fetchzip {

      url = "https://github.com/IUPAC-InChI/InChI/releases/download/v1.07.3/INCHI-1-SRC.zip";

      hash = "sha256-TUC2175HifB63EfSsg/ixA3wYzAxsvUnY6ZyNjVR/Fc=";

    };

  };

  boost' = boost.override { enableNumpy = true; };

in

buildPythonPackage rec {

  pname = "rdkit";

  version = "2024.09.1";

  version = "2025.03.6";

  pyproject = false;



  src =
@@ -59,8 +87,8 @@ buildPythonPackage rec { 
    fetchFromGitHub {

      owner = "rdkit";

      repo = "rdkit";

      rev = "Release_${versionTag}";

      hash = "sha256-UsyPlAJ8FISblF8szEmRqWansunIhW/gbEBZx13YM+A=";

      tag = "Release_${versionTag}";

      hash = "sha256-DqnwfT+lX7OnArIcFlCBrDl+QDmNpbPO9u7OGwu8fJo=";

    };



  unpackPhase = ''
@@ -72,19 +100,46 @@ buildPythonPackage rec { 
    # see https://github.com/rdkit/rdkit/pull/5928

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



    mkdir External/ChemDraw/chemdraw

    cp -r ${external.chemdraw}/* External/ChemDraw/chemdraw/

    chmod -R +w External/ChemDraw/chemdraw



    mkdir External/YAeHMOP/yaehmop

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



    mkdir -p External/FreeSASA/freesasa

    mkdir 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 ${external.pubchem-align3d} External/pubchem_shape/pubchem-align3d

    mkdir External/pubchem_shape/pubchem-align3d

    cp -r ${external.pubchem-align3d}/* External/pubchem_shape/pubchem-align3d



    mkdir External/INCHI-API/src

    ln -s ${external.inchi}/* External/INCHI-API/src



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

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

  '';



  patches = [

    (replaceVars ./dont-fetch-better-enums.patch {

      inherit (external) better_enums;

    })

  ];



  # Prevent linking to libpython which fails on darwin with:

  # Undefined symbols for architecture arm64

  # Reverts https://github.com/rdkit/rdkit/commit/470df8cd2fab78d64ef1dd254576097b651c3dd9

  postPatch = ''

    substituteInPlace \

      CMakeLists.txt \

      External/pubchem_shape/Wrap/CMakeLists.txt \

      --replace-fail \

        "find_package(Python3 COMPONENTS Interpreter Development.Module NumPy" \

        "find_package(Python3 COMPONENTS Interpreter Development NumPy" \

  '';



  nativeBuildInputs = [ cmake ];



  buildInputs = [
@@ -93,7 +148,6 @@ buildPythonPackage rec { 
    catch2_3

    coordgenlibs

    eigen

    inchi

    maeparser

  ];
@@ -126,8 +180,8 @@ buildPythonPackage rec { 
    (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")

    (lib.cmakeFeature "maeparser_DIR" "${maeparser}/lib/cmake")

    (lib.cmakeFeature "coordgen_DIR" "${coordgenlibs}/lib/cmake")

  ];



  checkPhase = ''
@@ -144,14 +198,14 @@ buildPythonPackage rec { 
    "rdkit.Chem.rdDetermineBonds"

  ];



  meta = with lib; {

  meta = {

    description = "Open source toolkit for cheminformatics";

    maintainers = with maintainers; [

    maintainers = with lib.maintainers; [

      rmcgibbo

      natsukium

    ];

    license = licenses.bsd3;

    license = lib.licenses.bsd3;

    homepage = "https://www.rdkit.org";

    changelog = "https://github.com/rdkit/rdkit/releases/tag/${src.rev}";

    changelog = "https://github.com/rdkit/rdkit/releases/tag/${src.tag}";

  };

}

pkgs/development/python-modules/rdkit/dont-fetch-better-enums.patch

0 → 100644
+14 −0
Original line number Diff line number Diff line 
diff --git a/CMakeLists.txt b/CMakeLists.txt

index 77939f452..9cace7fe1 100644

--- a/CMakeLists.txt

+++ b/CMakeLists.txt

@@ -184,8 +184,7 @@ Include(FetchContent)

 

 FetchContent_Declare(

   better_enums

-  GIT_REPOSITORY https://github.com/aantron/better-enums.git

-  GIT_TAG        c35576bed0295689540b39873126129adfa0b4c8 # 0.11.3

+  URL @better_enums@

 )

 

 if(RDK_INSTALL_INTREE)