commit 4d218c31af3d869bf293586f7c0f7b58d86ed1ea · pyrox.dev/nixpkgs

+73 -19

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

···

       1
        
       {

     

       2
        
         lib,

     

       3
       -
         stdenv,

     

       4
        
         buildPythonPackage,

     

       5
        
         fetchFromGitHub,

     

       0
        
       
     

       0
        
       
     

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       6
        
         cmake,

     

       7
        
         comic-neue,

     

       8
        
         boost,

     

       9
        
         catch2_3,

     

       10
       -
         inchi,

     

       11
        
         cairo,

     

       12
        
         eigen,

     

       13
        
         python,

     
···

       26
        
             rev = "AvalonToolkit_2.0.5-pre.3";

     

       27
        
             hash = "sha256-2MuFZgRIHXnkV7Nc1da4fa7wDx57VHUtwLthrmjk+5o=";

     

       28
        
           };

     

       29
       -
           yaehmop = fetchFromGitHub {

     

       30
       -
             owner = "greglandrum";

     

       31
       -
             repo = "yaehmop";

     

       32
       -
             rev = "v2024.03.1";

     

       33
       -
             hash = "sha256-rhR7Ev+9Fk/Ks7R2x2SjWu1L/48a4zHDHUBohx1Dw/M=";

     

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       34
        
           };

     

       35
        
           freesasa = fetchFromGitHub {

     

       36
        
             owner = "mittinatten";

     
···

       44
        
             rev = "daefab3dd0c90ca56da9d3d5e375fe4d651e6be3";

     

       45
        
             hash = "sha256-tQB4wqza9rlSoy4Uj9bA99ddawjxGyN9G7DYbcv/Qdo=";

     

       46
        
           };

     

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       47
        
         };

     

       48
        
         boost' = boost.override { enableNumpy = true; };

     

       49
        
       in

     

       50
        
       buildPythonPackage rec {

     

       51
        
         pname = "rdkit";

     

       52
       -
         version = "2024.09.1";

     

       53
        
         pyproject = false;

     

       54
        
       

     

       55
        
         src =

     
···

       59
        
           fetchFromGitHub {

     

       60
        
             owner = "rdkit";

     

       61
        
             repo = "rdkit";

     

       62
       -
             rev = "Release_${versionTag}";

     

       63
       -
             hash = "sha256-UsyPlAJ8FISblF8szEmRqWansunIhW/gbEBZx13YM+A=";

     

       64
        
           };

     

       65
        
       

     

       66
        
         unpackPhase = ''

     
···

       71
        
           # In buildPhase, CMake patches the file in this directory

     

       72
        
           # see https://github.com/rdkit/rdkit/pull/5928

     

       73
        
           cp -r ${external.avalon}/* External/AvalonTools/avalon

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       74
        
       

     

       75
        
           mkdir External/YAeHMOP/yaehmop

     

       76
        
           ln -s ${external.yaehmop}/* External/YAeHMOP/yaehmop

     

       77
        
       

     

       78
       -
           mkdir -p External/FreeSASA/freesasa

     

       79
        
           cp -r ${external.freesasa}/* External/FreeSASA/freesasa

     

       80
        
           chmod +w External/FreeSASA/freesasa/src

     

       81
        
           cp External/FreeSASA/freesasa2.c External/FreeSASA/freesasa/src

     

       82
        
       

     

       83
       -
           ln -s ${external.pubchem-align3d} External/pubchem_shape/pubchem-align3d

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       84
        
           ln -s ${rapidjson} External/rapidjson-1.1.0

     

       85
        
           ln -s ${comic-neue}/share/fonts/truetype/ComicNeue-Regular.ttf Data/Fonts/

     

       86
        
         '';

     

       87
        
       

     

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       88
        
         nativeBuildInputs = [ cmake ];

     

       89
        
       

     

       90
        
         buildInputs = [

     
···

       93
        
           catch2_3

     

       94
        
           coordgenlibs

     

       95
        
           eigen

     

       96
       -
           inchi

     

       97
        
           maeparser

     

       98
        
         ];

     

       99
        
       

     
···

       126
        
           (lib.cmakeBool "RDK_USE_URF" false)

     

       127
        
           (lib.cmakeFeature "AVALONTOOLS_DIR" "avalon")

     

       128
        
           (lib.cmakeFeature "FREESASA_SRC_DIR" "freesasa")

     

       129
       -
           (lib.cmakeFeature "INCHI_INCLUDE_DIR" "${inchi}/include/inchi")

     

       130
       -
           (lib.cmakeFeature "PUBCHEMSHAPE_DIR" "External/pubchem_shape/pubchem-align3d")

     

       131
        
         ];

     

       132
        
       

     

       133
        
         checkPhase = ''

     
···

       144
        
           "rdkit.Chem.rdDetermineBonds"

     

       145
        
         ];

     

       146
        
       

     

       147
       -
         meta = with lib; {

     

       148
        
           description = "Open source toolkit for cheminformatics";

     

       149
       -
           maintainers = with maintainers; [

     

       150
        
             rmcgibbo

     

       151
        
             natsukium

     

       152
        
           ];

     

       153
       -
           license = licenses.bsd3;

     

       154
        
           homepage = "https://www.rdkit.org";

     

       155
       -
           changelog = "https://github.com/rdkit/rdkit/releases/tag/${src.rev}";

     

       156
        
         };

     

       157
        
       }

···

       1
        
       {

     

       2
        
         lib,

     

       0
        
       
     

       3
        
         buildPythonPackage,

     

       4
        
         fetchFromGitHub,

     

       5
       +
         fetchzip,

     

       6
       +
         applyPatches,

     

       7
       +
         replaceVars,

     

       8
        
         cmake,

     

       9
        
         comic-neue,

     

       10
        
         boost,

     

       11
        
         catch2_3,

     

       0
        
       
     

       12
        
         cairo,

     

       13
        
         eigen,

     

       14
        
         python,

     
···

       27
        
             rev = "AvalonToolkit_2.0.5-pre.3";

     

       28
        
             hash = "sha256-2MuFZgRIHXnkV7Nc1da4fa7wDx57VHUtwLthrmjk+5o=";

     

       29
        
           };

     

       30
       +
           chemdraw = fetchFromGitHub {

     

       31
       +
             owner = "Glysade";

     

       32
       +
             repo = "chemdraw";

     

       33
       +
             tag = "v1.0.10";

     

       34
       +
             hash = "sha256-ee2Oxvo2d7Yb59lN0zkrbFqy/3rOvVLo6qdS+f23wVQ=";

     

       35
       +
           };

     

       36
       +
           yaehmop = applyPatches {

     

       37
       +
             src = fetchFromGitHub {

     

       38
       +
               owner = "greglandrum";

     

       39
       +
               repo = "yaehmop";

     

       40
       +
               rev = "v2025.03.1";

     

       41
       +
               hash = "sha256-rhR7Ev+9Fk/Ks7R2x2SjWu1L/48a4zHDHUBohx1Dw/M=";

     

       42
       +
             };

     

       43
       +
       

     

       44
       +
             # Compatibility with CMake < 3.5 has been removed from CMake.

     

       45
       +
             postPatch = ''

     

       46
       +
               substituteInPlace tightbind/CMakeLists.txt \

     

       47
       +
                 --replace-fail \

     

       48
       +
                   "cmake_minimum_required(VERSION 3.0)" \

     

       49
       +
                   "cmake_minimum_required(VERSION 3.5)"

     

       50
       +
             '';

     

       51
        
           };

     

       52
        
           freesasa = fetchFromGitHub {

     

       53
        
             owner = "mittinatten";

     
···

       61
        
             rev = "daefab3dd0c90ca56da9d3d5e375fe4d651e6be3";

     

       62
        
             hash = "sha256-tQB4wqza9rlSoy4Uj9bA99ddawjxGyN9G7DYbcv/Qdo=";

     

       63
        
           };

     

       64
       +
           better_enums = fetchFromGitHub {

     

       65
       +
             owner = "aantron";

     

       66
       +
             repo = "better-enums";

     

       67
       +
             tag = "0.11.3";

     

       68
       +
             hash = "sha256-UYldCOkRTySc78oEOJzgoY9h2lB386W/D5Rz3KjVCO8=";

     

       69
       +
           };

     

       70
       +
           # We cannot use the inchi from nixpkgs as the version is too old

     

       71
       +
           inchi = fetchzip {

     

       72
       +
             url = "https://github.com/IUPAC-InChI/InChI/releases/download/v1.07.3/INCHI-1-SRC.zip";

     

       73
       +
             hash = "sha256-TUC2175HifB63EfSsg/ixA3wYzAxsvUnY6ZyNjVR/Fc=";

     

       74
       +
           };

     

       75
        
         };

     

       76
        
         boost' = boost.override { enableNumpy = true; };

     

       77
        
       in

     

       78
        
       buildPythonPackage rec {

     

       79
        
         pname = "rdkit";

     

       80
       +
         version = "2025.03.6";

     

       81
        
         pyproject = false;

     

       82
        
       

     

       83
        
         src =

     
···

       87
        
           fetchFromGitHub {

     

       88
        
             owner = "rdkit";

     

       89
        
             repo = "rdkit";

     

       90
       +
             tag = "Release_${versionTag}";

     

       91
       +
             hash = "sha256-DqnwfT+lX7OnArIcFlCBrDl+QDmNpbPO9u7OGwu8fJo=";

     

       92
        
           };

     

       93
        
       

     

       94
        
         unpackPhase = ''

     
···

       99
        
           # In buildPhase, CMake patches the file in this directory

     

       100
        
           # see https://github.com/rdkit/rdkit/pull/5928

     

       101
        
           cp -r ${external.avalon}/* External/AvalonTools/avalon

     

       102
       +
       

     

       103
       +
           mkdir External/ChemDraw/chemdraw

     

       104
       +
           cp -r ${external.chemdraw}/* External/ChemDraw/chemdraw/

     

       105
       +
           chmod -R +w External/ChemDraw/chemdraw

     

       106
        
       

     

       107
        
           mkdir External/YAeHMOP/yaehmop

     

       108
        
           ln -s ${external.yaehmop}/* External/YAeHMOP/yaehmop

     

       109
        
       

     

       110
       +
           mkdir External/FreeSASA/freesasa

     

       111
        
           cp -r ${external.freesasa}/* External/FreeSASA/freesasa

     

       112
        
           chmod +w External/FreeSASA/freesasa/src

     

       113
        
           cp External/FreeSASA/freesasa2.c External/FreeSASA/freesasa/src

     

       114
        
       

     

       115
       +
           mkdir External/pubchem_shape/pubchem-align3d

     

       116
       +
           cp -r ${external.pubchem-align3d}/* External/pubchem_shape/pubchem-align3d

     

       117
       +
       

     

       118
       +
           mkdir External/INCHI-API/src

     

       119
       +
           ln -s ${external.inchi}/* External/INCHI-API/src

     

       120
       +
       

     

       121
        
           ln -s ${rapidjson} External/rapidjson-1.1.0

     

       122
        
           ln -s ${comic-neue}/share/fonts/truetype/ComicNeue-Regular.ttf Data/Fonts/

     

       123
        
         '';

     

       124
        
       

     

       125
       +
         patches = [

     

       126
       +
           (replaceVars ./dont-fetch-better-enums.patch {

     

       127
       +
             inherit (external) better_enums;

     

       128
       +
           })

     

       129
       +
         ];

     

       130
       +
       

     

       131
       +
         # Prevent linking to libpython which fails on darwin with:

     

       132
       +
         # Undefined symbols for architecture arm64

     

       133
       +
         # Reverts https://github.com/rdkit/rdkit/commit/470df8cd2fab78d64ef1dd254576097b651c3dd9

     

       134
       +
         postPatch = ''

     

       135
       +
           substituteInPlace \

     

       136
       +
             CMakeLists.txt \

     

       137
       +
             External/pubchem_shape/Wrap/CMakeLists.txt \

     

       138
       +
             --replace-fail \

     

       139
       +
               "find_package(Python3 COMPONENTS Interpreter Development.Module NumPy" \

     

       140
       +
               "find_package(Python3 COMPONENTS Interpreter Development NumPy" \

     

       141
       +
         '';

     

       142
       +
       

     

       143
        
         nativeBuildInputs = [ cmake ];

     

       144
        
       

     

       145
        
         buildInputs = [

     
···

       148
        
           catch2_3

     

       149
        
           coordgenlibs

     

       150
        
           eigen

     

       0
        
       
     

       151
        
           maeparser

     

       152
        
         ];

     

       153
        
       

     
···

       180
        
           (lib.cmakeBool "RDK_USE_URF" false)

     

       181
        
           (lib.cmakeFeature "AVALONTOOLS_DIR" "avalon")

     

       182
        
           (lib.cmakeFeature "FREESASA_SRC_DIR" "freesasa")

     

       183
       +
           (lib.cmakeFeature "maeparser_DIR" "${maeparser}/lib/cmake")

     

       184
       +
           (lib.cmakeFeature "coordgen_DIR" "${coordgenlibs}/lib/cmake")

     

       185
        
         ];

     

       186
        
       

     

       187
        
         checkPhase = ''

     
···

       198
        
           "rdkit.Chem.rdDetermineBonds"

     

       199
        
         ];

     

       200
        
       

     

       201
       +
         meta = {

     

       202
        
           description = "Open source toolkit for cheminformatics";

     

       203
       +
           maintainers = with lib.maintainers; [

     

       204
        
             rmcgibbo

     

       205
        
             natsukium

     

       206
        
           ];

     

       207
       +
           license = lib.licenses.bsd3;

     

       208
        
           homepage = "https://www.rdkit.org";

     

       209
       +
           changelog = "https://github.com/rdkit/rdkit/releases/tag/${src.tag}";

     

       210
        
         };

     

       211
        
       }

+14

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

···

       1
       +
       diff --git a/CMakeLists.txt b/CMakeLists.txt

     

       2
       +
       index 77939f452..9cace7fe1 100644

     

       3
       +
       --- a/CMakeLists.txt

     

       4
       +
       +++ b/CMakeLists.txt

     

       5
       +
       @@ -184,8 +184,7 @@ Include(FetchContent)

     

       6
       +
        

     

       7
       +
        FetchContent_Declare(

     

       8
       +
          better_enums

     

       9
       +
       -  GIT_REPOSITORY https://github.com/aantron/better-enums.git

     

       10
       +
       -  GIT_TAG        c35576bed0295689540b39873126129adfa0b4c8 # 0.11.3

     

       11
       +
       +  URL @better_enums@

     

       12
       +
        )

     

       13
       +
        

     

       14
       +
        if(RDK_INSTALL_INTREE)