python3Packages.rdkit: 2024.09.1 -> 2025.03.1

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

@@ -1,13 +1,14 @@
 {
   lib,
-  stdenv,
   buildPythonPackage,
   fetchFromGitHub,
+  fetchzip,
+  applyPatches,
+  replaceVars,
   cmake,
   comic-neue,
   boost,
   catch2_3,
-  inchi,
   cairo,
   eigen,
   python,
@@ -26,11 +27,27 @@ let
       rev = "AvalonToolkit_2.0.5-pre.3";
       hash = "sha256-2MuFZgRIHXnkV7Nc1da4fa7wDx57VHUtwLthrmjk+5o=";
     };
-    yaehmop = fetchFromGitHub {
-      owner = "greglandrum";
-      repo = "yaehmop";
-      rev = "v2024.03.1";
-      hash = "sha256-rhR7Ev+9Fk/Ks7R2x2SjWu1L/48a4zHDHUBohx1Dw/M=";
+    chemdraw = fetchFromGitHub {
+      owner = "Glysade";
+      repo = "chemdraw";
+      tag = "v1.0.10";
+      hash = "sha256-ee2Oxvo2d7Yb59lN0zkrbFqy/3rOvVLo6qdS+f23wVQ=";
+    };
+    yaehmop = applyPatches {
+      src = fetchFromGitHub {
+        owner = "greglandrum";
+        repo = "yaehmop";
+        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";
@@ -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

@@ -0,0 +1,14 @@
+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)