From 30c188124d90e2b323df3245af6c7de673be3c0a Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sat, 30 Dec 2023 11:57:18 +0900
Subject: [PATCH 1/4] coordgenlibs: fix build with clang

---
 pkgs/development/libraries/coordgenlibs/default.nix | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/pkgs/development/libraries/coordgenlibs/default.nix b/pkgs/development/libraries/coordgenlibs/default.nix
index 1d89025a51fa..36cfc5e03762 100644
--- a/pkgs/development/libraries/coordgenlibs/default.nix
+++ b/pkgs/development/libraries/coordgenlibs/default.nix
@@ -21,6 +21,10 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ cmake ];
   buildInputs = [ boost zlib maeparser ];
 
+  env = lib.optionalAttrs stdenv.cc.isClang {
+    NIX_CFLAGS_COMPILE = "-Wno-unused-but-set-variable";
+  };
+
   meta = with lib; {
     description = "Schrodinger-developed 2D Coordinate Generation";
     maintainers = [ maintainers.rmcgibbo ];

From 1881026b3d5e4979fc3b791ec905701b7ab95629 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sat, 30 Dec 2023 12:04:53 +0900
Subject: [PATCH 2/4] coordgenlibs: enable tests

---
 pkgs/development/libraries/coordgenlibs/default.nix | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pkgs/development/libraries/coordgenlibs/default.nix b/pkgs/development/libraries/coordgenlibs/default.nix
index 36cfc5e03762..1a457535ad05 100644
--- a/pkgs/development/libraries/coordgenlibs/default.nix
+++ b/pkgs/development/libraries/coordgenlibs/default.nix
@@ -25,6 +25,8 @@ stdenv.mkDerivation rec {
     NIX_CFLAGS_COMPILE = "-Wno-unused-but-set-variable";
   };
 
+  doCheck = true;
+
   meta = with lib; {
     description = "Schrodinger-developed 2D Coordinate Generation";
     maintainers = [ maintainers.rmcgibbo ];

From 4fa311aa43cc527d5a407da25e0bde2be7e41551 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sat, 30 Dec 2023 12:07:06 +0900
Subject: [PATCH 3/4] coordgenlibs: refactor

---
 pkgs/development/libraries/coordgenlibs/default.nix | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/pkgs/development/libraries/coordgenlibs/default.nix b/pkgs/development/libraries/coordgenlibs/default.nix
index 1a457535ad05..4febe03ef04d 100644
--- a/pkgs/development/libraries/coordgenlibs/default.nix
+++ b/pkgs/development/libraries/coordgenlibs/default.nix
@@ -7,15 +7,15 @@
 , maeparser
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "coordgenlibs";
   version = "3.0.2";
 
   src = fetchFromGitHub {
     owner = "schrodinger";
-    repo = pname;
-    rev = "v${version}";
-    sha256 = "sha256-casFPNbPv9mkKpzfBENW7INClypuCO1L7clLGBXvSvI=";
+    repo = "coordgenlibs";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-casFPNbPv9mkKpzfBENW7INClypuCO1L7clLGBXvSvI=";
   };
 
   nativeBuildInputs = [ cmake ];
@@ -29,7 +29,9 @@ stdenv.mkDerivation rec {
 
   meta = with lib; {
     description = "Schrodinger-developed 2D Coordinate Generation";
+    homepage = "https://github.com/schrodinger/coordgenlibs";
+    changelog = "https://github.com/schrodinger/coordgenlibs/releases/tag/${finalAttrs.version}";
     maintainers = [ maintainers.rmcgibbo ];
     license = licenses.bsd3;
   };
-}
+})

From 07964df9f55546110cc02f6a648a2ad0dfc84fd5 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sat, 30 Dec 2023 11:30:16 +0900
Subject: [PATCH 4/4] python311Packages.rdkit: 2023.09.1 -> 2023.09.3

Diff: https://github.com/rdkit/rdkit/compare/Release_2023_09_1...Release_2023_09_3

Changelog: https://github.com/rdkit/rdkit/releases/tag/Release_2023_09_3
---
 pkgs/development/python-modules/rdkit/default.nix | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/pkgs/development/python-modules/rdkit/default.nix b/pkgs/development/python-modules/rdkit/default.nix
index 56cca6c1af85..7d0632ebc836 100644
--- a/pkgs/development/python-modules/rdkit/default.nix
+++ b/pkgs/development/python-modules/rdkit/default.nix
@@ -5,7 +5,7 @@
 , cmake
 , comic-neue
 , boost
-, catch2
+, catch2_3
 , inchi
 , cairo
 , eigen
@@ -42,8 +42,8 @@ let
 in
 buildPythonPackage rec {
   pname = "rdkit";
-  version = "2023.09.1";
-  format = "other";
+  version = "2023.09.3";
+  pyproject = false;
 
   src =
     let
@@ -53,7 +53,7 @@ buildPythonPackage rec {
       owner = pname;
       repo = pname;
       rev = "Release_${versionTag}";
-      hash = "sha256-qaYD/46oCTnso1FbD08zr2JuatKmSSqNBhOYlfeIiAA=";
+      hash = "sha256-bewOdmpnm6cArD5iaMKNqT8z4GUIpih+JzJ+wdo/lrI=";
     };
 
   unpackPhase = ''
@@ -84,6 +84,7 @@ buildPythonPackage rec {
   buildInputs = [
     boost
     cairo
+    catch2_3
   ] ++ lib.optionals (stdenv.system == "x86_64-darwin") [
     memorymappingHook
   ];
@@ -109,7 +110,6 @@ buildPythonPackage rec {
   '';
 
   cmakeFlags = [
-    "-DCATCH_DIR=${catch2}/include/catch2"
     "-DINCHI_LIBRARY=${inchi}/lib/libinchi.so"
     "-DINCHI_LIBRARIES=${inchi}/lib/libinchi.so"
     "-DINCHI_INCLUDE_DIR=${inchi}/include/inchi"