pymol: fix build

pkgs/by-name/py/pymol/package.nix

@@ -2,6 +2,7 @@
   stdenv,
   lib,
   fetchFromGitHub,
+  fetchpatch,
   makeDesktopItem,
   cmake,
   python3Packages,
@@ -57,11 +58,31 @@ python3Packages.buildPythonApplication rec {
 
   # A script is already created by the `[project.scripts]` directive
   # in `pyproject.toml`.
-  patches = [ ./script-already-exists.patch ];
+  patches = [ 
+    ./script-already-exists.patch
+
+    # Fix python3.13 and numpy 2 compatibility
+    (fetchpatch {
+      url="https://github.com/schrodinger/pymol-open-source/commit/fef4a026425d195185e84d46ab88b2bbd6d96cf8.patch";
+      hash = "sha256-F/5UcYwgHgcMQ+zeigedc1rr3WkN9rhxAxH+gQfWKIY=";
+    })
+    (fetchpatch {
+      url="https://github.com/schrodinger/pymol-open-source/commit/97cc1797695ee0850621762491e93dc611b04165.patch";
+      hash = "sha256-H2PsRFn7brYTtLff/iMvJbZ+RZr7GYElMSINa4RDYdA=";
+    })
+    # Fixes failing test testLoadPWG
+    (fetchpatch {
+      url="https://github.com/schrodinger/pymol-open-source/commit/17c6cbd96d52e9692fd298daec6c9bda273a8aad.patch";
+      hash = "sha256-dcYRzUhiaGlR3CjQ0BktA5L+8lFyVdw0+hIz3Li7gDQ=";
+    })
+  ];
 
   postPatch = ''
     substituteInPlace setup.py \
       --replace-fail "self.install_libbase" '"${placeholder "out"}/${python3Packages.python.sitePackages}"'
+
+    substituteInPlace pyproject.toml \
+      --replace-fail '"cmake>=3.13.3",' ""
   '';
 
   env.PREFIX_PATH = lib.optionalString (!stdenv.hostPlatform.isDarwin) "${msgpack}";
@@ -74,7 +95,7 @@ python3Packages.buildPythonApplication rec {
   ];
 
   buildInputs = [
-    python3Packages.numpy_1
+    python3Packages.numpy
     python3Packages.pyqt5
     qt5.qtbase
     glew
@@ -115,6 +136,7 @@ python3Packages.buildPythonApplication rec {
     python3Packages.msgpack
     pillow
     pytestCheckHook
+    requests
   ];
 
   # some tests hang for some reason