pyscf: backport of h5py fixes, closes #138127

pyscf: adding patch explanation

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

@@ -13,6 +13,10 @@ buildPythonPackage rec {
     sha256  = "0xbwkjxxysfpqz72qn6n4a0zr2h6sprbcal8j7kzymh7swjy117w";
   };
 
+  # Backport from the 2.0.0 alpha releases of PySCF.
+  # H5Py > 3.3 deprecates the file modes, that PySCF sets.
+  patches = [ ./h5py.patch ];
+
   buildInputs = [
     libcint
     libxc

pkgs/development/python-modules/pyscf/h5py.patch

@@ -0,0 +1,13 @@
+diff --git a/pyscf/lib/misc.py b/pyscf/lib/misc.py
+index ed43689ff..a8a0d0e20 100644
+--- a/pyscf/lib/misc.py
++++ b/pyscf/lib/misc.py
+@@ -42,8 +42,6 @@ if h5py.version.version[:4] == '2.2.':
+     sys.stderr.write('h5py-%s is found in your environment. '
+                      'h5py-%s has bug in threading mode.\n'
+                      'Async-IO is disabled.\n' % ((h5py.version.version,)*2))
+-if h5py.version.version[:2] == '3.':
+-    h5py.get_config().default_file_mode = 'a'
+ 
+ c_double_p = ctypes.POINTER(ctypes.c_double)
+ c_int_p = ctypes.POINTER(ctypes.c_int)