From 9c6998f54232127bd5a083de19e5207a872ef0cf Mon Sep 17 00:00:00 2001
From: Phillip Seeber <phillip.seeber@googlemail.com>
Date: Thu, 16 Sep 2021 14:43:15 +0200
Subject: [PATCH] pyscf: backport of h5py fixes, closes #138127

pyscf: adding patch explanation
---
 pkgs/development/python-modules/pyscf/default.nix |  4 ++++
 pkgs/development/python-modules/pyscf/h5py.patch  | 13 +++++++++++++
 2 files changed, 17 insertions(+)
 create mode 100644 pkgs/development/python-modules/pyscf/h5py.patch

diff --git a/pkgs/development/python-modules/pyscf/default.nix b/pkgs/development/python-modules/pyscf/default.nix
index 0af38e3f8bea..0be40b5dfe7c 100644
--- a/pkgs/development/python-modules/pyscf/default.nix
+++ b/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
diff --git a/pkgs/development/python-modules/pyscf/h5py.patch b/pkgs/development/python-modules/pyscf/h5py.patch
new file mode 100644
index 000000000000..160128633208
--- /dev/null
+++ b/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)