python.pkgs.pygraphviz: add graphviz path

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

@@ -13,8 +13,18 @@ buildPythonPackage rec {
   buildInputs = [ doctest-ignore-unicode mock nose ];
   propagatedBuildInputs = [ graphviz pkgconfig ];
 
-  # the tests are currently failing:
-  # check status of pygraphviz/pygraphviz#129
+  patches = [
+    # pygraphviz depends on graphviz being in PATH. This patch always prepends
+    # graphviz to PATH.
+    ./graphviz-path.patch
+  ];
+  postPatch = ''
+    substituteInPlace pygraphviz/agraph.py --subst-var-by graphvizPath '${graphviz}/bin'
+  '';
+
+  # The tests are currently failing because of a bug in graphviz 2.40.1.
+  # Upstream does not want to skip the relevant tests:
+  # https://github.com/pygraphviz/pygraphviz/pull/129
   doCheck = false;
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/pygraphviz/graphviz-path.patch

@@ -0,0 +1,13 @@
+diff --git a/pygraphviz/agraph.py b/pygraphviz/agraph.py
+index 8f72024..2d8358e 100644
+--- a/pygraphviz/agraph.py
++++ b/pygraphviz/agraph.py
+@@ -1557,7 +1557,7 @@ class AGraph(object):
+         import os
+         import glob
+ 
+-        paths = os.environ["PATH"]
++        paths = '@graphvizPath@:' + os.environ["PATH"]
+         if os.name == "nt":
+             exe = ".exe"
+         else:

pkgs/top-level/python-packages.nix

@@ -3033,7 +3033,9 @@ in {
 
   graphviz = callPackage ../development/python-modules/graphviz { };
 
-  pygraphviz = callPackage ../development/python-modules/pygraphviz { };
+  pygraphviz = callPackage ../development/python-modules/pygraphviz {
+    graphviz = pkgs.graphviz; # not the python package
+  };
 
   pymc3 = callPackage ../development/python-modules/pymc3 { };