python3Packages.shapely: fix build with geos 3.9.0

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

@@ -1,17 +1,25 @@
-{ lib, stdenv, buildPythonPackage, fetchPypi, substituteAll, pythonOlder
-, geos, pytest, cython
+{ lib
+, stdenv
+, buildPythonPackage
+, fetchPypi
+, substituteAll
+, pythonOlder
+, geos
+, pytest
+, cython
 , numpy
+, fetchpatch
 }:
 
 buildPythonPackage rec {
   pname = "Shapely";
   version = "1.7.1";
+  disabled = pythonOlder "3.5";
 
   src = fetchPypi {
     inherit pname version;
     sha256 = "0adiz4jwmwxk7k1awqifb1a9bj5x4nx4gglb5dz9liam21674h8n";
   };
-  disabled = pythonOlder "3.5";
 
   nativeBuildInputs = [
     geos # for geos-config
@@ -26,6 +34,18 @@ buildPythonPackage rec {
   GEOS_LIBRARY_PATH = "${geos}/lib/libgeos_c${stdenv.hostPlatform.extensions.sharedLibrary}";
 
   patches = [
+    # Fix with geos 3.9. This patch will be part of the next release after 1.7.1
+    (fetchpatch {
+      url = "https://github.com/Toblerity/Shapely/commit/77879a954d24d1596f986d16ba3eff5e13861164.patch";
+      sha256 = "1w7ngjqbpf9vnvrfg4nyv34kckim9a60gvx20h6skc79xwihd4m5";
+      excludes = [
+        "tests/test_create_inconsistent_dimensionality.py"
+        "appveyor.yml"
+        ".travis.yml"
+      ];
+    })
+
+    # Patch to search form GOES .so/.dylib files in a Nix-aware way
     (substituteAll {
       src = ./library-paths.patch;
       libgeos_c = GEOS_LIBRARY_PATH;