python3Packages.shapely: keep version 1.8

Keep old version of package due to requirements
of following packages:

* kikit

pkgs/development/python-modules/shapely/1.8.nix

···
+{ lib
+, stdenv
+, buildPythonPackage
+, fetchPypi
+, pytestCheckHook
+, pythonOlder
+, substituteAll
+
+, cython
+, geos311
+, numpy
+, oldest-supported-numpy
+, setuptools
+, wheel
+}:
+
+buildPythonPackage rec {
+  pname = "Shapely";
+  version = "1.8.5";
+  format = "pyproject";
+
+  disabled = pythonOlder "3.7";
+
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-6CttYOz7EkEgyI/hBqR4WWu+qxQhFtfn9ko2TayQKpI=";
+  };
+
+  # Environment variable used in shapely/_buildcfg.py
+  GEOS_LIBRARY_PATH = "${geos311}/lib/libgeos_c${stdenv.hostPlatform.extensions.sharedLibrary}";
+
+  patches = [
+    # Patch to search form GOES .so/.dylib files in a Nix-aware way
+    (substituteAll {
+      src = ./library-paths.patch;
+      libgeos_c = GEOS_LIBRARY_PATH;
+      libc = lib.optionalString (!stdenv.isDarwin) "${stdenv.cc.libc}/lib/libc${stdenv.hostPlatform.extensions.sharedLibrary}.6";
+    })
+  ];
+
+  postPatch = ''
+    substituteInPlace pyproject.toml --replace "setuptools<64" "setuptools"
+  '';
+
+  nativeBuildInputs = [
+    cython
+    geos311 # for geos-config
+    oldest-supported-numpy
+    setuptools
+    wheel
+  ];
+
+  buildInputs = [
+    geos311
+  ];
+
+  propagatedBuildInputs = [
+    numpy
+  ];
+
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
+
+  preCheck = ''
+    rm -r shapely # prevent import of local shapely
+  '';
+
+  disabledTests = lib.optionals (stdenv.isDarwin && stdenv.isAarch64) [
+    # FIXME(lf-): these logging tests are broken, which is definitely our
+    # fault. I've tried figuring out the cause and failed.
+    #
+    # It is apparently some sandbox or no-sandbox related thing on macOS only
+    # though.
+    "test_error_handler_exception"
+    "test_error_handler"
+    "test_info_handler"
+  ];
+
+  pythonImportsCheck = [ "shapely" ];
+
+  meta = with lib; {
+    changelog = "https://github.com/shapely/shapely/blob/${version}/CHANGES.txt";
+    description = "Manipulation and analysis of geometric objects";
+    homepage = "https://github.com/shapely/shapely";
+    license = licenses.bsd3;
+    maintainers = teams.geospatial.members;
+  };
+}

pkgs/development/python-modules/shapely/library-paths.patch

···
+diff --git a/shapely/geos.py b/shapely/geos.py
+index 88c5f53..1ccd6e4 100644
+--- a/shapely/geos.py
++++ b/shapely/geos.py
+@@ -96,6 +96,7 @@ if sys.platform.startswith('linux'):
+         alt_paths = [
+             'libgeos_c.so.1',
+             'libgeos_c.so',
++            '@libgeos_c@',
+         ]
+         _lgeos = load_dll('geos_c', fallbacks=alt_paths)
+
+@@ -160,6 +161,7 @@ elif sys.platform == 'darwin':
+             "/usr/local/lib/libgeos_c.dylib",
+             # homebrew Apple Silicon
+             "/opt/homebrew/lib/libgeos_c.dylib",
++            "@libgeos_c@",
+         ]
+         _lgeos = load_dll('geos_c', fallbacks=alt_paths)
+
+diff --git a/tests/test_dlls.py b/tests/test_dlls.py
+index c71da8e..c36262c 100644
+--- a/tests/test_dlls.py
++++ b/tests/test_dlls.py
+@@ -18,4 +18,5 @@ class LoadingTestCase(unittest.TestCase):
+             '/opt/homebrew/lib/libgeos_c.dylib',  # homebrew (macOS)
+             os.path.join(sys.prefix, "lib", "libgeos_c.so"), # anaconda (Linux)
+             'libgeos_c.so.1',
+-            'libgeos_c.so'])
++            'libgeos_c.so',
++            '@libgeos_c@'])

pkgs/top-level/python-packages.nix

···
 
   shapely = callPackage ../development/python-modules/shapely { };
 
+  shapely18 = callPackage ../development/python-modules/shapely/1.8.nix { };
+
   shaperglot = callPackage ../development/python-modules/shaperglot { };
 
   sharedmem = callPackage ../development/python-modules/sharedmem { };