Merge pull request #309998 from TomaSajt/glymur

python312Packages.glymur: 0.12.5 -> 0.13.2, unbreak, refactor

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

@@ -1,10 +1,13 @@
 { lib
 , stdenv
 , buildPythonPackage
+, substituteAll
+, glibc
+, libtiff
+, openjpeg
 , fetchFromGitHub
 , lxml
 , numpy
-, openjpeg
 , pytestCheckHook
 , pythonOlder
 , scikit-image
@@ -13,54 +16,66 @@
 
 buildPythonPackage rec {
   pname = "glymur";
-  version = "0.12.5";
+  version = "0.13.2";
-  format = "pyproject";
+  pyproject = true;
 
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "quintusdias";
-    repo = pname;
+    repo = "glymur";
     rev = "refs/tags/v${version}";
-    hash = "sha256-9NMSAt5yFRnlCUDP37/ozhDsS8FTdRkfjUz8kQwWzVc=";
+    hash = "sha256-GUqe9mdMm2O/cbZw8Reohh4X1kO+xOMWHb83PjNvdu8=";
   };
 
-  nativeBuildInputs = [
+  patches = [
+    (substituteAll {
+      src = ./set-lib-paths.patch;
+      openjp2_lib = "${lib.getLib openjpeg}/lib/libopenjp2${stdenv.hostPlatform.extensions.sharedLibrary}";
+      tiff_lib = "${lib.getLib libtiff}/lib/libtiff${stdenv.hostPlatform.extensions.sharedLibrary}";
+    })
+  ];
+
+  postPatch = lib.optionalString (!stdenv.isDarwin) ''
+    substituteInPlace glymur/lib/tiff.py \
+        --replace-fail "glymur_config('c')" "ctypes.CDLL('${lib.getLib glibc}/lib/libc.so.6')"
+  '';
+
+  __propagatedImpureHostDeps = lib.optional stdenv.isDarwin "/usr/lib/libc.dylib";
+
+  build-system = [
     setuptools
   ];
 
-  propagatedBuildInputs = [
+  dependencies = [
+    lxml
     numpy
   ];
 
   nativeCheckInputs = [
-    lxml
     pytestCheckHook
     scikit-image
   ];
 
-  postConfigure = ''
+  preCheck = ''
-    substituteInPlace glymur/config.py \
+    export PATH="$out/bin:$PATH"
-    --replace "path = read_config_file(libname)" "path = '${openjpeg}/lib/lib' + libname + ${if stdenv.isDarwin then "'.dylib'" else "'.so'"}"
   '';
 
   disabledTestPaths = [
     # this test involves glymur's different ways of finding the openjpeg path on
     # fsh systems by reading an .rc file and such, and is obviated by the patch
-    # in postConfigure
     "tests/test_config.py"
-    "tests/test_tiff2jp2.py"
   ];
 
   pythonImportsCheck = [
     "glymur"
   ];
 
-  meta = with lib; {
+  meta = {
     description = "Tools for accessing JPEG2000 files";
     homepage = "https://github.com/quintusdias/glymur";
     changelog = "https://github.com/quintusdias/glymur/blob/v${version}/CHANGES.txt";
-    license = licenses.mit;
+    license = lib.licenses.mit;
-    maintainers = with maintainers; [ ];
+    maintainers = with lib.maintainers; [ tomasajt ];
   };
 }

pkgs/development/python-modules/glymur/set-lib-paths.patch

@@ -0,0 +1,16 @@
+diff --git a/glymur/config.py b/glymur/config.py
+index 962e299..dab44ba 100644
+--- a/glymur/config.py
++++ b/glymur/config.py
+@@ -53,6 +53,11 @@ def _determine_full_path(libname):
+     if path is not None:
+         return path
+ 
++    if libname == "openjp2":
++        return "@openjp2_lib@"
++    if libname == "tiff":
++        return "@tiff_lib@"
++
+     # No joy on config file.  Cygwin?  Cygwin is a bit of an odd case.
+     if platform.system().startswith('CYGWIN'):
+         g = pathlib.Path('/usr/bin').glob('cygopenjp2*.dll')