eggnog-mapper: 2.1.13 -> 2.1.14, fix for python 3.12+ and migrate to pyproject (#528766)

pkgs/by-name/eg/eggnog-mapper/package.nix

@@ -2,6 +2,7 @@
   lib,
   autoPatchelfHook,
   fetchFromGitHub,
+  fetchpatch2,
   python3Packages,
   wget,
   zlib,
@@ -9,38 +10,53 @@
 
 python3Packages.buildPythonApplication (finalAttrs: {
   pname = "eggnog-mapper";
-  version = "2.1.13";
-  format = "setuptools";
+  version = "2.1.14";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "eggnogdb";
     repo = "eggnog-mapper";
-    tag = finalAttrs.version;
-    hash = "sha256-Gu4D8DBvgCPlO+2MjeNZy6+lNqsIlksegWmmYvEZmUU=";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-rjQojz6JA7T03s4PojjXJuDZhdAx9VhPQrlRTGZaYZg=";
   };
 
-  postPatch = ''
-    # Not a great solution...
-    substituteInPlace setup.cfg \
-      --replace "==" ">="
-  '';
+  patches = [
+    # From https://github.com/eggnogdb/eggnog-mapper/pull/599
+    (fetchpatch2 {
+      name = "replace-distutils.patch";
+      url = "https://github.com/eggnogdb/eggnog-mapper/commit/998129d3766e060ff450e8f950b5361c6318b0a2.patch?full_index=1";
+      hash = "sha256-xYNd9p5BhGpvFXCWXRSEkZf+Lt4hCRGYeV9Oe4mDz3I=";
+    })
+  ];
 
   nativeBuildInputs = [
     autoPatchelfHook
   ];
 
+  build-system = with python3Packages; [
+    setuptools
+  ];
+
   buildInputs = [
     zlib
   ];
 
   propagatedBuildInputs = [
     wget
-  ]
-  ++ (with python3Packages; [
+  ];
+
+  dependencies = with python3Packages; [
     biopython
     psutil
     xlsxwriter
-  ]);
+  ];
+
+  # Upstream already relaxed these dependencies, but that is not yet included in 2.1.14
+  pythonRelaxDeps = [
+    "biopython"
+    "psutil"
+    "xlsxwriter"
+  ];
 
   # Tests rely on some of the databases being available, which is not bundled
   # with this package as (1) in total, they represent >100GB of data, and (2)