From c39fadf32ddf23c35164bfd047e6dfeeb0c62808 Mon Sep 17 00:00:00 2001
From: Timo Gottszky <timogottszky+git@gmail.com>
Date: Sat, 6 Jun 2026 12:50:29 +0200
Subject: [PATCH 1/3] eggnog-mapper: 2.1.13 -> 2.1.14

---
 pkgs/by-name/eg/eggnog-mapper/package.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/by-name/eg/eggnog-mapper/package.nix b/pkgs/by-name/eg/eggnog-mapper/package.nix
index 2960d5485476..063f7fba8a97 100644
--- a/pkgs/by-name/eg/eggnog-mapper/package.nix
+++ b/pkgs/by-name/eg/eggnog-mapper/package.nix
@@ -9,14 +9,14 @@
 
 python3Packages.buildPythonApplication (finalAttrs: {
   pname = "eggnog-mapper";
-  version = "2.1.13";
+  version = "2.1.14";
   format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "eggnogdb";
     repo = "eggnog-mapper";
-    tag = finalAttrs.version;
-    hash = "sha256-Gu4D8DBvgCPlO+2MjeNZy6+lNqsIlksegWmmYvEZmUU=";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-rjQojz6JA7T03s4PojjXJuDZhdAx9VhPQrlRTGZaYZg=";
   };
 
   postPatch = ''

From 467477e61abd30f71d5264ee3dad5b9a1bab4c61 Mon Sep 17 00:00:00 2001
From: Timo Gottszky <timogottszky+git@gmail.com>
Date: Sat, 6 Jun 2026 13:24:33 +0200
Subject: [PATCH 2/3] eggnogg-mapper: fix for python 3.12+

distutils was removed in python 3.12, upstream already fixed this but
the fix is not available in v2.1.14
---
 pkgs/by-name/eg/eggnog-mapper/package.nix | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/pkgs/by-name/eg/eggnog-mapper/package.nix b/pkgs/by-name/eg/eggnog-mapper/package.nix
index 063f7fba8a97..d29d73728d3c 100644
--- a/pkgs/by-name/eg/eggnog-mapper/package.nix
+++ b/pkgs/by-name/eg/eggnog-mapper/package.nix
@@ -2,6 +2,7 @@
   lib,
   autoPatchelfHook,
   fetchFromGitHub,
+  fetchpatch2,
   python3Packages,
   wget,
   zlib,
@@ -19,6 +20,15 @@ python3Packages.buildPythonApplication (finalAttrs: {
     hash = "sha256-rjQojz6JA7T03s4PojjXJuDZhdAx9VhPQrlRTGZaYZg=";
   };
 
+  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=";
+    })
+  ];
+
   postPatch = ''
     # Not a great solution...
     substituteInPlace setup.cfg \

From fdab2a416e569b1393c902b79805f18aca09da6b Mon Sep 17 00:00:00 2001
From: Timo Gottszky <timogottszky+git@gmail.com>
Date: Sat, 6 Jun 2026 13:31:05 +0200
Subject: [PATCH 3/3] eggnog-mapper: migrate to pyproject

---
 pkgs/by-name/eg/eggnog-mapper/package.nix | 26 ++++++++++++++---------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/pkgs/by-name/eg/eggnog-mapper/package.nix b/pkgs/by-name/eg/eggnog-mapper/package.nix
index d29d73728d3c..704794daac0c 100644
--- a/pkgs/by-name/eg/eggnog-mapper/package.nix
+++ b/pkgs/by-name/eg/eggnog-mapper/package.nix
@@ -11,7 +11,7 @@
 python3Packages.buildPythonApplication (finalAttrs: {
   pname = "eggnog-mapper";
   version = "2.1.14";
-  format = "setuptools";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "eggnogdb";
@@ -29,28 +29,34 @@ python3Packages.buildPythonApplication (finalAttrs: {
     })
   ];
 
-  postPatch = ''
-    # Not a great solution...
-    substituteInPlace setup.cfg \
-      --replace "==" ">="
-  '';
-
   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)