From defff9f32746ad847b0a170c13637d13a1fc600a Mon Sep 17 00:00:00 2001
From: chillcicada <2210227279@qq.com>
Date: Thu, 5 Mar 2026 10:27:29 +0800
Subject: [PATCH 1/3] avogadrolibs: migrate to by-name

---
 .../default.nix => by-name/av/avogadrolibs/package.nix}         | 0
 pkgs/top-level/all-packages.nix                                 | 2 --
 2 files changed, 2 deletions(-)
 rename pkgs/{development/libraries/science/chemistry/avogadrolibs/default.nix => by-name/av/avogadrolibs/package.nix} (100%)

diff --git a/pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix b/pkgs/by-name/av/avogadrolibs/package.nix
similarity index 100%
rename from pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix
rename to pkgs/by-name/av/avogadrolibs/package.nix
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index aacd720403d5..128c06d12fd9 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -11404,8 +11404,6 @@ with pkgs;
 
   ### SCIENCE/CHEMISTY
 
-  avogadrolibs = callPackage ../development/libraries/science/chemistry/avogadrolibs { };
-
   molequeue = libsForQt5.callPackage ../development/libraries/science/chemistry/molequeue { };
 
   avogadro2 = callPackage ../applications/science/chemistry/avogadro2 { };

From 207a37af3d5302582d99d7b668c2257773664a40 Mon Sep 17 00:00:00 2001
From: chillcicada <2210227279@qq.com>
Date: Thu, 5 Mar 2026 10:41:01 +0800
Subject: [PATCH 2/3] molequeue: migrate to by-name

---
 .../mo/molequeue/package.nix}                  | 18 ++++++++++--------
 pkgs/top-level/all-packages.nix                |  2 --
 2 files changed, 10 insertions(+), 10 deletions(-)
 rename pkgs/{development/libraries/science/chemistry/molequeue/default.nix => by-name/mo/molequeue/package.nix} (79%)

diff --git a/pkgs/development/libraries/science/chemistry/molequeue/default.nix b/pkgs/by-name/mo/molequeue/package.nix
similarity index 79%
rename from pkgs/development/libraries/science/chemistry/molequeue/default.nix
rename to pkgs/by-name/mo/molequeue/package.nix
index 33aa58bd73df..a6475b67ae16 100644
--- a/pkgs/development/libraries/science/chemistry/molequeue/default.nix
+++ b/pkgs/by-name/mo/molequeue/package.nix
@@ -3,27 +3,27 @@
   stdenv,
   fetchFromGitHub,
   cmake,
-  qttools,
-  wrapQtAppsHook,
+  qt5,
+  nix-update-script,
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "molequeue";
   version = "0.9.0";
 
   src = fetchFromGitHub {
     owner = "OpenChemistry";
     repo = "molequeue";
-    rev = version;
+    tag = finalAttrs.version;
     hash = "sha256-+NoY8YVseFyBbxc3ttFWiQuHQyy1GN8zvV1jGFjmvLg=";
   };
 
   nativeBuildInputs = [
     cmake
-    wrapQtAppsHook
+    qt5.wrapQtAppsHook
   ];
 
-  buildInputs = [ qttools ];
+  buildInputs = [ qt5.qttools ];
 
   postPatch = ''
     substituteInPlace CMakeLists.txt \
@@ -33,9 +33,11 @@ stdenv.mkDerivation rec {
   # Fix the broken CMake files to use the correct paths
   postInstall = ''
     substituteInPlace $out/lib/cmake/molequeue/MoleQueueConfig.cmake \
-      --replace "$out/" ""
+      --replace-fail "$out/" ""
   '';
 
+  passthru.updateScript = nix-update-script { };
+
   meta = {
     description = "Desktop integration of high performance computing resources";
     mainProgram = "molequeue";
@@ -44,4 +46,4 @@ stdenv.mkDerivation rec {
     platforms = lib.platforms.linux;
     license = lib.licenses.bsd3;
   };
-}
+})
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 128c06d12fd9..433e88ed0b99 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -11404,8 +11404,6 @@ with pkgs;
 
   ### SCIENCE/CHEMISTY
 
-  molequeue = libsForQt5.callPackage ../development/libraries/science/chemistry/molequeue { };
-
   avogadro2 = callPackage ../applications/science/chemistry/avogadro2 { };
 
   libxc_7 = pkgs.libxc.override { version = "7.0.0"; };

From 9309cdf32700c43207537012f604541f7f3bc0b4 Mon Sep 17 00:00:00 2001
From: chillcicada <2210227279@qq.com>
Date: Thu, 5 Mar 2026 10:41:39 +0800
Subject: [PATCH 3/3] avogadro2: migrate to by-name

---
 .../avogadro2/default.nix => by-name/av/avogadro2/package.nix}  | 0
 pkgs/top-level/all-packages.nix                                 | 2 --
 2 files changed, 2 deletions(-)
 rename pkgs/{applications/science/chemistry/avogadro2/default.nix => by-name/av/avogadro2/package.nix} (100%)

diff --git a/pkgs/applications/science/chemistry/avogadro2/default.nix b/pkgs/by-name/av/avogadro2/package.nix
similarity index 100%
rename from pkgs/applications/science/chemistry/avogadro2/default.nix
rename to pkgs/by-name/av/avogadro2/package.nix
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 433e88ed0b99..1fde13e51249 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -11404,8 +11404,6 @@ with pkgs;
 
   ### SCIENCE/CHEMISTY
 
-  avogadro2 = callPackage ../applications/science/chemistry/avogadro2 { };
-
   libxc_7 = pkgs.libxc.override { version = "7.0.0"; };
 
   molbar = with python3Packages; toPythonApplication molbar;