flake.lock: Update

Flake lock file updates:

• Updated input 'flake-utils':
    'github:numtide/flake-utils/cfacdce06f30d2b68473a46042957675eebb3401' (2023-04-11)
  → 'github:numtide/flake-utils/1ef2e671c3b0c19053962c07dbda38332dcebf26' (2024-01-15)
• Updated input 'nixpkgs':
    'github:NixOS/nixpkgs/daa7efafc2cf6e5efa7ff1c1d24f91127a2d8da4' (2023-05-23)
  → 'github:NixOS/nixpkgs/9a333eaa80901efe01df07eade2c16d183761fa3' (2024-01-22)

flake.lock

@@ -5,11 +5,11 @@
         "systems": "systems"
       },
       "locked": {
-        "lastModified": 1681202837,
+        "lastModified": 1705309234,
-        "narHash": "sha256-H+Rh19JDwRtpVPAWp64F+rlEtxUWBAQW28eAi3SRSzg=",
+        "narHash": "sha256-uNRRNRKmJyCRC/8y1RqBkqWBLM034y4qN7EprSdmgyA=",
         "owner": "numtide",
         "repo": "flake-utils",
-        "rev": "cfacdce06f30d2b68473a46042957675eebb3401",
+        "rev": "1ef2e671c3b0c19053962c07dbda38332dcebf26",
         "type": "github"
       },
       "original": {
@@ -20,11 +20,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1684854566,
+        "lastModified": 1705957679,
-        "narHash": "sha256-Swfk4jyHzDoqZUGeYHTWC5jOJ2PI7yBiAZqLeG6+zVU=",
+        "narHash": "sha256-Q8LJaVZGJ9wo33wBafvZSzapYsjOaNjP/pOnSiKVGHY=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "daa7efafc2cf6e5efa7ff1c1d24f91127a2d8da4",
+        "rev": "9a333eaa80901efe01df07eade2c16d183761fa3",
         "type": "github"
       },
       "original": {

flake.nix

@@ -13,6 +13,10 @@
       pkgs = import nixpkgs {
         inherit system;
         config.allowAliases = false;
+        config.permittedInsecurePackages = [
+          "python-2.7.18.6"
+          "python-2.7.18.6-env"
+        ];
         overlays = [ self.overlays.default ];
       };
       inherit (pkgs) lib;
@@ -30,7 +34,6 @@
         (system == "x86_64-linux" ) (attributesToAttrset overlayAttributes.right);
       hydraJobs = pkgs.lib.optionalAttrs
         (system == "x86_64-linux" ) self.packages;
-
     }
   ));
 }

pkgs/all-packages.nix

@@ -19,13 +19,13 @@ final: prev: with prev; {
   
   mfixsolver = callPackage ./mfix/mfixsolver.nix { };
 
-  inherit (callPackage ./opengl/default.nix { inherit prev; }) libGL mesa_glxgallium;
+  # inherit (callPackage ./opengl/default.nix { inherit prev; }) libGL mesa_glxgallium;
 
   openfoam = callPackage ./openfoam.nix { };
 
   openslide = callPackage ./openslide { };
 
-  ovito = libsForQt5.callPackage ./ovito.nix { };
+  ovito = qt6Packages.callPackage ./ovito.nix { };
 
   pythonOverrides = lib.composeExtensions prev.pythonOverrides (import ./python-packages.nix pkgs);
 

pkgs/lumpy.nix

@@ -1,8 +1,27 @@
 { stdenv, lib, fetchFromGitHub, which, autoconf, automake
 , zlib, curl
-, python2, hexdump, sambamba, samblaster, samtools }:
+, python2, fetchPypi, hexdump, sambamba, samblaster, samtools }: let
-
+  python = python2.override {
-stdenv.mkDerivation rec {
+    packageOverrides = final: prev: {
+      numpy = prev.numpy.overridePythonAttrs(old: rec {
+        version = "1.16.6";
+        disabled = false;
+        src = fetchPypi {
+          inherit version;
+          pname = "numpy";
+          extension = "zip";
+          sha256 = "e5cf3fdf13401885e8eea8170624ec96225e2174eb0c611c6f26dd33b489e3ff";
+        };
+        nativeCheckInputs = [
+          prev.pytest
+          # "hypothesis" indirectly depends on numpy to build its documentation.
+          prev.hypothesis
+          prev.typing-extensions
+        ];
+      });
+    };
+  };
+in stdenv.mkDerivation rec {
   version = "0.3.0";
   name = "lumpy-${version}";
 
@@ -39,7 +58,12 @@ stdenv.mkDerivation rec {
     automake
     zlib
     curl
-    (python2.withPackages (packages: with packages; [ numpy pysam ]))
+    (python.withPackages (packages: with packages;
+      [
+        numpy
+        pysam
+      ]
+    ))
     hexdump
     sambamba
     samblaster

pkgs/opengl/default.nix

@@ -28,7 +28,7 @@ let
           patchelf --set-rpath /usr/lib${stdenv.lib.optionalString stdenv.is64bit "64"}/nvidia:"$(patchelf --print-rpath $out/lib/libvglfaker.so)" $out/lib/libvglfaker.so
         '';
       } );
-      fltk = prev.fltk.override { inherit libGL libGLU freeglut; };
+      fltk = prev.fltk.override { inherit libGL libGLU; };
       freeglut = prev.freeglut.override { inherit libGL libGLU; };
     in
       substituteAll {

pkgs/ovito.nix

@@ -1,30 +1,55 @@
-{ mkDerivation, lib, fetchFromGitLab, cmake
+{ stdenv
-, boost, netcdf, hdf5, fftwSinglePrec, muparser, openssl, ffmpeg, python38
+, lib
-, qtbase, qtsvg, qttools, qscintilla }:
+, fetchFromGitLab
+, cmake
+, ninja
+, wrapQtAppsHook
+, qtbase
+, qtnetworkauth
+, qtscxml
+, qtsvg
+, ffmpeg
+, netcdf
+, libssh
+, boost
+, hdf5
+, python3 ? python3
+}:
 
-mkDerivation rec {
+stdenv.mkDerivation rec {
   pname = "ovito";
-  version = "3.4.0";
+  version = "3.8.4";
 
   src = fetchFromGitLab {
     owner = "stuko";
     repo = "ovito";
     rev = "v${version}";
-    sha256 = "1y3wr6yzpsl0qm7cicp2mppfszxd0fgx8hm99in9wff9qd0r16b5";
+    sha256 = "Vw9mB+huQHLg8OqyGo9KEg55ag3NQG+nTJj3tB++eQk=";
   };
 
-  buildInputs = [
+  nativeBuildInputs = [
     cmake
-    boost
+    ninja
-    netcdf hdf5
+    wrapQtAppsHook
-    fftwSinglePrec
-    muparser
-    openssl
-    ffmpeg
-    python38
-    qtbase qtsvg qttools qscintilla
   ];
 
+  buildInputs = [
+    qtbase
+    qtnetworkauth
+    qtscxml
+    qtsvg
+    ffmpeg
+    netcdf
+    libssh
+    boost
+    hdf5
+    python3
+  ];
+
+  cmakeFlags = [
+    "-DOVITO_BUILD_PYPI=${if python3 != null then "ON" else "OFF"}"
+  ];
+  
   meta = with lib; {
     description = "Scientific visualization and analysis software for atomistic and particle simulation data";
     homepage = https://ovito.org;