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,
-        "narHash": "sha256-H+Rh19JDwRtpVPAWp64F+rlEtxUWBAQW28eAi3SRSzg=",
+        "lastModified": 1705309234,
+        "narHash": "sha256-uNRRNRKmJyCRC/8y1RqBkqWBLM034y4qN7EprSdmgyA=",
         "owner": "numtide",
         "repo": "flake-utils",
-        "rev": "cfacdce06f30d2b68473a46042957675eebb3401",
+        "rev": "1ef2e671c3b0c19053962c07dbda38332dcebf26",
         "type": "github"
       },
       "original": {
@@ -20,11 +20,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1684854566,
-        "narHash": "sha256-Swfk4jyHzDoqZUGeYHTWC5jOJ2PI7yBiAZqLeG6+zVU=",
+        "lastModified": 1705957679,
+        "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/fastqc.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub
+{ stdenv, lib, fetchFromGitHub
 , jdk, ant, makeWrapper
 , jre, perl }:
 
@@ -25,7 +25,7 @@ stdenv.mkDerivation rec {
     makeWrapper $out/share/FastQC/fastqc $out/bin/fastqc --add-flags --java=${jre}/bin/java
   '';
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = https://www.bioinformatics.babraham.ac.uk/projects/fastqc/;
     description = "A quality control tool for high throughput sequence data";
     longDescription = ''

pkgs/firedrake/exodus.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, cmake, gfortran
+{ stdenv, lib, fetchurl, cmake, gfortran
 , netcdf, hdf5 }:
 
 stdenv.mkDerivation rec {
@@ -21,7 +21,7 @@ stdenv.mkDerivation rec {
   patches = ./exodus-include.patch;
   sourceRoot = "${name}/exodus";
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "http://gsjaardema.github.io/seacas";
     description = "A model developed to store and retrieve data for finite element analyses.";
     license = licenses.bsd3;

pkgs/firedrake/hypre.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, cmake
+{ stdenv, lib, fetchFromGitHub, cmake
 , openmpi }:
 
 stdenv.mkDerivation rec {
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
 
   makeFlags = [ "VERBOSE=1" ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "http://www.llnl.gov/casc/hypre";
     description = "Parallel solvers for sparse linear systems featuring multigrid methods.";
     license = licenses.gpl2;

pkgs/firedrake/metis.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromBitbucket, cmake }:
+{ stdenv, lib, fetchFromBitbucket, cmake }:
 
 stdenv.mkDerivation rec {
   version = "5.1.0-p4";
@@ -17,7 +17,7 @@ stdenv.mkDerivation rec {
 
   makeFlags = [ "VERBOSE=1" ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://bitbucket.org/petsc/metis";
     description = "A set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices.";
   };

pkgs/firedrake/parmetis.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromBitbucket, cmake
+{ stdenv, lib, fetchFromBitbucket, cmake
 , openmpi
 , metis }:
 
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
   cmakeFlags = [ "-DGKLIB_PATH=../headers" ];
   makeFlags = [ "VERBOSE=1" ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "http://glaros.dtc.umn.edu/gkhome/metis/parmetis";
     description = "An MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.";
   };

pkgs/firedrake/petsc.nix

@@ -1,4 +1,4 @@
-{ stdenv, callPackage, writeText, fetchFromGitHub, python, gfortran
+{ stdenv, lib, callPackage, writeText, fetchFromGitHub, python, gfortran
 , openmpi, blas, liblapack, hdf5, netcdf, eigen
 , sowing, metis, hypre, parmetis, exodus }:
 
@@ -45,7 +45,7 @@ stdenv.mkDerivation rec {
 
   setupHook = writeText "setupHook.sh" "export PETSC_DIR=@out@";
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://github.com/firedrakeproject/petsc";
     description = "A suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.";
     license = licenses.bsd2;

pkgs/firedrake/sowing.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromBitbucket, ghostscript }:
+{ stdenv, lib, fetchFromBitbucket, ghostscript }:
 
 stdenv.mkDerivation rec {
   version = "1.1.25-p1";
@@ -16,7 +16,7 @@ stdenv.mkDerivation rec {
     ghostscript
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://bitbucket.org/petsc/pkg-sowing";
     description = "Tools that are part of the petsc program development and maintenance environment.";
   };

pkgs/ghmm/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchsvn, autoreconfHook, pkg-config
+{ stdenv, lib, fetchsvn, autoreconfHook, pkg-config
 , libxml2, python2Packages, swig }:
 
 stdenv.mkDerivation rec {
@@ -45,7 +45,7 @@ stdenv.mkDerivation rec {
 
   hardeningDisable = [ "format" ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "The General Hidden Markov Model library (GHMM) is a freely available C library implementing efficient data structures and algorithms for basic and extended HMMs with discrete and continous emissions.";
     homepage = http://ghmm.sourceforge.net;
     platforms = platforms.all;

pkgs/gsort/default.nix

@@ -1,5 +1,5 @@
 # This file was generated by https://github.com/kamilchm/go2nix v1.3.0
-{ stdenv, buildGoPackage, fetchgit, fetchhg, fetchbzr, fetchsvn }:
+{ stdenv, lib, buildGoPackage, fetchgit, fetchhg, fetchbzr, fetchsvn }:
 
 buildGoPackage rec {
   name = "gsort-${version}";
@@ -15,7 +15,7 @@ buildGoPackage rec {
 
   goDeps = ./deps.nix;
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = https://github.com/brentp/gsort;
     description = "A tool to sort genomic files according to a genomefile.";
     platforms = platforms.all;

pkgs/idba.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl
+{ stdenv, lib, fetchurl
 , bash }:
 
 stdenv.mkDerivation rec {
@@ -25,7 +25,7 @@ stdenv.mkDerivation rec {
   #   stdenv
   # ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = https://github.com/loneknightpy/idba/;
     description = "Basic iterative de Bruijn graph assembler for second-generation sequencing reads";
     longDescription = "IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a generic purpose assembler and especially good for single-cell and metagenomic sequencing data. IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for RNA-Seq data.";

pkgs/lumpy.nix

@@ -1,8 +1,27 @@
-{ stdenv, fetchFromGitHub, which, autoconf, automake
+{ stdenv, lib, fetchFromGitHub, which, autoconf, automake
 , zlib, curl
-, python2, hexdump, sambamba, samblaster, samtools }:
-
-stdenv.mkDerivation rec {
+, python2, fetchPypi, hexdump, sambamba, samblaster, samtools }: let
+  python = python2.override {
+    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}";
 
@@ -39,14 +58,19 @@ stdenv.mkDerivation rec {
     automake
     zlib
     curl
-    (python2.withPackages (packages: with packages; [ numpy pysam ]))
+    (python.withPackages (packages: with packages;
+      [
+        numpy
+        pysam
+      ]
+    ))
     hexdump
     sambamba
     samblaster
     samtools
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "A probabilistic framework for structural variant discovery.";
     homepage = https://github.com/arq5x/lumpy-sv;
     platforms = platforms.all;

pkgs/meraculous.nix

@@ -1,4 +1,4 @@
-{ stdenv, overrideCC, gcc49, fetchurl, makeWrapper, gzip, cmake
+{ stdenv, lib, overrideCC, gcc49, fetchurl, makeWrapper, gzip, cmake
 , boost, perl, perlPackages, gnuplot }:
 
 # gcc 5.x c++11 requires istream to be explicitly cast to bool
@@ -30,7 +30,7 @@ stdenv.mkDerivation rec {
     gnuplot
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = http://jgi.doe.gov/data-and-tools/meraculous;
     description = "Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes.";
     platforms = platforms.all;

pkgs/mfix/mfixsolver.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, fetchFromGitHub
+{ stdenv, lib, fetchurl, fetchFromGitHub
 , cmake, gfortran, python38, pkg-config
 , openmpi, netcdf, boost }:
 
@@ -67,7 +67,7 @@ stdenv.mkDerivation rec {
     # netcdf
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = https://mfix.netl.doe.gov;
     description = "An open-source multiphase flow solver";
     platforms = platforms.all;

pkgs/openfoam.nix

@@ -1,4 +1,4 @@
-{ stdenv, bashInteractive, fetchFromGitHub, makeWrapper, flex, bison
+{ stdenv, lib, bashInteractive, fetchFromGitHub, makeWrapper, flex, bison
 , zlib, boost, openmpi, readline, gperftools, cgal, metis, scotch, mpfr }:
 
 
@@ -84,7 +84,7 @@ stdenv.mkDerivation rec {
     mpfr
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = http://www.openfoam.com;
     description = "Free open-source CFD software";
     platforms = platforms.linux;

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/openslide/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, autoreconfHook, pkg-config, fetchFromGitHub
+{ stdenv, lib, autoreconfHook, pkg-config, fetchFromGitHub
 , zlib, openjpeg, libtiff, cairo, libpng, gdk-pixbuf, libxml2, sqlite }:
 
 stdenv.mkDerivation rec {
@@ -30,7 +30,7 @@ stdenv.mkDerivation rec {
     sed -i -e 's|AM_CONDITIONAL(\[WINDOWS_RESOURCES\], \[test x$RC != x\])|AM_CONDITIONAL([WINDOWS_RESOURCES], [false])|' configure.ac
   '';
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = http://openslide.org;
     description = "A C library that provides a simple interface to read whole-slide images.";
     platforms = platforms.all;

pkgs/ovito.nix

@@ -1,30 +1,55 @@
-{ mkDerivation, lib, fetchFromGitLab, cmake
-, boost, netcdf, hdf5, fftwSinglePrec, muparser, openssl, ffmpeg, python38
-, qtbase, qtsvg, qttools, qscintilla }:
+{ stdenv
+, lib
+, 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
-    netcdf hdf5
-    fftwSinglePrec
-    muparser
-    openssl
-    ffmpeg
-    python38
-    qtbase qtsvg qttools qscintilla
+    ninja
+    wrapQtAppsHook
   ];
 
+  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;

pkgs/sambamba.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, ldc
+{ stdenv, lib, fetchFromGitHub, ldc
 , python3, glibc, which, zlib }:
 
 stdenv.mkDerivation rec {
@@ -27,7 +27,7 @@ stdenv.mkDerivation rec {
     zlib
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = https://github.com/lomereiter/sambamba/wiki;
     description = "Sambamba is a set of command-line tools for working with SAM/BAM file formats which are used for storing next generation sequencing (NGS) datasets.";
     platforms = platforms.all;

pkgs/samblaster.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub }:
+{ stdenv, lib, fetchFromGitHub }:
 
 stdenv.mkDerivation rec {
   version = "0.1.24";
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "A fast and flexible program for marking duplicates in read-id grouped paired-end SAM files.";
     homepage = https://github.com/GregoryFaust/samblaster;
     platforms = platforms.all;

pkgs/smoove/default.nix

@@ -1,5 +1,5 @@
 # This file was generated by https://github.com/kamilchm/go2nix v1.3.0
-{ stdenv, buildGoPackage, fetchgit, fetchhg, fetchbzr, fetchsvn, makeWrapper
+{ stdenv, lib, buildGoPackage, fetchgit, fetchhg, fetchbzr, fetchsvn, makeWrapper
 , gzip, gsort, htslib, lumpy, samtools, svtyper, mosdepth }:
 
 buildGoPackage rec {
@@ -31,7 +31,7 @@ buildGoPackage rec {
     makeWrapper
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = https://github.com/brentp/smoove;
     description = "Wrap existing software and adds some internal read-filtering to simplify calling and genotyping structural variants.";
     platforms = platforms.all;

pkgs/sumo.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, unzip
+{ stdenv, lib, fetchurl, unzip
 , lzma, bzip2, zlib, libjpeg, libtiff, openssl
 , mesa, xorg
 , fox, xercesc, proj, gdal, hdf5, curl }:
@@ -24,7 +24,7 @@ stdenv.mkDerivation rec {
     curl
   ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = http://software.dlr.de/p/sumo/home;
     description = "SUMO is an open source, highly portable, microscopic and continuous road traffic simulation package designed to handle large road networks";
     platforms = platforms.all;