Merge branch 'master' into haskell-updates

6 files changed, 76 insertions, 74 deletions

diff --git a/pkgs/applications/science/chemistry/octopus/default.nix b/pkgs/applications/science/chemistry/octopus/default.nix
index 93fec7149604b..a3a385802aaaa 100644
--- a/pkgs/applications/science/chemistry/octopus/default.nix
+++ b/pkgs/applications/science/chemistry/octopus/default.nix
@@ -1,6 +1,9 @@
 { lib
 , stdenv
 , fetchFromGitLab
+, cmake
+, pkg-config
+, ninja
 , gfortran
 , which
 , perl
@@ -14,15 +17,12 @@
 , gsl
 , netcdf
 , arpack
-, autoreconfHook
+, spglib
+, metis
 , scalapack
 , mpi
 , enableMpi ? true
 , python3
-, enableFma ? stdenv.hostPlatform.fmaSupport
-, enableFma4 ? stdenv.hostPlatform.fma4Support
-, enableAvx ? stdenv.hostPlatform.avx2Support
-, enableAvx512 ? stdenv.hostPlatform.avx512Support
 }:
 
 assert (!blas.isILP64) && (!lapack.isILP64);
@@ -30,21 +30,23 @@ assert (blas.isILP64 == arpack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "octopus";
-  version = "13.0";
+  version = "14.0";
 
   src = fetchFromGitLab {
     owner = "octopus-code";
     repo = "octopus";
     rev = version;
-    sha256 = "sha256-CZ+Qmv6aBQ6w11mLvTP6QAJzaGs+vmmXuNGnSyAqVDU=";
+    sha256 = "sha256-wQ2I+10ZHLKamW3j6AUtq2KZVm6d29+JxYgwvBKz9DU=";
   };
 
   nativeBuildInputs = [
     which
     perl
     procps
-    autoreconfHook
+    cmake
     gfortran
+    pkg-config
+    ninja
   ];
 
   buildInputs = [
@@ -57,34 +59,20 @@ stdenv.mkDerivation rec {
     netcdf
     arpack
     libvdwxc
+    spglib
+    metis
     (python3.withPackages (ps: [ ps.pyyaml ]))
   ] ++ lib.optional enableMpi scalapack;
 
   propagatedBuildInputs = lib.optional enableMpi mpi;
   propagatedUserEnvPkgs = lib.optional enableMpi mpi;
 
-  configureFlags = with lib; [
-    "--with-yaml-prefix=${lib.getDev libyaml}"
-    "--with-blas=-lblas"
-    "--with-lapack=-llapack"
-    "--with-fftw-prefix=${lib.getDev fftw}"
-    "--with-gsl-prefix=${lib.getDev gsl}"
-    "--with-libxc-prefix=${lib.getDev libxc}"
-    "--with-libvdwxc"
-    "--enable-openmp"
-  ]
-  ++ optional enableFma "--enable-fma3"
-  ++ optional enableFma4 "--enable-fma4"
-  ++ optional enableAvx "--enable-avx"
-  ++ optional enableAvx512 "--enable-avx512"
-  ++ optionals enableMpi [
-    "--enable-mpi"
-    "--with-scalapack=-lscalapack"
-    "CC=mpicc"
-    "FC=mpif90"
+  cmakeFlags = [
+    (lib.cmakeBool "OCTOPUS_MPI" enableMpi)
+    (lib.cmakeBool "OCTOPUS_ScaLAPACK" enableMpi)
+    (lib.cmakeBool "OCTOPUS_OpenMP" true)
   ];
 
-
   nativeCheckInputs = lib.optional.enableMpi mpi;
   doCheck = false;
   checkTarget = "check-short";
diff --git a/pkgs/applications/science/machine-learning/labelimg/default.nix b/pkgs/applications/science/machine-learning/labelimg/default.nix
index 244eaa05d695d..21174305b9e3e 100644
--- a/pkgs/applications/science/machine-learning/labelimg/default.nix
+++ b/pkgs/applications/science/machine-learning/labelimg/default.nix
@@ -1,38 +1,51 @@
-{ lib, python3Packages, fetchFromGitHub, qt5 }:
-  python3Packages.buildPythonApplication rec {
-    pname = "labelImg";
-    version = "1.8.3";
-    src = fetchFromGitHub {
-      owner = "tzutalin";
-      repo = "labelImg";
-      rev = "v${version}";
-      sha256 = "07v106fzlmxrbag4xm06m4mx9m0gckb27vpwsn7sap1bbgc1pap5";
-    };
-    nativeBuildInputs = with python3Packages; [
-      pyqt5
-      qt5.wrapQtAppsHook
-    ];
-    propagatedBuildInputs = with python3Packages; [
-      pyqt5
-      lxml
-      sip4
-    ];
-    preBuild = ''
-      make qt5py3
-    '';
-    postInstall = ''
-      cp libs/resources.py $out/${python3Packages.python.sitePackages}/libs
-    '';
-    dontWrapQtApps = true;
-    preFixup = ''
-      makeWrapperArgs+=("''${qtWrapperArgs[@]}")
-    '';
-    meta = with lib; {
-      description = "A graphical image annotation tool and label object bounding boxes in images";
-      mainProgram = "labelImg";
-      homepage = "https://github.com/tzutalin/labelImg";
-      license = licenses.mit;
-      platforms = platforms.linux;
-      maintainers = [ maintainers.cmcdragonkai ];
-    };
-  }
+{
+  lib,
+  python3Packages,
+  fetchFromGitHub,
+  fetchpatch,
+  qt5,
+}:
+python3Packages.buildPythonApplication rec {
+  pname = "labelImg";
+  version = "1.8.6";
+  src = fetchFromGitHub {
+    owner = "tzutalin";
+    repo = "labelImg";
+    rev = "v${version}";
+    hash = "sha256-RJxCtiDOePajlrjy9cpKETSKsWlH/Dlu1iFMj2aO4XU=";
+  };
+  nativeBuildInputs = with python3Packages; [
+    pyqt5
+    qt5.wrapQtAppsHook
+  ];
+  patches = [
+    # fixes https://github.com/heartexlabs/labelImg/issues/838
+    # can be removed after next upstream version bump
+    (fetchpatch {
+      url = "https://github.com/heartexlabs/labelImg/commit/5c38b6bcddce895d646e944e3cddcb5b43bf8b8b.patch";
+      hash = "sha256-BmbnJS95RBfoNQT0E6JDJ/IZfBa+tv1C69+RVOSFdRA=";
+    })
+  ];
+  propagatedBuildInputs = with python3Packages; [
+    pyqt5
+    lxml
+  ];
+  preBuild = ''
+    make qt5py3
+  '';
+  postInstall = ''
+    cp libs/resources.py $out/${python3Packages.python.sitePackages}/libs
+  '';
+  dontWrapQtApps = true;
+  preFixup = ''
+    makeWrapperArgs+=("''${qtWrapperArgs[@]}")
+  '';
+  meta = with lib; {
+    description = "A graphical image annotation tool and label object bounding boxes in images";
+    mainProgram = "labelImg";
+    homepage = "https://github.com/tzutalin/labelImg";
+    license = licenses.mit;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.cmcdragonkai ];
+  };
+}
diff --git a/pkgs/applications/science/math/pspp/default.nix b/pkgs/applications/science/math/pspp/default.nix
index 032ae257c5641..420b495e736e6 100644
--- a/pkgs/applications/science/math/pspp/default.nix
+++ b/pkgs/applications/science/math/pspp/default.nix
@@ -6,11 +6,11 @@
 
 stdenv.mkDerivation rec {
   pname = "pspp";
-  version = "2.0.0";
+  version = "2.0.1";
 
   src = fetchurl {
     url = "mirror://gnu/pspp/${pname}-${version}.tar.gz";
-    sha256 = "sha256-qPbLiGr1sIOENXm81vsZHAVKzOKMxotY58XwmZai2N8=";
+    sha256 = "sha256-jtuw8J6M+AEMrZ4FWeAjDX/FquRyHHVsNQVU3zMCTAA=";
   };
 
   nativeBuildInputs = [ pkg-config texinfo python3 makeWrapper ];
diff --git a/pkgs/applications/science/math/rofi-calc/default.nix b/pkgs/applications/science/math/rofi-calc/default.nix
index 6b15073675f73..be126e5fa3974 100644
--- a/pkgs/applications/science/math/rofi-calc/default.nix
+++ b/pkgs/applications/science/math/rofi-calc/default.nix
@@ -12,13 +12,13 @@
 
 stdenv.mkDerivation rec {
   pname = "rofi-calc";
-  version = "2.2.0";
+  version = "2.2.1";
 
   src = fetchFromGitHub {
     owner = "svenstaro";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-SGDORHX+lk6PS5/sPAmKZLfZD99/A7XvDPDnuAygDAM=";
+    sha256 = "sha256-uXaI8dwTRtg8LnFxopgXr9x/vEl8ixzIGOsSQQkAkoQ=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix
index 628b40cd13008..1027590d0de84 100644
--- a/pkgs/applications/science/misc/snakemake/default.nix
+++ b/pkgs/applications/science/misc/snakemake/default.nix
@@ -6,14 +6,14 @@
 
 python3.pkgs.buildPythonApplication rec {
   pname = "snakemake";
-  version = "8.4.12";
+  version = "8.10.4";
   format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = pname;
     rev = "refs/tags/v${version}";
-    hash = "sha256-ehQIrTw1+klFW+Hu4WsWaCJ0YoN2hIqryqqaoNQb1us=";
+    hash = "sha256-SZf//Z1rLHyvW/f0U6kEBzV1NjDEDG1OcFl9/JR+i/g=";
     # https://github.com/python-versioneer/python-versioneer/issues/217
     postFetch = ''
       sed -i "$out"/snakemake/_version.py -e 's#git_refnames = ".*"#git_refnames = " (tag: v${version})"#'
@@ -48,6 +48,7 @@ python3.pkgs.buildPythonApplication rec {
     snakemake-interface-executor-plugins
     snakemake-interface-common
     snakemake-interface-storage-plugins
+    snakemake-interface-report-plugins
     stopit
     tabulate
     throttler
diff --git a/pkgs/applications/science/molecular-dynamics/lammps/default.nix b/pkgs/applications/science/molecular-dynamics/lammps/default.nix
index 4c2a80c2f1b73..b881d339300c4 100644
--- a/pkgs/applications/science/molecular-dynamics/lammps/default.nix
+++ b/pkgs/applications/science/molecular-dynamics/lammps/default.nix
@@ -7,7 +7,7 @@
 , blas
 , lapack
 , cmake
-, cudaPackages
+, autoAddDriverRunpath
 , pkg-config
 # Available list of packages can be found near here:
 #
@@ -63,7 +63,7 @@ stdenv.mkDerivation (finalAttrs: {
     pkg-config
     # Although not always needed, it is needed if cmakeFlags include
     # GPU_API=cuda, and it doesn't users that don't enable the GPU package.
-    cudaPackages.autoAddDriverRunpath
+    autoAddDriverRunpath
   ];
 
   passthru = {