Merge branch 'nixos-unstable-small' of https://github.com/NixOS/nixpkgs

Conflicts:
	nixpkgs/nixos/modules/services/mail/rss2email.nix
	nixpkgs/pkgs/build-support/go/module.nix

15 files changed, 104 insertions, 66 deletions

diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/default.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/default.nix
index 3fae85187deb..f0d25defe122 100644
--- a/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/default.nix
@@ -15,17 +15,18 @@
 , gsl
 , fftw
 , gtest
+, indi-full
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "indilib";
-  version = "2.0.5";
+  version = "2.0.6";
 
   src = fetchFromGitHub {
     owner = "indilib";
     repo = "indi";
-    rev = "v${version}";
-    hash = "sha256-n1zj1U26l30JYr5Tio5zwv8v/e2cjEeIRGsyncMtt9I=";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-3MeF2G/rr//c7cgGzqDzmqoNKvR+7Kkbid1g8znKPkg=";
   };
 
   nativeBuildInputs = [
@@ -48,7 +49,7 @@ stdenv.mkDerivation rec {
   cmakeFlags = [
     "-DCMAKE_INSTALL_LIBDIR=lib"
     "-DUDEVRULES_INSTALL_DIR=lib/udev/rules.d"
-  ] ++ lib.optional doCheck [
+  ] ++ lib.optional finalAttrs.finalPackage.doCheck [
     "-DINDI_BUILD_UNITTESTS=ON"
     "-DINDI_BUILD_INTEGTESTS=ON"
   ];
@@ -68,13 +69,19 @@ stdenv.mkDerivation rec {
     done
   '';
 
+  passthru.tests = {
+    # make sure 3rd party drivers compile with this indilib
+    indi-full = indi-full.override {
+      indilib = finalAttrs.finalPackage;
+    };
+  };
 
   meta = with lib; {
     homepage = "https://www.indilib.org/";
     description = "Implementation of the INDI protocol for POSIX operating systems";
-    changelog = "https://github.com/indilib/indi/releases/tag/v${version}";
+    changelog = "https://github.com/indilib/indi/releases/tag/v${finalAttrs.version}";
     license = licenses.lgpl2Plus;
     maintainers = with maintainers; [ hjones2199 sheepforce ];
     platforms = platforms.unix;
   };
-}
+})
diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-full.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-full.nix
index e2018ce7c2b0..4dd80c3f0275 100644
--- a/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-full.nix
+++ b/nixpkgs/pkgs/development/libraries/science/astronomy/indilib/indi-full.nix
@@ -6,7 +6,7 @@ let
     owner = "indilib";
     repo = "indi-3rdparty";
     rev = "v${version}";
-    hash = "sha256-EtwN3yuMsT9CV+CapkKDy3e92u9Blvy+ySrQU586Z1s=";
+    hash = "sha256-KNoyYldZWsXB9ubu0EYDgckRtpQgSCmzKlx7Erx4MRQ=";
   };
   indi-firmware = callPackage ./indi-firmware.nix {
     inherit version;
diff --git a/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix
deleted file mode 100644
index 7a6122fbc8db..000000000000
--- a/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix
+++ /dev/null
@@ -1,32 +0,0 @@
-{ lib, stdenv, fetchFromGitHub, cmake, libminc }:
-
-stdenv.mkDerivation rec {
-  pname = "EBTKS";
-  version  = "unstable-2017-09-23";
-
-  src = fetchFromGitHub {
-    owner  = "BIC-MNI";
-    repo   = pname;
-    rev    = "67e4e197d8a32d6462c9bdc7af44d64ebde4fb5c";
-    sha256 = "1a1qw6i47fs1izx60l1ysabpmyx9j5sjnbdv8b47wi2xcc9i3hpq";
-  };
-
-  # error: use of undeclared identifier 'finite'; did you mean 'isfinite'?
-  postPatch = ''
-    substituteInPlace templates/EBTKS/SimpleArray.h \
-      --replace "#define FINITE(x) finite(x)" "#define FINITE(x) isfinite(x)"
-  '';
-
-  nativeBuildInputs = [ cmake ];
-  buildInputs = [ libminc ];
-
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ];
-
-  meta = with lib; {
-    homepage = "https://github.com/BIC-MNI/${pname}";
-    description = "Library for working with MINC files";
-    maintainers = with maintainers; [ bcdarwin ];
-    platforms = platforms.unix;
-    license   = licenses.free;
-  };
-}
diff --git a/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix
index d89b6dbbe679..8b1aa7d01e81 100644
--- a/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "htslib";
-  version = "1.19";
+  version = "1.19.1";
 
   src = fetchurl {
     url = "https://github.com/samtools/htslib/releases/download/${version}/${pname}-${version}.tar.bz2";
-    sha256 = "sha256-h1HEDE+n0fI6aGTFsgpzdE+L5oI5U1rncpxffTlNBzY=";
+    sha256 = "sha256-Ii1001dPtnsVjGmIyYDuqrqKBlb15P+3a1+lfwNZM+w=";
   };
 
   # perl is only used during the check phase.
diff --git a/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix
index b6adf67cbe82..9af6793ef997 100644
--- a/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix
@@ -47,6 +47,8 @@ stdenv.mkDerivation rec {
     install -Dm644 -t "$out/share/bash-completion/completions/mirtk" share/completion/bash/mirtk
   '';
 
+  env.NIX_CFLAGS_COMPILE = "-Wno-changes-meaning";
+
   nativeBuildInputs = [ cmake ];
   buildInputs = [
     boost
diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/simple-dftd3/python.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/simple-dftd3/python.nix
new file mode 100644
index 000000000000..74f24e10f55f
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/chemistry/simple-dftd3/python.nix
@@ -0,0 +1,42 @@
+{ buildPythonPackage
+, pkg-config
+, meson
+, simple-dftd3
+, cffi
+, numpy
+, toml
+, qcengine
+, pyscf
+, ase
+, pytestCheckHook
+}:
+
+buildPythonPackage {
+  inherit (simple-dftd3) pname version src meta;
+
+  # pytest is also required for installation, not only testing
+  nativeBuildInputs = [ pytestCheckHook ];
+
+  buildInputs = [ simple-dftd3 ];
+
+  propagatedBuildInputs = [
+    cffi
+    numpy
+    toml
+  ];
+
+  checkInputs = [
+    ase
+    qcengine
+    pyscf
+  ];
+
+  preConfigure = ''
+    cd python
+  '';
+
+  # The compiled CFFI is not placed correctly before pytest invocation
+  preCheck = ''
+    find . -name "_libdftd3*" -exec cp {} ./dftd3/. \;
+  '';
+}
diff --git a/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix b/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix
index cea4d5b4c6fa..a76c2f878ba7 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix
@@ -12,13 +12,13 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "ipopt";
-  version = "3.14.13";
+  version = "3.14.14";
 
   src = fetchFromGitHub {
     owner = "coin-or";
     repo = "Ipopt";
     rev = "releases/${version}";
-    sha256 = "sha256-51isH1hlzgbD0JVtGp3NuaGY5l2CeS1S7oVeRYG+vWI=";
+    sha256 = "sha256-qMPdJVLIXFePhTA6qRr1Pth/BjJ62cj9y8C1HKQJGDQ=";
   };
 
   CXXDEFS = [ "-DHAVE_RAND" "-DHAVE_CSTRING" "-DHAVE_CSTDIO" ];
diff --git a/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix b/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix
index 3bf16057f835..595ba2aa5713 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix
@@ -11,13 +11,13 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "liblapack";
-  version = "3.11";
+  version = "3.12.0";
 
   src = fetchFromGitHub {
     owner = "Reference-LAPACK";
     repo = "lapack";
     rev = "v${finalAttrs.version}";
-    sha256 = "sha256-AYD78u70y8cY19hmM/aDjQEzxO8u9lPWhCFxRe5cqXI=";
+    sha256 = "sha256-xn9HL4YF8JPka1gwet5bGGo2k505H3RfWpxkUIYNecQ=";
   };
 
   nativeBuildInputs = [ gfortran cmake ];
diff --git a/nixpkgs/pkgs/development/libraries/science/math/magma/generic.nix b/nixpkgs/pkgs/development/libraries/science/math/magma/generic.nix
index b27b42bf3ae8..7ef60e0418ed 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/magma/generic.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/magma/generic.nix
@@ -142,6 +142,8 @@ stdenv.mkDerivation {
   ] ++ lists.optionals rocmSupport [
     "-DCMAKE_C_COMPILER=${rocmPackages.clr}/bin/hipcc"
     "-DCMAKE_CXX_COMPILER=${rocmPackages.clr}/bin/hipcc"
+  ] ++ lists.optionals (cudaPackages.cudaAtLeast "12.0.0") [
+    (lib.cmakeBool "USE_FORTRAN" false)
   ];
 
   buildFlags = [
diff --git a/nixpkgs/pkgs/development/libraries/science/math/mongoose/default.nix b/nixpkgs/pkgs/development/libraries/science/math/mongoose/default.nix
index df645809a445..29b901277f61 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/mongoose/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/mongoose/default.nix
@@ -7,11 +7,11 @@
 }:
 
 let
-  suitesparseVersion = "7.5.1";
+  suitesparseVersion = "7.6.0";
 in
 stdenv.mkDerivation {
   pname = "mongoose";
-  version = "3.3.1";
+  version = "3.3.2";
 
   outputs = [ "bin" "out" "dev" ];
 
@@ -19,7 +19,7 @@ stdenv.mkDerivation {
     owner = "DrTimothyAldenDavis";
     repo = "SuiteSparse";
     rev = "v${suitesparseVersion}";
-    hash = "sha256-6eC26rag9kZ1E4qJ5KY/dLXGld+EHP2OUpyikjXQhQk=";
+    hash = "sha256-zZXbUNXxVi4mpI4j4GjyVYraoPFWcuep9q5jl1XdqEo=";
   };
 
   nativeBuildInputs = [
diff --git a/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix b/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix
index c5b9f9019e06..7ecd6a88d13c 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix
@@ -6,14 +6,14 @@
 # Multi-threaded applications must not call a threaded OpenBLAS
 # (the only exception is when an application uses OpenMP as its
 # *only* form of multi-threading). See
-#     https://github.com/xianyi/OpenBLAS/wiki/Faq/4bded95e8dc8aadc70ce65267d1093ca7bdefc4c#multi-threaded
-#     https://github.com/xianyi/OpenBLAS/issues/2543
+#     https://github.com/OpenMathLib/OpenBLAS/wiki/Faq/4bded95e8dc8aadc70ce65267d1093ca7bdefc4c#multi-threaded
+#     https://github.com/OpenMathLib/OpenBLAS/issues/2543
 # This flag builds a single-threaded OpenBLAS using the flags
 # stated in thre.
 , singleThreaded ? false
 , buildPackages
 # Select a specific optimization target (other than the default)
-# See https://github.com/xianyi/OpenBLAS/blob/develop/TargetList.txt
+# See https://github.com/OpenMathLib/OpenBLAS/blob/develop/TargetList.txt
 , target ? null
 # Select whether DYNAMIC_ARCH is enabled or not.
 , dynamicArch ? null
@@ -30,6 +30,7 @@
 , octave
 , opencv
 , python3
+, openmp ? null
 }:
 
 let blas64_ = blas64; in
@@ -141,15 +142,15 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "openblas";
-  version = "0.3.25";
+  version = "0.3.26";
 
   outputs = [ "out" "dev" ];
 
   src = fetchFromGitHub {
-    owner = "xianyi";
+    owner = "OpenMathLib";
     repo = "OpenBLAS";
     rev = "v${version}";
-    hash = "sha256-eY/R7gLDOls3csuwZkUS+x+v3GeL3dCsOD+4STxDpCg=";
+    hash = "sha256-AA3+x3SXkcg3g7bROZYLpWAbxnRedmQBZPe+rBJKxJ8=";
   };
 
   postPatch = ''
@@ -179,6 +180,8 @@ stdenv.mkDerivation rec {
     which
   ];
 
+  buildInputs = lib.optional (stdenv.cc.isClang && config.USE_OPENMP) openmp;
+
   depsBuildBuild = [
     buildPackages.gfortran
     buildPackages.stdenv.cc
@@ -206,10 +209,12 @@ stdenv.mkDerivation rec {
         else stdenv.hostPlatform != stdenv.buildPlatform;
     # This disables automatic build job count detection (which honours neither enableParallelBuilding nor NIX_BUILD_CORES)
     # and uses the main make invocation's job count, falling back to 1 if no parallelism is used.
-    # https://github.com/xianyi/OpenBLAS/blob/v0.3.20/getarch.c#L1781-L1792
+    # https://github.com/OpenMathLib/OpenBLAS/blob/v0.3.20/getarch.c#L1781-L1792
     MAKE_NB_JOBS = 0;
-  } // (lib.optionalAttrs singleThreaded {
-    # As described on https://github.com/xianyi/OpenBLAS/wiki/Faq/4bded95e8dc8aadc70ce65267d1093ca7bdefc4c#multi-threaded
+  } // (lib.optionalAttrs stdenv.cc.isClang {
+    LDFLAGS = "-L${lib.getLib buildPackages.gfortran.cc}/lib"; # contains `libgfortran.so`; building with clang needs this, gcc has it implicit
+  }) // (lib.optionalAttrs singleThreaded {
+    # As described on https://github.com/OpenMathLib/OpenBLAS/wiki/Faq/4bded95e8dc8aadc70ce65267d1093ca7bdefc4c#multi-threaded
     USE_THREAD = false;
     USE_LOCKING = true; # available with openblas >= 0.3.7
     USE_OPENMP = false; # openblas will refuse building with both USE_OPENMP=1 and USE_THREAD=0
@@ -220,7 +225,7 @@ stdenv.mkDerivation rec {
 
   postInstall = ''
     # Write pkgconfig aliases. Upstream report:
-    # https://github.com/xianyi/OpenBLAS/issues/1740
+    # https://github.com/OpenMathLib/OpenBLAS/issues/1740
     for alias in blas cblas lapack; do
       cat <<EOF > $out/lib/pkgconfig/$alias.pc
 Name: $alias
@@ -257,7 +262,7 @@ EOF
   meta = with lib; {
     description = "Basic Linear Algebra Subprograms";
     license = licenses.bsd3;
-    homepage = "https://github.com/xianyi/OpenBLAS";
+    homepage = "https://github.com/OpenMathLib/OpenBLAS";
     platforms = attrNames configs;
     maintainers = with maintainers; [ ttuegel ];
   };
diff --git a/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix b/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix
index 8a00d9ae521e..648e05376529 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix
@@ -1,4 +1,5 @@
-{ lib, stdenv
+{ lib
+, stdenv
 , fetchFromGitHub
 , cmake
 , gnum4
@@ -6,7 +7,7 @@
 
 stdenv.mkDerivation rec {
   pname = "suitesparse-graphblas";
-  version = "7.4.4";
+  version = "9.0.1";
 
   outputs = [ "out" "dev" ];
 
@@ -14,7 +15,7 @@ stdenv.mkDerivation rec {
     owner = "DrTimothyAldenDavis";
     repo = "GraphBLAS";
     rev = "v${version}";
-    sha256 = "sha256-4NLYNapIiEXntXHrsyq63jIbuBJxR77X3VbLFbvtT9A=";
+    hash = "sha256-eNd6jlpW3KiRvOCKvNP5ttpgjPPXt2M2vLhk1Zn4gTE=";
   };
 
   nativeBuildInputs = [
@@ -22,11 +23,15 @@ stdenv.mkDerivation rec {
     gnum4
   ];
 
+  preConfigure = ''
+    export HOME=$(mktemp -d)
+  '';
+
   meta = with lib; {
     description = "Graph algorithms in the language of linear algebra";
-    homepage = "http://faculty.cse.tamu.edu/davis/GraphBLAS.html";
+    homepage = "https://people.engr.tamu.edu/davis/GraphBLAS.html";
     license = licenses.asl20;
-    maintainers = with maintainers; [];
+    maintainers = with maintainers; [ wegank ];
     platforms = with platforms; unix;
   };
 }
diff --git a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix
index 45ea5900e286..9561cf2ed779 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix
@@ -9,6 +9,7 @@
 , config
 , enableCuda ? config.cudaSupport
 , cudaPackages
+, openmp ? null
 }:
 
 stdenv.mkDerivation rec {
@@ -38,6 +39,8 @@ stdenv.mkDerivation rec {
     gfortran.cc.lib
     gmp
     mpfr
+  ] ++ lib.optionals stdenv.cc.isClang [
+    openmp
   ] ++ lib.optionals enableCuda [
     cudaPackages.cuda_cudart.dev
     cudaPackages.cuda_cudart.lib
diff --git a/nixpkgs/pkgs/development/libraries/science/math/tensorflow-lite/default.nix b/nixpkgs/pkgs/development/libraries/science/math/tensorflow-lite/default.nix
index 1ac08ce0cd2f..1bee7f46d37c 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/tensorflow-lite/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/tensorflow-lite/default.nix
@@ -84,6 +84,10 @@ buildBazelPackage rec {
 
   postPatch = ''
     rm .bazelversion
+
+    # Fix gcc-13 build failure by including missing include headers
+    sed -e '1i #include <cstdint>' -i \
+      tensorflow/lite/kernels/internal/spectrogram.cc
   '';
 
   preConfigure = ''
diff --git a/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix b/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix
index dd28553d60e9..fa6e5e48f846 100644
--- a/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix
@@ -120,7 +120,7 @@ stdenv.mkDerivation rec {
     "-DPython3_EXECUTABLE=${pythonEnv}/bin/python"
     "-DNS3_PYTHON_BINDINGS=ON"
     "-DNS3_DES_METRICS=ON"
-    "-DNS3_BINDINGS_INSTALL_DIR=lib/${pythonEnv.libPrefix}/site-packages"
+    "-DNS3_BINDINGS_INSTALL_DIR=${pythonEnv.sitePackages}"
     "-DNS3_LOG=ON"
     "-DNS3_ASSERT=ON"
     "-DNS3_GTK3=ON"