Merge commit 'd8fe5e6c'

Conflicts:
	nixpkgs/pkgs/build-support/go/module.nix

12 files changed, 108 insertions, 119 deletions

diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/libxisf/default.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/libxisf/default.nix
index 19fb83ca78be..d19dd2788745 100644
--- a/nixpkgs/pkgs/development/libraries/science/astronomy/libxisf/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/astronomy/libxisf/default.nix
@@ -11,14 +11,14 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "libxisf";
-  version = "0.2.11";
+  version = "0.2.12";
 
   src = fetchFromGitea {
     domain = "gitea.nouspiro.space";
     owner = "nou";
     repo = "libXISF";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-wXIbU9/xUyECluL6k1oKS3NBpoC/qjQdW9e485qmlgo=";
+    hash = "sha256-QhshgKyf9s5U5JMa5TZelIo1tpJGlsOQePPG1kEfbq8=";
   };
 
   patches = [
diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/dftd4/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/dftd4/default.nix
index 087c6e7d01de..ea7aafd156ae 100644
--- a/nixpkgs/pkgs/development/libraries/science/chemistry/dftd4/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/chemistry/dftd4/default.nix
@@ -1,8 +1,11 @@
 { stdenv
 , lib
 , fetchFromGitHub
-, cmake
 , gfortran
+, meson
+, ninja
+, pkg-config
+, python3
 , blas
 , lapack
 , mctc-lib
@@ -23,23 +26,20 @@ stdenv.mkDerivation rec {
     hash = "sha256-VIV9953hx0MZupOARdH+P1h7JtZeJmTlqtO8si+lwdU=";
   };
 
-  nativeBuildInputs = [ cmake gfortran ];
+  nativeBuildInputs = [ gfortran meson ninja pkg-config python3 ];
 
   buildInputs = [ blas lapack mctc-lib mstore multicharge ];
 
   outputs = [ "out" "dev" ];
 
-  # Fix the Pkg-Config files for doubled store paths
+  doCheck = true;
+
   postPatch = ''
-    substituteInPlace config/template.pc \
-      --replace "\''${prefix}/" ""
+    patchShebangs --build \
+      config/install-mod.py \
+      app/tester.py
   '';
 
-  cmakeFlags = [
-    "-DBUILD_SHARED_LIBS=${if stdenv.hostPlatform.isStatic then "OFF" else "ON"}"
-  ];
-
-  doCheck = true;
   preCheck = ''
     export OMP_NUM_THREADS=2
   '';
diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/mctc-lib/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/mctc-lib/default.nix
index a8c27b3eec56..58c1fdaf04e2 100644
--- a/nixpkgs/pkgs/development/libraries/science/chemistry/mctc-lib/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/chemistry/mctc-lib/default.nix
@@ -2,9 +2,11 @@
 , lib
 , fetchFromGitHub
 , gfortran
+, meson
+, ninja
 , pkg-config
+, python3
 , json-fortran
-, cmake
 }:
 
 stdenv.mkDerivation rec {
@@ -18,24 +20,18 @@ stdenv.mkDerivation rec {
     hash = "sha256-AXjg/ZsitdDf9fNoGVmVal1iZ4/sxjJb7A9W4yye/rg=";
   };
 
-  nativeBuildInputs = [ gfortran pkg-config cmake ];
+  nativeBuildInputs = [ gfortran meson ninja pkg-config python3 ];
 
   buildInputs = [ json-fortran ];
 
   outputs = [ "out" "dev" ];
 
-  # Fix the Pkg-Config files for doubled store paths
+  doCheck = true;
+
   postPatch = ''
-    substituteInPlace config/template.pc \
-      --replace "\''${prefix}/" ""
+    patchShebangs --build config/install-mod.py
   '';
 
-  cmakeFlags = [
-    "-DBUILD_SHARED_LIBS=${if stdenv.hostPlatform.isStatic then "OFF" else "ON"}"
-  ];
-
-  doCheck = true;
-
   meta = with lib; {
     description = "Modular computation tool chain library";
     mainProgram = "mctc-convert";
diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/mstore/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/mstore/default.nix
index 948d11435461..e187a9a9833f 100644
--- a/nixpkgs/pkgs/development/libraries/science/chemistry/mstore/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/chemistry/mstore/default.nix
@@ -1,8 +1,11 @@
 { stdenv
 , lib
 , fetchFromGitHub
-, cmake
 , gfortran
+, meson
+, ninja
+, pkg-config
+, python3
 , mctc-lib
 }:
 
@@ -17,22 +20,16 @@ stdenv.mkDerivation rec {
     hash = "sha256-dN2BulLS/ENRFVdJIrZRxgBV8S4d5+7BjTCGnhBbf4I=";
   };
 
-  nativeBuildInputs = [ cmake gfortran ];
+  nativeBuildInputs = [ gfortran meson ninja pkg-config python3 ];
 
   buildInputs = [ mctc-lib ];
 
   outputs = [ "out" "dev" ];
 
-  # Fix the Pkg-Config files for doubled store paths
   postPatch = ''
-    substituteInPlace config/template.pc \
-      --replace "\''${prefix}/" ""
+    patchShebangs --build config/install-mod.py
   '';
 
-  cmakeFlags = [
-    "-DBUILD_SHARED_LIBS=${if stdenv.hostPlatform.isStatic then "OFF" else "ON"}"
-  ];
-
   meta = with lib; {
     description = "Molecular structure store for testing";
     license = licenses.asl20;
diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/multicharge/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/multicharge/default.nix
index 020390737139..3660705242f6 100644
--- a/nixpkgs/pkgs/development/libraries/science/chemistry/multicharge/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/chemistry/multicharge/default.nix
@@ -1,8 +1,12 @@
 { stdenv
 , lib
 , fetchFromGitHub
-, cmake
+, fetchpatch2
 , gfortran
+, meson
+, ninja
+, pkg-config
+, python3
 , blas
 , lapack
 , mctc-lib
@@ -22,23 +26,28 @@ stdenv.mkDerivation rec {
     hash = "sha256-oUI5x5/Gd0EZBb1w+0jlJUF9X51FnkHFu8H7KctqXl0=";
   };
 
-  nativeBuildInputs = [ cmake gfortran ];
+  patches = [
+    # Fix finding of MKL for Intel 2021 and newer
+    # Also fix finding mstore
+    # https://github.com/grimme-lab/multicharge/pull/20
+    (fetchpatch2 {
+      url = "https://github.com/grimme-lab/multicharge/commit/98a11ac524cd2a1bd9e2aeb8f4429adb2d76ee8.patch";
+      hash = "sha256-zZ2pcbyaHjN2ZxpMhlqUtIXImrVsLk/8WIcb9IYPgBw=";
+    })
+  ];
+
+  nativeBuildInputs = [ gfortran meson ninja pkg-config python3 ];
 
   buildInputs = [ blas lapack mctc-lib mstore ];
 
   outputs = [ "out" "dev" ];
 
-  # Fix the Pkg-Config files for doubled store paths
+  doCheck = true;
+
   postPatch = ''
-    substituteInPlace config/template.pc \
-      --replace "\''${prefix}/" ""
+    patchShebangs --build config/install-mod.py
   '';
 
-  cmakeFlags = [
-    "-DBUILD_SHARED_LIBS=${if stdenv.hostPlatform.isStatic then "OFF" else "ON"}"
-  ];
-
-  doCheck = true;
   preCheck = ''
     export OMP_NUM_THREADS=2
   '';
diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/simple-dftd3/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/simple-dftd3/default.nix
index d4f81e3a24cb..eb8fa56455e4 100644
--- a/nixpkgs/pkgs/development/libraries/science/chemistry/simple-dftd3/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/chemistry/simple-dftd3/default.nix
@@ -2,7 +2,9 @@
 , lib
 , fetchFromGitHub
 , gfortran
-, cmake
+, meson
+, ninja
+, pkg-config
 , mctc-lib
 , mstore
 , toml-f
@@ -22,21 +24,12 @@ stdenv.mkDerivation rec {
     hash = "sha256-dfXiKKCGJ69aExSKpVC3Bp//COy256R9PDyxCNmDsfo=";
   };
 
-  nativeBuildInputs = [ cmake gfortran ];
+  nativeBuildInputs = [ gfortran meson ninja pkg-config ];
 
   buildInputs = [ mctc-lib mstore toml-f blas ];
 
   outputs = [ "out" "dev" ];
 
-  # Fix the Pkg-Config files for doubled store paths
-  postPatch = ''
-    substituteInPlace config/template.pc \
-      --replace "\''${prefix}/" ""
-  '';
-  cmakeFlags = [
-    "-DBUILD_SHARED_LIBS=${if stdenv.hostPlatform.isStatic then "OFF" else "ON"}"
-  ];
-
   doCheck = true;
   preCheck = ''
     export OMP_NUM_THREADS=2
@@ -47,7 +40,7 @@ stdenv.mkDerivation rec {
     mainProgram = "s-dftd3";
     license = with licenses; [ lgpl3Only gpl3Only ];
     homepage = "https://github.com/dftd3/simple-dftd3";
-    platforms = [ "x86_64-linux" ];
+    platforms = platforms.linux;
     maintainers = [ maintainers.sheepforce ];
   };
 }
diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/default.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/default.nix
index 64374972c295..4f8c43a08e49 100644
--- a/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/default.nix
@@ -2,8 +2,10 @@
 , lib
 , fetchFromGitHub
 , fetchpatch
-, cmake
 , gfortran
+, meson
+, ninja
+, pkg-config
 , blas
 , lapack
 , mctc-lib
@@ -35,13 +37,12 @@ stdenv.mkDerivation rec {
     })
   ];
 
-  # Fix the Pkg-Config files for doubled store paths
-  postPatch = ''
-    substituteInPlace config/template.pc \
-      --replace "\''${prefix}/" ""
-  '';
-
-  nativeBuildInputs = [ cmake gfortran ];
+  nativeBuildInputs = [
+    gfortran
+    meson
+    ninja
+    pkg-config
+  ];
 
   buildInputs = [
     blas
@@ -56,10 +57,6 @@ stdenv.mkDerivation rec {
 
   outputs = [ "out" "dev" ];
 
-  cmakeFlags = [
-    "-DBUILD_SHARED_LIBS=${if stdenv.hostPlatform.isStatic then "OFF" else "ON"}"
-  ];
-
   doCheck = true;
   preCheck = ''
     export OMP_NUM_THREADS=2
diff --git a/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/python.nix b/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/python.nix
index 3a72cfaaa6a3..cfe8668204e2 100644
--- a/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/python.nix
+++ b/nixpkgs/pkgs/development/libraries/science/chemistry/tblite/python.nix
@@ -1,4 +1,6 @@
-{ buildPythonPackage
+{ lib
+, buildPythonPackage
+, pythonAtLeast
 , fetchpatch
 , meson
 , ninja
@@ -15,6 +17,7 @@
 , toml-f
 , multicharge
 , dftd4
+, setuptools
 }:
 
 buildPythonPackage {
@@ -27,6 +30,8 @@ buildPythonPackage {
     pkg-config
     gfortran
     mctc-lib
+  ] ++ lib.optionals (pythonAtLeast "3.12") [
+    setuptools
   ];
 
   buildInputs = [
diff --git a/nixpkgs/pkgs/development/libraries/science/math/flintqs/default.nix b/nixpkgs/pkgs/development/libraries/science/math/flintqs/default.nix
deleted file mode 100644
index c5426ed67fc7..000000000000
--- a/nixpkgs/pkgs/development/libraries/science/math/flintqs/default.nix
+++ /dev/null
@@ -1,40 +0,0 @@
-{ lib, stdenv
-, fetchFromGitHub
-, autoreconfHook
-, gmp
-}:
-
-stdenv.mkDerivation rec {
-  version = "1.0";
-  pname = "flintqs";
-
-  src = fetchFromGitHub {
-    owner = "sagemath";
-    repo = "FlintQS";
-    rev = "v${version}";
-    sha256 = "1f0lnayz6j6qgasx8pbq61d2fqam0wwhsmh6h15l4vq58l1vvbwj";
-  };
-
-  preAutoreconf = ''
-    touch ChangeLog
-  '';
-
-  buildInputs = [
-    gmp
-  ];
-
-  nativeBuildInputs = [
-    autoreconfHook
-  ];
-
-  doCheck = true;
-
-  meta = with lib; {
-    description = "Highly optimized multi-polynomial quadratic sieve for integer factorization";
-    homepage = "https://github.com/sagemath/FlintQS";
-    license = with licenses; [ gpl2 ];
-    maintainers = teams.sage.members;
-    mainProgram = "QuadraticSieve";
-    platforms = platforms.all;
-  };
-}
diff --git a/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix b/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix
index 214f27046527..ac513297f159 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix
@@ -21,6 +21,9 @@ stdenv.mkDerivation rec {
     m4ri
   ];
 
+  # does not compile correctly with -O2 on LLVM clang; see
+  # https://bitbucket.org/malb/m4rie/issues/23/trying-to-compile-on-apple-m1
+  makeFlags = [] ++ lib.optionals stdenv.isDarwin [ "CFLAGS=-O0" ];
   nativeBuildInputs = [
     autoreconfHook
   ];
@@ -35,7 +38,5 @@ stdenv.mkDerivation rec {
     license = licenses.gpl2Plus;
     maintainers = teams.sage.members;
     platforms = platforms.unix;
-    # never built on aarch64-darwin since first introduction in nixpkgs
-    broken = stdenv.isDarwin && stdenv.isAarch64;
   };
 }
diff --git a/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix b/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix
index 505457edd64f..8f3fbe345126 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix
@@ -2,6 +2,7 @@
 , fetchurl
 , fetchpatch
 , coreutils
+, dos2unix
 }:
 
 stdenv.mkDerivation rec {
@@ -24,24 +25,54 @@ stdenv.mkDerivation rec {
     "PREFIX=$(out)"
   ];
 
+  nativeBuildInputs = [ dos2unix ];
+
+  prePatch = ''
+    find ./dietz/ -type f -exec dos2unix {} \;
+  '';
+
   patches = [
     # Fix makefiles which use all the variables in all the wrong ways and
     # hardcode values for some variables.
     (fetchpatch {
-      url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/rubiks/patches/dietz-cu2-Makefile.patch";
-      sha256 = "1ry3w1mk9q4jqd91zlaa1bdiiplld4hpfjaldbhlmzlgrrc99qmq";
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/dietz-cu2-Makefile.patch";
+      sha256 = "bRU7MJ/6BgCp2PUqZOragJhm38Q3E8ShStXQIYwIjvw=";
+    })
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/dietz-mcube-Makefile.patch";
+      sha256 = "f53z4DogXKax1vUNkraOTt3TQ4bvT7CdQK/hOaaBS38=";
+    })
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/dietz-solver-Makefile.patch";
+      sha256 = "7gMC8y9elyIy2KvXYcp7YjPBNqn9PVhUle+/GrYAAdE=";
+    })
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/reid-Makefile.patch";
+      sha256 = "rp3SYtx02vVBtSlg1vJpdIoXNcdBNKDLCLqLAKwOYeQ=";
+    })
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/fedora-1-rubiks-includes.patch";
+      sha256 = "QYJ1KQ73HTEGY/beMVbcU215g/B8rHDjYD1YM2WZ7sk=";
+    })
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/fedora-2-rubiks-ansi-c.patch";
+      sha256 = "Rnu7uphE9URxnbg2K8mkymnB61magweH+WxVWR9JC4s=";
+    })
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/fedora-3-rubiks-prototypes.patch";
+      sha256 = "Wi038g+y7No1TNMiITtAdipjRi0+g6h0Sspslm5rZGU=";
     })
     (fetchpatch {
-      url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/rubiks/patches/dietz-mcube-Makefile.patch";
-      sha256 = "0zsbh6k3kqdg82fv0kzghr1x7pafisv943gmssqscp107bhg77bz";
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/fedora-4-rubiks-longtype.patch";
+      sha256 = "6pNuxFM69CZ/TQGZfHXLlCN5g5lf3RiYYZKzMvLJwkw=";
     })
     (fetchpatch {
-      url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/rubiks/patches/dietz-solver-Makefile.patch";
-      sha256 = "0vhw70ylnmydgjhwx8jjlb2slccj4pfqn6vzirkyz1wp8apsmfhp";
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/fedora-5-rubiks-signed.patch";
+      sha256 = "CCGXBMYvSjTm4YKQZAQMi6pWGjyHDYYQzdMZDSW2vFE=";
     })
     (fetchpatch {
-      url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/rubiks/patches/reid-Makefile.patch";
-      sha256 = "1r311sn012xs135s0d21qwsig2kld7rdcq19nm0zbnklviid57df";
+      url = "https://raw.githubusercontent.com/sagemath/sage/2a9a4267f93588cf33119cbacc032ed9acc433e5/build/pkgs/rubiks/patches/fedora-6-rubiks-attributes.patch";
+      sha256 = "RhlzMb33iaLfeBoF7Y0LIgEzOB/EC+AoWMSkRPCICaU=";
     })
   ];
 
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 ac08cb876253..84949e0a5344 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix
@@ -7,7 +7,7 @@
 
 stdenv.mkDerivation rec {
   pname = "suitesparse-graphblas";
-  version = "9.0.3";
+  version = "9.1.0";
 
   outputs = [ "out" "dev" ];
 
@@ -15,7 +15,7 @@ stdenv.mkDerivation rec {
     owner = "DrTimothyAldenDavis";
     repo = "GraphBLAS";
     rev = "v${version}";
-    hash = "sha256-qRRrxMshLLEltCzXFv/j6NgRi6x1SHlAuKG5NfLiBFs=";
+    hash = "sha256-YK0REOqoNa55tQt6NH/0QQ07pzAImDR5kC00sbFILH8=";
   };
 
   nativeBuildInputs = [