Merge master into staging-next

15 files changed, 418 insertions, 10 deletions

diff --git a/pkgs/development/libraries/bobcat/default.nix b/pkgs/development/libraries/bobcat/default.nix
index 3047cf539ceb..4e328fe2b2a9 100644
--- a/pkgs/development/libraries/bobcat/default.nix
+++ b/pkgs/development/libraries/bobcat/default.nix
@@ -4,10 +4,10 @@
 
 stdenv.mkDerivation rec {
   pname = "bobcat";
-  version = "5.10.01";
+  version = "5.11.01";
 
   src = fetchFromGitLab {
-    sha256 = "sha256-QhjUIaPSDAvOt0ZCzQWASpG+GJaTviosGDrzrckhuhs=";
+    sha256 = "sha256-JLJKaJmztputIon9JkKzpm3Ch60iwm4Imh9p42crYzA=";
     domain = "gitlab.com";
     rev = version;
     repo = "bobcat";
diff --git a/pkgs/development/libraries/drumstick/default.nix b/pkgs/development/libraries/drumstick/default.nix
index 36a4c56bbaf7..6d7352e87742 100644
--- a/pkgs/development/libraries/drumstick/default.nix
+++ b/pkgs/development/libraries/drumstick/default.nix
@@ -5,11 +5,11 @@
 
 stdenv.mkDerivation rec {
   pname = "drumstick";
-  version = "2.6.1";
+  version = "2.7.0";
 
   src = fetchurl {
     url = "mirror://sourceforge/drumstick/${version}/${pname}-${version}.tar.bz2";
-    hash = "sha256-5O9yD3MexorJUm5tv6oghDb4J/b3SO10mDQR9dT2jlA=";
+    hash = "sha256-Yb5SrXJ5ZK0IJ8XbnxAGLlfqKGOrfv2VET9Ba8dKItU=";
   };
 
   patches = [
diff --git a/pkgs/development/libraries/freetds/default.nix b/pkgs/development/libraries/freetds/default.nix
index a473b708a279..29d7d178db2b 100644
--- a/pkgs/development/libraries/freetds/default.nix
+++ b/pkgs/development/libraries/freetds/default.nix
@@ -8,11 +8,11 @@ assert odbcSupport -> unixODBC != null;
 
 stdenv.mkDerivation rec {
   pname = "freetds";
-  version = "1.3.13";
+  version = "1.3.17";
 
   src = fetchurl {
     url    = "https://www.freetds.org/files/stable/${pname}-${version}.tar.bz2";
-    sha256 = "sha256-1M+QCUFR/c3aEo7RjLCmv2WzCL41K1NEmUO1JJxbSPI=";
+    sha256 = "sha256-+AzAGg71u+M+fLs3Au2SSqteJaxuzNk8lJ6H3+98WYQ=";
   };
 
   buildInputs = [
diff --git a/pkgs/development/libraries/json-fortran/default.nix b/pkgs/development/libraries/json-fortran/default.nix
new file mode 100644
index 000000000000..422248520fc4
--- /dev/null
+++ b/pkgs/development/libraries/json-fortran/default.nix
@@ -0,0 +1,37 @@
+{ stdenv, lib, fetchFromGitHub, gfortran, cmake }:
+
+stdenv.mkDerivation rec {
+  pname = "json-fortran";
+  version = "8.3.0";
+
+  src = fetchFromGitHub {
+    owner = "jacobwilliams";
+    repo = pname;
+    rev = version;
+    hash = "sha256-96W9bzWEZ3EN4wtnDT3G3pvLdcI4SIhGJWBVPU3rNZ4=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    gfortran
+  ];
+
+  cmakeFlags = [
+    "-DUSE_GNU_INSTALL_CONVENTION=ON"
+  ];
+
+  # Due to some misconfiguration in CMake the Fortran modules end up in $out/$out.
+  # Move them back to the desired location.
+  postInstall = ''
+    mv $out/$out/include $out/.
+    rm -r $out/nix
+  '';
+
+  meta = with lib; {
+    description = "Modern Fortran JSON API";
+    homepage = "https://github.com/jacobwilliams/json-fortran";
+    license = licenses.mit;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/pkgs/development/libraries/science/chemistry/dftd4/default.nix b/pkgs/development/libraries/science/chemistry/dftd4/default.nix
new file mode 100644
index 000000000000..a099a14a8e63
--- /dev/null
+++ b/pkgs/development/libraries/science/chemistry/dftd4/default.nix
@@ -0,0 +1,47 @@
+{ stdenv
+, lib
+, fetchFromGitHub
+, cmake
+, gfortran
+, blas
+, lapack
+, mctc-lib
+, mstore
+, multicharge
+}:
+
+assert !blas.isILP64 && !lapack.isILP64;
+
+stdenv.mkDerivation rec {
+  pname = "dftd4";
+  version = "3.5.0";
+
+  src = fetchFromGitHub {
+    owner = "dftd4";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-ZCoFbjTNQD7slq5sKwPRPkrHSHofsxU9C9h/bF5jmZI=";
+  };
+
+  nativeBuildInputs = [ cmake gfortran ];
+
+  buildInputs = [ blas lapack mctc-lib mstore multicharge ];
+
+  postInstall = ''
+    substituteInPlace $out/lib/pkgconfig/${pname}.pc \
+      --replace "''${prefix}" ""
+  '';
+
+  doCheck = true;
+  preCheck = ''
+    export OMP_NUM_THREADS=2
+  '';
+
+  meta = with lib; {
+    description = "Generally Applicable Atomic-Charge Dependent London Dispersion Correction";
+    license = with licenses; [ lgpl3Plus gpl3Plus ];
+    homepage = "https://github.com/grimme-lab/dftd4";
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/pkgs/development/libraries/science/chemistry/mctc-lib/default.nix b/pkgs/development/libraries/science/chemistry/mctc-lib/default.nix
new file mode 100644
index 000000000000..e9be83970fbf
--- /dev/null
+++ b/pkgs/development/libraries/science/chemistry/mctc-lib/default.nix
@@ -0,0 +1,39 @@
+{ stdenv
+, lib
+, fetchFromGitHub
+, gfortran
+, pkg-config
+, json-fortran
+, cmake
+}:
+
+stdenv.mkDerivation rec {
+  pname = "mctc-lib";
+  version = "0.3.1";
+
+  src = fetchFromGitHub {
+    owner = "grimme-lab";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-AXjg/ZsitdDf9fNoGVmVal1iZ4/sxjJb7A9W4yye/rg=";
+  };
+
+  nativeBuildInputs = [ gfortran pkg-config cmake ];
+
+  buildInputs = [ json-fortran ];
+
+  postInstall = ''
+    substituteInPlace $out/lib/pkgconfig/${pname}.pc \
+      --replace "''${prefix}" ""
+  '';
+
+  doCheck = true;
+
+  meta = with lib; {
+    description = "Modular computation tool chain library";
+    homepage = "https://github.com/grimme-lab/mctc-lib";
+    license = licenses.asl20;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/pkgs/development/libraries/science/chemistry/mstore/default.nix b/pkgs/development/libraries/science/chemistry/mstore/default.nix
new file mode 100644
index 000000000000..7fcdfbdf5492
--- /dev/null
+++ b/pkgs/development/libraries/science/chemistry/mstore/default.nix
@@ -0,0 +1,36 @@
+{ stdenv
+, lib
+, fetchFromGitHub
+, cmake
+, gfortran
+, mctc-lib
+}:
+
+stdenv.mkDerivation rec {
+  pname = "mstore";
+  version = "0.2.0";
+
+  src = fetchFromGitHub {
+    owner = "grimme-lab";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-dN2BulLS/ENRFVdJIrZRxgBV8S4d5+7BjTCGnhBbf4I=";
+  };
+
+  nativeBuildInputs = [ cmake gfortran ];
+
+  buildInputs = [ mctc-lib ];
+
+  postInstall = ''
+    substituteInPlace $out/lib/pkgconfig/${pname}.pc \
+      --replace "''${prefix}" ""
+  '';
+
+  meta = with lib; {
+    description = "Molecular structure store for testing";
+    license = licenses.asl20;
+    homepage = "https://github.com/grimme-lab/mstore";
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/pkgs/development/libraries/science/chemistry/multicharge/default.nix b/pkgs/development/libraries/science/chemistry/multicharge/default.nix
new file mode 100644
index 000000000000..5a5046cd2a54
--- /dev/null
+++ b/pkgs/development/libraries/science/chemistry/multicharge/default.nix
@@ -0,0 +1,46 @@
+{ stdenv
+, lib
+, fetchFromGitHub
+, cmake
+, gfortran
+, blas
+, lapack
+, mctc-lib
+, mstore
+}:
+
+assert !blas.isILP64 && !lapack.isILP64;
+
+stdenv.mkDerivation rec {
+  pname = "multicharge";
+  version = "0.2.0";
+
+  src = fetchFromGitHub {
+    owner = "grimme-lab";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-oUI5x5/Gd0EZBb1w+0jlJUF9X51FnkHFu8H7KctqXl0=";
+  };
+
+  nativeBuildInputs = [ cmake gfortran ];
+
+  buildInputs = [ blas lapack mctc-lib mstore ];
+
+  postInstall = ''
+    substituteInPlace $out/lib/pkgconfig/${pname}.pc \
+      --replace "''${prefix}" ""
+  '';
+
+  doCheck = true;
+  preCheck = ''
+    export OMP_NUM_THREADS=2
+  '';
+
+  meta = with lib; {
+    description = "Electronegativity equilibration model for atomic partial charges";
+    license = licenses.asl20;
+    homepage = "https://github.com/grimme-lab/multicharge";
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/pkgs/development/libraries/science/chemistry/simple-dftd3/default.nix b/pkgs/development/libraries/science/chemistry/simple-dftd3/default.nix
new file mode 100644
index 000000000000..a9bd2c8faa73
--- /dev/null
+++ b/pkgs/development/libraries/science/chemistry/simple-dftd3/default.nix
@@ -0,0 +1,46 @@
+{ stdenv
+, lib
+, fetchFromGitHub
+, gfortran
+, cmake
+, mctc-lib
+, mstore
+, toml-f
+, blas
+}:
+
+assert !blas.isILP64;
+
+stdenv.mkDerivation rec {
+  pname = "simple-dftd3";
+  version = "0.7.0";
+
+  src = fetchFromGitHub {
+    owner = "dftd3";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-5OvmMgjD8ujjKHkuw4NT8hEXKh5YPxuBl/Mu6g2/KIA=";
+  };
+
+  nativeBuildInputs = [ cmake gfortran ];
+
+  buildInputs = [ mctc-lib mstore toml-f blas ];
+
+  postInstall = ''
+    substituteInPlace $out/lib/pkgconfig/s-dftd3.pc \
+      --replace "''${prefix}" ""
+  '';
+
+  doCheck = true;
+  preCheck = ''
+    export OMP_NUM_THREADS=2
+  '';
+
+  meta = with lib; {
+    description = "Reimplementation of the DFT-D3 program";
+    license = with licenses; [lgpl3Only gpl3Only];
+    homepage = "https://github.com/dftd3/simple-dftd3";
+    platforms = [ "x86_64-linux" ];
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/pkgs/development/libraries/science/chemistry/tblite/default.nix b/pkgs/development/libraries/science/chemistry/tblite/default.nix
new file mode 100644
index 000000000000..0f05315b9d88
--- /dev/null
+++ b/pkgs/development/libraries/science/chemistry/tblite/default.nix
@@ -0,0 +1,59 @@
+{ stdenv
+, lib
+, fetchFromGitHub
+, cmake
+, gfortran
+, blas
+, lapack
+, mctc-lib
+, mstore
+, toml-f
+, multicharge
+, dftd4
+, simple-dftd3
+}:
+
+assert !blas.isILP64 && !lapack.isILP64;
+
+stdenv.mkDerivation rec {
+  pname = "tblite";
+  version = "0.3.0";
+
+  src = fetchFromGitHub {
+    owner = "tblite";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-R7CAFG/x55k5Ieslxeq+DWq1wPip4cI+Yvn1cBbeVNs=";
+  };
+
+  nativeBuildInputs = [ cmake gfortran ];
+
+  buildInputs = [
+    blas
+    lapack
+    mctc-lib
+    mstore
+    toml-f
+    multicharge
+    dftd4
+    simple-dftd3
+  ];
+
+  doCheck = true;
+  preCheck = ''
+    export OMP_NUM_THREADS=2
+  '';
+
+  postInstall = ''
+    substituteInPlace $out/lib/pkgconfig/${pname}.pc \
+      --replace "''${prefix}" ""
+  '';
+
+  meta = with lib; {
+    description = "Light-weight tight-binding framework";
+    license = with licenses; [ gpl3Plus lgpl3Plus ];
+    homepage = "https://github.com/tblite/tblite";
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/pkgs/development/libraries/science/chemistry/tblite/python.nix b/pkgs/development/libraries/science/chemistry/tblite/python.nix
new file mode 100644
index 000000000000..00301d957662
--- /dev/null
+++ b/pkgs/development/libraries/science/chemistry/tblite/python.nix
@@ -0,0 +1,28 @@
+{ buildPythonPackage
+, meson
+, ninja
+, pkg-config
+, tblite
+, cffi
+}:
+
+buildPythonPackage rec {
+  inherit (tblite) pname version src meta;
+
+  nativeBuildInputs = [ meson ninja pkg-config ];
+
+  buildInputs = [ tblite ];
+
+  propagatedBuildInputs = [ cffi ];
+
+  format = "other";
+
+  configurePhase = ''
+    runHook preConfigure
+
+    meson setup build python --prefix=$out
+    cd build
+
+    runHook postConfigure
+  '';
+}
diff --git a/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix b/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix
index 0d5409c6817d..f6baae932ba2 100644
--- a/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix
+++ b/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix
@@ -6,7 +6,7 @@
 
 stdenv.mkDerivation rec {
   pname = "suitesparse-graphblas";
-  version = "7.2.0";
+  version = "7.4.3";
 
   outputs = [ "out" "dev" ];
 
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
     owner = "DrTimothyAldenDavis";
     repo = "GraphBLAS";
     rev = "v${version}";
-    sha256 = "sha256-N3TBuKWQRisXE5DQ0c+N2cv0darQ8mz4g2oe7pKst9E=";
+    sha256 = "sha256-myUaSzBlt34L3UJDKB9VXetaPCc3SZCzpbsSn1j+MPw=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/development/libraries/test-drive/default.nix b/pkgs/development/libraries/test-drive/default.nix
new file mode 100644
index 000000000000..b858f39498c2
--- /dev/null
+++ b/pkgs/development/libraries/test-drive/default.nix
@@ -0,0 +1,32 @@
+{ stdenv, lib, fetchFromGitHub, gfortran, cmake }:
+
+stdenv.mkDerivation rec {
+  pname = "test-drive";
+  version = "0.4.0";
+
+  src = fetchFromGitHub {
+    owner = "fortran-lang";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-ObAnHFP1Hp0knf/jtGHynVF0CCqK47eqetePx4NLmlM=";
+  };
+
+  postPatch = ''
+    substituteInPlace config/template.pc \
+      --replace 'libdir=''${prefix}/@CMAKE_INSTALL_LIBDIR@' "libdir=@CMAKE_INSTALL_LIBDIR@" \
+      --replace 'includedir=''${prefix}/@CMAKE_INSTALL_INCLUDEDIR@' "includedir=@CMAKE_INSTALL_INCLUDEDIR@"
+  '';
+
+  nativeBuildInputs = [
+    gfortran
+    cmake
+  ];
+
+  meta = with lib; {
+    description = "Procedural Fortran testing framework";
+    homepage = "https://github.com/fortran-lang/test-drive";
+    license = with licenses; [ asl20 mit ] ;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/pkgs/development/libraries/toml-f/default.nix b/pkgs/development/libraries/toml-f/default.nix
new file mode 100644
index 000000000000..d28447c40046
--- /dev/null
+++ b/pkgs/development/libraries/toml-f/default.nix
@@ -0,0 +1,38 @@
+{ stdenv
+, lib
+, fetchFromGitHub
+, gfortran
+, cmake
+, test-drive
+}:
+
+stdenv.mkDerivation rec {
+  pname = "toml-f";
+  version = "0.3.1";
+
+  src = fetchFromGitHub {
+    owner = pname;
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-8FbnUkeJUP4fiuJCroAVDo6U2M7ZkFLpG2OYrapMYtU=";
+  };
+
+  nativeBuildInputs = [ gfortran cmake ];
+
+  buildInputs = [ test-drive ];
+
+  postInstall = ''
+    substituteInPlace $out/lib/pkgconfig/${pname}.pc \
+      --replace "''${prefix}/" ""
+  '';
+
+  doCheck = true;
+
+  meta = with lib; {
+    description = "TOML parser implementation for data serialization and deserialization in Fortran";
+    license = with licenses; [ asl20 mit ];
+    homepage = "https://github.com/toml-f/toml-f";
+    platforms = [ "x86_64-linux" ];
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
diff --git a/pkgs/development/libraries/xsimd/default.nix b/pkgs/development/libraries/xsimd/default.nix
index db8cc787dee4..ec2d166ef580 100644
--- a/pkgs/development/libraries/xsimd/default.nix
+++ b/pkgs/development/libraries/xsimd/default.nix
@@ -1,12 +1,12 @@
 { lib, stdenv, fetchFromGitHub, cmake, gtest }:
 stdenv.mkDerivation rec {
   pname = "xsimd";
-  version = "8.1.0";
+  version = "9.0.1";
   src = fetchFromGitHub {
     owner = "xtensor-stack";
     repo = "xsimd";
     rev = version;
-    sha256 = "sha256-Aqs6XJkGjAjGAp0PprabSM4m+32M/UXpSHppCHdzaZk=";
+    sha256 = "sha256-onALN6agtrHWigtFlCeefD9CiRZI4Y690XTzy2UDnrk=";
   };
 
   nativeBuildInputs = [ cmake ];