Nix-QChem · markuskowa · Dec 25, 2024 · Dec 25, 2024 · Dec 25, 2024 · Dec 25, 2024
diff --git a/flake.lock b/flake.lock
diff --git a/nixpkgs-opt.nix b/nixpkgs-opt.nix
@@ -40,7 +40,9 @@ let
     libint = recallPackage libint {};
     libmbd = recallPackage libmbd {};
     libvori = recallPackage libvori {};
+    libvdwxc = recallPackage libvdwxc {};
     libxc = recallPackage libxc {};
+    mpb = recallPackage mpb {};
     meep = python3.pkgs.toPythonApplication (recallPackage python3.pkgs.meep {});
     mkl = recallPackage mkl {};
     molden = recallPackage molden {};
@@ -63,6 +65,7 @@ let
     scalapack = recallPackage scalapack {};
     siesta = recallPackage siesta {};
     siesta-mpi = recallPackage siesta-mpi {};
+    sirius = recallPackage sirius {};
     spglib = recallPackage spglib {};
 
     fftwSinglePrec = self.fftw.override { precision = "single"; };

diff --git a/overlay.nix b/overlay.nix
@@ -99,7 +99,9 @@ let
         #
         ambertools = super.python311.pkgs.toPythonApplication self.python311.pkgs.ambertools;
 
-        autodock-vina = callPackage ./pkgs/apps/autodock-vina { };
+        autodock-vina = callPackage ./pkgs/apps/autodock-vina {
+          boost = final.boost182;
+        };
 
         autoint = super.python3.pkgs.toPythonApplication self.python3.pkgs.pyphspu;
 

diff --git a/pkgs/apps/autodock-vina/python.nix b/pkgs/apps/autodock-vina/python.nix
@@ -1,6 +1,4 @@
 { buildPythonPackage
-, lib
-, fetchFromGitHub
 , boost
 , swig
 , numpy
@@ -9,7 +7,7 @@
 , openbabel-bindings
 }:
 
-buildPythonPackage rec {
+buildPythonPackage {
   inherit (autodock-vina) pname version src meta;
 
   # Remove hardcoded include paths and fix version constraint formats
@@ -25,6 +23,8 @@ buildPythonPackage rec {
     export PATH=$PATH:${swig}/bin
   '';
 
+  env.NIX_CFLAGS_COMPILE = "-Wno-error=parentheses";
+
   nativeBuildInputs = [ sphinx ];
 
   buildInputs = [ swig ];

diff --git a/pkgs/apps/sharc/unwrapped.nix b/pkgs/apps/sharc/unwrapped.nix
@@ -1,14 +1,12 @@
 { stdenv
 , lib
 , fetchFromGitHub
-, makeWrapper
 , which
 , gfortran
 , blas
 , lapack
 , fftw
 , python3
-, gnuplot
 , wfoverlap
 , enablePysharc ? true
 , hdf5
@@ -18,7 +16,7 @@
 }:
 
 let
-  version = "3.0.1";
+  version = "3.0.2";
   python = python3.withPackages (p: with p; [
     numpy
     openbabel-bindings
@@ -33,11 +31,14 @@ in stdenv.mkDerivation {
     owner = "sharc-md";
     repo = "sharc";
     rev = "v${version}";
-    hash = "sha256-aTFrLrp2PTZXvMI4UkXw/hAv225rADwo9W+k09td52U=";
+    hash = "sha256-B4cnqp9YRG4GdkhXSzPJ1uYE55MIT0MwXxxAGuuMDGg=";
   };
 
   outputs = [ "out" "doc" "tests" ];
 
+  # Needed to build with gcc-14
+  env.NIX_CFLAGS_COMPILE = "-Wno-error=incompatible-pointer-types -Wno-error=int-conversion";
+
   passthru = { inherit python; };
 
   nativeBuildInputs = [ which gfortran ];

diff --git a/pkgs/apps/vmd/default.nix b/pkgs/apps/vmd/default.nix
@@ -20,6 +20,8 @@ let
 
     sourceRoot = "plugins";
 
+    env.NIX_CFLAGS_COMPILE = "-Wno-error=implicit-function-declaration";
+
     makeFlags = [ "LINUXAMD64" ];
 
     preBuild = ''
@@ -67,6 +69,8 @@ in stdenv.mkDerivation {
   sourceRoot = "vmd-${version}";
 
 
+  env.NIX_CFLAGS_COMPILE = "-Wno-error=implicit-function-declaration";
+
   # non-standard configure script
   configurePhase = ''
     patchShebangs ./configure

diff --git a/pkgs/by-name/gabedit/package.nix b/pkgs/by-name/gabedit/package.nix
@@ -43,7 +43,7 @@ stdenv.mkDerivation rec {
     OMPCFLAGS = -fopenmp
     DRAWGEOMGL = -DDRAWGEOMGL
 
-    COMMONCFLAGS = -Wformat -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -O2 -DENABLE_DEPRECATED $(OMPCFLAGS) $(DRAWGEOMGL) -Wformat-security -Wno-unused-variable
+    COMMONCFLAGS = -Wformat -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -O2 -DENABLE_DEPRECATED $(OMPCFLAGS) $(DRAWGEOMGL) -Wformat-security -Wno-unused-variable -Wno-error=implicit-function-declaration -Wno-error=int-conversion
     LDFLAGS = -Wl,-z,relro
     EOF
   '';

diff --git a/pkgs/by-name/gamess-us/package.nix b/pkgs/by-name/gamess-us/package.nix
@@ -1,5 +1,5 @@
-{ stdenv, lib, makeWrapper, fetchFromGitLab, requireFile, mpiCheckPhaseHook, gfortran, writeTextFile, cmake, perl
-, tcsh, mpi, openblas, hostname, openssh, gnused, libxc, ncurses
+{ stdenv, lib, makeWrapper, fetchFromGitLab, requireFile, mpiCheckPhaseHook, gfortran, cmake, perl
+, tcsh, mpi, openblas, hostname, openssh, gnused, ncurses
 , enableMpi ? true
 }:
 
@@ -10,7 +10,7 @@ in stdenv.mkDerivation rec {
 
   # The website always provides "gamess-current.tar.gz". However, we expect the file to be renamed,
   # to a more reasonable name.
-  src = requireFile rec {
+  src = requireFile {
     name = "${pname}-${version}.tar.gz";
     sha256 = "sha256-mQUe3sPLh2aCLh93t7Qc+fLULOYeZnE+S1El9zV83qk=";
     url = "https://www.msg.chem.iastate.edu/gamess/download.html";
@@ -73,6 +73,9 @@ in stdenv.mkDerivation rec {
       substituteInPlace lked --replace "libopenblas.a" "libopenblas.so"
     '';
 
+  # Needed to build with gcc-14
+  env.NIX_CFLAGS_COMPILE = "-Wno-error=int-conversion";
+
   # The interactive config script of gamess. Pretty standard build with MPI parallelism, but
   # without additional interfaces (such as libxc, qcengine, tinker, ...)
   configurePhase =

diff --git a/pkgs/by-name/libvdwxc/package.nix b/pkgs/by-name/libvdwxc/package.nix
diff --git a/pkgs/python-by-name/cclib/package.nix b/pkgs/python-by-name/cclib/package.nix
@@ -1,6 +1,7 @@
 { buildPythonPackage
 , lib
 , fetchFromGitHub
+, fetchpatch
 , isPy311
 , setuptools
 , pytestCheckHook
@@ -30,6 +31,12 @@ buildPythonPackage rec {
     hash = "sha256-XYFVSJ11MGx2dq/yYa5jaC2XsrStZCT5WzwSCelEV3U=";
   };
 
+  patches = [(fetchpatch {
+    name = "numpy-2";
+    url = "https://github.com/cclib/cclib/pull/1513/commits/bfca15ca759f2d8fbb34b4cce24b91c4cd48b20f.patch";
+    hash = "sha256-Pm3CGk6WEzh7Ov9JUrXHESxPanBFNGA49YpVrZBObYk=";
+  })];
+
   pyproject = true;
 
   postPatch = ''

diff --git a/pkgs/python-by-name/gator/package.nix b/pkgs/python-by-name/gator/package.nix
@@ -51,6 +51,7 @@ buildPythonPackage rec {
     homepage = "https://github.com/gator-program/gator";
     license = licenses.gpl3Only;
     maintainers = [ maintainers.markuskowa ];
+    broken = true; # Needs an update to the latest version
   };
 }
 
diff --git a/pkgs/python-by-name/mendeleev/package.nix b/pkgs/python-by-name/mendeleev/package.nix
@@ -4,6 +4,7 @@
 , pythonRelaxDepsHook
 , numpy
 , colorama
+, pydantic
 , pyfiglet
 , pygments
 , pandas
@@ -12,22 +13,28 @@
 , plotly
 , seaborn
 , poetry-core
+, deprecated
 }:
 
 buildPythonPackage rec {
   pname = "mendeleev";
-  version = "0.17.0";
+  version = "0.20.1";
 
   src = fetchFromGitHub {
     owner = "lmmentel";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-LYWMbQARuOJXhu4yMAuQqeHckDFVgjwD73bpx5GR15U=";
+    hash = "sha256-NA0pgfhgk1XBA1Ei8IUtYuw8rh53Dp4XBqZ+5btzhYU=";
   };
 
-  format = "pyproject";
+  pyproject = true;
 
-  propagatedBuildInputs = [
+  build-system = [
+    poetry-core
+  ];
+
+  dependencies = [
+    pydantic
     numpy
     colorama
     pyfiglet
@@ -37,7 +44,7 @@ buildPythonPackage rec {
     bokeh
     plotly
     seaborn
-    poetry-core
+    deprecated
   ];
 
   nativeBuildInputs = [

diff --git a/pkgs/python-by-name/pyastronomy/package.nix b/pkgs/python-by-name/pyastronomy/package.nix
@@ -18,13 +18,13 @@
 
 buildPythonPackage rec {
   pname = "PyAstronomy";
-  version = "0.19.0";
+  version = "0.22.0";
 
   src = with lib.versions; fetchFromGitHub {
     owner = "sczesla";
     repo = pname;
     rev = "v_${major version}-${minor version}-${patch version}";
-    hash = "sha256-HFlPTvnUtfCrXV2P8kTrqpo2Ph2PoixyoCDXi+kT8ic=";
+    hash = "sha256-eZorxlBHRE6NZH4elF0bRDNo8NY8DFij55uctv+YrK4=";
   };
 
   propagatedBuildInputs = [

diff --git a/pkgs/python-by-name/qmcpack/package.nix b/pkgs/python-by-name/qmcpack/package.nix
@@ -21,13 +21,13 @@
 
 buildPythonPackage rec {
   pname = "qmcpack";
-  version = "3.17.1";
+  version = "unstable-2025-01-16";
 
   src = fetchFromGitHub {
     owner = "QMCPACK";
     repo = "qmcpack";
-    rev = "v${version}";
-    sha256 = "sha256-D/wcKULhAsOkyGHN1AlVs3av0yeOvouPMHLcmNmOUo8=";
+    rev = "0373d2c6c20ef45412805cd973b522e5a988d832";
+    sha256 = "sha256-CyCGj8cY907RjkMZexnMyC8wEtuXcDYyJe/jeWrWDg8=";
   };
 
   format = "other";

diff --git a/pkgs/python-by-name/veloxchem/package.nix b/pkgs/python-by-name/veloxchem/package.nix
@@ -75,6 +75,7 @@ buildPythonPackage rec {
     homepage = "https://veloxchem.org";
     license = [ licenses.lgpl3 ];
     maintainers = [ maintainers.markuskowa ];
+    broken = true; # Needs an update to the latest version
   };
 }