cp2k: 2025.2 -> 2026.1, update tblite, multicharge, dftd4, jonquil (#532430)

pkgs/by-name/cp/cp2k/package.nix

@@ -26,7 +26,7 @@
   pkg-config,
   plumed,
   zlib,
-  hdf5-fortran,
+  hdf5-fortran-mpi,
   sirius,
   libvdwxc,
   spla,
@@ -131,13 +131,13 @@ let
 in
 stdenv.mkDerivation (finalAttrs: {
   pname = "cp2k";
-  version = "2025.2";
+  version = "2026.1-unstable-2026-06-16";
 
   src = fetchFromGitHub {
     owner = "cp2k";
     repo = "cp2k";
-    rev = "v${finalAttrs.version}";
-    hash = "sha256-vfl5rCoFeGtYuZ7LcsVsESjKxFbN5IYDvBSzOqsd64w=";
+    rev = "c28f603b5956aa638ef130b21b091da4e3a17639";
+    hash = "sha256-LIghR2gCYbJDux4bFfeKCi+a+VDVbjcZfcVpYwjPkEg=";
     fetchSubmodules = true;
   };
 
@@ -175,7 +175,7 @@ stdenv.mkDerivation (finalAttrs: {
     dbcsr
     plumed
     zlib
-    hdf5-fortran
+    hdf5-fortran-mpi
     spla
     spfft
     libvdwxc
@@ -207,9 +207,6 @@ stdenv.mkDerivation (finalAttrs: {
 
   postPatch = ''
     patchShebangs tools exts/dbcsr/tools/build_utils exts/dbcsr/.cp2k
-    substituteInPlace exts/build_dbcsr/Makefile \
-      --replace '/usr/bin/env python3' '${python3}/bin/python' \
-      --replace 'SHELL = /bin/sh' 'SHELL = bash'
   '';
 
   cmakeFlags = [

pkgs/by-name/df/dftd4/build-paths.patch

@@ -1,5 +1,5 @@
 diff --git a/CMakeLists.txt b/CMakeLists.txt
-index f222aab..262b505 100644
+index 3db5442..64fa14a 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
 @@ -89,7 +89,6 @@ target_include_directories(
@@ -20,29 +20,38 @@ index f222aab..262b505 100644
  if(WITH_API)
    enable_language("C")
 diff --git a/config/template.cmake b/config/template.cmake
-index 8b5141d..8f94d66 100644
+index 8b5141d..76654d1 100644
 --- a/config/template.cmake
 +++ b/config/template.cmake
-@@ -6,7 +6,6 @@ set("@PROJECT_NAME@_WITH_OpenMP" @WITH_OpenMP@)
+@@ -5,8 +5,7 @@ set("@PROJECT_NAME@_WITH_API_V2" @WITH_API_V2@)
+ set("@PROJECT_NAME@_WITH_OpenMP" @WITH_OpenMP@)
  set(
    "@PROJECT_NAME@_INCLUDE_DIRS"
-   "@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_INCLUDEDIR@"
+-  "@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_INCLUDEDIR@"
 -  "@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_INCLUDEDIR@/@module-dir@"
++  "@CMAKE_INSTALL_FULL_INCLUDEDIR@"
  )
  list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}")
  
 diff --git a/config/template.pc b/config/template.pc
-index 3d6efbb..fea69e4 100644
+index 3d6efbb..55b899f 100644
 --- a/config/template.pc
 +++ b/config/template.pc
-@@ -6,4 +6,4 @@ Name: @PROJECT_NAME@
+@@ -1,9 +1,9 @@
+ prefix=@CMAKE_INSTALL_PREFIX@
+-libdir=${prefix}/@CMAKE_INSTALL_LIBDIR@
+-includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@
++libdir=@CMAKE_INSTALL_FULL_LIBDIR@
++includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
+ 
+ Name: @PROJECT_NAME@
  Description: @PROJECT_DESCRIPTION@
  Version: @PROJECT_VERSION@
  Libs: -L${libdir} -l@PROJECT_NAME@
 -Cflags: -I${includedir} -I${includedir}/@module-dir@
 +Cflags: -I${includedir} -I${includedir}/
 diff --git a/meson.build b/meson.build
-index c9e9c58..ac8f0bd 100644
+index 7de7d61..81b8a7d 100644
 --- a/meson.build
 +++ b/meson.build
 @@ -83,7 +83,7 @@ if install

pkgs/by-name/df/dftd4/cmake.patch

@@ -1,13 +0,0 @@
-diff --git a/config/template.pc b/config/template.pc
-index 3d6efbb..e338a42 100644
---- a/config/template.pc
-+++ b/config/template.pc
-@@ -1,6 +1,6 @@
- prefix=@CMAKE_INSTALL_PREFIX@
--libdir=${prefix}/@CMAKE_INSTALL_LIBDIR@
--includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@
-+libdir=@CMAKE_INSTALL_FULL_LIBDIR@
-+includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
- 
- Name: @PROJECT_NAME@
- Description: @PROJECT_DESCRIPTION@

pkgs/by-name/df/dftd4/package.nix

@@ -26,21 +26,18 @@ assert (
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "dftd4";
-  version = "3.7.0";
+  version = "4.2.0";
 
   src = fetchFromGitHub {
     owner = "dftd4";
     repo = "dftd4";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-dixPCLH5dWkE2/7ghGEXJmX2/g1DN30dB4jX2d7fmio=";
+    hash = "sha256-uKjNOIza3/I0oREp88oFESoNqEdumo1AztIjcrVb1O8=";
   };
 
   patches = [
-    # Make sure fortran headers are installed directly in /include
-    ./fortran-module-dir.patch
-
-    # Fix wrong generation of package config include paths
-    ./cmake.patch
+    # Fix pkg-config, meson and cmake paths for include and lib dirs
+    ./build-paths.patch
   ];
 
   nativeBuildInputs = [

pkgs/by-name/jo/jonquil/package.nix

@@ -21,13 +21,13 @@ assert (
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "jonquil";
-  version = "0.3.0";
+  version = "0.3.1";
 
   src = fetchFromGitHub {
     owner = "toml-f";
     repo = "jonquil";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-2JCTHA0nyA7xE0IA+LNrEAulHU2eIbNRvFGQ7YSQMRE=";
+    hash = "sha256-xKL3EWZaHdMAuUK7pL2vjfRk8Fq2uNL65TrGUyFQ5cc=";
   };
 
   patches = [

pkgs/by-name/mc/mctc-lib/package.nix

@@ -50,7 +50,9 @@ stdenv.mkDerivation (finalAttrs: {
   ]
   ++ lib.optional (buildType == "cmake") cmake;
 
-  buildInputs = [
+  propagatedBuildInputs = [
+    # jonquil (and the toml-f it propagates) appears in mctc-lib.pc's Requires.private, so it must
+    # be propagated for pkg-config consumers (e.g. dftd4) to resolve mctc-lib
     jonquil
   ];
 

pkgs/by-name/mu/multicharge/package.nix

@@ -25,13 +25,13 @@ assert (
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "multicharge";
-  version = "0.3.1";
+  version = "0.5.0";
 
   src = fetchFromGitHub {
     owner = "grimme-lab";
     repo = "multicharge";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-8qwM3dpvFoL2WrMWNf14zYtRap0ijdfZ95XaTlkHhqQ=";
+    hash = "sha256-hswqC+fvC6tuxDpuUgowyqm72ubVikzpR4EzXtTM5cs=";
   };
 
   patches = [
@@ -69,6 +69,11 @@ stdenv.mkDerivation (finalAttrs: {
 
   postPatch = ''
     patchShebangs --build config/install-mod.py
+
+    # custom blas and lapack need to be explicitly found for transitive dependencies
+    # otherwise CMAKE builds can not proceed.
+    echo 'set(custom-blas_FOUND TRUE)' >> config/cmake/Findcustom-blas.cmake
+    echo 'set(custom-lapack_FOUND TRUE)' >> config/cmake/Findcustom-lapack.cmake
   '';
 
   preCheck = ''

pkgs/development/libraries/science/chemistry/tblite/default.nix

@@ -1,6 +1,6 @@
 {
-  stdenv,
   lib,
+  stdenv,
   fetchFromGitHub,
   gfortran,
   buildType ? "meson",
@@ -29,13 +29,13 @@ assert (
 
 stdenv.mkDerivation rec {
   pname = "tblite";
-  version = "0.5.0";
+  version = "0.6.0";
 
   src = fetchFromGitHub {
     owner = "tblite";
     repo = "tblite";
     rev = "v${version}";
-    hash = "sha256-hePy/slEeM2o1gtrAbq/nkEUILa6oQjkD2ddDstQ2Zc=";
+    hash = "sha256-z0g+bf6APqNLB9mDE49FelitQ9ptZXdFQuYeXIT0NIw=";
   };
 
   patches = [
@@ -45,10 +45,18 @@ stdenv.mkDerivation rec {
     ./pkgconfig.patch
   ];
 
-  # Python scripts in test subdirectories to run the tests
-  postPatch = ''
-    patchShebangs ./
-  '';
+  postPatch =
+    # Python scripts in test subdirectories to run the tests
+    ''
+      patchShebangs ./
+    ''
+
+    # libquadmath is only shipped by GCC on architectures that lack native
+    # quad-precision support (e.g. x86_64); on aarch64 it does not exist.
+    + lib.optionalString (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64) ''
+      substituteInPlace config/meson.build \
+        --replace-fail "lib_deps += cc.find_library('quadmath')" ""
+    '';
 
   nativeBuildInputs = [
     gfortran

pkgs/development/libraries/science/chemistry/tblite/python.nix

@@ -23,6 +23,7 @@ buildPythonPackage {
     pname
     version
     src
+    postPatch
     meta
     ;