Merge pull request #335598 from doronbehar/pkg/lammps

python31{2,1}Packages.lammps: init at 2Aug2023_update3

pkgs/applications/science/molecular-dynamics/lammps/default.nix

@@ -75,8 +75,9 @@ stdenv.mkDerivation (finalAttrs: {
     inherit extraBuildInputs;
   };
   cmakeFlags = [
+    (lib.cmakeBool "BUILD_SHARED_LIBS" true)
   ]
-  ++ (builtins.map (p: "-DPKG_${p}=ON") (builtins.attrNames (lib.filterAttrs (n: v: v) packages)))
+  ++ (lib.mapAttrsToList (n: v: lib.cmakeBool "PKG_${n}" v) packages)
   ++ (lib.mapAttrsToList (n: v: "-D${n}=${v}") extraCmakeFlags)
   ;
 
@@ -99,7 +100,7 @@ stdenv.mkDerivation (finalAttrs: {
     ln -s $out/share/vim-plugins/lammps $out/share/nvim/site
   '';
 
-  meta = with lib; {
+  meta = {
     description = "Classical Molecular Dynamics simulation code";
     longDescription = ''
       LAMMPS is a classical molecular dynamics simulation code designed to
@@ -109,13 +110,16 @@ stdenv.mkDerivation (finalAttrs: {
       under the terms of the GNU Public License (GPL).
       '';
     homepage = "https://www.lammps.org";
-    license = licenses.gpl2Only;
-    platforms = platforms.linux;
+    license = lib.licenses.gpl2Only;
+    platforms = lib.platforms.linux;
     # compiling lammps with 64 bit support blas and lapack might cause runtime
     # segfaults. In anycase both blas and lapack should have the same #bits
     # support.
     broken = (blas.isILP64 && lapack.isILP64);
-    maintainers = [ maintainers.costrouc maintainers.doronbehar ];
+    maintainers = with lib.maintainers; [
+      costrouc
+      doronbehar
+    ];
     mainProgram = "lmp";
   };
 })

pkgs/development/python-modules/lammps/default.nix

@@ -0,0 +1,46 @@
+{
+  lib,
+  lammps,
+  stdenv,
+  buildPythonPackage,
+}:
+
+let
+  LAMMPS_SHARED_LIB = "${lib.getLib lammps}/lib/liblammps${stdenv.hostPlatform.extensions.library}";
+in
+buildPythonPackage {
+  inherit (lammps) pname version src;
+
+  env = {
+    inherit LAMMPS_SHARED_LIB;
+  };
+  preConfigure = ''
+    cd python
+    # Upstream assumes that the shared library is located in the same directory
+    # as the core.py file. We want to separate the shared library (built by
+    # cmake) and the Python library, so we perform this substitution:
+    substituteInPlace lammps/core.py \
+      --replace-fail \
+        "from inspect import getsourcefile" \
+        "getsourcefile = lambda f: \"${LAMMPS_SHARED_LIB}\""
+  '';
+
+  pythonImportsCheck = [
+    "lammps"
+    "lammps.pylammps"
+  ];
+
+  # We could potentially run other examples, but some of them are so old that
+  # they don't run with nowadays' LAMMPS. This one is simple enough and recent
+  # enough and it works.
+  checkPhase = ''
+    python examples/mc.py examples/in.mc
+  '';
+
+  meta = {
+    description = "Python Bindings for LAMMPS";
+    homepage = "https://docs.lammps.org/Python_head.html";
+    inherit (lammps.meta) license;
+    maintainers = with lib.maintainers; [ doronbehar ];
+  };
+}

pkgs/top-level/python-packages.nix

@@ -6744,6 +6744,10 @@ self: super: with self; {
 
   lakeside = callPackage ../development/python-modules/lakeside { };
 
+  lammps = callPackage ../development/python-modules/lammps {
+    inherit (pkgs) lammps;
+  };
+
   lancedb = callPackage ../development/python-modules/lancedb { };
 
   langchain = callPackage ../development/python-modules/langchain { };