packages.py4vasp: fix

flake.lock

@@ -447,24 +447,6 @@
       "inputs": {
         "systems": "systems_4"
       },
-      "locked": {
-        "lastModified": 1726560853,
-        "narHash": "sha256-X6rJYSESBVr3hBoH0WbKE5KvhPU5bloyZ2L4K60/fPQ=",
-        "owner": "numtide",
-        "repo": "flake-utils",
-        "rev": "c1dfcf08411b08f6b8615f7d8971a2bfa81d5e8a",
-        "type": "github"
-      },
-      "original": {
-        "owner": "numtide",
-        "repo": "flake-utils",
-        "type": "github"
-      }
-    },
-    "flake-utils_5": {
-      "inputs": {
-        "systems": "systems_6"
-      },
       "locked": {
         "lastModified": 1710146030,
         "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
@@ -777,27 +759,6 @@
         "type": "github"
       }
     },
-    "nix-github-actions_2": {
-      "inputs": {
-        "nixpkgs": [
-          "poetry2nix",
-          "nixpkgs"
-        ]
-      },
-      "locked": {
-        "lastModified": 1729742964,
-        "narHash": "sha256-B4mzTcQ0FZHdpeWcpDYPERtyjJd/NIuaQ9+BV1h+MpA=",
-        "owner": "nix-community",
-        "repo": "nix-github-actions",
-        "rev": "e04df33f62cdcf93d73e9a04142464753a16db67",
-        "type": "github"
-      },
-      "original": {
-        "owner": "nix-community",
-        "repo": "nix-github-actions",
-        "type": "github"
-      }
-    },
     "nix-index-database": {
       "inputs": {
         "nixpkgs": [
@@ -1162,30 +1123,6 @@
         "type": "github"
       }
     },
-    "poetry2nix": {
-      "inputs": {
-        "flake-utils": "flake-utils_4",
-        "nix-github-actions": "nix-github-actions_2",
-        "nixpkgs": [
-          "nixpkgs"
-        ],
-        "systems": "systems_5",
-        "treefmt-nix": "treefmt-nix_4"
-      },
-      "locked": {
-        "lastModified": 1731205797,
-        "narHash": "sha256-F7N1mxH1VrkVNHR3JGNMRvp9+98KYO4b832KS8Gl2xI=",
-        "owner": "nix-community",
-        "repo": "poetry2nix",
-        "rev": "f554d27c1544d9c56e5f1f8e2b8aff399803674e",
-        "type": "github"
-      },
-      "original": {
-        "owner": "nix-community",
-        "repo": "poetry2nix",
-        "type": "github"
-      }
-    },
     "pre-commit-hooks-nix": {
       "inputs": {
         "flake-compat": "flake-compat_5",
@@ -1286,7 +1223,6 @@
         "openxlsx": "openxlsx",
         "plasma-manager": "plasma-manager",
         "pocketfft": "pocketfft",
-        "poetry2nix": "poetry2nix",
         "py4vasp": "py4vasp",
         "qchem": "qchem",
         "rsshub": "rsshub",
@@ -1497,35 +1433,6 @@
         "type": "github"
       }
     },
-    "systems_5": {
-      "locked": {
-        "lastModified": 1681028828,
-        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
-        "owner": "nix-systems",
-        "repo": "default",
-        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
-        "type": "github"
-      },
-      "original": {
-        "id": "systems",
-        "type": "indirect"
-      }
-    },
-    "systems_6": {
-      "locked": {
-        "lastModified": 1681028828,
-        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
-        "owner": "nix-systems",
-        "repo": "default",
-        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
-        "type": "github"
-      },
-      "original": {
-        "owner": "nix-systems",
-        "repo": "default",
-        "type": "github"
-      }
-    },
     "tgbot-cpp": {
       "flake": false,
       "locked": {
@@ -1605,27 +1512,6 @@
         "type": "github"
       }
     },
-    "treefmt-nix_4": {
-      "inputs": {
-        "nixpkgs": [
-          "poetry2nix",
-          "nixpkgs"
-        ]
-      },
-      "locked": {
-        "lastModified": 1730120726,
-        "narHash": "sha256-LqHYIxMrl/1p3/kvm2ir925tZ8DkI0KA10djk8wecSk=",
-        "owner": "numtide",
-        "repo": "treefmt-nix",
-        "rev": "9ef337e492a5555d8e17a51c911ff1f02635be15",
-        "type": "github"
-      },
-      "original": {
-        "owner": "numtide",
-        "repo": "treefmt-nix",
-        "type": "github"
-      }
-    },
     "ufo": {
       "flake": false,
       "locked": {
@@ -1678,7 +1564,7 @@
     "winapps": {
       "inputs": {
         "flake-compat": "flake-compat_6",
-        "flake-utils": "flake-utils_5",
+        "flake-utils": "flake-utils_4",
         "nixpkgs": [
           "nixpkgs"
         ]

flake.nix

@@ -29,7 +29,6 @@
     gricad = { url = "github:Gricad/nur-packages"; flake = false; };
     catppuccin.url = "github:catppuccin/nix";
     bscpkgs = { url = "git+https://git.chn.moe/chn/bscpkgs.git"; inputs.nixpkgs.follows = "nixpkgs"; };
-    poetry2nix = { url = "github:nix-community/poetry2nix"; inputs.nixpkgs.follows = "nixpkgs"; };
     winapps = { url = "github:winapps-org/winapps/feat-nix-packaging"; inputs.nixpkgs.follows = "nixpkgs"; };
     aagl = { url = "github:ezKEa/aagl-gtk-on-nix/release-24.11"; inputs.nixpkgs.follows = "nixpkgs"; };
 

flake/src.nix

@@ -7,4 +7,10 @@
       + "/nixos-plasma6-24.11beta709057.0c582677378f-x86_64-linux.iso";
     sha256 = "000wmfn6k5awqwsx9qldhdgahv4k09w4yzmvf0djs51qjdpha082";
   };
+  nglview = pkgs.fetchPypi
+  {
+    pname = "nglview";
+    version = "3.1.2";
+    hash = "sha256-f2cu+itsoNs03paOW1dmsUsbPa3iEtL4oIPGAKETRc4=";
+  };
 }

modules/default.nix

@@ -24,7 +24,6 @@ inputs:
           [
             topInputs.qchem.overlays.default
             topInputs.bscpkgs.overlays.default
-            topInputs.poetry2nix.overlays.default
             topInputs.aagl.overlays.default
             (final: prev:
             {

modules/packages/vasp.nix

@@ -8,12 +8,16 @@ inputs:
   # TODO: add more options to correctly configure VASP
   config = let inherit (inputs.config.nixos.packages) vasp; in inputs.lib.mkIf (vasp != null)
   {
-    nixos.packages.packages._packages = with inputs.pkgs;
+    nixos.packages.packages = with inputs.pkgs;
-    (
+    {
-      [ localPackages.vasp.intel localPackages.vasp.vtstscripts localPackages.py4vasp localPackages.vaspkit wannier90 ]
+      _packages =
-        ++ (inputs.lib.optional
+      (
-          (let inherit (inputs.config.nixos.system.nixpkgs) cuda; in cuda.enable && cuda.capabilities != null)
+        [ localPackages.vasp.intel localPackages.vasp.vtstscripts localPackages.vaspkit wannier90 ]
-          localPackages.vasp.nvidia)
+          ++ (inputs.lib.optional
-    );
+            (let inherit (inputs.config.nixos.system.nixpkgs) cuda; in cuda.enable && cuda.capabilities != null)
+            localPackages.vasp.nvidia)
+      );
+      _pythonPackages = [(_: [ localPackages.py4vasp ])];
+    };
   };
 }

packages/default.nix

@@ -92,13 +92,14 @@ inputs: rec
   sockpp = inputs.pkgs.callPackage ./sockpp.nix { src = inputs.topInputs.sockpp; };
   git-lfs-transfer = inputs.pkgs.callPackage ./git-lfs-transfer.nix
     { src = inputs.topInputs.git-lfs-transfer; hash = inputs.topInputs.self.src.git-lfs-transfer; };
-  py4vasp = inputs.pkgs.callPackage ./py4vasp { src = inputs.topInputs.py4vasp; };
+  py4vasp = inputs.pkgs.python3Packages.callPackage ./py4vasp.nix { src = inputs.topInputs.py4vasp; inherit nglview; };
   pocketfft = inputs.pkgs.callPackage ./pocketfft.nix { src = inputs.topInputs.pocketfft; };
   spectroscopy = inputs.pkgs.callPackage ./spectroscopy.nix { src = inputs.topInputs.spectroscopy; };
   mirism = inputs.pkgs.callPackage ./mirism { inherit biu; stdenv = inputs.pkgs.clang18Stdenv; };
   vaspberry = inputs.pkgs.callPackage ./vaspberry.nix { src = inputs.topInputs.vaspberry; };
   highfive = inputs.pkgs.callPackage ./highfive.nix { src = inputs.topInputs.highfive; };
   stickerpicker = inputs.pkgs.python3Packages.callPackage ./stickerpicker.nix { src = inputs.topInputs.stickerpicker; };
+  nglview = inputs.pkgs.python3Packages.callPackage ./nglview.nix { src = inputs.topInputs.self.src.nglview; };
 
   fromYaml = content: builtins.fromJSON (builtins.readFile
     (inputs.pkgs.runCommand "toJSON" {}

packages/nglview.nix

@@ -0,0 +1,18 @@
+# from https://github.com/NixOS/nixpkgs/pull/267893
+{
+  buildPythonPackage, src,
+  ipywidgets, jupyter-packaging, jupyterlab-widgets, numpy, setuptools, versioneer, wheel, notebook
+}: buildPythonPackage
+{
+  name = "nglview";
+  pyproject = true;
+  inherit src;
+  build-system = [ jupyter-packaging setuptools versioneer wheel ];
+  dependencies = [ ipywidgets jupyterlab-widgets numpy notebook ];
+  postPatch =
+  ''
+    substituteInPlace pyproject.toml \
+      --replace "jupyter_packaging~=0.7.9" "jupyter_packaging" \
+      --replace '"versioneer-518"' ""
+  '';
+}

packages/py4vasp.nix

@@ -0,0 +1,11 @@
+{
+  src, buildPythonPackage,
+  poetry-core, numpy, h5py, pandas, ase, plotly, kaleido, ipython, scipy, nglview
+}: buildPythonPackage
+{
+  name = "py4vasp";
+  pyproject = true;
+  inherit src;
+  build-system = [ poetry-core ];
+  dependencies = [ numpy h5py pandas ase plotly kaleido ipython scipy nglview ];
+}

packages/py4vasp/default.nix

@@ -1,10 +0,0 @@
-{ src, poetry2nix, runCommand }:
-let
-  package = poetry2nix.mkPoetryApplication
-  {
-    projectDir = src;
-    overrides = poetry2nix.overrides.withDefaults (final: prev:
-      { numpy = prev.numpy.overridePythonAttrs { patches = prev.patches or [] ++ [ ./numpy.patch ]; }; });
-  };
-  python = package.python.withPackages (p: [ package p.mdtraj ]);
-in runCommand "py4vasp" {} "mkdir -p $out/bin; ln -s ${python}/bin/python $out/bin/py4vasp"

packages/py4vasp/numpy.patch

@@ -1,70 +0,0 @@
-From f391623a00aff45f510bf815ddfb1817ae833059 Mon Sep 17 00:00:00 2001
-From: Katie Rust <katie@ktpanda.org>
-Date: Mon, 16 Sep 2024 13:04:22 -0500
-Subject: [PATCH] BUG: Stub out `get_build_msvc_version` if
- `distutils.msvccompiler` cannot be imported (fixes #27405)
-
----
- numpy/distutils/mingw32ccompiler.py | 8 +++++++-
- 1 file changed, 7 insertions(+), 1 deletion(-)
-
-diff --git a/numpy/distutils/mingw32ccompiler.py b/numpy/distutils/mingw32ccompiler.py
-index 39905a784088..2599a9e9a807 100644
---- a/numpy/distutils/mingw32ccompiler.py
-+++ b/numpy/distutils/mingw32ccompiler.py
-@@ -24,7 +24,13 @@
- 
- import distutils.cygwinccompiler
- from distutils.unixccompiler import UnixCCompiler
--from distutils.msvccompiler import get_build_version as get_build_msvc_version
-+
-+try:
-+    from distutils.msvccompiler import get_build_version as get_build_msvc_version
-+except ImportError:
-+    def get_build_msvc_version():
-+        return None
-+
- from distutils.errors import UnknownFileError
- from numpy.distutils.misc_util import (msvc_runtime_library,
-                                        msvc_runtime_version,
-diff --git a/numpy/distutils/msvccompiler.py b/numpy/distutils/msvccompiler.py
-index 2b93221baa..d1fae7b6ca 100644
---- a/numpy/distutils/msvccompiler.py
-+++ b/numpy/distutils/msvccompiler.py
-@@ -1,5 +1,4 @@
- import os
--from distutils.msvccompiler import MSVCCompiler as _MSVCCompiler
- 
- from .system_info import platform_bits
- 
-@@ -36,27 +35,12 @@ def _merge(old, new):
-     return ';'.join([old, new])
- 
- 
--class MSVCCompiler(_MSVCCompiler):
-+class MSVCCompiler:
-     def __init__(self, verbose=0, dry_run=0, force=0):
--        _MSVCCompiler.__init__(self, verbose, dry_run, force)
-+        pass
- 
-     def initialize(self):
--        # The 'lib' and 'include' variables may be overwritten
--        # by MSVCCompiler.initialize, so save them for later merge.
--        environ_lib = os.getenv('lib', '')
--        environ_include = os.getenv('include', '')
--        _MSVCCompiler.initialize(self)
--
--        # Merge current and previous values of 'lib' and 'include'
--        os.environ['lib'] = _merge(environ_lib, os.environ['lib'])
--        os.environ['include'] = _merge(environ_include, os.environ['include'])
--
--        # msvc9 building for 32 bits requires SSE2 to work around a
--        # compiler bug.
--        if platform_bits == 32:
--            self.compile_options += ['/arch:SSE2']
--            self.compile_options_debug += ['/arch:SSE2']
--
-+        pass
- 
- def lib_opts_if_msvc(build_cmd):
-     """ Add flags if we are using MSVC compiler