Merge pull request #26317 from Mounium/pymol

pymol: added Pmw + python version bump

pkgs/applications/science/chemistry/pymol/default.nix

@@ -1,24 +1,50 @@
-{ stdenv, fetchurl, python27Packages, glew, freeglut, libpng, libxml2, tk, freetype }:
+{ stdenv, fetchurl, makeDesktopItem
+, python3, python3Packages
+, glew, freeglut, libpng, libxml2, tk, freetype }:
+
+
+with stdenv.lib;
 
 let
-  version = "1.8.4.0";
+  pname = "pymol";
+  ver_maj = "1.8";
+  ver_min = "4";
+  version = "${ver_maj}.${ver_min}.0";
+  description = "A Python-enhanced molecular graphics tool";
+
+  desktopItem = makeDesktopItem {
+    name = "${pname}";
+    exec = "${pname}";
+    desktopName = "PyMol Molecular Graphics System";
+    genericName = "Molecular Modeller";
+    comment = description;
+    mimeType = "chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;";
+    categories = "Graphics;Education;Science;Chemistry;";
+  };
 in
-python27Packages.buildPythonApplication {
+python3Packages.buildPythonApplication {
   name = "pymol-${version}";
   src = fetchurl {
-    url = "mirror://sourceforge/project/pymol/pymol/1.8/pymol-v1.8.4.0.tar.bz2";
+    url = "mirror://sourceforge/project/pymol/pymol/${ver_maj}/pymol-v${version}.tar.bz2";
     sha256 = "0yfj8g5yic9zz6f0bw2n8h6ifvgsn8qvhq84alixsi28wzppn55n";
   };
 
-  buildInputs = [ python27Packages.numpy glew freeglut libpng libxml2 tk freetype ];
+  buildInputs = [ python3Packages.numpy glew freeglut libpng libxml2 tk freetype ];
   NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2";
 
   installPhase = ''
     python setup.py install --home=$out
+    cp -r ${desktopItem}/share/ $out/
+    runHook postInstall
   '';
 
-  meta = with stdenv.lib; {
+  postInstall = with python3Packages; ''
-    description = "A Python-enhanced molecular graphics tool";
+    wrapProgram $out/bin/pymol \
+      --prefix PYTHONPATH : ${makeSearchPathOutput "lib" python3.sitePackages [ Pmw tkinter ]}
+  '';
+
+  meta = {
+    description = description;
     homepage = "https://www.pymol.org/";
     license = licenses.psfl;
   };

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

@@ -0,0 +1,24 @@
+{ lib , buildPythonPackage , fetchPypi, tkinter }:
+
+buildPythonPackage rec {
+  pname = "Pmw";
+  version = "2.0.1";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "080iml3868nxniyn56kcwnbghm10j7fw74a5nj0s19sm4zsji78b";
+  };
+
+  propagatedBuildInputs = [ tkinter ];
+
+  # Disable tests due to their xserver requirement
+  doCheck = false;
+
+  meta = {
+    description = "A toolkit for building high-level compound widgets in Python using the Tkinter module";
+    homepage = "http://pmw.sourceforge.net/";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ mounium ];
+  };
+}

pkgs/top-level/python-packages.nix

@@ -240,6 +240,8 @@ in {
 
   plantuml = callPackage ../tools/misc/plantuml { };
 
+  Pmw = callPackage ../development/python-modules/Pmw { };
+
   pyaes = callPackage ../development/python-modules/pyaes.nix { };
 
   pyatspi = if isPy3k then callPackage ../development/python-modules/pyatspi { } else throw "pyatspi not supported for interpreter ${python.executable}";