small fixes for OSX

Author: rbetz

README.md

@@ -1,7 +1,9 @@
 # vmd-python
 Installable VMD as a python module
 
-*NEW*: Version 3.0 has the following new features
+*NEW*: Support for new arm64 macs!
+
+Version 3.0 has the following new features
 
 * Atomselection attributes can be accessed or set more easily:
   `atomsel.get("x")` can be written as `atomsel.x`!
@@ -12,8 +14,6 @@ Installable VMD as a python module
 * More rigorous reference counting / fewer memory leaks
 * Much prettier code
 
-*NEW*: Support for Python 3!!!
-
 ![CI status](https://img.shields.io/travis/Eigenstate/vmd-python.svg)
 ![Downloads](https://anaconda.org/rbetz/vmd-python/badges/downloads.svg)
 ![Conda](https://anaconda.org/rbetz/vmd-python/badges/installer/conda.svg)
@@ -105,7 +105,7 @@ The easiest way to install the module is by using the [Conda](https://conda.io/e
 Python package manager. Vmd-python is in the [conda forge](https://conda-forge.org/)
 channel:
 
-Simple binary installation with conda (currently linux-x86\_64 only)
+Simple binary installation with conda:
 
     conda install -c conda-forge vmd-python
 
@@ -136,21 +136,16 @@ and `libopengl0` packages. To build:
 
 Please file issues if you have problems with this!!
 
-### OSX support
-
-Users have reported that on OSX with Tcl/Tk 8.6 the module will
-segfault on import. Unfortunately I'm the only developer of this software and
-don't have access to a machine running OSX with which to debug the issue.
-
 ## Dependencies
 vmd-python has the following dependencies:
 
-    * python 2.7 or 3.6
+    * python>2.7 or>3.6
     * numpy
     * libnetcdf >= 4.3
     * expat
     * sqlite
-    * Tcl/Tk = 8.5 (8.6 will crash on OSX)
+    * Tcl/Tk
+    * importlib_resources
 
 To build on Debian, that's the following packages:
 

test/test_vmd.py

@@ -1,8 +1,9 @@
 # Tests covalently bonded ligand
 import inspect
-import pytest
 import os
 
+import pytest
+
 dir = os.path.dirname(__file__)
 
 #==============================================================================
@@ -22,20 +23,20 @@ def test_caps_import():
 #==============================================================================
 
 def test_load_mae(file_rho):
-    from vmd import molecule, atomsel
+    from vmd import atomsel, molecule
     assert callable(atomsel)
 
     molecule.load('mae', file_rho)
-    chrg = set(atomsel().get('charge'))
+    chrg = set(atomsel().charge)
     assert chrg == set([0.0, 1.0, -1.0])
 
-    ins = set(atomsel().get('insertion'))
+    ins = set(atomsel().insertion)
     assert set(_.strip() for _ in ins) == set(['', 'A'])
 
 #==============================================================================
 
 def test_evaltcl(file_rho):
-    from vmd import evaltcl, atomsel, molecule
+    from vmd import atomsel, evaltcl, molecule
 
     molid = int(evaltcl("mol new"))
     assert molecule.get_top() == molid

vmd/install.sh

@@ -13,12 +13,6 @@ export VMDINSTALLBINDIR="$VMDDIR"
 export VMDINSTALLLIBRARYDIR="$VMDDIR"
 export PLUGINDIR="$VMDDIR/plugins"
 
-# Clean up previous installation
-if [[ -d $PLUGINDIR ]]; then
-    echo "Deleting previous plugin directory $PLUGINDIR"
-    rm -r $PLUGINDIR
-fi
-
 # Compile the plugins
 echo "Compiling plugins to $PLUGINDIR"
 mkdir -p $PLUGINDIR
@@ -57,7 +51,7 @@ cd $vmd_src/plugins
 make clean
 
 # Remove symlink so install doesn't freak out
-rm $vmd_src/vmd_src/plugins
+rm -f $vmd_src/vmd_src/plugins
 
 # Copy init.py file into build directory
 cp "$vmd_src/vmd_src/__init__.py" "$VMDDIR"

vmd/vmd_src/configure

@@ -2168,6 +2168,9 @@ if ($config_arch eq "MACOSXX86" || $config_arch eq "MACOSXX86_64" || $config_arc
     } else {
       $arch_lopts       .= "";
     }
+    if ($config_shared) {
+      $arch_cppopts    .= " -DVMD_SHARED";
+    }
 
     # Mesa version uses X11 just like other Unix versions,
     # but the OpenGL version uses native MacOS X, no X11.

vmd/vmd_src/python/Molecule.py

@@ -27,6 +27,7 @@
 
 from vmd import molecule, molrep
 
+
 class Molecule:
   """
   The Molecule class is a proxy for molecules loaded into VMD.  Most
@@ -91,7 +92,7 @@ def _guessFiletype(self, filename):
     if ind >= 0:
       filetype = filename[ind+1:]
     else:
-      if len(filename) is 4:
+      if len(filename) == 4:
         filetype = 'webpdb'
     return filetype