Update msspec against its dependencies.

MsSpec is now compatible with latest version of WX, of numpy,
scipy, matplotlib...

Makefile

@@ -19,7 +19,7 @@ endif
 .PHONY: pybinding install devel venv doc clean
 
 
-pybinding: venv
+pybinding:
 	@+. $(VENV_PATH)/bin/activate && $(MAKE) -C src pybinding
 
 
@@ -28,7 +28,7 @@ venv:
 	@. $(VENV_PATH)/bin/activate && pip install --upgrade pip && pip install -r src/pip.freeze
 
 
-install: pybinding
+install: venv pybinding
 	@+. $(VENV_PATH)/bin/activate && $(MAKE) -C src sdist
 	@+. $(VENV_PATH)/bin/activate && $(MAKE) -C src frontend
 	@+. $(VENV_PATH)/bin/activate && pip install src/dist/msspec-$(VERSION).tar.gz
@@ -36,7 +36,7 @@ install: pybinding
 
 
 devel: VENV_PATH = ./_venv
-devel: pybinding venv
+devel: venv pybinding
 	@. $(VENV_PATH)/bin/activate && pip install -e src/
 
 

src/msspec/calculator.py

@@ -59,6 +59,7 @@ from subprocess import Popen
 import ase.atom
 import ase.atoms
 import ase.data
+from ase.io.extxyz import write_xyz
 import numpy as np
 from ase.calculators.calculator import Calculator
 from terminaltables.ascii_table import AsciiTable
@@ -548,7 +549,8 @@ class _MSCALCULATOR(Calculator):
     def add_cluster_to_dset(self, dset):
         clusbuf = StringIO()
         self.atoms.info['absorber'] = self.atoms.absorber
-        self.atoms.write(clusbuf, format='xyz')
+        #self.atoms.write(clusbuf, format='xyz')
+        write_xyz(clusbuf, self.atoms)
         dset.add_parameter(group='Cluster', name='cluster', value=clusbuf.getvalue(), hidden="True")
 
     def shutdown(self):
@@ -756,10 +758,11 @@ class _PED(_MSCALCULATOR):
                             legend=r'$\Re(f(\theta))$')
 
         # save the cluster
-        clusbuf = StringIO()
-        self.atoms.info['absorber'] = self.atoms.absorber
-        self.atoms.write(clusbuf, format='xyz')
-        dset.add_parameter(group='Cluster', name='cluster', value=clusbuf.getvalue(), hidden="True")
+        #clusbuf = StringIO()
+        #self.atoms.info['absorber'] = self.atoms.absorber
+        #self.atoms.write(clusbuf, format='xyz')
+        #dset.add_parameter(group='Cluster', name='cluster', value=clusbuf.getvalue(), hidden="True")
+        self.add_cluster_to_dset(dset)
 
         LOGGER.info('%s scan computing done!', scan_type)
 

src/msspec/iodata.py

@@ -75,6 +75,7 @@ from io import StringIO
 from datetime import datetime
 
 import ase.io
+from ase.io.extxyz import read_xyz, write_xyz
 import h5py
 import numpy as np
 import wx.grid
@@ -180,8 +181,8 @@ class DataSet(object):
                          float: '{:<20.10e}', complex: 's'}
         self._formats = ((np.integer, '{:<20d}'),
                          (np.floating, '{:<20.10e}'),
-                         (np.complex, '({0.real:<.10e} {0.imag:<.10e}j)'),
-                         (np.bool, '{:s}'),
+                         (complex, '({0.real:<.10e} {0.imag:<.10e}j)'),
+                         (bool, '{:s}'),
                          (str, '{:s}'))
 
 
@@ -395,9 +396,13 @@ class DataSet(object):
         :return: The cluster
         :rtype: :py:class:`ase.Atoms`
         """
+        p = self.get_parameter(group='Cluster', name='cluster')['value']
         s = StringIO()
         s.write(self.get_parameter(group='Cluster', name='cluster')['value'])
-        return ase.io.read(s, format='xyz')
+        s.seek(0)
+        #return ase.io.read(s, format='xyz')
+        cluster = list(read_xyz(s))[-1]
+        return cluster
 
 
     def select(self, *args, **kwargs):
@@ -730,13 +735,13 @@ class Data(object):
                 dset = output.add_dset(dset_name)
                 dset.notes = fd['DATA'][dset_name].attrs['notes']
                 for h5dset in fd['DATA'][dset_name]:
-                    dset.add_columns(**{h5dset: fd['DATA'][dset_name][h5dset].value})
+                    dset.add_columns(**{h5dset: fd['DATA'][dset_name][h5dset][...]})
 
             try:
                 vfile = LooseVersion(fd['MsSpec viewer metainfo'].attrs['version'])
                 if vfile > LooseVersion(msspec.__version__):
                     raise NameError('File was saved with a more recent format')
-                xml = fd['MsSpec viewer metainfo']['info'].value.tostring()
+                xml = fd['MsSpec viewer metainfo']['info'][...].tobytes()
                 root = etree.fromstring(xml)
                 for elt0 in root.iter('parameters'):
                     dset_name = elt0.attrib['dataset']
@@ -868,7 +873,8 @@ class _DataSetView(object):
             if np.shape(values)[0] == 1:
                 xvalues = list(range(len(values[0])))
                 axes.bar(xvalues, values[0], label=label,
-                          picker=5)
+                         # picker=5
+                         )
                 axes.set_xticks(xvalues)
             else:
                 if proj in ('ortho', 'stereo'):
@@ -890,7 +896,7 @@ class _DataSetView(object):
 
                 elif proj == 'polar':
                     values[0] = np.radians(values[0])
-                    axes.plot(*values, label=label, picker=5,
+                    axes.plot(*values, label=label, #picker=5,
                               marker=opts['marker'])
                 else:
                     if scale == 'semilogx':
@@ -901,7 +907,7 @@ class _DataSetView(object):
                         pltcmd = axes.loglog
                     else:
                         pltcmd = axes.plot
-                    pltcmd(*values, label=label, picker=5,
+                    pltcmd(*values, label=label, #picker=5,
                            marker=opts['marker'])
             axes.grid(opts['grid'])
             axes.set_title(opts['title'])
@@ -909,6 +915,7 @@ class _DataSetView(object):
             axes.set_ylabel(opts['ylabel'])
             axes.set_xlim(*opts['xlim'])
             axes.set_ylim(*opts['ylim'])
+            #axes.set_pickradius(5)
             if label:
                 axes.legend()
         axes.autoscale(enable=opts['autoscale'])
@@ -1221,9 +1228,14 @@ class _DataWindow(wx.Frame):
         cluster_viewer = ClusterViewer(win, size=wx.Size(480, 340))
 
         dset = self.data[self._current_dset]
-        s = StringIO()
-        s.write(dset.get_parameter(group='Cluster', name='cluster')['value'])
-        atoms = ase.io.read(s, format='xyz')
+        #s = StringIO()
+        #s.write(dset.get_parameter(group='Cluster', name='cluster')['value'])
+        #_s = dset.get_parameter(group='Cluster', name='cluster')['value']
+        #print(_s)
+        # rewind to the begining of the string
+        #s.seek(0)
+        #atoms = ase.io.read(s, format='xyz')
+        atoms = dset.get_cluster()
         cluster_viewer.set_atoms(atoms, rescale=True, center=True)
         cluster_viewer.rotate_atoms(0., 180.)
         cluster_viewer.rotate_atoms(-45., -45.)
@@ -1388,7 +1400,8 @@ class _DataWindow(wx.Frame):
         menu = self.GetMenuBar().GetMenu(menu_id)
         for item in menu.GetMenuItems():
             if item.IsChecked():
-                sb.SetStatusText("%s" % item.GetText(), 1)
+                #sb.SetStatusText("%s" % item.GetText(), 1)
+                sb.SetStatusText("%s" % item.GetItemLabelText(), 1)
                 break
 
     def update_title(self):

src/pip.freeze

@@ -1,14 +1,13 @@
-ase==3.19.1
-h5py==2.10.0
-ipython==7.13.0
-lxml==4.5.0
-matplotlib==2.1.1
-numpy==1.18.2
-Pint==0.11
-#pip==20.0.2
-pycairo==1.19.1
-scipy==1.4.1
-setuptools-scm==3.5.0
-terminaltables==3.1.0
+ase
+h5py
+ipython
+lxml
+matplotlib
+numpy
+Pint
+pycairo
+scipy
+setuptools-scm
+terminaltables
 #wxPython@https://extras.wxpython.org/wxPython4/extras/linux/gtk3/debian-10/wxPython-4.1.0-cp37-cp37m-linux_x86_64.whl
 #wxPython@https://extras.wxpython.org/wxPython4/extras/linux/gtk3/debian-9/wxPython-4.0.7.post2-cp35-cp35m-linux_x86_64.whl