From ebb450024b2181c117f3c69075c23ffb986bd8a3 Mon Sep 17 00:00:00 2001 From: Sylvain Tricot Date: Fri, 19 Feb 2021 08:22:47 +0100 Subject: [PATCH] Update msspec against its dependencies. MsSpec is now compatible with latest version of WX, of numpy, scipy, matplotlib... --- Makefile | 6 +++--- src/msspec/calculator.py | 13 ++++++++----- src/msspec/iodata.py | 37 +++++++++++++++++++++++++------------ src/pip.freeze | 23 +++++++++++------------ 4 files changed, 47 insertions(+), 32 deletions(-) diff --git a/Makefile b/Makefile index b96333b..760ecab 100644 --- a/Makefile +++ b/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 @. $(VENV_PATH)/bin/activate && pip install -e src/ diff --git a/src/msspec/calculator.py b/src/msspec/calculator.py index 9fe21cc..dc5d682 100644 --- a/src/msspec/calculator.py +++ b/src/msspec/calculator.py @@ -59,6 +59,7 @@ from subprocess import Popen import ase.atom import ase.atoms import ase.data +from ase.io.extxyz import write_xyz import numpy as np from ase.calculators.calculator import Calculator from terminaltables.ascii_table import AsciiTable @@ -548,7 +549,8 @@ class _MSCALCULATOR(Calculator): def add_cluster_to_dset(self, dset): clusbuf = StringIO() self.atoms.info['absorber'] = self.atoms.absorber - self.atoms.write(clusbuf, format='xyz') + #self.atoms.write(clusbuf, format='xyz') + write_xyz(clusbuf, self.atoms) dset.add_parameter(group='Cluster', name='cluster', value=clusbuf.getvalue(), hidden="True") def shutdown(self): @@ -756,10 +758,11 @@ class _PED(_MSCALCULATOR): legend=r'$\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) diff --git a/src/msspec/iodata.py b/src/msspec/iodata.py index 998485b..b15e3c3 100644 --- a/src/msspec/iodata.py +++ b/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): diff --git a/src/pip.freeze b/src/pip.freeze index 0a7d654..8502bcf 100644 --- a/src/pip.freeze +++ b/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