Merge pull request #58 from JuDFTteam/release-0.4.10

Release 0.4.10

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.9
+current_version = 0.4.10
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

masci_tools/__init__.py

@@ -13,6 +13,6 @@
 '''
 import logging
 
-__version__ = '0.4.9'
+__version__ = '0.4.10'
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())

masci_tools/tools/greensfunction.py

@@ -192,6 +192,7 @@ def _read_element_header(hdffile, index):
     onsite = element.attrs['l_onsite'][0] == 1
     contour = element.attrs['iContour'][0]
     atomDiff = np.array(element.attrs['atomDiff'])
+    atomDiff[abs(atomDiff) < 1e-12] = 0.0
     nLO = element.attrs['numLOs'][0]
 
     return GreensfElement(l, lp, atomType, atomTypep, sphavg, onsite, contour, nLO, atomDiff)
@@ -431,7 +432,7 @@ def printElements(elements, index=None, mark=None):
         atomdiff_str = np.array2string(element.atomDiff,
                                        precision=2,
                                        separator=',',
-                                       suppress_small=False,
+                                       suppress_small=True,
                                        sign=' ',
                                        floatmode='fixed')
         print(

masci_tools/vis/bokeh_plots.py

@@ -400,10 +400,11 @@ def bokeh_dos(dosdata,
 
     if 'limits' in kwargs:
         limits = kwargs.pop('limits')
-        if xyswitch:
-            limits['x'], limits['y'] = limits.pop('dos', None), limits.pop('energy', None)
-        else:
-            limits['x'], limits['y'] = limits.pop('energy', None), limits.pop('dos', None)
+        if 'x' not in limits and 'y' not in limits:
+            if xyswitch:
+                limits['x'], limits['y'] = limits.pop('dos', None), limits.pop('energy', None)
+            else:
+                limits['x'], limits['y'] = limits.pop('energy', None), limits.pop('dos', None)
         kwargs['limits'] = {k: v for k, v in limits.items() if v is not None}
 
     lines = {'horizontal': 0}
@@ -475,10 +476,11 @@ def bokeh_spinpol_dos(dosdata,
 
     if 'limits' in kwargs:
         limits = kwargs.pop('limits')
-        if xyswitch:
-            limits['x'], limits['y'] = limits.pop('dos', None), limits.pop('energy', None)
-        else:
-            limits['x'], limits['y'] = limits.pop('energy', None), limits.pop('dos', None)
+        if 'x' not in limits and 'y' not in limits:
+            if xyswitch:
+                limits['x'], limits['y'] = limits.pop('dos', None), limits.pop('energy', None)
+            else:
+                limits['x'], limits['y'] = limits.pop('energy', None), limits.pop('dos', None)
         kwargs['limits'] = {k: v for k, v in limits.items() if v is not None}
 
     lines = {'horizontal': 0}

masci_tools/vis/bokeh_plotter.py

@@ -218,7 +218,13 @@ def __init__(self, **kwargs):
                          key_descriptions=self._BOKEH_DESCRIPTIONS,
                          **kwargs)
 
-    def plot_kwargs(self, ignore=None, extra_keys=None, plot_type='default', post_process=True, **kwargs):
+    def plot_kwargs(self,
+                    ignore=None,
+                    extra_keys=None,
+                    plot_type='default',
+                    post_process=True,
+                    list_of_dicts=True,
+                    **kwargs):
         """
         Creates a dict or list of dicts (for multiple plots) with the defined parameters
         for the plotting calls fo matplotlib
@@ -269,7 +275,8 @@ def plot_kwargs(self, ignore=None, extra_keys=None, plot_type='default', post_pr
         if 'marker_size' in plot_kwargs:
             plot_kwargs['size'] = plot_kwargs.pop('marker_size')
 
-        plot_kwargs = self.dict_of_lists_to_list_of_dicts(plot_kwargs, self.single_plot, self.num_plots)
+        if list_of_dicts:
+            plot_kwargs = self.dict_of_lists_to_list_of_dicts(plot_kwargs, self.single_plot, self.num_plots)
 
         return plot_kwargs
 

masci_tools/vis/fleur.py

@@ -313,6 +313,9 @@ def plot_fleur_dos(dosdata,
     recipe from :py:mod:`~masci_tools.io.parsers.hdf5.recipes` or something
     producing equivalent data
 
+    The limits for the axes can be specified either with ``x`` and ``y`` or
+    ``energy`` and ``dos``. Mixing the two options is not possible
+
     :param dosdata: dataset dict produced by the `FleurDOS` recipe
     :param attributes: attributes dict produced by the `FleurDOS` recipe
     :param spinpol: bool, if True (default) use the plot for spin-polarized dos if the data is spin-polarized
@@ -363,7 +366,7 @@ def plot_fleur_dos(dosdata,
     #Select the keys
     legend_labels, keys = np.array(legend_labels)[key_mask].tolist(), np.array(keys)[key_mask].tolist()
 
-    kwargs = _process_dos_kwargs(keys, **kwargs)
+    kwargs = _process_dos_kwargs(keys, bokeh_plot=bokeh_plot, **kwargs)
 
     if bokeh_plot:
         if spinpol:
@@ -385,7 +388,7 @@ def plot_fleur_dos(dosdata,
     return fig
 
 
-def _process_dos_kwargs(ordered_keys, **kwargs):
+def _process_dos_kwargs(ordered_keys, bokeh_plot=False, **kwargs):
     """
     Convert any kwarg in dict form with str keys to the correct dict with integer index
     for the plotting functions.
@@ -394,8 +397,17 @@ def _process_dos_kwargs(ordered_keys, **kwargs):
 
     :returns: kwargs with the dicts converted to integer indexed dicts
     """
+    from .matplotlib_plotter import MatplotlibPlotter
+    from .bokeh_plotter import BokehPlotter
+
+    if bokeh_plot:
+        params = BokehPlotter()
+    else:
+        params = MatplotlibPlotter()
 
     for key, value in kwargs.items():
+        if params.is_general(key):
+            continue
         if isinstance(value, dict):
             new_dict = value.copy()
             for plot_label, val in value.items():

masci_tools/vis/matplotlib_plotter.py

@@ -313,7 +313,13 @@ def __init__(self, **kwargs):
                          key_descriptions=self._MATPLOTLIB_DESCRIPTIONS,
                          **kwargs)
 
-    def plot_kwargs(self, ignore=None, extra_keys=None, plot_type='default', post_process=True, **kwargs):
+    def plot_kwargs(self,
+                    ignore=None,
+                    extra_keys=None,
+                    plot_type='default',
+                    post_process=True,
+                    list_of_dicts=True,
+                    **kwargs):
         """
         Creates a dict or list of dicts (for multiple plots) with the defined parameters
         for the plotting calls fo matplotlib
@@ -394,9 +400,17 @@ def plot_kwargs(self, ignore=None, extra_keys=None, plot_type='default', post_pr
 
                 plot_kwargs['cmap'] = self.truncate_colormap(plot_kwargs['cmap'], *self['sub_colormap'])
 
-        plot_kwargs = self.dict_of_lists_to_list_of_dicts(plot_kwargs, self.single_plot, self.num_plots)
+        if list_of_dicts:
+            plot_kwargs = self.dict_of_lists_to_list_of_dicts(plot_kwargs, self.single_plot, self.num_plots)
 
-        if not self.single_plot:
+        if not list_of_dicts and 'label' in plot_kwargs:
+            label = plot_kwargs.pop('label')
+            if isinstance(label, list):
+                plot_kwargs['label'] = [value if value is not None else '' for value in label]
+            else:
+                plot_kwargs['label'] = label if label is not None else ''
+
+        if not self.single_plot and list_of_dicts:
             for index, value in enumerate(plot_kwargs):
                 if self[('area_plot', index)]:
                     value.pop('marker', None)

masci_tools/vis/parameters.py

@@ -129,10 +129,21 @@ def _generate_plot_parameters_table(defaults, descriptions):
             value = f'``{value}``'
 
         descr = descriptions.get(key, 'No Description available')
+        descr = descr.replace('{',' ``{')
+        descr = descr.replace('}','}`` ')
 
         table.extend([f'       * - ``{key}``',
-                      f'         - {descr}',
-                      f'         - {value}'])
+                      f'         - {descr}'])
+
+        if not isinstance(value, dict):
+            table.append(f'         - {value}')
+        else:
+            string_value = [f"'{key}': {val}," for key, val in value.items()]
+            string_value[0] = '{' + string_value[0]
+            string_value[-1] = string_value[-1].rstrip(',') + '}'
+
+            table.extend(['         - .. code-block::', ''] + \
+                         [f'                {string}' for string in string_value])
 
     table.append('')
     #yapf: enable
@@ -387,7 +398,7 @@ def __setitem__(self, key, value):
         if key not in self._params:
             raise KeyError(f'Unknown parameter: {key}')
 
-        if key not in self._GENERAL_KEYS:
+        if not self.is_general(key):
             value = self.convert_to_complete_list(value,
                                                   self.single_plot,
                                                   self.num_plots,
@@ -582,6 +593,17 @@ def get_description(self, key):
         else:
             warnings.warn(f'{key} is not a known parameter')
 
+    def is_general(self, key):
+        """
+        Return, whether the key is general
+        (meaning only related to the whole plots)
+
+        :param key: str of the key to check
+
+        :returns: bool, whether the key is general
+        """
+        return key in self._GENERAL_KEYS
+
     @property
     def _hardcoded_defaults(self):
         """

masci_tools/vis/plot_methods.py

@@ -777,6 +777,12 @@ def histogram(xdata,
     If the arguments are not recognized they are passed on to the matplotlib function `hist`
     """
 
+    if not isinstance(xdata[0], (list, np.ndarray, pd.Series)):
+        xdata = [xdata]
+
+    plot_params.single_plot = False
+    plot_params.num_plots = len(xdata)
+
     if 'label' in kwargs:
         warnings.warn('Please use plot_label instead of label', DeprecationWarning)
         kwargs['plot_label'] = kwargs.pop('label')
@@ -804,7 +810,7 @@ def histogram(xdata,
 
     ax = plot_params.prepare_plot(title=title, xlabel=xlabel, ylabel=ylabel, axis=axis, minor=True)
 
-    plot_kwargs = plot_params.plot_kwargs(plot_type='histogram')
+    plot_kwargs = plot_params.plot_kwargs(plot_type='histogram', list_of_dicts=False)
     n, bins, patches = ax.hist(xdata,
                                density=density,
                                histtype=histtype,
@@ -1538,9 +1544,9 @@ def plot_lattice_constant(scaling,
             with NestedPlotParameters(plot_params):
                 ax = single_scatterplot(scaling,
                                         fit_y,
-                                        xlabel,
-                                        ylabel,
-                                        title,
+                                        xlabel=xlabel,
+                                        ylabel=ylabel,
+                                        title=title,
                                         axis=ax,
                                         show=False,
                                         save_plots=False,
@@ -1595,10 +1601,11 @@ def plot_dos(energy_grid,
 
     if 'limits' in kwargs:
         limits = kwargs.pop('limits')
-        if xyswitch:
-            limits['x'], limits['y'] = limits.pop('dos', None), limits.pop('energy', None)
-        else:
-            limits['x'], limits['y'] = limits.pop('energy', None), limits.pop('dos', None)
+        if 'x' not in limits and 'y' not in limits:
+            if xyswitch:
+                limits['x'], limits['y'] = limits.pop('dos', None), limits.pop('energy', None)
+            else:
+                limits['x'], limits['y'] = limits.pop('energy', None), limits.pop('dos', None)
         kwargs['limits'] = {k: v for k, v in limits.items() if v is not None}
 
     lines = {'horizontal': 0}
@@ -1668,10 +1675,11 @@ def plot_spinpol_dos(energy_grid,
 
     if 'limits' in kwargs:
         limits = kwargs.pop('limits')
-        if xyswitch:
-            limits['x'], limits['y'] = limits.pop('dos', None), limits.pop('energy', None)
-        else:
-            limits['x'], limits['y'] = limits.pop('energy', None), limits.pop('dos', None)
+        if 'x' not in limits and 'y' not in limits:
+            if xyswitch:
+                limits['x'], limits['y'] = limits.pop('dos', None), limits.pop('energy', None)
+            else:
+                limits['x'], limits['y'] = limits.pop('energy', None), limits.pop('dos', None)
         kwargs['limits'] = {k: v for k, v in limits.items() if v is not None}
 
     if isinstance(spin_up_data[0], (list, np.ndarray)):

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools", "wheel"]
 
 [tool.poetry]
 name = "masci_tools"
-version = "0.4.9"
+version = "0.4.10"
 description = "Tools for Materials science. Vis contains wrapers of matplotlib functionality to visualalize common material science data. Plus wrapers of visualisation for aiida-fleur workflow nodes"
 readme = "README.md"
 authors = ["Jens Bröder <[email protected]>",

setup.py

@@ -17,7 +17,7 @@
 if __name__ == '__main__':
     setup(
         name='masci_tools',
-        version='0.4.9',
+        version='0.4.10',
         description='Tools for Materials science. Vis contains wrappers of matplotlib functionality to visualize common material science data. Plus wrappers of visualisation for aiida-fleur workflow nodes',
         # add long_description from readme.md:
         long_description = long_description, # add contents of README.md

tests/test_fleur_vis.py

@@ -154,6 +154,30 @@ def test_plot_dos_param_change_by_label_mpl():
     return gcf()
 
 
+@pytest.mark.mpl_image_compare(baseline_dir='files/fleur_vis/', filename='dos_param_by_label_with_general_params.png')
+def test_plot_dos_param_change_by_label_general_dicts_mpl():
+    from masci_tools.io.parsers.hdf5 import HDF5Reader
+    from masci_tools.io.parsers.hdf5.recipes import FleurDOS
+    from masci_tools.vis.fleur import plot_fleur_dos
+
+    TEST_BANDDOS_FILE = os.path.join(HDFTEST_DIR, 'banddos_dos.hdf')
+
+    with HDF5Reader(TEST_BANDDOS_FILE) as h5reader:
+        data, attributes = h5reader.read(recipe=FleurDOS)
+
+    gcf().clear()
+
+    plot_fleur_dos(data,
+                   attributes,
+                   show=False,
+                   color={'MT:1_up': 'red'},
+                   linewidth={'Total_up': 6},
+                   limits={'energy': (-5, 5)},
+                   lines={'vertical': [-1, 0, 1]})
+
+    return gcf()
+
+
 @pytest.mark.mpl_image_compare(baseline_dir='files/fleur_vis/', filename='spinpol_dos_defaults.png')
 def test_plot_spinpol_dos_defaults_mpl():
     from masci_tools.io.parsers.hdf5 import HDF5Reader

tests/test_plot_methods.py

@@ -1049,6 +1049,57 @@ def test_param_change(self):
         # need to return the figure in order for mpl checks to work
         return gcf()
 
+    @pytest.mark.mpl_image_compare(baseline_dir='files/plot_methods/matplotlib/histogram/', filename='stacked.png')
+    def test_defaults_stacked(self):
+        """
+        Test of histogram plot with default values
+        """
+        import numpy as np
+        from masci_tools.vis.plot_methods import histogram
+
+        np.random.seed(19680801)
+        N_points = 10000
+
+        # Generate a normal distribution, center at x=0 and y=5
+        x = np.random.randn(N_points)
+        x2 = np.random.randn(N_points)
+
+        gcf().clear()
+
+        histogram([x, x2], show=False, histtype='barstacked')
+
+        # need to return the figure in order for mpl checks to work
+        return gcf()
+
+    @pytest.mark.mpl_image_compare(baseline_dir='files/plot_methods/matplotlib/histogram/',
+                                   filename='stacked_param_change.png')
+    def test_param_changed_stacked(self):
+        """
+        Test of histogram plot with default values
+        """
+        import numpy as np
+        from masci_tools.vis.plot_methods import histogram
+
+        np.random.seed(19680801)
+        N_points = 10000
+
+        # Generate a normal distribution, center at x=0 and y=5
+        x = np.random.randn(N_points)
+        x2 = np.random.randn(N_points)
+
+        gcf().clear()
+
+        histogram([x, x2],
+                  color=['darkblue', 'darkred'],
+                  histtype='barstacked',
+                  linewidth=2,
+                  legend=True,
+                  plot_label={1: 'This is on top'},
+                  show=False)
+
+        # need to return the figure in order for mpl checks to work
+        return gcf()
+
 
 class TestBarchartPlot(object):  #pylint: disable=missing-class-docstring