Merge pull request #34 from 1313e/dev

Mark release of v1.2.2.

docs/source/user/hdf5.inc

@@ -16,13 +16,13 @@ HDF5-files can be viewed freely by the user using the `HDFView`_ application mad
 ----
 
 The general file contains:
-    - Attributes (9/10): Describe the general non-changeable properties of the emulator, which include:
+    - Attributes (11/12): Describe the general non-changeable properties of the emulator, which include:
 
         - Emulator type and method;
         - Gaussian parameters;
         - Name of used :class:`~prism.modellink.ModelLink` subclass;
         - Used *PRISM* version;
-        - Polynomial order;
+        - Regression parameters;
         - Bools for using mock data or regression covariance;
         - Mock data parameters if mock data was used.
 

docs/source/user/parameters.inc

@@ -38,6 +38,15 @@ Below are descriptions of all the parameters that can be provided to *PRISM* in
     This number is multiplied by the difference between the upper and lower value boundaries of the model parameters to obtain the Gaussian correlation length for every model parameter.
     This value must be positive, normalized and either a scalar or a list of :attr:`~prism.modellink.ModelLink.n_par` scalars (where the values correspond to the sorted list of model parameters).
 
+:attr:`~prism.emulator.Emulator.f_infl` (Default: 0.2)
+    .. versionadded:: 1.2.2
+
+    The residual variance inflation factor.
+    The variance values for all known samples in an emulator iteration are inflated by this number multiplied by :attr:`~prism.emulator.Emulator.rsdl_var`.
+    This can be used to adjust for the underestimation of the emulator variance.
+    Setting this to zero causes no variance inflation to be performed.
+    This value must be non-negative.
+
 :attr:`~prism.Pipeline.impl_cut` (Default: [0.0, 4.0, 3.8, 3.5])
     A list of implausibility cut-off values that specifies the maximum implausibility values a parameter set is allowed to have to be considered 'plausible'.
     A zero can be used as a filler value, either taking on the preceding value or acting as a wildcard if the preceding value is a wildcard or non-existent.

prism/__version__.py

@@ -10,7 +10,7 @@
 
 # %% VERSIONS
 # Default/Latest/Current version
-__version__ = '1.2.1'
+__version__ = '1.2.2'
 
 # Compatibility versions
 compat_version = ['1.0.0rc12']

prism/_docstrings.py

@@ -292,7 +292,7 @@
 
 # Description of proj_par
 proj_par_doc =\
-        """proj_par : 1D array_like of {{int, str}} or None{0}{1}
+        """proj_par : 1D array_like of {{int; str}} or None{0}{1}
             For which model parameters to construct the projection figures.
             If 1D array_like, construct projection figures for all combinations
             of provided model parameters that are active, with a string
@@ -424,18 +424,18 @@ class that was created for drawing *{0}*.
         --------------
         keyword : {1}
             String specifying the type of data that needs to be saved.
-        data : {{int, float, str, array_like}} or dict
+        data : {{int; float; str; array_like}} or dict
             The actual data that needs to be saved at data keyword `keyword`.
             If dict, save every item individually.
 
         Generates
         ---------
         The specified data is saved to the HDF5-file."""
 save_data_doc_p = save_data_doc.format(
-    "", "{'impl_par', 'impl_sam', 'n_eval_sam'}")
+    "", "{'impl_par'; 'impl_sam'; 'n_eval_sam'}")
 save_data_doc_e = save_data_doc.format(
-    std_emul_i_doc+"\n\t"+lemul_s_doc+"\n\t", "{'active_par', "
-    "'active_par_data', 'cov_mat', 'exp_dot_term', 'mod_real_set', "
+    std_emul_i_doc+"\n\t"+lemul_s_doc+"\n\t", "{'active_par'; "
+    "'active_par_data'; 'cov_mat'; 'exp_dot_term'; 'mod_real_set'; "
     "'regression'}")
 save_data_doc_pr = save_data_doc.format(std_emul_i_doc+"\n\t",
                                         "{'nD_proj_hcube'}")

prism/_gui/widgets/overview.py

@@ -370,7 +370,7 @@ def show_unavailable_context_menu(self):
         """
 
         # If there is currently at least one item selected, show context menu
-        if len(self.proj_list_u.selectedItems()):
+        if self.proj_list_u.selectedItems():
             self.context_menu_u.popup(QG.QCursor.pos())
 
     # This function shows a list of projection figures in the viewing area
@@ -761,7 +761,7 @@ def save_projection_figures(self, list_items=None, *, choose=False):
                     **options)
 
                 # If filename was provided, save image
-                if(filename != ''):
+                if filename:
                     fig.savefig(filename)
                 # Else, break the loop
                 else:

prism/_gui/widgets/preferences/custom_boxes.py

@@ -16,6 +16,7 @@
 from itertools import chain
 
 # Package imports
+import cmasher as cmr
 from e13tools.utils import docstring_substitute
 from matplotlib import cm, rcParams
 from matplotlib.colors import BASE_COLORS, CSS4_COLORS, to_rgba
@@ -437,10 +438,20 @@ def __init__(self, *args, **kwargs):
 
     # This function creates a combobox with colormaps
     def init(self):
-        # Obtain a list with default colormaps that should be at the top
-        std_cmaps = sset(['cividis', 'dusk', 'freeze', 'gothic', 'heat',
-                          'inferno', 'magma', 'plasma', 'rainforest',
-                          'sunburst', 'viridis'])
+        # Define set of CMasher colormaps that should be at the top
+        cmr_cmaps = sset(['dusk', 'freeze', 'gothic', 'heat', 'rainforest',
+                          'sunburst'])
+
+        # Check that all of those colormaps are available in CMasher
+        cmr_cmaps.intersection_update(cmr.cm.cmap_d)
+
+        # Obtain a set with default MPL colormaps that should be at the top
+        std_cmaps = sset(['cividis', 'inferno', 'magma', 'plasma', 'viridis'])
+
+        # Add CMasher colormaps to it
+        std_cmaps.update(['cmr.'+cmap for cmap in cmr_cmaps])
+
+        # Obtain reversed set of recommended colormaps
         std_cmaps_r = sset([cmap+'_r' for cmap in std_cmaps])
 
         # Obtain a list with all colormaps and their reverses
@@ -464,8 +475,13 @@ def init(self):
                 cmap_icons[cmap] = self.create_cmap_icon(cmap, cmap_size)
             ColorMapBox.cmap_icons = cmap_icons
 
+        # Create a layout for this widget
+        box_layout = QW.QHBoxLayout(self)
+        box_layout.setContentsMargins(0, 0, 0, 0)
+        self.setToolTip("Colormap to be used for the corresponding plot type")
+
         # Create a combobox for cmaps
-        cmaps_box = QW_QComboBox(self)
+        cmaps_box = QW_QComboBox()
         for cmap in chain(*cmaps):
             cmap_icon = self.cmap_icons[cmap]
             cmaps_box.addItem(cmap_icon, cmap)
@@ -478,9 +494,10 @@ def init(self):
         # Set remaining properties
         set_box_value(cmaps_box, rcParams['image.cmap'])
         cmaps_box.setIconSize(QC.QSize(*cmap_size))
-        cmaps_box.setToolTip("Colormap to be used for the corresponding plot "
-                             "type")
         cmaps_box.currentTextChanged.connect(self.cmap_selected)
+
+        # Add cmaps_box to layout
+        box_layout.addWidget(cmaps_box)
         self.cmaps_box = cmaps_box
 
     # This function creates an icon of a colormap

prism/_gui/widgets/preferences/kwargs_dicts.py

@@ -376,7 +376,7 @@ def get_box_value(self):
             entry_type = get_box_value(entry_type_item.widget())
 
             # If the entry_type is empty or banned, skip this row
-            if(entry_type == '' or entry_type in self.banned_entries):
+            if not entry_type or entry_type in self.banned_entries:
                 continue
 
             # Obtain the value of the corresponding field box
@@ -419,7 +419,7 @@ def set_box_value(self, page_dict):
             entry_type = get_box_value(entry_type_item.widget())
 
             # Delete this entry if not in page_dict or if it is not allowed
-            if(entry_type not in page_dict or (entry_type == '') or
+            if(entry_type not in page_dict or not entry_type or
                entry_type in self.banned_entries):
                 self.remove_editable_entry(entry_type_item.widget())
                 continue
@@ -552,7 +552,7 @@ def entry_type_selected(self, entry_type, kwargs_box):
         cur_box = self.kwargs_grid.itemAt(index+1).widget()
 
         # Check what entry_type is given and act accordingly
-        if(entry_type == ''):
+        if not entry_type:
             # If '' is selected, use an empty label widget
             field_box = QW.QLabel('')
         elif entry_type in self.banned_entries:

prism/_gui/widgets/preferences/tests/test_kwargs_dicts.py

@@ -254,7 +254,7 @@ class TestKwargsDictDialog_EntryTypes(object):
     @pytest.mark.parametrize(
         "page_name, entry_type, field_type, field_value",
         [('impl_kwargs_2D', 'alpha', QW.QDoubleSpinBox, 0.5),
-         ('impl_kwargs_3D', 'cmap', ColorMapBox, cm.get_cmap('rainforest')),
+         ('impl_kwargs_3D', 'cmap', ColorMapBox, cm.get_cmap('cmr.freeze')),
          ('los_kwargs_2D', 'color', ColorBox, 'cyan'),
          ('fig_kwargs', 'dpi', QW.QSpinBox, 175),
          ('fig_kwargs', 'figsize', FigSizeBox, (13, 13)),

prism/_gui/widgets/viewing_area.py

@@ -167,7 +167,7 @@ def save_view(self):
             **options)
 
         # If filename was provided, save image
-        if(filename != ''):
+        if filename:
             # Grab the current state of the projection area as a Pixmap
             pixmap = self.proj_area.grab()
 

prism/_internal.py

@@ -274,7 +274,7 @@ def check_vals(values, name, *args):
         raise_error(err_msg, InputError, logger)
 
     # Loop over all criteria
-    while len(args):
+    while args:
         # Check for bool
         if 'bool' in args:
             # Convert values to str

prism/_pipeline.py

@@ -246,7 +246,6 @@ def __repr__(self):
 
             # Add the default parameter dicts to it
             default_dict.update(self._get_default_parameters())
-            default_dict.update(self._emulator._get_default_parameters())
             default_dict.update(self._Projection__get_default_parameters())
 
             # Loop over all items in prism_dict and check if it is default
@@ -263,7 +262,9 @@ def __repr__(self):
                         par_repr.append("%r: %r" % (key, val))
 
             # Convert par_repr from list to dict and add it to str_repr
-            str_repr.append("prism_par={%s}" % (", ".join(map(str, par_repr))))
+            if par_repr:
+                str_repr.append("prism_par={%s}"
+                                % (", ".join(map(str, par_repr))))
 
         # Add the emul_type representation if it is not default
         emul_repr = "%s.%s" % (self._emulator.__class__.__module__,
@@ -1106,7 +1107,7 @@ def _get_paths(self, root_dir, working_dir, prefix):
                 emul_dirs.sort(key=lambda x: x[1], reverse=True)
 
                 # If no working directory exists, create a new one
-                if not len(emul_dirs):
+                if not emul_dirs:
                     working_dir = ''.join([prefix_new, '0'])
                     self._working_dir = path.join(self._root_dir, working_dir)
                     os.mkdir(self._working_dir)
@@ -1119,6 +1120,19 @@ def _get_paths(self, root_dir, working_dir, prefix):
                     logger.info("Working directories found, set to %r."
                                 % (path.basename(self._working_dir)))
 
+            # If one specified a working directory, use it
+            elif isinstance(working_dir, str):
+                self._working_dir = path.join(self._root_dir, working_dir)
+                logger.info("Working directory set to %r." % (working_dir))
+
+                # Check if this directory already exists and create it if not
+                try:
+                    os.mkdir(self._working_dir)
+                except OSError:
+                    pass
+                else:
+                    logger.info("Working directory did not exist, created it.")
+
             # If one requested a new working directory
             elif working_dir is True:
                 # Obtain list of working directories that satisfy naming scheme
@@ -1152,25 +1166,6 @@ def _get_paths(self, root_dir, working_dir, prefix):
                 logger.info("New working directory requested, created %r."
                             % (path.basename(working_dir)))
 
-            # If one specified a working directory, use it
-            elif isinstance(working_dir, str):
-                self._working_dir = path.join(self._root_dir, working_dir)
-                logger.info("Working directory set to %r." % (working_dir))
-
-                # Check if this directory already exists and create it if not
-                try:
-                    os.mkdir(self._working_dir)
-                except OSError:
-                    pass
-                else:
-                    logger.info("Working directory did not exist, created it.")
-
-            # If one provided an integer, raise warning about it
-            elif isinstance(working_dir, int):
-                err_msg = ("Input argument 'working_dir' cannot be of type "
-                           "int!")
-                raise_error(err_msg, TypeError, logger)
-
             # If anything else is given, it is invalid
             else:
                 err_msg = "Input argument 'working_dir' is invalid!"
@@ -2235,7 +2230,7 @@ def _evaluate_sam_set(self, emul_i, sam_set, exec_code):
                 sam_idx = self._comm.bcast(sam_idx, 0)
 
                 # Check that sam_idx is still holding plausible samples
-                if not len(sam_idx):
+                if not sam_idx.size:
                     # If not, stop analysis
                     break
                 else:
@@ -2327,9 +2322,9 @@ def analyze(self, *, impl_cut=None):
 
             # Save impl_par to hdf5
             self._save_data({
-                    'impl_par': {
-                        'impl_cut': self._impl_cut[emul_i],
-                        'cut_idx': self._cut_idx[emul_i]}})
+                'impl_par': {
+                    'impl_cut': self._impl_cut[emul_i],
+                    'cut_idx': self._cut_idx[emul_i]}})
 
             # Create an emulator evaluation sample set
             eval_sam_set = self._get_eval_sam_set(emul_i)
@@ -2959,29 +2954,29 @@ def f(x):
                             'active_par_data' in ccheck_flat[i]]
                 print("  - {0: <{1}}\t{2}".format(
                     "'active_par_data'?", width-4, "No (%s)" % (ccheck_i) if
-                    len(ccheck_i) else "Yes"))
+                    ccheck_i else "Yes"))
 
                 # Check if all regression processes have been done if requested
                 if self._emulator._method in ('regression', 'full'):
                     ccheck_i = [i for i in range(n_emul_s) if
                                 'regression' in ccheck_flat[i]]
                     print("  - {0: <{1}}\t{2}".format(
                         "'regression'?", width-4, "No (%s)" % (ccheck_i) if
-                        len(ccheck_i) else "Yes"))
+                        ccheck_i else "Yes"))
 
                 # Check if all covariance matrices have been determined
                 ccheck_i = [i for i in range(n_emul_s) if
                             'cov_mat' in ccheck_flat[i]]
                 print("  - {0: <{1}}\t{2}".format(
                     "'cov_mat'?", width-4, "No (%s)" % (ccheck_i) if
-                    len(ccheck_i) else "Yes"))
+                    ccheck_i else "Yes"))
 
                 # Check if all exp_dot_terms have been determined
                 ccheck_i = [i for i in range(n_emul_s) if
                             'exp_dot_term' in ccheck_flat[i]]
                 print("  - {0: <{1}}\t{2}".format(
                     "'exp_dot_term'?", width-4, "No (%s)" % (ccheck_i) if
-                    len(ccheck_i) else "Yes"))
+                    ccheck_i else "Yes"))
             print("-"*width)
 
             # PARAMETER SPACE
@@ -3430,9 +3425,9 @@ def _process_call_str(pipeline_obj, string):
         str_list = string.split('.')
 
         # If the first element is 'pipe', it refers to a Pipeline attribute
-        if str_list.pop(0) == 'pipe':
+        if(str_list.pop(0) == 'pipe'):
             # Remove 'pipe' again in case 'pipe.pipe.xxx' was provided
-            if len(str_list) and str_list[0] == 'pipe':
+            if str_list and (str_list[0] == 'pipe'):
                 str_list.pop(0)
 
             # Retrieve the attribute that string refers to

prism/_projection.py

@@ -138,7 +138,7 @@ def project(self, emul_i=None, proj_par=None, **kwargs):
             implausibility (top/left) plot in the 2D projection figures. It
             takes all arguments that can be provided to the
             :func:`~matplotlib.pyplot.plot` function.
-        impl_kwargs_3D : dict. Default: {'cmap': 'rainforest_r'}
+        impl_kwargs_3D : dict. Default: {'cmap': 'cmr.rainforest_r'}
             Dict of keyword arguments to be used for making the minimum
             implausibility (top/left) plot in the 3D projection figures. It
             takes all arguments that can be provided to the
@@ -148,7 +148,7 @@ def project(self, emul_i=None, proj_par=None, **kwargs):
             (bottom/right) plot in the 2D projection figures. It takes all
             arguments that can be provided to the
             :func:`~matplotlib.pyplot.plot` function.
-        los_kwargs_3D : dict. Default: {'cmap': 'freeze'}
+        los_kwargs_3D : dict. Default: {'cmap': 'cmr.freeze'}
             Dict of keyword arguments to be used for making the line-of-sight
             (bottom/right) plot in the 3D projection figures. It takes all
             arguments that can be provided to the
@@ -594,8 +594,8 @@ def __draw_3D_proj_fig(self, hcube, impl_min, impl_los, proj_res):
             # Therefore, values up to max(z_los)/N has the color for 0
             min_los = min(1, np.max(z_los))/self.__los_kwargs_3D['cmap'].N
 
-            # Set all z_min to impl_cut if its corresponding z_los <= min_los
-            z_min[z_los <= min_los] = impl_cut
+            # Set all z_min to impl_cut if its corresponding z_los < min_los
+            z_min[z_los < min_los] = impl_cut
 
         # Create plotted parameter value grid
         x = np.linspace(*self._modellink._par_rng[par1], gridsize[0])
@@ -818,7 +818,7 @@ def __get_req_hcubes(self, emul_i, proj_par):
                 hcubes.extend(proj_par[np_array(hcube_idx)].tolist())
             if self.__proj_3D:
                 hcube_idx = list(combinations(range(len(proj_par)), 2))
-                if len(hcube_idx):
+                if hcube_idx:
                     hcubes.extend(proj_par[np_array(hcube_idx)].tolist())
 
             # Add the emulator iteration in front of all hcubes
@@ -984,9 +984,9 @@ def __get_default_input_arguments(self):
         # Create input argument dicts with default figure parameters
         fig_kwargs = {'dpi': 100}
         impl_kwargs_2D = {}
-        impl_kwargs_3D = {'cmap': 'rainforest_r'}
+        impl_kwargs_3D = {'cmap': 'cmr.rainforest_r'}
         los_kwargs_2D = {}
-        los_kwargs_3D = {'cmap': 'freeze'}
+        los_kwargs_3D = {'cmap': 'cmr.freeze'}
         line_kwargs_est = {'linestyle': '--',
                            'color': 'grey'}
         line_kwargs_cut = {'color': 'r'}