Merge branch 'master' of https://github.com/1313e/PRISM

README.rst

@@ -178,13 +178,13 @@ And, finally, if you use *PRISM* as part of your workflow in a scientific public
 
 Acknowledgements
 ================
-Special thanks to Alan Duffy, Darren Croton, Simon Mutch and Manodeep Sinha for providing many valuable suggestions and constructive feedback points.
+Special thanks to Darren Croton, Alan Duffy, Michael Goldstein, Simon Mutch, Manodeep Sinha and Ian Vernon for providing many valuable suggestions and constructive feedback points.
 Huge thanks to James Josephides for making the *PRISM* logo.
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/prism.svg?logo=pypi&logoColor=white&label=PyPI
     :target: https://pypi.python.org/pypi/prism
     :alt: PyPI - Latest Release
-.. |Python| image:: https://img.shields.io/pypi/pyversions/prism.svg?logo=python&logoColor=white&label=Python
+.. |Python| image:: https://img.shields.io/badge/Python-3.5%2B-blue?logo=python&logoColor=white
     :target: https://pypi.python.org/pypi/prism
     :alt: PyPI - Python Versions
 .. |Azure| image:: https://img.shields.io/azure-devops/build/1313e/2f7c67c7-61eb-4e70-9ff3-7f54f8e39987/1?logo=azure-pipelines&logoColor=white&label=Azure

docs/source/conf.py

@@ -60,6 +60,7 @@
                        'matplotlib': ('https://matplotlib.org', None),
                        'h5py': ('https://h5py.readthedocs.io/en/stable', None),
                        'e13tools': ('https://e13tools.readthedocs.io', None),
+                       'cmasher': ('https://cmasher.readthedocs.io', None),
                        'PyQt5': ('https://www.riverbankcomputing.com/static/Docs/PyQt5', None)}
 
 # Autodoc configuration

docs/source/user/call_model.inc

@@ -11,9 +11,12 @@ Input arguments
 ###############
 Depending on the values of the :attr:`~prism.modellink.ModelLink.multi_call` and :attr:`~prism.modellink.ModelLink.MPI_call` flags (where the first is set by the :attr:`~prism.modellink.ModelLink.call_type` flag), the :obj:`~prism.Pipeline` instance will use the :meth:`~prism.modellink.ModelLink.call_model` method differently.
 As explained in :ref:`writing_modellink`, every model evaluation sample is requested individually in serial by default, which corresponds to :attr:`~prism.modellink.ModelLink.multi_call` is :pycode:`False` and :attr:`~prism.modellink.ModelLink.MPI_call` is :pycode:`False`.
-When single-calling a model, *PRISM* expects an array-like container back with shape :pycode:`(n_data)`, where the order of the elements is the same as the order of the requested :pycode:`data_idx`.
+When single-calling a model, *PRISM* expects an array-like container back with shape :pycode:`(n_data,)`, where the order of the elements is the same as the order of the requested :pycode:`data_idx`.
 If we assume that we have an instance of the :class:`LineLink` class (introduced in `line_link.py`_) called :pycode:`modellink_obj` and want to evaluate the model three times for all data points, then the model would be called as (solely by the controller rank)::
 
+    # Import SortedDict class
+    from sortedcontainers import SortedDict as sdict
+
     # Get emul_i, sam_set and data_idx
     emul_i = 1
     sam_set = np.random.rand(3, modellink_obj.n_par)

docs/source/user/hybrid_sampling.inc

@@ -115,7 +115,7 @@ For this, we need to define an `lnpost()` function, for which we will use a simp
         data_var = [err[0]**2 for err in pipe.modellink.data_err]
 
         # Calculate the posterior probability and return it
-        sigma_2 = md_var+data_var
+        sigma2 = md_var+data_var
         diff = pipe.modellink.data_val-mod_out
         return(-0.5*(np.sum(diff**2/sigma2)))
 

docs/source/user/projections.inc

@@ -128,15 +128,22 @@ It should therefore only be used when necessary.
     If :pycode:`False`, only the parameter space in which the emulator is defined is shown, which more often than not allows for more details to be seen in the projection figure.
     If :pycode:`True`, the full model parameter space is used for the axes limits, allowing projection figures from different iterations to be compared with each other more easily.
 
+.. versionadded:: 1.2.4
+    The `full_impl_rng` argument is a bool, which controls whether the lower limit for the minimum implausibility plot should be set to zero (:pycode:`True`) or to the lowest implausibility value plotted (:pycode:`False`), with the latter being the default.
+    If :pycode:`False`, only the implausibility range in which plausible samples are plotted will be used, which increases the amount of detail in the minimum implausibility plot.
+    If :pycode:`True`, the entire implausibility range that can hold plausible samples is used, allowing for the relative implausibility difference between samples to be interpreted correctly.
+    Set this value to :pycode:`True` if one wishes to have the same plotting behavior as in versions earlier than v1.2.4.
+
 The `force` argument is a bool, which controls what to do if a projection is requested for which data already exists.
 If :pycode:`False` (default), it will use the previously acquired projection data to create the projection figure if it does not exist, skip if it does or return the figure data if `figure` is :pycode:`False`.
 If :pycode:`True`, the projection data and all associated projection figures will be deleted, and the projection will be recalculated.
 
-The remaining seven arguments are keyword argument dicts, that need to be passed to the various different plotting functions that are used for creating the projection figures.
+The remaining eight arguments are keyword argument dicts, that need to be passed to the various different plotting functions that are used for creating the projection figures.
 The `fig_kwargs` dict is passed to the :func:`~matplotlib.pyplot.figure` function when creating the projection figure instance.
 The `impl_kwargs_2D` and `los_kwargs_2D` dicts are passed to the :func:`~matplotlib.pyplot.plot` function when making the minimum implausibility and line-of-sight depth subplots, respectively, for the 2D projections.
 Similarly, the `impl_kwargs_3D` and `los_kwargs_3D` dicts are passed to the :func:`~matplotlib.pyplot.hexbin` function for 3D projections.
-And, finally, the `line_kwargs_est` and `line_kwargs_cut` dicts are passed to the :func:`~matplotlib.pyplot.draw` function for drawing the parameter estimate and implausibility cut-off lines.
+The `line_kwargs_est` and `line_kwargs_cut` dicts are passed to the :func:`~matplotlib.pyplot.draw` function for drawing the parameter estimate and implausibility cut-off lines.
+And, finally, the `arrow_kwargs_est` dict is passed to the :func:`~matplotlib.pyplot.arrow` function for drawing the parameter estimate arrow in case its line is out-of-range.
 
 Crystal (GUI)
 #############

prism/__version__.py

@@ -10,7 +10,7 @@
 
 # %% VERSIONS
 # Default/Latest/Current version
-__version__ = '1.2.3'
+__version__ = '1.3.1'
 
 # Compatibility versions
-compat_version = ['1.0.0rc12']
+compat_version = ['1.0.0rc12', '1.2.2']

prism/_gui/widgets/conftest.py

@@ -5,7 +5,7 @@
 from os import path
 
 # Package imports
-from qtpy import QtWidgets as QW
+from qtpy import QtCore as QC, QtWidgets as QW
 import pytest
 
 # PRISM imports
@@ -14,6 +14,10 @@
 from prism.modellink.tests.modellink import GaussianLink3D
 
 
+# Set the default Locale to English
+QC.QLocale.setDefault(QC.QLocale(31))
+
+
 # %% GLOBALS
 DIR_PATH = path.abspath(path.dirname(__file__))     # Path to tests directory
 

prism/_gui/widgets/preferences/custom_boxes.py

@@ -20,6 +20,7 @@
 import e13tools as e13
 from matplotlib import cm, rcParams
 from matplotlib.colors import BASE_COLORS, CSS4_COLORS, to_rgba
+import matplotlib.pyplot as plt
 import numpy as np
 from qtpy import QtCore as QC, QtGui as QG, QtWidgets as QW
 from sortedcontainers import SortedDict as sdict, SortedSet as sset
@@ -31,7 +32,7 @@
     QW_QSpinBox, get_box_value, set_box_value)
 
 # All declaration
-__all__ = ['ColorBox', 'ColorMapBox', 'DefaultBox', 'FigSizeBox']
+__all__ = ['ColorBox', 'ColorMapBox', 'DefaultBox']
 
 
 # %% CLASS DEFINITIONS
@@ -455,9 +456,10 @@ def init(self):
         std_cmaps_r = sset([cmap+'_r' for cmap in std_cmaps])
 
         # Obtain a list with all colormaps and their reverses
-        all_cmaps = sset([cmap for cmap in cm.cmap_d
+        all_cmaps = sset([cmap for cmap in plt.colormaps()
                           if not cmap.endswith('_r')])
-        all_cmaps_r = sset([cmap for cmap in cm.cmap_d if cmap.endswith('_r')])
+        all_cmaps_r = sset([cmap for cmap in plt.colormaps()
+                            if cmap.endswith('_r')])
 
         # Gather all sets together
         cmaps = (std_cmaps, std_cmaps_r, all_cmaps, all_cmaps_r)
@@ -804,106 +806,3 @@ def set_box_value(self, value):
 
         set_box_value(self.type_box, self.type_dict[type(value)])
         set_box_value(self.value_box, value)
-
-
-# Make class with a special box for setting the figsize
-class FigSizeBox(BaseBox):
-    """
-    Defines the :class:`~FigSizeBox` class.
-
-    This class is used for making the 'figsize' entry in the
-    :class:`~prism._gui.widgets.preferences.KwargsDictDialogPage` class.
-
-    """
-
-    @e13.docstring_substitute(optional=kwargs_doc.format(
-        'prism._gui.widgets.core.BaseBox'))
-    def __init__(self, *args, **kwargs):
-        """
-        Initialize an instance of the :class:`~FigSizeBox` class.
-
-        %(optional)s
-
-        """
-
-        # Call super constructor
-        super().__init__(*args, **kwargs)
-
-        # Create the figsize box
-        self.init()
-
-    # This function creates the figsize box
-    def init(self):
-        """
-        Sets up the figure size entry after it has been initialized.
-
-        This function is mainly responsible for simply creating the two double
-        spinboxes that allow for the width and height to be set.
-
-        """
-
-        # Create the box_layout
-        box_layout = QW.QHBoxLayout(self)
-        box_layout.setContentsMargins(0, 0, 0, 0)
-        self.setToolTip("Figure size dimensions to use for the projection "
-                        "figure")
-
-        # Create two double spinboxes for the width and height
-        # WIDTH
-        width_box = QW_QDoubleSpinBox()
-        width_box.setRange(1, 9999999)
-        width_box.setSuffix("'")
-        width_box.setStepType(width_box.AdaptiveDecimalStepType)
-        width_box.setToolTip("Width (in inches) of projection figure")
-        self.width_box = width_box
-
-        # HEIGHT
-        height_box = QW_QDoubleSpinBox()
-        height_box.setRange(1, 9999999)
-        height_box.setSuffix("'")
-        height_box.setToolTip("Height (in inches) of projection figure")
-        self.height_box = height_box
-
-        # Also create a textlabel with 'X'
-        x_label = QW.QLabel('X')
-        x_label.setSizePolicy(QW.QSizePolicy.Fixed, QW.QSizePolicy.Fixed)
-
-        # Add everything to the box_layout
-        box_layout.addWidget(width_box)
-        box_layout.addWidget(x_label)
-        box_layout.addWidget(height_box)
-
-        # Set default value
-        set_box_value(self, rcParams['figure.figsize'])
-
-    # This function retrieves a value of this special box
-    def get_box_value(self):
-        """
-        Returns the current width and height of this figsize box and returns
-        it.
-
-        Returns
-        -------
-        figsize : tuple
-            A tuple containing the width and height values of the figsize,
-            formatted as `(width, height)`.
-
-        """
-
-        return((get_box_value(self.width_box), get_box_value(self.height_box)))
-
-    # This function sets the value of this special box
-    def set_box_value(self, value):
-        """
-        Sets the current value of the figsize box to `value`.
-
-        Parameters
-        ----------
-        value : tuple
-            A tuple containing the width and height values of the figsize,
-            formatted as `(width, height)`.
-
-        """
-
-        set_box_value(self.width_box, value[0])
-        set_box_value(self.height_box, value[1])

prism/_gui/widgets/preferences/kwargs_dicts.py

@@ -24,7 +24,7 @@
     BaseBox, QW_QComboBox, QW_QDoubleSpinBox, QW_QEditableComboBox, QW_QLabel,
     QW_QSpinBox, get_box_value, set_box_value)
 from prism._gui.widgets.preferences.custom_boxes import (
-    ColorBox, ColorMapBox, DefaultBox, FigSizeBox)
+    ColorBox, ColorMapBox, DefaultBox)
 
 # All declaration
 __all__ = ['KwargsDictBoxLayout', 'KwargsDictDialog', 'KwargsDictDialogPage']
@@ -496,12 +496,13 @@ def add_editable_entry(self):
             delete_but.setText('X')
 
         # Determine the number of entries currently in kwargs_grid
-        n_rows = self.kwargs_grid.count()//3
+        next_row = self.kwargs_grid.getItemPosition(
+            self.kwargs_grid.count()-1)[0]+1
 
         # Make a new editable entry
-        self.kwargs_grid.addWidget(delete_but, n_rows, 0)
-        self.kwargs_grid.addWidget(kwargs_box, n_rows, 1)
-        self.kwargs_grid.addWidget(QW.QLabel(''), n_rows, 2)
+        self.kwargs_grid.addWidget(delete_but, next_row, 0)
+        self.kwargs_grid.addWidget(kwargs_box, next_row, 1)
+        self.kwargs_grid.addWidget(QW.QLabel(''), next_row, 2)
 
     # This function deletes an editable entry
     @QC.Slot(QW.QComboBox)
@@ -614,11 +615,6 @@ def create_type_dpi(self):
                            "figure")
         return(dpi_box)
 
-    # This function creates a figsize box
-    @e13.docstring_append(create_type_doc.format('figsize'))
-    def create_type_figsize(self):
-        return(FigSizeBox())
-
     # This function creates a linestyle box
     @e13.docstring_append(create_type_doc.format('linestyle'))
     def create_type_linestyle(self):
@@ -678,6 +674,70 @@ def create_type_markersize(self):
         set_box_value(markersize_box, rcParams['lines.markersize'])
         return(markersize_box)
 
+    # This function creates a fh_arrowlength box
+    @e13.docstring_append(create_type_doc.format('fh_arrowlength'))
+    def create_type_fh_arrowlength(self):
+        # Make a double spinbox for arrow head length
+        head_length_box = QW_QDoubleSpinBox()
+        head_length_box.setRange(0, 9999999)
+        head_length_box.setDecimals(4)
+        head_length_box.setToolTip("Scaling factor for the length of the "
+                                   "plotted arrow head")
+        return(head_length_box)
+
+    # This function creates a ft_arrowlength box
+    @e13.docstring_append(create_type_doc.format('ft_arrowlength'))
+    def create_type_ft_arrowlength(self):
+        # Make a double spinbox for arrow tail length
+        tail_length_box = QW_QDoubleSpinBox()
+        tail_length_box.setRange(0, 9999999)
+        tail_length_box.setDecimals(2)
+        tail_length_box.setToolTip("Length of the plotted arrow tail relative "
+                                   "to the length of its head")
+        return(tail_length_box)
+
+    # This function creates a fh_arrowwidth box
+    @e13.docstring_append(create_type_doc.format('fh_arrowwidth'))
+    def create_type_fh_arrowwidth(self):
+        # Make a double spinbox for arrow head width
+        head_length_box = QW_QDoubleSpinBox()
+        head_length_box.setRange(0, 9999999)
+        head_length_box.setDecimals(4)
+        head_length_box.setToolTip("Scaling factor for the width of the "
+                                   "plotted arrow head")
+        return(head_length_box)
+
+    # This function creates a ft_arrowwidth box
+    @e13.docstring_append(create_type_doc.format('ft_arrowwidth'))
+    def create_type_ft_arrowwidth(self):
+        # Make a double spinbox for arrow tail width
+        tail_length_box = QW_QDoubleSpinBox()
+        tail_length_box.setRange(0, 9999999)
+        tail_length_box.setDecimals(4)
+        tail_length_box.setToolTip("Scaling factor for the width of the "
+                                   "plotted arrow tail")
+        return(tail_length_box)
+
+    # This function creates a rel_xpos box
+    @e13.docstring_append(create_type_doc.format('rel_xpos'))
+    def create_type_rel_xpos(self):
+        # Make a double spinbox for arrow relative x-position
+        x_pos_box = QW_QDoubleSpinBox()
+        x_pos_box.setRange(0, 1)
+        x_pos_box.setDecimals(4)
+        x_pos_box.setToolTip("Relative x-position of the arrow.")
+        return(x_pos_box)
+
+    # This function creates a rel_xpos box
+    @e13.docstring_append(create_type_doc.format('rel_ypos'))
+    def create_type_rel_ypos(self):
+        # Make a double spinbox for arrow relative y-position
+        y_pos_box = QW_QDoubleSpinBox()
+        y_pos_box.setRange(0, 1)
+        y_pos_box.setDecimals(4)
+        y_pos_box.setToolTip("Relative y-position of the arrow.")
+        return(y_pos_box)
+
     # This function creates a scale box
     def create_type_scale(self, axis):
         """