Merge pull request #2810 from PMEAL/dev #patch

Release v3.2.1

.github/workflows/tests.yml

@@ -1,6 +1,6 @@
 name: Tests
 
-on: [push]
+on: [pull_request]
 
 jobs:
   build:
@@ -15,7 +15,6 @@ jobs:
       max-parallel: 9
       matrix:
         python-version: ['3.9', '3.10', '3.11']
-        # Add macos-latest to the next line once #2451 is fixed
         os: [ubuntu-latest, windows-latest, macos-latest]
         include:
         - os: ubuntu-latest

openpnm/__version__.py

@@ -1 +1 @@
-__version__ = '3.2.0.dev0'
+__version__ = '3.2.0.dev4'

openpnm/algorithms/__init__.py

@@ -13,6 +13,8 @@
 from ._transient_advection_diffusion import *
 
 from ._fourier_conduction import *
+from ._transient_fourier_conduction import *
+
 from ._ohmic_conduction import *
 
 from ._drainage import *

openpnm/algorithms/_transient_fourier_conduction.py

@@ -0,0 +1,30 @@
+import logging
+from openpnm.algorithms import TransientReactiveTransport, FourierConduction
+
+
+__all__ = ['TransientFourierConduction']
+
+
+logger = logging.getLogger(__name__)
+
+
+class TransientFourierConductionSettings():
+    r"""
+
+    Parameters
+    ----------
+    %(TransientFourierConduction.parameters)s
+
+    """
+    quantity = 'pore.temperature'
+    conductance = 'throat.thermal_conductance'
+    pore_volume = 'pore.volume'
+
+
+class TransientFourierConduction(TransientReactiveTransport, FourierConduction):
+    r"""
+    A class to simulate transient thermal diffusion with heat source
+    """
+
+    def __init__(self, name='trans_fourier_?', **kwargs):
+        super().__init__(name=name, **kwargs)

openpnm/algorithms/_transport.py

@@ -312,7 +312,7 @@ def rate(self, pores=[], throats=[], mode='group'):
             g = np.tile(g, (2, 1)).T    # Make conductance an Nt by 2 matrix
         # The next line is critical for rates to be correct
         g = np.flip(g, axis=1)
-        Qt = np.diff(g*X12, axis=1).squeeze()
+        Qt = np.diff(g*X12, axis=1).ravel()
 
         if throats.size:
             R = np.absolute(Qt[throats])

openpnm/core/_base2.py

@@ -315,7 +315,7 @@ def _get_name(self):
     name = property(_get_name, _set_name)
 
     def _get_project(self):
-        for proj in ws.values():
+        for proj in list(ws.values()):
             if self in proj:
                 return proj
 

openpnm/phase/_phase.py

@@ -57,12 +57,12 @@ def __setitem__(self, key, value):
         if '@' not in key:
             super().__setitem__(key, value)
         else:
+            # Deal with the fact that the label might only exist on the network
             propname, domain = key.split('@')
             element, prop = propname.split('.', 1)
-            # Fetch array from self
-            try:
+            try:  # Fetch array from self if present
                 temp = self[element + '.' + prop]
-            except KeyError:
+            except KeyError:  # Otherwise create it
                 temp = self._initialize_empty_array_like(value, element)
                 self[element + '.' + prop] = temp
             # Insert values into masked locations

openpnm/topotools/_topotools.py

@@ -210,9 +210,6 @@ def trim(network, pores=[], throats=[]):
         if (obj.Np == Np_old) and (obj.Nt == Nt_old):
             Ps = Pkeep_inds
             Ts = Tkeep_inds
-        else:  # If subdomain object then Np/Nt < Np/Nt_old
-            Ps = obj.to_local(pores=Pkeep_inds, missing_vals=None)
-            Ts = obj.to_local(throats=Tkeep_inds, missing_vals=None)
         for key in list(obj.keys()):
             temp = obj.pop(key)
             if key.split('.', 1)[0] == 'throat':

openpnm/utils/_project.py

@@ -15,44 +15,9 @@
 
 __all__ = [
     'Project',
-    'SimpleList',
 ]
 
 
-class SimpleList:
-    """A simple list class that prevents duplicates, and more!"""
-    def __init__(self, data=None):
-        if (data is not None):
-            self._list = list(data)
-        else:
-            self._list = list()
-
-    def __repr__(self):  # pragma: no cover
-        return self._list.__repr__()
-
-    def __len__(self):
-        return len(self._list)
-
-    def __getitem__(self, ii):
-        if isinstance(ii, slice):
-            return self.__class__(self._list[ii])
-        else:
-            return self._list[ii]
-
-    def __delitem__(self, ii):
-        del self._list[ii]
-
-    def __str__(self):  # pragma: no cover
-        return str(self._list)
-
-    def __iter__(self):
-        return self._list.__iter__()
-
-    def append(self, item):
-        if item not in self._list:
-            self._list.append(item)
-
-
 class ProjectSettings(SettingsAttr):
     r"""
     uuid : str
@@ -74,7 +39,7 @@ def name(self, name):
         self._name = name
 
 
-class Project(SimpleList):
+class Project(list):
     r"""
     This class provides a container for all OpenPNM objects in a given
     simulation.
@@ -109,16 +74,14 @@ def __init__(self, *args, **kwargs):
         ws[self.settings['name']] = self
 
     def __getitem__(self, key):
-        if isinstance(key, str):  # Enable dict-style retrieval if key is a string
-            obj = None
-            for item in self:
-                if item.name == key:
-                    obj = item
-            if obj is None:
-                raise KeyError(key)
-        else:
-            obj = super().__getitem__(key)
-        return obj
+        try:
+            return super().__getitem__(key)
+        except TypeError:
+            if isinstance(key, str):  # Enable dict-style lookup if key is a string
+                for item in self:
+                    if item.name == key:
+                        return item
+            raise KeyError(key)
 
     def copy(self, name=None):
         r"""

openpnm/utils/_workspace.py

@@ -123,7 +123,7 @@ def _validate_name(self, name=None):
                 name = name + '_01'
             prefix, count = name.rsplit('_', 1)
             n = [0]
-            for item in self.keys():
+            for item in list(self.keys()):
                 if item.startswith(prefix+'_'):
                     n.append(int(item.split(prefix+'_')[1]))
             name = prefix+'_'+str(max(n)+1).zfill(2)

openpnm/visualization/_plottools.py

@@ -27,6 +27,7 @@ def plot_connections(network,
                      ax=None,
                      size_by=None,
                      color_by=None,
+                     label_by=None,
                      cmap='jet',
                      color='b',
                      alpha=1.0,
@@ -55,8 +56,10 @@ def plot_connections(network,
         An ndarray of throat values (e.g. alg['throat.rate']).  These
         values are used to scale the ``linewidth``, so if the lines are too
         thin, then increase ``linewidth``.
-    color_by : str or array_like (optional)
+    color_by : array_like (optional)
         An ndarray of throat values (e.g. alg['throat.rate']).
+    label_by : array_like (optional)
+        An array or list of values to use as labels
     cmap : str or cmap object (optional)
         The matplotlib colormap to use if specfying a throat property
         for ``color_by``
@@ -71,6 +74,9 @@ def plot_connections(network,
         Controls the thickness of drawn lines.  Is used to scale the thickness
         if ``size_by`` is given. Default is 1. If a value is provided for
         ``size_by`` then they are used to scale the ``linewidth``.
+    font : dict
+        A dictionary of key-value pairs that are used to control the font
+        appearance if `label_by` is provided.
     **kwargs : dict
         All other keyword arguments are passed on to the ``Line3DCollection``
         class of matplotlib, so check their documentation for additional
@@ -149,20 +155,35 @@ class of matplotlib, so check their documentation for additional
     if 'c' in kwargs.keys():
         color = kwargs.pop('c')
     color = mcolors.to_rgb(color) + tuple([alpha])
+    if isinstance(cmap, str):
+        try:
+            cmap = plt.colormaps.get_cmap(cmap)
+        except AttributeError:
+            cmap = plt.cm.get_cmap(cmap)
     # Override colors with color_by if given
     if color_by is not None:
+        color_by = np.array(color_by, dtype=np.float16)
         if len(color_by) != len(Ts):
             color_by = color_by[Ts]
         if not np.all(np.isfinite(color_by)):
             color_by[~np.isfinite(color_by)] = 0
             logger.warning('nans or infs found in color_by array, setting to 0')
-        color = cm.get_cmap(name=cmap)(color_by / color_by.max())
+        vmin = kwargs.pop('vmin', color_by.min())
+        vmax = kwargs.pop('vmax', color_by.max())
+        cscale = (color_by - vmin) / (vmax - vmin)
+        color = cmap(cscale)
         color[:, 3] = alpha
     if size_by is not None:
+        if len(size_by) != len(Ts):
+            size_by = size_by[Ts]
         if not np.all(np.isfinite(size_by)):
             size_by[~np.isfinite(size_by)] = 0
             logger.warning('nans or infs found in size_by array, setting to 0')
         linewidth = size_by / size_by.max() * linewidth
+    if label_by is not None:
+        if len(label_by) != len(Ts):
+            label_by = label_by[Ts]
+    fontkws = kwargs.pop('font', {})
 
     if ThreeD:
         lc = Line3DCollection(throat_pos, colors=color, cmap=cmap,
@@ -172,6 +193,12 @@ class of matplotlib, so check their documentation for additional
         lc = LineCollection(throat_pos, colors=color, cmap=cmap,
                             linestyles=linestyle, linewidths=linewidth,
                             antialiaseds=np.ones_like(network.Ts), **kwargs)
+        if label_by is not None:
+            for count, (P1, P2) in enumerate(network.conns[Ts, :]):
+                i, j, k = np.mean(network.coords[[P1, P2], :], axis=0)
+                ax.text(i, j, label_by[count],
+                        ha='center', va='center',
+                        **fontkws)
     ax.add_collection(lc)
 
     if np.size(Ts) > 0:
@@ -187,6 +214,7 @@ def plot_coordinates(network,
                      ax=None,
                      size_by=None,
                      color_by=None,
+                     label_by=None,
                      cmap='jet',
                      color='r',
                      alpha=1.0,
@@ -215,6 +243,8 @@ def plot_coordinates(network,
         you should do `size_by=net['pore.diameter']**2`.
     color_by : str or array_like
         An ndarray of pore values (e.g. alg['pore.concentration']).
+    label_by : array_like (optional)
+        An array or list of values to use as labels
     cmap : str or cmap object
         The matplotlib colormap to use if specfying a pore property
         for ``color_by``
@@ -228,6 +258,9 @@ def plot_coordinates(network,
     markersize : scalar
         Controls size of marker, default is 1.0.  This value is used to scale
         the ``size_by`` argument if given.
+    font : dict
+        A dictionary of key-value pairs that are used to control the font
+        appearance if `label_by` is provided.
     **kwargs
         All other keyword arguments are passed on to the ``scatter``
         function of matplotlib, so check their documentation for additional
@@ -310,18 +343,33 @@ def plot_coordinates(network,
         color = kwargs.pop('c')
     if 's' in kwargs.keys():
         markersize = kwargs.pop('s')
+    if isinstance(cmap, str):
+        try:
+            cmap = plt.colormaps.get_cmap(cmap)
+        except AttributeError:
+            cmap = plt.cm.get_cmap(cmap)
     if color_by is not None:
-        color_by = color_by[Ps]
+        color_by = np.array(color_by, dtype=np.float16)
+        if len(color_by) != len(Ps):
+            color_by = color_by[Ps]
         if not np.all(np.isfinite(color_by)):
             color_by[~np.isfinite(color_by)] = 0
             logger.warning('nans or infs found in color_by array, setting to 0')
-        color = cm.get_cmap(name=cmap)(color_by / color_by.max())
+        vmin = kwargs.pop('vmin', color_by.min())
+        vmax = kwargs.pop('vmax', color_by.max())
+        cscale = (color_by - vmin) / (vmax - vmin)
+        color = cmap(cscale)
     if size_by is not None:
+        if len(size_by) != len(Ps):
+            size_by = size_by[Ps]
         if not np.all(np.isfinite(size_by)):
             size_by[~np.isfinite(size_by)] = 0
             logger.warning('nans or infs found in size_by array, setting to 0')
         markersize = size_by / size_by.max() * markersize
-
+    if label_by is not None:
+        if len(label_by) != len(Ps):
+            label_by = label_by[Ps]
+    fontkws = kwargs.pop('font', {})
     if ThreeD:
         sc = ax.scatter(X, Y, Z,
                         c=color,
@@ -338,6 +386,11 @@ def plot_coordinates(network,
                         marker=marker,
                         alpha=alpha,
                         **kwargs)
+        if label_by is not None:
+            for count, (i, j, k) in enumerate(network.coords[Ps, :]):
+                ax.text(i, j, label_by[count],
+                        ha='center', va='center',
+                        **fontkws)
         _scale_axes(ax=ax, X=Xl, Y=Yl, Z=np.zeros_like(Yl))
 
     _label_axes(ax=ax, X=Xl, Y=Yl, Z=Zl)

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.2.0.dev0
+current_version = 3.2.0.dev4
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)\.(?P<release>\D+)(?P<build>\d+)?
 serialize = {major}.{minor}.{patch}.{release}{build}