Port to latest holoviews

topo/__init__.py

@@ -53,7 +53,6 @@
 
 import os
 import param
-import imagen
 
 
 def version_int(v):

topo/analysis/__init__.py

@@ -7,7 +7,7 @@
 
 import numpy as np
 
-from holoviews.interface.collector import Reference
+from holoviews.core.io import Reference
 from holoviews import HSV, Image
 from holoviews.core.options import Compositor
 from holoviews.ipython import IPTestCase
@@ -29,10 +29,10 @@
 
 
 
-CoG_spec = "Image.X CoG * Image.Y CoG * Image.BlueChannel"
-XYCoG = chain.instance(group='XYCoG', name='XYCoG',
-                       operations = [image_overlay.instance(spec=CoG_spec), factory.instance()])
-Compositor.register(Compositor("Image.X CoG * Image.Y CoG", XYCoG, 'XYCoG', 'display'))
+# CoG_spec = "Image.X CoG * Image.Y CoG * Image.BlueChannel"
+# XYCoG = chain.instance(group='XYCoG', name='XYCoG',
+#                        operations = [image_overlay.instance(spec=CoG_spec), factory.instance()])
+# Compositor.register(Compositor("Image.X CoG * Image.Y CoG", XYCoG, 'XYCoG', 'display'))
 
 
 import param

topo/analysis/command.py

@@ -205,9 +205,9 @@ def _update_proj_cog(self, p, proj):
 
         timestamp = topo.sim.time()
         lbrt = sheet.bounds.lbrt()
-        xsv = Image(xcog, sheet.bounds, label=proj.name, group='X CoG',
+        xsv = Image(xcog, bounds=sheet.bounds, label=proj.name, group='X CoG',
                     vdims=[Dimension('X CoG', range=(lbrt[0], lbrt[2]))])
-        ysv = Image(ycog, sheet.bounds, label=proj.name, group='Y CoG',
+        ysv = Image(ycog, bounds=sheet.bounds, label=proj.name, group='Y CoG',
                     vdims=[Dimension('Y CoG', range=(lbrt[1], lbrt[3]))])
 
         lines = []

topo/analysis/featureresponses.py

@@ -16,7 +16,7 @@
 
 from holoviews import Image, HoloMap
 from holoviews.ipython.widgets import ProgressBar
-from holoviews.interface.collector import AttrDict
+from topo.misc.attrdict import AttrDict
 
 import topo
 import topo.base.sheetcoords
@@ -52,14 +52,14 @@ def update_sheet_activity(sheet_name, force=False):
                         src_name=sheet.name, shape=sheet.activity.shape,
                         timestamp=time)
     if not view:
-        im = Image(np.array(sheet.activity), sheet.bounds)
+        im = Image(np.array(sheet.activity), bounds=sheet.bounds)
         im.metadata=metadata
-        view = HoloMap((time, im), key_dimensions=[Time])
+        view = HoloMap((time, im), kdims=[Time])
         view.metadata = metadata
         sheet.views.Maps[name] = view
     else:
         if force or view.range('Time')[1] < time:
-            im = Image(np.array(sheet.activity), sheet.bounds)
+            im = Image(np.array(sheet.activity), bounds=sheet.bounds)
             im.metadata=metadata
             view[time] = im
     return view

topo/analysis/weights.py

@@ -105,7 +105,7 @@ def _process(self, tree, key=None):
 
             # Construct Elements
             label =' '.join([s, p])
-            histogram = Histogram(bins, edges, group="Weight Isotropy",
+            histogram = Histogram((edges, bins), group="Weight Isotropy",
                                   kdims=[Dimension('Azimuth')], label=label)
             layout.WeightIsotropy['_'.join([s, p])] = histogram
         return layout
@@ -148,7 +148,7 @@ def _process(self, tree, key=None):
             featurepref = preferences[s]
             if isinstance(featurepref, HoloMap):
                 featurepref = featurepref.last
-            feature = featurepref.value_dimensions[0]
+            feature = featurepref.vdims[0]
             feature_arr = featurepref.data.flat
             cfs = tree.CFs[p]
             deltas, weights = [], []
@@ -171,7 +171,7 @@ def _process(self, tree, key=None):
             # Construct Elements
             label = ' '.join([s,p])
             group = '%s Weight Distribution' % self.p.feature
-            histogram = Histogram(bins, edges, group=group, label=label,
+            histogram = Histogram((edges, bins), group=group, label=label,
                                   kdims=[' '.join([self.p.feature, 'Difference'])],
                                   vdims=['Weight'])
 

topo/base/cf.py

@@ -23,7 +23,7 @@
 
 import param
 from holoviews import GridSpace, Dimension, HoloMap, Layout
-from holoviews.interface.collector import AttrDict
+from topo.misc.attrdict import AttrDict
 from holoviews.core import BoundingBox, BoundingRegionParameter, Slice
 
 import patterngenerator
@@ -782,7 +782,7 @@ def view(self, sheet_x, sheet_y, timestamp=None, situated=False, **kwargs):
             matrix_data = cf.weights.copy()
             bounds = roi_bounds
 
-        sv = CFView(matrix_data, bounds, situated_bounds=situated_bounds,
+        sv = CFView(matrix_data, bounds=bounds, situated_bounds=situated_bounds,
                     input_sheet_slice=(r1, r2, c1, c2), roi_bounds=roi_bounds,
                     label=self.name, group='CF Weight')
         sv.metadata=AttrDict(timestamp=timestamp)

topo/base/generatorsheet.py

@@ -8,7 +8,7 @@
 from topo.base.patterngenerator import PatternGenerator,Constant
 from topo.base.simulation import FunctionEvent, PeriodicEventSequence
 
-from holoviews.interface.collector import AttrDict
+from topo.misc.attrdict import AttrDict
 from holoviews import Image
 
 import numpy as np
@@ -279,7 +279,7 @@ def __getitem__(self, coords):
         else:
             arr = self.activity.copy()
 
-        im = Image(arr, self.bounds,
+        im = Image(arr, bounds=self.bounds,
                    label=self.name+' Activity', group='Activity')[coords]
         im.metadata=metadata
         return im

topo/base/projection.py

@@ -12,7 +12,7 @@
 
 from imagen import Disk
 from holoviews import Image, Layout
-from holoviews.interface.collector import AttrDict
+from topo.misc.attrdict import AttrDict
 
 from sheet import Sheet
 from simulation import EPConnection
@@ -326,7 +326,7 @@ def projection_view(self, timestamp=None):
         """Returns the activity in a single projection"""
         if timestamp is None:
             timestamp = self.src.simulation.time()
-        im = Image(self.activity.copy(), self.dest.bounds,
+        im = Image(self.activity.copy(), bounds=self.dest.bounds,
                    label=self.name, group='Activity')
         im.metadata=AttrDict(proj_src_name=self.src.name,
                              precedence=self.src.precedence,

topo/base/sheet.py

@@ -24,7 +24,7 @@
 
 from holoviews import Image, Layout
 from holoviews.core import BoundingBox, BoundingRegionParameter, SheetCoordinateSystem
-from holoviews.interface.collector import AttrDict
+from topo.misc.attrdict import AttrDict
 
 from simulation import EventProcessor
 from functionfamily import TransferFn
@@ -309,7 +309,7 @@ def __getitem__(self, coords):
                             row_precedence=self.row_precedence,
                             timestamp=self.simulation.time())
 
-        image = Image(self.activity.copy(), self.bounds,
+        image = Image(self.activity.copy(), bounds=self.bounds,
                    label=self.name, group='Activity')[coords]
         image.metadata=metadata
         return image

topo/base/sheetview.py

@@ -117,7 +117,7 @@ def situated(self):
         r1, r2, c1, c2 = self.input_sheet_slice
         data[r1:r2, c1:c2] = self.data
 
-        return CFView(data, self.situated_bounds, roi_bounds=self.bounds,
+        return CFView(data, bounds=self.situated_bounds, roi_bounds=self.bounds,
                       situated_bounds=self.situated_bounds,
                       label=self.label, group=self.group)
 

topo/base/simulation.py

@@ -56,7 +56,7 @@
 import time
 import bisect
 
-from holoviews.interface.collector import AttrDict
+from topo.misc.attrdict import AttrDict
 
 #: Default path to the current simulation, from main
 #: Only to be used by script_repr(), to allow it to generate

topo/misc/commandline.py

@@ -23,26 +23,20 @@
 from param.parameterized import Parameterized
 from topo.base.simulation import OptionalSingleton
 
-try:
-    # By default, use a non-GUI backend for matplotlib.
-    from matplotlib import pyplot as plt
-    plt.switch_backend('agg')
-
-    matplotlib_imported=True
-except ImportError:
-    matplotlib_imported=False
-
 # Dummy object just for messages
 cmdline_main=Parameterized(name="CommandLine")
 
 ipython_shell_interface = None
 ipython_prompt_interface = None
 try:
     try:
-         from IPython.terminal.embed import InteractiveShellEmbed as IPShell
+        from IPython.terminal.embed import InteractiveShellEmbed as IPShell
+        from traitlets.config.loader import Config
+        from IPython.terminal.prompts import Prompts, Token
+        import IPython.lib.inputhook
     except ImportError: # Prior to IPython 1.0, InteractiveShellEmbed was found in the frontend package
         from IPython.frontend.terminal.embed import InteractiveShellEmbed as IPShell # pyflakes:ignore (try/except import)
-    from IPython.config.loader import Config
+        from IPython.config.loader import Config
     ipython_shell_interface = "InteractiveShellEmbed"
     try:
         from IPython.core.prompts import PromptManager  # pyflakes:ignore (try/except import)
@@ -224,6 +218,34 @@ def get_format(cls):
         return cls._format
 
 
+class IPythonCommandPrompt(Prompts):
+    """
+    Control over input prompt.
+
+    Several predefined formats are provided, and any of these (or any
+    arbitrary string) can be used by calling set_format() with their
+    values.
+
+    See the IPython manual for details:
+    https://ipython.readthedocs.io/en/5.x/config/details.html?highlight=Prompts
+    """
+    def in_prompt_tokens(self, cli=None):
+
+        return [
+             (Token, 'Topographica '),
+             (Token.Prompt, 'In <'),
+             (Token.PromptNum, str(self.shell.execution_count)),
+             (Token.Prompt, '>: '),
+             ]
+
+    def out_prompt_tokens(self):
+        return [
+             (Token.OutPrompt, 'Out<'),
+             (Token.OutPromptNum, str(self.shell.execution_count)),
+             (Token.OutPrompt, '>: '),
+         ]
+
+
 class CommandPrompt(IPCommandPromptHandler):
     """
     Control over input prompt.
@@ -455,11 +477,44 @@ def o_action(option,opt_str,value,parser):
 		       help="set the default output path")
 
 
+if ipython_shell_interface == "InteractiveShellEmbed":
+    # IPython 0.11 and later
+
+    config = Config()
+    if ipython_prompt_interface == "PromptManager":
+        config.PromptManager.in_template = CommandPrompt.get_format()
+        config.PromptManager.in2_template = CommandPrompt2.get_format()
+        config.PromptManager.out_template = OutputPrompt.get_format()
+        config.InteractiveShell.confirm_exit = False
+    else:
+        config.TerminalInteractiveShell.prompts_class=IPythonCommandPrompt
+        config.InteractiveShell.confirm_exit = False
+
+
 def gui(start=True,exit_on_quit=True):
     """Start the GUI as if -g were supplied in the command used to launch Topographica."""
-    if matplotlib_imported:
+    # 
+    # To integrate with Tk we need to 
+    # create ipshell *before* calling enable_gui
+    # it is important that you use instance(), instead of the class
+    # constructor, so that it creates the global InteractiveShell singleton
+
+    IPShell.instance(config=config)
+
+    try:
+        # Need to connect Tk before import of pyplot
+        import matplotlib
+        matplotlib.use("TkAgg")
+
+#         # By default, use a non-GUI backend for matplotlib.
+#         from matplotlib import pyplot as plt
+#         plt.ioff()
+#         plt.switch_backend('agg')
+
         from holoviews.plotting import mpl
-        plt.switch_backend('TkAgg')
+    except:
+        pass
+
     auto_import_commands()
     if start:
         import topo.tkgui
@@ -708,8 +763,6 @@ def exec_startup_files():
         if os.path.exists(startup_file):
             cmdline_main.warning("Ignoring %s; location for startup file is %s (UNIX/Linux/Mac OS X) or %s (Windows)."%(startup_file,rcpath,inipath))
 
-
-
 ### Execute what is specified by the options.
 
 def process_argv(argv):
@@ -799,19 +852,16 @@ def process_argv(argv):
         elif ipython_shell_interface == "InteractiveShellEmbed":
             # IPython 0.11 and later
 
-            config = Config()
-
             if ipython_prompt_interface == "PromptManager":
                 config.PromptManager.in_template = CommandPrompt.get_format()
                 config.PromptManager.in2_template = CommandPrompt2.get_format()
                 config.PromptManager.out_template = OutputPrompt.get_format()
-            else:
-                config.InteractiveShell.prompt_in1 = CommandPrompt.get_format()
-                config.InteractiveShell.prompt_in2 = CommandPrompt2.get_format()
-                config.InteractiveShell.prompt_out = OutputPrompt.get_format()
-            config.InteractiveShell.confirm_exit = False
-            ipshell = IPShell(config=config,user_ns=__main__.__dict__,
-                              banner1="",exit_msg="")
+                config.InteractiveShell.confirm_exit = False
+
+            IPython.lib.inputhook.enable_gui(gui='tk')
+
+
+            ipshell = IPShell.instance()
             if option.pdb:
                 ipshell.call_pdb = True
 
@@ -822,7 +872,7 @@ def process_argv(argv):
                 cmdline_main.warning(
                     "Could not load IPython extension 'topo.misc.ipython'; ignored error was:\n%s"%traceback.format_exc())
 
-            ipshell()
+            ipshell.mainloop(local_ns=__main__.__dict__)
 
     global return_code
     if return_code != 0:

topo/misc/lancext.py

@@ -15,7 +15,7 @@
 import param
 
 from holoviews import NdMapping, Layout
-from holoviews.interface.collector import Collector
+from featuremapper.collector import Collector
 from holoviews.core.element import Collator
 from holoviews.core.io import Pickler
 

topo/submodel/specifications.py

@@ -57,8 +57,13 @@ def __lt__(self, other):
 
 
     def __eq__(self, other):
-        return self.sort_precedence == other.sort_precedence
-
+        try:
+            return self.sort_precedence == other.sort_precedence
+        except Exception as e:
+            # Change in holoviews
+            if type(other) == str:
+                return False
+            raise e
 
     def __init__(self, object_type):
         self._object_type = object_type

topo/tests/unit/testcf.py

@@ -1,6 +1,10 @@
 import unittest
 import numpy
 
+# Need to load TkAgg before any calls to pyplot in the imports
+import matplotlib
+matplotlib.use("TkAgg")
+
 from topo.base.simulation import Simulation
 from topo.base.boundingregion import BoundingBox
 from topo.base.cf import CFIter,ResizableCFProjection,CFSheet