3.6.0b7 - Better cubic plotting & new template config. Fixed windows req

bsb/__init__.py

@@ -1,3 +1,3 @@
-__version__ = "3.6.0b6"
+__version__ = "3.6.0b7"
 
 from .reporting import set_verbosity, report, warn

bsb/cli.py

@@ -157,7 +157,7 @@ def start_cli():
         "-t",
         "--template",
         action="store",
-        default="mouse_cerebellum_cortex_noTouch.json",
+        default="template.json",
         help="Name of the template config file.",
     )
     parser_config.add_argument(

bsb/configurations/.gitignore

@@ -6,3 +6,4 @@
 !touch.json
 !mouse_cerebellum_cortex_noTouch.json
 !mouse_cerebellum_cortex_io_dcn.json
+!template.json

bsb/configurations/template.json

@@ -0,0 +1,45 @@
+{
+  "name": "Empty template",
+  "network_architecture": {
+    "simulation_volume_x": 400.0,
+    "simulation_volume_z": 400.0
+  },
+  "output": {
+    "format": "bsb.output.HDF5Formatter"
+  },
+  "layers": {
+    "base_layer": {
+      "thickness": 100
+    }
+  },
+  "cell_types": {
+    "base_type": {
+      "placement": {
+        "class": "bsb.placement.ParticlePlacement",
+        "layer": "base_layer",
+        "soma_radius": 2.5,
+        "density": 3.9e-4
+      },
+      "morphology": {
+        "class": "bsb.morphologies.NoGeometry"
+      },
+      "plotting": {
+        "display_label": "Template cell",
+        "color": "#E62314",
+        "opacity": 0.5
+      }
+    }
+  },
+  "after_placement": {
+
+  },
+  "connection_types": {
+
+  },
+  "after_connectivity": {
+
+  },
+  "simulations": {
+
+  }
+}

bsb/plotting.py

@@ -200,7 +200,8 @@ def wrapper_function(*args, fig=None, input_region=None, **kwargs):
     return wrapper_function
 
 
-def _plot_network(network, fig, swapaxes):
+def _plot_network(network, fig, cubic, swapaxes):
+    xmin, xmax, ymin, ymax, zmin, zmax = tuple([0] * 6)
     for type in network.configuration.cell_types.values():
         if type.entity:
             continue
@@ -217,6 +218,21 @@ def _plot_network(network, fig, swapaxes):
                 name=type.plotting.label,
             )
         )
+        xmin = min(xmin, np.min(pos[:, 0], initial=0))
+        xmax = max(xmax, np.max(pos[:, 0], initial=0))
+        ymin = min(ymin, np.min(pos[:, 1], initial=0))
+        ymax = max(ymax, np.max(pos[:, 1], initial=0))
+        zmin = min(zmin, np.min(pos[:, 2], initial=0))
+        zmax = max(zmax, np.max(pos[:, 2], initial=0))
+    if cubic:
+        rng = max(xmax - xmin, ymax - ymin, zmax - zmin)
+        fig.layout.scene.xaxis.range = [xmin, xmin + rng]
+        if swapaxes:
+            fig.layout.scene.yaxis.range = [ymin, ymin + rng]
+            fig.layout.scene.zaxis.range = [zmin, zmin + rng]
+        else:
+            fig.layout.scene.yaxis.range = [ymin, ymin + rng]
+            fig.layout.scene.zaxis.range = [zmin, zmin + rng]
 
 
 @_network_figure
@@ -227,15 +243,15 @@ def plot_network(
     Plot a network, either from the current cache or the storage.
     """
     if from_memory:
-        _plot_network(network, fig, swapaxes)
+        _plot_network(network, fig, cubic, swapaxes)
     else:
         network.reset_network_cache()
         for type in network.configuration.cell_types.values():
             if type.entity:
                 continue
             # Load from HDF5
             network.get_cells_by_type(type.name)
-        _plot_network(network, fig, swapaxes)
+        _plot_network(network, fig, cubic, swapaxes)
     return fig
 
 

setup.py

@@ -23,7 +23,7 @@
     # Add all packages with binary dependencies that cannot be installed on RTD here.
     requires.extend(
         [
-            "rtree-linux==0.9.4",
+            "rtree-linux>=0.9.4",
         ]
     )