From 8f8b53613193754075f21a398284ed48b00f37f5 Mon Sep 17 00:00:00 2001
From: Utkarsha Dunde <Utkarsha@Vipuls-MacBook-Pro.local>
Date: Sat, 14 Mar 2026 18:02:27 +0530
Subject: [PATCH 1/7] Fix: correctly pipe keyword arguments to plot_dendrogram

---
 brian2tools/plotting/base.py       |  5 +----
 brian2tools/plotting/morphology.py | 12 ++++++++----
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/brian2tools/plotting/base.py b/brian2tools/plotting/base.py
index 28bb385d..83749c15 100644
--- a/brian2tools/plotting/base.py
+++ b/brian2tools/plotting/base.py
@@ -106,10 +106,7 @@ def brian_plot(brian_obj,
             kwds['rate_unit'] = _get_best_unit(smooth_rate)
         return plot_rate(brian_obj.t, smooth_rate, axes=axes, **kwds)
     elif isinstance(brian_obj, Morphology):
-        if kwds:
-            logger.warn('plot_dendrogram does not take any additional keyword '
-                        'arguments, ignoring them.')
-        return plot_dendrogram(brian_obj, axes=axes)
+        return plot_dendrogram(brian_obj, axes=axes, **kwds)
     elif isinstance(brian_obj, Synapses):
         if len(brian_obj) == 0:
             raise TypeError('Synapses object does not have any synapses.')
diff --git a/brian2tools/plotting/morphology.py b/brian2tools/plotting/morphology.py
index 08cdbfdf..49b380fa 100644
--- a/brian2tools/plotting/morphology.py
+++ b/brian2tools/plotting/morphology.py
@@ -353,7 +353,7 @@ def plot_morphology(morphology, plot_3d=None, show_compartments=False,
     return axes
 
 
-def plot_dendrogram(morphology, axes=None):
+def plot_dendrogram(morphology, axes=None, **kwds):
     '''
     Plot a "dendrogram" of a morphology, i.e. an abstract representation which
     visualizes the branching structure and the length of each section.
@@ -366,6 +366,10 @@ def plot_dendrogram(morphology, axes=None):
         The `~matplotlib.axes.Axes` instance used for plotting. Defaults to
         ``None`` which means that a new `~matplotlib.axes.Axes` will be
         created for the plot.
+    kwds : dict, optional
+        Any additional keywords command will be handed over to matplotlib's
+        `~matplotlib.axes.Axes.plot` command. This can be used to set plot
+        properties such as the ``color``.
 
     Returns
     -------
@@ -427,7 +431,7 @@ def plot_dendrogram(morphology, axes=None):
 
     # Plot the dendogram with lengths of the vertical lines representing the
     # total distance to the root
-    plt.plot(x_values[0], length_metric[0], 'ko', clip_on=False)
+    plt.plot(x_values[0], length_metric[0], marker='o', clip_on=False, **kwds)
     for sec, (x, depth) in enumerate(zip(x_values, length_metric)):
         child_start_idx = (sec+1)*max_children
         num_children = flat_morpho.morph_children_num[sec+1]
@@ -435,8 +439,8 @@ def plot_dendrogram(morphology, axes=None):
             child_indices = children[child_start_idx:child_start_idx+num_children]
             child_depth = length_metric[child_indices-1]
             child_x = x_values[child_indices-1]
-            axes.vlines(child_x, depth, child_depth, clip_on=False, lw=2)
-            axes.hlines(depth, min(child_x), max(child_x), lw=2)
+            axes.vlines(child_x, depth, child_depth, clip_on=False, lw=2, **kwds)
+            axes.hlines(depth, min(child_x), max(child_x), lw=2, **kwds)
     axes.set_xticks([])
     axes.set_ylabel('distance from root (um)')
     axes.set_xlim(-1, terminal_counter)

From 9344604fa65e80b399d11b7094f90e4b7cc4759b Mon Sep 17 00:00:00 2001
From: Utkarsha Dunde <Utkarsha@Vipuls-MacBook-Pro.local>
Date: Sat, 14 Mar 2026 18:26:48 +0530
Subject: [PATCH 2/7] Test: fix unimplemented device export test

---
 brian2tools/tests/test_baseexport.py | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/brian2tools/tests/test_baseexport.py b/brian2tools/tests/test_baseexport.py
index ea5b1926..6c680b63 100644
--- a/brian2tools/tests/test_baseexport.py
+++ b/brian2tools/tests/test_baseexport.py
@@ -873,9 +873,18 @@ def test_ExportDevice_unsupported():
     g :1
     '''
     G = NeuronGroup(1, eqn)
-    _ = PoissonInput(G, 'g', 1, 1 * Hz, 1)
-    # with pytest.raises(NotImplementedError):
-    run(10 * ms)
+    run(1*ms)
+    
+    from brian2.core.base import BrianObject
+    class UnsupportedObject(BrianObject):
+        def __init__(self):
+            super().__init__(name='unsupported*')
+    
+    obj = UnsupportedObject()
+    net = Network(obj)
+    with pytest.raises(NotImplementedError):
+        net.run(10 * ms)
+    device.reinit()
 
 
 if __name__ == '__main__':

From f9ba7403ae9f4209369774b141fd2d4badc60b79 Mon Sep 17 00:00:00 2001
From: Utkarsha Dunde <utkarshadunde@gmail.com>
Date: Sat, 21 Mar 2026 19:51:29 +0530
Subject: [PATCH 3/7] Addressing review comments

---
 brian2tools/tests/test_baseexport.py | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/brian2tools/tests/test_baseexport.py b/brian2tools/tests/test_baseexport.py
index dc587540..910d4d58 100644
--- a/brian2tools/tests/test_baseexport.py
+++ b/brian2tools/tests/test_baseexport.py
@@ -4,6 +4,7 @@
                     PopulationRateMonitor, EventMonitor, set_device,
                     run, device, Network, Synapses, PoissonInput, TimedArray,
                     Function)
+from brian2.core.base import BrianObject
 from brian2.core.namespace import get_local_namespace
 from brian2.equations.equations import (DIFFERENTIAL_EQUATION,
                                         FLOAT, SUBEXPRESSION,
@@ -898,14 +899,7 @@ def test_ExportDevice_unsupported():
     """
     start_scope()
     set_device('exporter')
-    eqn = '''
-    v = 1 :1
-    g :1
-    '''
-    G = NeuronGroup(1, eqn)
-    run(1*ms)
-    
-    from brian2.core.base import BrianObject
+
     class UnsupportedObject(BrianObject):
         def __init__(self):
             super().__init__(name='unsupported*')
@@ -935,7 +929,6 @@ def __init__(self):
     test_Synapses()
     test_ExportDevice_options()
     test_ExportDevice_basic()
-    test_ExportDevice_unsupported()  # TODO: not checking anything
     test_synapse_init()
     test_synapse_connect_cond()
     test_synapse_connect_generator()

From 1cf325526a170576502383a8eb300c19b1a73b9a Mon Sep 17 00:00:00 2001
From: Utkarsha Dunde <utkarshadunde@gmail.com>
Date: Sat, 21 Mar 2026 20:23:37 +0530
Subject: [PATCH 4/7] Addressing review comments : Fix pipeline

---
 brian2tools/mdexport/expander.py     | 15 ++++++++-------
 brian2tools/plotting/morphology.py   | 16 ++++++++--------
 brian2tools/tests/test_baseexport.py |  7 ++++---
 3 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/brian2tools/mdexport/expander.py b/brian2tools/mdexport/expander.py
index 75085d43..500ae746 100644
--- a/brian2tools/mdexport/expander.py
+++ b/brian2tools/mdexport/expander.py
@@ -704,8 +704,9 @@ def expand_initializer(self, initializer):
                 (initializer['index'] != 'True' and initializer['index'] != 'False')):
             init_str += ' if ' + self.render_expression(initializer['index'])
         elif (isinstance(initializer['index'], bool) or
-            (initializer['index'] == 'True' or
-             initializer['index'] == 'False')):
+            (isinstance(initializer['index'], str) and
+             (initializer['index'] == 'True' or
+              initializer['index'] == 'False'))):
             if initializer['index'] is True or initializer['index'] == 'True':
                 init_str += ''  # "to all members" implied
             else:
@@ -796,10 +797,10 @@ def expand_connector(self, connector):
                         self.expand_identifiers(connector['identifiers']))
         return con_str + '.' + endll
 
-    
-       
 
-  
+
+
+
     def expand_pathway(self, pathway):
         """
         Expand `SynapticPathway`
@@ -864,7 +865,7 @@ def expand_summed_variables(self, sum_variables):
             sum_var_str += self.expand_summed_variable(sum_var)
         return sum_var_str
 
-   
+
 
     def expand_runregularly(self, run_reg):
         """
@@ -880,4 +881,4 @@ def expand_runregularly(self, run_reg):
                 ' code: ' +
                 self.prepare_math_statements(run_reg['code'], separate=True) +
                 ' will be executed' + endll)
-        return md_str
+        return md_str
\ No newline at end of file
diff --git a/brian2tools/plotting/morphology.py b/brian2tools/plotting/morphology.py
index 4cf6b5c9..24d8cc6f 100644
--- a/brian2tools/plotting/morphology.py
+++ b/brian2tools/plotting/morphology.py
@@ -34,15 +34,15 @@ def _plot_morphology2D(morpho, axes, colors,
         color = colors[color_counter % len(colors)]
 
     if isinstance(morpho, Soma):
-        x, y = morpho.x/um, morpho.y/um
-        radius = morpho.diameter/um/2
+        x, y = float(morpho.x/um), float(morpho.y/um)
+        radius = float(morpho.diameter/um/2)
         circle = Circle((x, y), radius=radius, color=color)
         axes.add_patch(circle)
-       
-      
+
+
     else:
         coords = morpho.coordinates/um
-    
+
         if show_diameter:
             coords_2d = coords[:, :2]
             directions = np.diff(coords_2d, axis=0)
@@ -56,7 +56,7 @@ def _plot_morphology2D(morpho, axes, colors,
                                 (coords_2d - orthogonal*radius[:, np.newaxis])[::-1]])
             patch = Polygon(points, color=color)
             axes.add_patch(patch)
-           
+
         else:
             axes.plot(coords[:, 0], coords[:, 1], color=color, lw=2)
         if show_compartments:
@@ -74,7 +74,7 @@ def _plot_morphology2D(morpho, axes, colors,
                            show_compartments=show_compartments,
                            show_diameter=show_diameter,
                            colors=colors, color_counter=color_counter+1)
-    
+
 def _plot_morphology3D(morpho, figure, colors, values, value_norm,
                        value_colormap,
                        show_diameters=True,
@@ -439,4 +439,4 @@ def plot_dendrogram(morphology, axes=None):
     axes.set_xticks([])
     axes.set_ylabel('distance from root (um)')
     axes.set_xlim(-1, terminal_counter)
-    return axes
+    return axes
\ No newline at end of file
diff --git a/brian2tools/tests/test_baseexport.py b/brian2tools/tests/test_baseexport.py
index 910d4d58..c0c73598 100644
--- a/brian2tools/tests/test_baseexport.py
+++ b/brian2tools/tests/test_baseexport.py
@@ -237,7 +237,7 @@ def test_spikegenerator():
     assert spike_gen_dict['indices'] == [0]
     assert spike_gen_dict['indices'].dtype == int
 
-    assert float(spike_gen_dict['times']) == float(time)
+    assert float(spike_gen_dict['times'][0]) == float(time[0])
     assert spike_gen_dict['times'][:].dimensions == second
     assert spike_gen_dict['times'].dtype == float
 
@@ -903,7 +903,7 @@ def test_ExportDevice_unsupported():
     class UnsupportedObject(BrianObject):
         def __init__(self):
             super().__init__(name='unsupported*')
-    
+
     obj = UnsupportedObject()
     net = Network(obj)
     with pytest.raises(NotImplementedError):
@@ -929,7 +929,8 @@ def __init__(self):
     test_Synapses()
     test_ExportDevice_options()
     test_ExportDevice_basic()
+    test_ExportDevice_unsupported()
     test_synapse_init()
     test_synapse_connect_cond()
     test_synapse_connect_generator()
-    test_synapse_connect_ij()
+    test_synapse_connect_ij()
\ No newline at end of file

From 3183e284dca074538c76589730f1228bfc6fce1a Mon Sep 17 00:00:00 2001
From: Utkarsha Dunde <utkarshadunde@gmail.com>
Date: Sat, 21 Mar 2026 20:32:04 +0530
Subject: [PATCH 5/7] Addressing review comments : Fix pipeline 2

---
 brian2tools/plotting/morphology.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/brian2tools/plotting/morphology.py b/brian2tools/plotting/morphology.py
index 24d8cc6f..b912ae86 100644
--- a/brian2tools/plotting/morphology.py
+++ b/brian2tools/plotting/morphology.py
@@ -34,8 +34,8 @@ def _plot_morphology2D(morpho, axes, colors,
         color = colors[color_counter % len(colors)]
 
     if isinstance(morpho, Soma):
-        x, y = float(morpho.x/um), float(morpho.y/um)
-        radius = float(morpho.diameter/um/2)
+        x, y = float(np.squeeze(morpho.x/um)), float(np.squeeze(morpho.y/um))
+        radius = float(np.squeeze(morpho.diameter/um/2))
         circle = Circle((x, y), radius=radius, color=color)
         axes.add_patch(circle)
 

From 56982fcf7681b71aceb15dfa15d6c7ad1d34695f Mon Sep 17 00:00:00 2001
From: Utkarsha Dunde <utkarshadunde@gmail.com>
Date: Sat, 21 Mar 2026 22:59:06 +0530
Subject: [PATCH 6/7] Addressing review comments.

---
 brian2tools/plotting/morphology.py | 10 ++++++----
 brian2tools/tests/test_plotting.py | 14 ++++++++++++++
 docs_sphinx/user/plotting.rst      |  8 +++++---
 3 files changed, 25 insertions(+), 7 deletions(-)

diff --git a/brian2tools/plotting/morphology.py b/brian2tools/plotting/morphology.py
index 69b2b5db..43c3477b 100644
--- a/brian2tools/plotting/morphology.py
+++ b/brian2tools/plotting/morphology.py
@@ -365,10 +365,12 @@ def plot_dendrogram(morphology, axes=None, **kwds):
         The `~matplotlib.axes.Axes` instance used for plotting. Defaults to
         ``None`` which means that a new `~matplotlib.axes.Axes` will be
         created for the plot.
-    kwds : dict, optional
-        Any additional keywords command will be handed over to matplotlib's
-        `~matplotlib.axes.Axes.plot` command. This can be used to set plot
-        properties such as the ``color``.
+    **kwds
+        Any additional keyword arguments are passed to matplotlib's
+        `~matplotlib.axes.Axes.plot`, `~matplotlib.axes.Axes.vlines`, and
+        `~matplotlib.axes.Axes.hlines` calls. Only arguments accepted by all
+        three functions should be used (e.g. ``color``, ``alpha``,
+        ``linewidth``).
 
     Returns
     -------
diff --git a/brian2tools/tests/test_plotting.py b/brian2tools/tests/test_plotting.py
index 1b6fd085..e1ec6a29 100644
--- a/brian2tools/tests/test_plotting.py
+++ b/brian2tools/tests/test_plotting.py
@@ -122,6 +122,20 @@ def test_plot_morphology():
     ax = plot_dendrogram(morpho)
     assert isinstance(ax, matplotlib.axes.Axes)
     plt.close()
+    # Test that styling kwargs are accepted and forwarded without error
+    ax = plot_dendrogram(morpho, color='red')
+    assert isinstance(ax, matplotlib.axes.Axes)
+    plt.close()
+    ax = plot_dendrogram(morpho, color='blue', alpha=0.5)
+    assert isinstance(ax, matplotlib.axes.Axes)
+    plt.close()
+    ax = plot_dendrogram(morpho, color='green', linewidth=3)
+    assert isinstance(ax, matplotlib.axes.Axes)
+    plt.close()
+    # brian_plot routes Morphology to plot_dendrogram, so kwargs must work there too
+    ax = brian_plot(morpho, color='purple')
+    assert isinstance(ax, matplotlib.axes.Axes)
+    plt.close()
     ax = plot_morphology(morpho)
     assert isinstance(ax, matplotlib.axes.Axes)
     plt.close()
diff --git a/docs_sphinx/user/plotting.rst b/docs_sphinx/user/plotting.rst
index 0b8420f4..815c489c 100644
--- a/docs_sphinx/user/plotting.rst
+++ b/docs_sphinx/user/plotting.rst
@@ -228,9 +228,11 @@ dendogram::
 
 .. image:: ../images/plot_dendrogram.svg
 
-The `~brian2tools.plotting.morphology.plot_dendrogram` function does the same thing, but in contrast to the other
-plot functions it does not allow any customization at the moment, so there is no benefit over using
-`~brian2tools.plotting.base.brian_plot`.
+The `~brian2tools.plotting.morphology.plot_dendrogram` function does the same thing, but also accepts additional
+keyword arguments (e.g. ``color``, ``alpha``, ``linewidth``) that are forwarded to the underlying
+`~matplotlib.axes.Axes.plot`, `~matplotlib.axes.Axes.vlines`, and `~matplotlib.axes.Axes.hlines` calls::
+
+    plot_dendrogram(morpho, color='red', alpha=0.7)
 
 .. _plotting_morphologies:
 

From 3ec09366965d25363185421ccb8948be02546bbe Mon Sep 17 00:00:00 2001
From: Utkarsha Dunde <utkarshadunde@gmail.com>
Date: Thu, 26 Mar 2026 17:24:11 +0530
Subject: [PATCH 7/7] Addressing review comments.

---
 brian2tools/plotting/morphology.py |  9 ++++++---
 docs_sphinx/user/plotting.rst      | 14 +++++++++++---
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/brian2tools/plotting/morphology.py b/brian2tools/plotting/morphology.py
index e0b0caa8..a42f78cf 100644
--- a/brian2tools/plotting/morphology.py
+++ b/brian2tools/plotting/morphology.py
@@ -430,9 +430,12 @@ def plot_dendrogram(morphology, axes=None, **kwds):
 
     x_values = (np.array(min_index) + np.array(max_index)) / 2.0
 
+    clip_on = kwds.pop('clip_on', False)
+    lw = kwds.pop('lw', kwds.pop('linewidth', 2))
+
     # Plot the dendogram with lengths of the vertical lines representing the
     # total distance to the root
-    plt.plot(x_values[0], length_metric[0], marker='o', clip_on=False, **kwds)
+    plt.plot(x_values[0], length_metric[0], marker='o', clip_on=clip_on, **kwds)
     for sec, (x, depth) in enumerate(zip(x_values, length_metric)):
         child_start_idx = (sec+1)*max_children
         num_children = flat_morpho.morph_children_num[sec+1]
@@ -440,8 +443,8 @@ def plot_dendrogram(morphology, axes=None, **kwds):
             child_indices = children[child_start_idx:child_start_idx+num_children]
             child_depth = length_metric[child_indices-1]
             child_x = x_values[child_indices-1]
-            axes.vlines(child_x, depth, child_depth, clip_on=False, lw=2, **kwds)
-            axes.hlines(depth, min(child_x), max(child_x), lw=2, **kwds)
+            axes.vlines(child_x, depth, child_depth, clip_on=clip_on, lw=lw, **kwds)
+            axes.hlines(depth, min(child_x), max(child_x), lw=lw, **kwds)
     axes.set_xticks([])
     axes.set_ylabel('distance from root (um)')
     axes.set_xlim(-1, terminal_counter)
diff --git a/docs_sphinx/user/plotting.rst b/docs_sphinx/user/plotting.rst
index 815c489c..2e87c2b2 100644
--- a/docs_sphinx/user/plotting.rst
+++ b/docs_sphinx/user/plotting.rst
@@ -228,12 +228,20 @@ dendogram::
 
 .. image:: ../images/plot_dendrogram.svg
 
-The `~brian2tools.plotting.morphology.plot_dendrogram` function does the same thing, but also accepts additional
-keyword arguments (e.g. ``color``, ``alpha``, ``linewidth``) that are forwarded to the underlying
-`~matplotlib.axes.Axes.plot`, `~matplotlib.axes.Axes.vlines`, and `~matplotlib.axes.Axes.hlines` calls::
+The `~brian2tools.plotting.morphology.plot_dendrogram` function does the same thing, but in contrast to the other
+plot functions it does not allow any customization that is not also available via
+`~brian2tools.plotting.base.brian_plot`. Both functions accept additional keyword arguments (e.g. ``color``,
+``alpha``, ``linewidth``) that are forwarded to the underlying `~matplotlib.axes.Axes.plot`,
+`~matplotlib.axes.Axes.vlines`, and `~matplotlib.axes.Axes.hlines` calls::
 
     plot_dendrogram(morpho, color='red', alpha=0.7)
 
+.. image:: ../images/plot_dendrogram_custom.svg
+
+The same customization is also possible via `~brian2tools.plotting.base.brian_plot`::
+
+    brian_plot(morpho, color='red', alpha=0.7)
+
 .. _plotting_morphologies:
 
 Morphologies in 2D or 3D