:format: format with black

Author: enryH

.github/workflows/cdci.yml

@@ -9,11 +9,11 @@ on:
     types: [published]
 
 jobs:
-  # format:
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v4
-  #     - uses: psf/black@stable 
+  format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: psf/black@stable
   # lint:
   #   name: Lint with ruff
   #   runs-on: ubuntu-latest
@@ -51,7 +51,6 @@ jobs:
           pip install -e .
       # - name: Run tests
       #   run: python -m pytest tests
-  
 
 
   publish:

src/vuecore/Dendrogram.py

@@ -3,8 +3,19 @@
 from collections import OrderedDict
 import plotly.graph_objs as go
 
-def plot_dendrogram(Z_dendrogram, cutoff_line=True, value=15, orientation='bottom', hang=30, hide_labels=False, labels=None,
-                    colorscale=None, hovertext=None, color_threshold=None):
+
+def plot_dendrogram(
+    Z_dendrogram,
+    cutoff_line=True,
+    value=15,
+    orientation="bottom",
+    hang=30,
+    hide_labels=False,
+    labels=None,
+    colorscale=None,
+    hovertext=None,
+    color_threshold=None,
+):
     """
     Modified version of Plotly _dendrogram.py that returns a dendrogram Plotly figure object with cutoff line.
 
@@ -36,25 +47,59 @@ def plot_dendrogram(Z_dendrogram, cutoff_line=True, value=15, orientation='botto
         figure = plot_dendrogram(dendro_tree, hang=0.9, cutoff_line=False)
     """
 
-    dendrogram = Dendrogram(Z_dendrogram, orientation, hang, hide_labels, labels, colorscale, hovertext=hovertext, color_threshold=color_threshold)
+    dendrogram = Dendrogram(
+        Z_dendrogram,
+        orientation,
+        hang,
+        hide_labels,
+        labels,
+        colorscale,
+        hovertext=hovertext,
+        color_threshold=color_threshold,
+    )
 
     if cutoff_line == True:
-        dendrogram.layout.update({'shapes':[{'type':'line',
-                                 'xref':'paper',
-                                 'yref':'y',
-                                 'x0':0, 'y0':value,
-                                 'x1':1, 'y1':value,
-                                 'line':{'color':'red'}}]})
+        dendrogram.layout.update(
+            {
+                "shapes": [
+                    {
+                        "type": "line",
+                        "xref": "paper",
+                        "yref": "y",
+                        "x0": 0,
+                        "y0": value,
+                        "x1": 1,
+                        "y1": value,
+                        "line": {"color": "red"},
+                    }
+                ]
+            }
+        )
 
     figure = dict(data=dendrogram.data, layout=dendrogram.layout)
-    figure['layout']['template'] = 'plotly_white'
+    figure["layout"]["template"] = "plotly_white"
 
     return figure
 
+
 class Dendrogram(object):
     """Refer to plot_dendrogram() for docstring."""
-    def __init__(self, Z_dendrogram, orientation='bottom', hang=1, hide_labels=False, labels=None, colorscale=None, hovertext=None,
-                 color_threshold=None, width=np.inf, height=np.inf, xaxis='xaxis', yaxis='yaxis'):
+
+    def __init__(
+        self,
+        Z_dendrogram,
+        orientation="bottom",
+        hang=1,
+        hide_labels=False,
+        labels=None,
+        colorscale=None,
+        hovertext=None,
+        color_threshold=None,
+        width=np.inf,
+        height=np.inf,
+        xaxis="xaxis",
+        yaxis="yaxis",
+    ):
         self.orientation = orientation
         self.labels = labels
         self.xaxis = xaxis
@@ -64,20 +109,19 @@ def __init__(self, Z_dendrogram, orientation='bottom', hang=1, hide_labels=False
         self.sign = {self.xaxis: 1, self.yaxis: 1}
         self.layout = {self.xaxis: {}, self.yaxis: {}}
 
-        if self.orientation in ['left', 'bottom']:
+        if self.orientation in ["left", "bottom"]:
             self.sign[self.xaxis] = 1
         else:
             self.sign[self.xaxis] = -1
 
-        if self.orientation in ['right', 'bottom']:
+        if self.orientation in ["right", "bottom"]:
             self.sign[self.yaxis] = 1
         else:
             self.sign[self.yaxis] = -1
 
-        (dd_traces, xvals, yvals,
-            ordered_labels, leaves) = self.get_dendrogram_traces(Z_dendrogram, hang, colorscale,
-                                                                 hovertext,
-                                                                 color_threshold)
+        (dd_traces, xvals, yvals, ordered_labels, leaves) = self.get_dendrogram_traces(
+            Z_dendrogram, hang, colorscale, hovertext, color_threshold
+        )
 
         self.labels = ordered_labels
         self.leaves = leaves
@@ -93,9 +137,9 @@ def __init__(self, Z_dendrogram, orientation='bottom', hang=1, hide_labels=False
         if len(self.zero_vals) > len(yvals) + 1:
             l_border = int(min(self.zero_vals))
             r_border = int(max(self.zero_vals))
-            correct_leaves_pos = range(l_border,
-                                       r_border + 1,
-                                       int((r_border - l_border) / len(yvals)))
+            correct_leaves_pos = range(
+                l_border, r_border + 1, int((r_border - l_border) / len(yvals))
+            )
             self.zero_vals = [v for v in correct_leaves_pos]
 
         self.zero_vals.sort()
@@ -113,26 +157,29 @@ def get_color_dict(self, colorscale):
 
         # These are the color codes returned for dendrograms
         # We're replacing them with nicer colors
-        d = {'r': 'red',
-             'g': 'green',
-             'b': 'blue',
-             'c': 'cyan',
-             'm': 'magenta',
-             'y': 'yellow',
-             'k': 'black',
-             'w': 'white'}
+        d = {
+            "r": "red",
+            "g": "green",
+            "b": "blue",
+            "c": "cyan",
+            "m": "magenta",
+            "y": "yellow",
+            "k": "black",
+            "w": "white",
+        }
         default_colors = OrderedDict(sorted(d.items(), key=lambda t: t[0]))
 
         if colorscale is None:
             colorscale = [
-                'rgb(0,116,217)',  # blue
-                'rgb(35,205,205)',  # cyan
-                'rgb(61,153,112)',  # green
-                'rgb(40,35,35)',  # black
-                'rgb(133,20,75)',  # magenta
-                'rgb(255,65,54)',  # red
-                'rgb(255,255,255)',  # white
-                'rgb(255,220,0)']  # yellow
+                "rgb(0,116,217)",  # blue
+                "rgb(35,205,205)",  # cyan
+                "rgb(61,153,112)",  # green
+                "rgb(40,35,35)",  # black
+                "rgb(133,20,75)",  # magenta
+                "rgb(255,65,54)",  # red
+                "rgb(255,255,255)",  # white
+                "rgb(255,220,0)",
+            ]  # yellow
 
         for i in range(len(default_colors.keys())):
             k = list(default_colors.keys())[i]  # PY3 won't index keys
@@ -150,32 +197,34 @@ def set_axis_layout(self, axis_key, hide_labels):
         :return (dict): An axis_key dictionary with set parameters.
         """
         axis_defaults = {
-                'type': 'linear',
-                'ticks': 'outside',
-                'mirror': 'allticks',
-                'rangemode': 'tozero',
-                'showticklabels': True,
-                'zeroline': False,
-                'showgrid': False,
-                'showline': True,
-            }
+            "type": "linear",
+            "ticks": "outside",
+            "mirror": "allticks",
+            "rangemode": "tozero",
+            "showticklabels": True,
+            "zeroline": False,
+            "showgrid": False,
+            "showline": True,
+        }
 
         if len(self.labels) != 0:
             axis_key_labels = self.xaxis
-            if self.orientation in ['left', 'right']:
+            if self.orientation in ["left", "right"]:
                 axis_key_labels = self.yaxis
             if axis_key_labels not in self.layout:
                 self.layout[axis_key_labels] = {}
-            self.layout[axis_key_labels]['tickvals'] = \
-                [zv*self.sign[axis_key] for zv in self.zero_vals]
-            self.layout[axis_key_labels]['ticktext'] = self.labels
-            self.layout[axis_key_labels]['tickmode'] = 'array'
+            self.layout[axis_key_labels]["tickvals"] = [
+                zv * self.sign[axis_key] for zv in self.zero_vals
+            ]
+            self.layout[axis_key_labels]["ticktext"] = self.labels
+            self.layout[axis_key_labels]["tickmode"] = "array"
 
         self.layout[axis_key].update(axis_defaults)
 
         if hide_labels == True:
-            self.layout[axis_key].update({'showticklabels': False})
-        else: pass
+            self.layout[axis_key].update({"showticklabels": False})
+        else:
+            pass
 
         return self.layout[axis_key]
 
@@ -191,24 +240,27 @@ def set_figure_layout(self, width, height, hide_labels):
         :type hide_labels: boolean
         :return: Plotly layout
         """
-        self.layout.update({
-            'showlegend': False,
-            'autosize': False,
-            'hovermode': 'closest',
-            'width': width,
-            'height': height
-        })
+        self.layout.update(
+            {
+                "showlegend": False,
+                "autosize": False,
+                "hovermode": "closest",
+                "width": width,
+                "height": height,
+            }
+        )
 
         self.set_axis_layout(self.xaxis, hide_labels=hide_labels)
         self.set_axis_layout(self.yaxis, hide_labels=False)
 
         return self.layout
 
-
-    def get_dendrogram_traces(self, Z_dendrogram, hang, colorscale, hovertext, color_threshold):
+    def get_dendrogram_traces(
+        self, Z_dendrogram, hang, colorscale, hovertext, color_threshold
+    ):
         """
         Calculates all the elements needed for plotting a dendrogram.
-        
+
         :param Z_dendrogram: Matrix of observations as array of arrays
         :type Z_dendrogram: ndarray
         :param hang: dendrogram distance of leaf lines
@@ -218,28 +270,28 @@ def get_dendrogram_traces(self, Z_dendrogram, hang, colorscale, hovertext, color
         :param hovertext: List of hovertext for constituent traces of dendrogram
         :type hovertext: list
         :return (tuple): Contains all the traces in the following order:
-         
+
                 a. trace_list: List of Plotly trace objects for dendrogram tree
                 b. icoord: All X points of the dendrogram tree as array of arrays with length 4
                 c. dcoord: All Y points of the dendrogram tree as array of arrays with length 4
                 d. ordered_labels: leaf labels in the order they are going to appear on the plot
                 e. Z_dendrogram['leaves']: left-to-right traversal of the leaves
         """
-        icoord = scp.array(Z_dendrogram['icoord'])
-        dcoord = scp.array(Z_dendrogram['dcoord'])
-        ordered_labels = scp.array(Z_dendrogram['ivl'])
-        color_list = scp.array(Z_dendrogram['color_list'])
+        icoord = scp.array(Z_dendrogram["icoord"])
+        dcoord = scp.array(Z_dendrogram["dcoord"])
+        ordered_labels = scp.array(Z_dendrogram["ivl"])
+        color_list = scp.array(Z_dendrogram["color_list"])
         colors = self.get_color_dict(colorscale)
 
         trace_list = []
 
         for i in range(len(icoord)):
-            if self.orientation in ['top', 'bottom']:
+            if self.orientation in ["top", "bottom"]:
                 xs = icoord[i]
             else:
                 xs = dcoord[i]
 
-            if self.orientation in ['top', 'bottom']:
+            if self.orientation in ["top", "bottom"]:
                 ys = dcoord[i]
             else:
                 ys = icoord[i]
@@ -264,28 +316,31 @@ def get_dendrogram_traces(self, Z_dendrogram, hang, colorscale, hovertext, color
                 y_coord.append(y)
 
             trace = dict(
-                type='scattergl',
+                type="scattergl",
                 x=np.multiply(self.sign[self.xaxis], x_coord),
                 y=np.multiply(self.sign[self.yaxis], y_coord),
-                mode='lines',
-                marker=dict(color='rgb(40,35,35)'),
-                line=dict(color='rgb(40,35,35)', width=1),      #dict(color=colors[color_key]),
+                mode="lines",
+                marker=dict(color="rgb(40,35,35)"),
+                line=dict(
+                    color="rgb(40,35,35)", width=1
+                ),  # dict(color=colors[color_key]),
                 text=hovertext_label,
-                hoverinfo='text')
+                hoverinfo="text",
+            )
 
             try:
                 x_index = int(self.xaxis[-1])
             except ValueError:
-                x_index = ''
+                x_index = ""
 
             try:
                 y_index = int(self.yaxis[-1])
             except ValueError:
-                y_index = ''
+                y_index = ""
 
-            trace['xaxis'] = 'x' + x_index
-            trace['yaxis'] = 'y' + y_index
+            trace["xaxis"] = "x" + x_index
+            trace["yaxis"] = "y" + y_index
 
             trace_list.append(trace)
 
-        return trace_list, icoord, dcoord, ordered_labels, Z_dendrogram['leaves']
+        return trace_list, icoord, dcoord, ordered_labels, Z_dendrogram["leaves"]