Update lint for pre-commit

Update

stuff

Astuff

Fixup

Author: jeromekelleher

app.py

@@ -1,6 +1,6 @@
-import sys
-import pathlib
 import logging
+import pathlib
+import sys
 
 import panel as pn
 import tskit

config.py

@@ -1,4 +1,4 @@
 # Global plot settings
 PLOT_WIDTH = 1000
 PLOT_HEIGHT = 600
-THRESHOLD = 1000  # max number of points to overlay on a plot
+THRESHOLD = 1000  # max number of points to overlay on a plot

model.py

@@ -1,9 +1,9 @@
 from functools import cached_property
 
-import tskit
-import numpy as np
 import numba
+import numpy as np
 import pandas as pd
+import tskit
 
 spec = [
     ("num_edges", numba.int64),
@@ -43,7 +43,7 @@ def __init__(
         self.in_range = np.zeros(2, dtype=np.int64)
         self.out_range = np.zeros(2, dtype=np.int64)
 
-    def next(self):
+    def next(self):  # noqa
         left = self.interval[1]
         j = self.in_range[1]
         k = self.out_range[1]
@@ -220,7 +220,7 @@ def mutations_df(self):
         unknown = tskit.is_unknown_time(mutations_time)
         mutations_time[unknown] = self.ts.nodes_time[mutations_node[unknown]]
 
-        node_flag = ts.nodes_flags[mutations_node]
+        # node_flag = ts.nodes_flags[mutations_node]
         position = ts.sites_position[ts.mutations_site]
 
         tables = self.ts.tables
@@ -440,90 +440,6 @@ def make_sliding_windows(self, iterable, size, overlap=0):
             end += step
         yield iterable[start:]
 
-    def plot_polytomy_fractions(
-        self, region_start=None, region_end=None, window_size=100_000, overlap=0
-    ):
-        """
-        Plots the fraction of polytomies in windows actoss the genomic sequence
-        """
-        if region_start is None:
-            region_start = max(0, self.ts.tables.sites.position[0] - 50_000)
-        if region_end is None:
-            region_end = self.ts.tables.sites.position[-1] + 50_000
-        fig, ax = plt.subplots(figsize=(20, 5))
-        polytomy_fractions = self.calc_polytomy_fractions()
-        poly_fracs_by_pos = self.map_stats_to_genome(polytomy_fractions)
-        poly_fracs_means = []
-        poly_fracs_sd = []
-        genomic_positions = []
-        for poly_win in self.make_sliding_windows(
-            poly_fracs_by_pos, window_size, overlap
-        ):
-            poly_fracs_means.append(np.mean(poly_win))
-            poly_fracs_sd.append(np.std(poly_win))
-        for gen_win in self.make_sliding_windows(
-            np.arange(1, self.ts.sequence_length), window_size, overlap
-        ):
-            genomic_positions.append(gen_win[0] / 1_000_000)
-        ax.plot(
-            genomic_positions,
-            poly_fracs_means,
-            label="mean",
-            linewidth=0.5,
-        )
-        ax.fill_between(
-            genomic_positions,
-            np.array(poly_fracs_means) - np.array(poly_fracs_sd),
-            np.array(poly_fracs_means) + np.array(poly_fracs_sd),
-            alpha=0.3,
-            label="mean +/- std",
-        )
-        missing_vals = np.take(genomic_positions, np.where(np.isnan(poly_fracs_means)))
-        ax.plot(
-            missing_vals,
-            np.zeros(len(missing_vals)),
-            color="red",
-            marker="o",
-            label="missing data",
-        )
-        ax.set_xlabel(f"Position on chr {self.chr}(Mb)", fontsize=10)
-        ax.set_ylabel("Window mean", fontsize=10)
-        ax.set_title("Polytomy score", fontsize=10)
-        ax.set_ylim(0, 1)
-        ax.set_xlim(region_start / 1_000_000, region_end / 1_000_000)
-        handles, labels = ax.get_legend_handles_labels()
-        unique = [
-            (h, l)
-            for i, (h, l) in enumerate(zip(handles, labels))
-            if l not in labels[:i]
-        ]
-        ax.legend(*zip(*unique))
-        plt.show()
-
-    def plot_mutations_per_site_along_seq(
-        self, region_start=None, region_end=None, hist_bins=1000
-    ):
-        count = self.sites_num_mutations
-        pos = self.ts.sites_position
-        if region_start is None:
-            region_start = pos[0]
-        if region_end is None:
-            region_end = pos[-1]
-        grid = sns.jointplot(
-            x=pos / 1_000_000,
-            y=count,
-            kind="scatter",
-            marginal_ticks=True,
-            alpha=0.5,
-            marginal_kws=dict(bins=hist_bins),
-            xlim=(region_start / 1_000_000, region_end / 1_000_000),
-        )
-        grid.ax_marg_y.remove()
-        grid.fig.set_figwidth(20)
-        grid.fig.set_figheight(8)
-        grid.ax_joint.set_xlabel("Position on genome (Mb)")
-        grid.ax_joint.set_ylabel("Number of mutations")
-
     def calc_mean_node_arity(self):
         span_sums = np.bincount(
             self.ts.edges_parent,

pages/__init__.py

@@ -1,12 +1,12 @@
-import os
 import importlib
+import os
 
 # List all files in the current directory
 for module_file in os.listdir(os.path.dirname(__file__)):
     # Check if it's a python file and not this __init__ file
-    if module_file.endswith('.py') and module_file != '__init__.py':
+    if module_file.endswith(".py") and module_file != "__init__.py":
         module_name = module_file[:-3]  # remove the .py extension
-        module = importlib.import_module('.' + module_name, package=__name__)
+        module = importlib.import_module("." + module_name, package=__name__)
 
         # Add the page function to the current module's namespace
         globals()[module_name] = module.page

pages/edge_explorer.py

@@ -1,8 +1,10 @@
-import panel as pn
-import holoviews as hv
 import bokeh.models as bkm
+import holoviews as hv
+import panel as pn
+
 import config
 
+
 def page(tsm):
     hv.extension("bokeh")
     edges_df = tsm.edges_df

pages/edges.py

@@ -1,9 +1,12 @@
+import bokeh.models as bkm
 import holoviews as hv
 import holoviews.operation.datashader as hd
 import panel as pn
+
 import config
-import bokeh.models as bkm
-from plot_helpers import filter_points, hover_points
+from plot_helpers import filter_points
+from plot_helpers import hover_points
+
 
 def page(tsm):
     hv.extension("bokeh")

pages/mutations.py

@@ -1,15 +1,19 @@
-import panel as pn
 import holoviews as hv
 import holoviews.operation.datashader as hd
 import hvplot.pandas  # noqa
 import numpy as np
+import panel as pn
 
 import config
-from plot_helpers import filter_points, hover_points
+from plot_helpers import filter_points
+from plot_helpers import hover_points
 
 
 def make_hist_on_axis(dimension, points, num_bins=30):
-    ### Make histogram function for a specified axis of a scatter plot
+    """
+    Make histogram function for a specified axis of a scatter plot
+    """
+
     def compute_hist(x_range, y_range):
         filtered_points = filter_points(points, x_range, y_range)
         hist = hv.operation.histogram(
@@ -21,7 +25,9 @@ def compute_hist(x_range, y_range):
 
 
 def make_hist(data, title, bins_range, log_y=True, plot_width=800):
-    ### Make histogram from given count data
+    """
+    Make histogram from given count data
+    """
     count, bins = np.histogram(data, bins=bins_range)
     ylabel = "log(Count)" if log_y else "Count"
     np.seterr(divide="ignore")
@@ -36,7 +42,9 @@ def make_hist(data, title, bins_range, log_y=True, plot_width=800):
 
 
 def make_hist_panel(tsm, log_y):
-    ### Make row of histograms for holoviews panel
+    """
+    Make row of histograms for holoviews panel
+    """
     overall_site_hist = make_hist(
         tsm.sites_num_mutations,
         "Mutations per site",

pages/nodes.py

@@ -1,13 +1,15 @@
 import functools
 
-import numpy as np
-import hvplot.pandas  # noqa
 import holoviews as hv
 import holoviews.operation.datashader as hd
+import hvplot.pandas  # noqa
+import numpy as np
 import panel as pn
 
 import config
-from plot_helpers import filter_points, hover_points, make_hist_matplotlib
+from plot_helpers import filter_points
+from plot_helpers import hover_points
+from plot_helpers import make_hist_matplotlib
 
 
 def page(tsm):

pages/overview.py

@@ -1,4 +1,5 @@
 import panel as pn
 
+
 def page(tsm):
-    return pn.pane.HTML(tsm.ts)
+    return pn.pane.HTML(tsm.ts)

pages/trees.py

@@ -1,7 +1,8 @@
-import panel as pn
+import functools
+
 import holoviews as hv
 import numpy as np
-import functools
+import panel as pn
 
 from plot_helpers import make_hist_matplotlib
 
@@ -70,7 +71,7 @@ def page(tsm):
     mean_arity_hist_func = functools.partial(
         make_hist_matplotlib,
         df_trees.mean_internal_arity,
-        f"Mean arity per tree \n(not yet implemented)",
+        "Mean arity per tree \n(not yet implemented)",
         num_bins=bins,
         log_y=True,
     )