Upgrade bokeh to 3.1 (#400)

* upgrade bokeh to 3.1

* rework plotting show and return values

* update poetry

malariagen_data/ag3.py

@@ -1867,8 +1867,9 @@ def plot_cnv_hmm_coverage_track(
 
         if show:
             bkplt.show(fig)
-
-        return fig
+            return None
+        else:
+            return fig
 
     def plot_cnv_hmm_coverage(
         self,
@@ -1914,11 +1915,6 @@ def plot_cnv_hmm_coverage(
         show : bool, optional
             If true, show the plot.
 
-        Returns
-        -------
-        fig : Figure
-            Bokeh figure.
-
         """
         debug = self._log.debug
 
@@ -1961,8 +1957,9 @@ def plot_cnv_hmm_coverage(
 
         if show:
             bkplt.show(fig)
-
-        return fig
+            return None
+        else:
+            return fig
 
     def plot_cnv_hmm_heatmap_track(
         self,
@@ -2113,7 +2110,9 @@ def plot_cnv_hmm_heatmap_track(
         fig.yaxis.major_label_text_font_size = f"{row_height}px"
 
         debug("add color bar")
-        color_bar = bkmod.ColorBar(
+        # For some reason, mypy reports: Module has no attribute "ColorBar"
+        # ...but this works fine, so ignore for now.
+        color_bar = bkmod.ColorBar(  # type: ignore
             title="Copy number",
             color_mapper=color_mapper,
             major_label_overrides={
@@ -2126,8 +2125,9 @@ def plot_cnv_hmm_heatmap_track(
 
         if show:
             bkplt.show(fig)
-
-        return fig
+            return None
+        else:
+            return fig
 
     def plot_cnv_hmm_heatmap(
         self,
@@ -2171,13 +2171,6 @@ def plot_cnv_hmm_heatmap(
             row_height.
         genes_height : int, optional
             Height of genes track in pixels (px).
-        show : bool, optional
-            If true, show the plot.
-
-        Returns
-        -------
-        fig : Figure
-            Bokeh figure.
 
         """
         debug = self._log.debug
@@ -2220,8 +2213,9 @@ def plot_cnv_hmm_heatmap(
 
         if show:
             bkplt.show(fig)
-
-        return fig
+            return None
+        else:
+            return fig
 
     def _view_alignments_add_site_filters_tracks(
         self, *, contig, visibility_window, tracks
@@ -2349,6 +2343,8 @@ def plot_aim_heatmap(
         colors="T10",
         xgap=0,
         ygap=0.5,
+        show=True,
+        renderer=None,
     ):
         """Plot a heatmap of ancestry-informative marker (AIM) genotypes.
 
@@ -2547,7 +2543,11 @@ def plot_aim_heatmap(
             height=max(300, row_height * len(samples) + 100),
         )
 
-        return fig
+        if show:
+            fig.show(renderer=renderer)
+            return None
+        else:
+            return fig
 
 
 @numba.njit("Tuple((int8, int64))(int8[:], int8)")

malariagen_data/anoph/genome_features.py

@@ -60,7 +60,7 @@ class gplt_params:
     genes_height_default: genes_height = 120
     show: TypeAlias = Annotated[
         bool,
-        "If true, show the plot.",
+        "If true, show the plot. If False, do not show the plot, but return the figure.",
     ]
     toolbar_location: TypeAlias = Annotated[
         Literal["above", "below", "left", "right"],
@@ -79,8 +79,8 @@ class gplt_params:
         # Use quite a broad type here to accommodate both single-panel figures
         # created via bokeh.plotting and multi-panel figures created via
         # bokeh.layouts.
-        bokeh.model.Model,
-        "A bokeh figure.",
+        Optional[bokeh.model.Model],
+        "A bokeh figure (only returned if show=False).",
     ]
 
 
@@ -234,6 +234,11 @@ def plot_transcript(
         if title is True:
             title = f"{transcript} ({parent.strand})"
 
+        if x_range is None:
+            x_range = bokeh.models.Range1d(
+                parent.start - 2_000, parent.end + 2_000, bounds="auto"
+            )
+
         debug("Define tooltips for hover.")
         tooltips = [
             ("Type", "@type"),
@@ -255,6 +260,7 @@ def plot_transcript(
             active_drag="xpan",
             tooltips=tooltips,
             x_range=x_range,
+            y_range=bokeh.models.Range1d(-0.6, 0.6),
         )
 
         debug("Find child components of the transcript.")
@@ -333,13 +339,13 @@ def plot_transcript(
 
         debug("Tidy up the figure.")
         fig.yaxis.ticker = []
-        fig.y_range = bokeh.models.Range1d(-0.6, 0.6)
         self._bokeh_style_genome_xaxis(fig, parent.contig)
 
         if show:
             bokeh.plotting.show(fig)
-
-        return fig
+            return None
+        else:
+            return fig
 
     @check_types
     @doc(
@@ -412,6 +418,7 @@ def plot_genes(
             active_drag="xpan",
             tooltips=tooltips,
             x_range=x_range,
+            y_range=bokeh.models.Range1d(-0.4, 2.2),
         )
 
         debug("add functionality to click through to vectorbase")
@@ -431,7 +438,6 @@ def plot_genes(
         )
 
         debug("tidy up the plot")
-        fig.y_range = bokeh.models.Range1d(-0.4, 2.2)
         fig.ygrid.visible = False
         yticks = [0.4, 1.4]
         yticklabels = ["-", "+"]
@@ -441,8 +447,9 @@ def plot_genes(
 
         if show:
             bokeh.plotting.show(fig)
-
-        return fig
+            return None
+        else:
+            return fig
 
     def _plot_genes_setup_data(self, *, region):
         attributes = [a for a in self._gff_default_attributes if a != "Parent"]

malariagen_data/anoph/snp_data.py

@@ -1069,8 +1069,9 @@ def plot_snps(
 
         if show:
             bokeh.plotting.show(fig)
-
-        return fig
+            return None
+        else:
+            return fig
 
     @check_types
     @doc(
@@ -1198,7 +1199,7 @@ def plot_snps_track(
             tooltips=tooltips,
         )
         hover_tool = fig.select(type=bokeh.models.HoverTool)
-        hover_tool.names = ["snps"]
+        hover_tool.name = "snps"
 
         # Plot gaps in the reference genome.
         df_n_runs = pd.DataFrame(
@@ -1247,8 +1248,9 @@ def plot_snps_track(
 
         if show:
             bokeh.plotting.show(fig)
-
-        return fig
+            return None
+        else:
+            return fig
 
     @check_types
     @doc(