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tedinburghtedinburgh
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Add linting
1 parent f807826 commit 183505e

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2 files changed

+57
-71
lines changed

2 files changed

+57
-71
lines changed

‎vertex/IsaricDraw.py‎

Lines changed: 48 additions & 60 deletions
Original file line numberDiff line numberDiff line change
@@ -1170,9 +1170,7 @@ def fig_forest_plot(
11701170
traces = []
11711171

11721172
# Add the point estimates as scatter plot points
1173-
traces.append(
1174-
go.Scatter(x=df[labels[1]], y=df[labels[0]], mode="markers", name="Odds Ratio", marker=marker)
1175-
)
1173+
traces.append(go.Scatter(x=df[labels[1]], y=df[labels[0]], mode="markers", name="Odds Ratio", marker=marker))
11761174

11771175
# Add the confidence intervals as lines
11781176
for index, row in df.iterrows():
@@ -1189,15 +1187,17 @@ def fig_forest_plot(
11891187
if noeffect_line is not None:
11901188
if isinstance(noeffect_line, dict) is False:
11911189
noeffect_line = {"color": "red", "width": 2}
1192-
add_shape = [{
1193-
# Line of no effect
1194-
"type": "line",
1195-
"x0": 1,
1196-
"y0": -0.5,
1197-
"x1": 1,
1198-
"y1": len(df[labels[0]]) - 0.5,
1199-
"line": noeffect_line,
1200-
}]
1190+
add_shape = [
1191+
{
1192+
# Line of no effect
1193+
"type": "line",
1194+
"x0": 1,
1195+
"y0": -0.5,
1196+
"x1": 1,
1197+
"y1": len(df[labels[0]]) - 0.5,
1198+
"line": noeffect_line,
1199+
}
1200+
]
12011201
else:
12021202
add_shape = None
12031203

@@ -1665,24 +1665,25 @@ def fig_bar_line_chart(
16651665

16661666

16671667
def fig_heatmaps(
1668-
data,
1669-
title="",
1670-
subplot_titles=None,
1671-
ylabel="",
1672-
xlabel="",
1673-
colorbar_label="",
1674-
index_column="index",
1675-
zmin=None,
1676-
zmax=None,
1677-
include_annotations=False,
1678-
base_color_map=None,
1679-
height=750,
1680-
suffix="",
1681-
filepath="",
1682-
save_inputs=False,
1683-
graph_id=None,
1684-
graph_label="",
1685-
graph_about=""):
1668+
data,
1669+
title="",
1670+
subplot_titles=None,
1671+
ylabel="",
1672+
xlabel="",
1673+
colorbar_label="",
1674+
index_column="index",
1675+
zmin=None,
1676+
zmax=None,
1677+
include_annotations=False,
1678+
base_color_map=None,
1679+
height=750,
1680+
suffix="",
1681+
filepath="",
1682+
save_inputs=False,
1683+
graph_id=None,
1684+
graph_label="",
1685+
graph_about="",
1686+
):
16861687
# ----
16871688
# Every figure must start with this
16881689
if save_inputs:
@@ -1699,20 +1700,17 @@ def fig_heatmaps(
16991700

17001701
# Create subplots for the heatmaps
17011702
fig = make_subplots(
1702-
rows=len(data), cols=1,
1703+
rows=len(data),
1704+
cols=1,
17031705
subplot_titles=subplot_titles,
17041706
vertical_spacing=0.1,
17051707
y_title=ylabel,
17061708
)
17071709

17081710
if zmin is None:
1709-
zmin = min(
1710-
data[ii].drop(columns=index_column).min().min()
1711-
for ii in range(len(data)))
1711+
zmin = min(data[ii].drop(columns=index_column).min().min() for ii in range(len(data)))
17121712
if zmax is None:
1713-
zmax = max(
1714-
data[ii].drop(columns=index_column).max().max()
1715-
for ii in range(len(data)))
1713+
zmax = max(data[ii].drop(columns=index_column).max().max() for ii in range(len(data)))
17161714
if base_color_map is None:
17171715
base_color_map = "viridis"
17181716

@@ -1735,9 +1733,10 @@ def fig_heatmaps(
17351733
zmax=zmax,
17361734
colorscale=base_color_map,
17371735
colorbar=({"title": colorbar_label} if ii == 0 else None),
1738-
showscale=(True if ii == 0 else False)
1736+
showscale=(True if ii == 0 else False),
17391737
),
1740-
row=(ii + 1), col=1
1738+
row=(ii + 1),
1739+
col=1,
17411740
)
17421741

17431742
# Update layout
@@ -1765,15 +1764,7 @@ def fig_heatmaps(
17651764
return fig, graph_id, graph_label, graph_about
17661765

17671766

1768-
def fig_sankey(
1769-
data,
1770-
height=500,
1771-
suffix="",
1772-
filepath="",
1773-
save_inputs=False,
1774-
graph_id="sankey",
1775-
graph_label="",
1776-
graph_about=""):
1767+
def fig_sankey(data, height=500, suffix="", filepath="", save_inputs=False, graph_id="sankey", graph_label="", graph_about=""):
17771768
# ----
17781769
# Every figure must start with this
17791770
if save_inputs:
@@ -1789,24 +1780,21 @@ def fig_sankey(
17891780
link = data[1].copy()
17901781
annotations = data[2].copy()
17911782

1792-
node_metadata = {
1793-
"hovertemplate": "%{customdata}",
1794-
"pad": 15,
1795-
"thickness": 20,
1796-
"line": {"color": "black", "width": 1.2}
1797-
}
1783+
node_metadata = {"hovertemplate": "%{customdata}", "pad": 15, "thickness": 20, "line": {"color": "black", "width": 1.2}}
17981784
link_metadata = {
17991785
"hovertemplate": "%{source.customdata} to %{target.customdata}",
18001786
"line": {"color": "rgba(0,0,0,0.3)", "width": 0.3},
18011787
}
18021788

18031789
fig = go.Figure(
1804-
data=[go.Sankey(
1805-
arrangement="snap",
1806-
valueformat=".0f",
1807-
node={**node.to_dict(orient="list"), **node_metadata},
1808-
link={**link.to_dict(orient="list"), **link_metadata},
1809-
)],
1790+
data=[
1791+
go.Sankey(
1792+
arrangement="snap",
1793+
valueformat=".0f",
1794+
node={**node.to_dict(orient="list"), **node_metadata},
1795+
link={**link.to_dict(orient="list"), **link_metadata},
1796+
)
1797+
],
18101798
layout=go.Layout(
18111799
annotations=annotations.to_dict(orient="records"),
18121800
height=height,

‎vertex/layout/filters.py‎

Lines changed: 9 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -96,21 +96,21 @@ def cid(base):
9696
if layout == "accordion":
9797
children = [
9898
html.Label(html.B("Sex at birth:")),
99-
html.Div(style={'margin-top': '5px'}),
99+
html.Div(style={"margin-top": "5px"}),
100100
sex_checklist,
101-
html.Div(style={'margin-top': '10px'}),
101+
html.Div(style={"margin-top": "10px"}),
102102
html.Label(html.B("Age:")),
103-
html.Div(style={'margin-top': '5px'}),
103+
html.Div(style={"margin-top": "5px"}),
104104
age_slider,
105-
html.Div(style={'margin-top': '10px'}),
105+
html.Div(style={"margin-top": "10px"}),
106106
country_section,
107-
html.Div(style={'margin-top': '15px'}),
107+
html.Div(style={"margin-top": "15px"}),
108108
html.Label(html.B("Admission date:")),
109-
html.Div(style={'margin-top': '5px'}),
109+
html.Div(style={"margin-top": "5px"}),
110110
admdate_slider,
111-
html.Div(style={'margin-top': '35px'}),
111+
html.Div(style={"margin-top": "35px"}),
112112
html.Label(html.B("Outcome:")),
113-
html.Div(style={'margin-top': '5px'}),
113+
html.Div(style={"margin-top": "5px"}),
114114
outcome_checklist,
115115
]
116116
comp = dbc.AccordionItem(
@@ -308,9 +308,7 @@ def get_filter_options(df_map):
308308
}
309309

310310
admdate_yyyymm = pd.date_range(
311-
start=df_map["pres_date"].min(),
312-
end=df_map["pres_date"].max() + pd.DateOffset(months=1),
313-
freq="MS"
311+
start=df_map["pres_date"].min(), end=df_map["pres_date"].max() + pd.DateOffset(months=1), freq="MS"
314312
)
315313
admdate_options = {
316314
"min": 0,

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