Fix pytest warnings in graphics tests (#824)

Author: tanghaibao

pyproject.toml

@@ -124,6 +124,9 @@ artifacts = [
 addopts = "-v --cov=jcvi --cov-branch --cov-report=xml --cov-report=term"
 testpaths = ["tests"]
 python_files = ["test_*.py"]
+filterwarnings = [
+    "ignore:invalid escape sequence.*:SyntaxWarning:ete3\\..*",
+]
 
 [tool.isort]
 profile = "black"

src/jcvi/graphics/grabseeds.py

@@ -84,8 +84,18 @@ def __init__(
         self.x, self.y = int(round(x)), int(round(y))
         self.location = f"{self.x}|{self.y}"
         self.area = int(round(props.area))
-        self.length = int(round(props.major_axis_length))
-        self.width = int(round(props.minor_axis_length))
+        major_axis_length = (
+            props.axis_major_length
+            if hasattr(props, "axis_major_length")
+            else props.major_axis_length
+        )
+        minor_axis_length = (
+            props.axis_minor_length
+            if hasattr(props, "axis_minor_length")
+            else props.minor_axis_length
+        )
+        self.length = int(round(major_axis_length))
+        self.width = int(round(minor_axis_length))
         self.props = props
         self.efds = efds
         self.circularity = 4 * pi * props.area / props.perimeter**2
@@ -798,7 +808,16 @@ def seeds(args):
         efds = efd_feature(contour)
         y0, x0 = props.centroid
         orientation = props.orientation
-        major, minor = props.major_axis_length, props.minor_axis_length
+        major = (
+            props.axis_major_length
+            if hasattr(props, "axis_major_length")
+            else props.major_axis_length
+        )
+        minor = (
+            props.axis_minor_length
+            if hasattr(props, "axis_minor_length")
+            else props.minor_axis_length
+        )
         major_dx = sin(orientation) * major / 2
         major_dy = cos(orientation) * major / 2
         minor_dx = cos(orientation) * minor / 2

src/jcvi/graphics/karyotype.py

@@ -455,7 +455,7 @@ def main(args: List[str]):
 
     seqidsfile, layoutfile = args
 
-    fig = plt.figure(1, (iopts.w, iopts.h))
+    fig = plt.figure(figsize=(iopts.w, iopts.h))
     root = fig.add_axes((0, 0, 1, 1))
 
     Karyotype(

src/jcvi/graphics/landscape.py

@@ -220,7 +220,7 @@ def mosdepth(args):
     logscale = opts.logscale
 
     # Construct a composite figure with N tracks indicated in the groups
-    fig = plt.figure(1, (iopts.w, iopts.h))
+    fig = plt.figure(figsize=(iopts.w, iopts.h))
     root = fig.add_axes((0, 0, 1, 1))
 
     rows = len(groups)
@@ -608,7 +608,7 @@ def depth(args):
 
     bedfiles = args
 
-    fig = plt.figure(1, (iopts.w, iopts.h))
+    fig = plt.figure(figsize=(iopts.w, iopts.h))
     root = fig.add_axes((0, 0, 1, 1))
 
     npanels = len(bedfiles)
@@ -788,7 +788,7 @@ def composite(args):
     plt.rcParams["xtick.major.size"] = 0
     plt.rcParams["ytick.major.size"] = 0
 
-    fig = plt.figure(1, (iopts.w, iopts.h))
+    fig = plt.figure(figsize=(iopts.w, iopts.h))
     root = fig.add_axes((0, 0, 1, 1))
 
     root.text(0.5, 0.95, chr, ha="center", color="darkslategray")
@@ -1072,7 +1072,7 @@ def heatmap(args):
     stacks = opts.stacks.split(",")
     heatmaps = opts.heatmaps.split(",")
 
-    fig = plt.figure(1, (iopts.w, iopts.h))
+    fig = plt.figure(figsize=(iopts.w, iopts.h))
     root_extent = (0, 0, 1, 1)
     root = fig.add_axes(root_extent)
 
@@ -1301,7 +1301,7 @@ def stack(args):
 
     stacks = opts.stacks.split(",")
 
-    fig = plt.figure(1, (iopts.w, iopts.h))
+    fig = plt.figure(figsize=(iopts.w, iopts.h))
     root_extent = (0, 0, 1, 1)
     root = fig.add_axes(root_extent)
 

src/jcvi/graphics/synteny.py

@@ -693,7 +693,7 @@ def main(args: List[str]):
     prune_features = not opts.noprune
 
     pf = datafile.rsplit(".", 1)[0]
-    fig = plt.figure(1, (iopts.w, iopts.h))
+    fig = plt.figure(figsize=(iopts.w, iopts.h))
     root = fig.add_axes((0, 0, 1, 1))
     Synteny(
         fig,