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Jun 7, 2022
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use min_time to allow negative times in ts #2215

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4 changes: 4 additions & 0 deletions python/CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,10 @@

**Changes**

- A ``min_time`` parameter in ``draw_svg`` enables the youngest node as the y axis min
value, allowing negative times.
(:user:`hyanwong`, :issue:`2197`, :pr:`2215`)

- ``VcfWriter.write`` now prints the site ID of variants in the ID field of the
output VCF files.
(:user:`roohy`, :issue:`2103`, :pr:`2107`)
Expand Down
113 changes: 105 additions & 8 deletions python/tests/test_drawing.py
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Expand Up @@ -221,6 +221,28 @@ def get_simple_ts(self, use_mutation_times=False):
tables.mutations.time = np.full_like(tables.mutations.time, tskit.UNKNOWN_TIME)
return tables.tree_sequence()

def get_ts_varying_min_times(self, *args, **kwargs):
"""
Like get_simple_ts but return a tree sequence with negative times, and some trees
with different min times (i.e. with dangling nonsample nodes at negative times)
"""
ts = self.get_simple_ts(*args, **kwargs)
tables = ts.dump_tables()
time = tables.nodes.time
time[time == 0] = 0.1
time[3] = -9.99
tables.nodes.time = time
# set node 3 to be non-sample node lower than the rest
flags = tables.nodes.flags
flags[3] = 0
tables.nodes.flags = flags
edges = tables.edges
assert edges[3].child == 3 and edges[3].parent == 5
edges[3] = edges[3].replace(left=ts.breakpoints(True)[1])
tables.sort()
tables.nodes.flags = flags
return tables.tree_sequence()

def fail(self, *args, **kwargs):
"""
Required for xmlunittest.XmlTestMixin to work with pytest not unittest
Expand Down Expand Up @@ -591,6 +613,8 @@ def test_unused_args(self):
t.draw(format=self.drawing_format, node_colours={})
with pytest.raises(ValueError):
t.draw(format=self.drawing_format, max_time=1234)
with pytest.raises(ValueError):
t.draw(format=self.drawing_format, min_time=1234)
with pytest.raises(ValueError):
with pytest.warns(FutureWarning):
t.draw(format=self.drawing_format, max_tree_height=1234)
Expand Down Expand Up @@ -1500,8 +1524,6 @@ def test_nonimplemented_base_class(self):
plot.set_spacing()
with pytest.raises(NotImplementedError):
plot.draw_x_axis(tick_positions=ts.breakpoints(as_array=True))
with pytest.raises(NotImplementedError):
plot.draw_y_axis(ticks={0: "0"})

def test_bad_tick_spacing(self):
# Integer y_ticks to give auto-generated tick locs is not currently implemented
Expand All @@ -1514,7 +1536,7 @@ def test_bad_tick_spacing(self):

def test_no_mixed_yscales(self):
ts = self.get_simple_ts()
with pytest.raises(ValueError, match="varying yscales"):
with pytest.raises(ValueError, match="vary in timescale"):
ts.draw_svg(y_axis=True, max_time="tree")

def test_draw_defaults(self):
Expand Down Expand Up @@ -1704,6 +1726,21 @@ def test_bad_max_time(self):
with pytest.warns(FutureWarning):
t.draw_svg(max_tree_height=bad_height)

def test_bad_min_time(self):
t = self.get_binary_tree()
for bad_min in ["te", "asdf", "", [], b"23"]:
with pytest.raises(ValueError):
t.draw_svg(min_time=bad_min)
with pytest.raises(ValueError):
with pytest.warns(FutureWarning):
t.draw_svg(max_tree_height=bad_min)

def test_bad_neg_log_time(self):
t = self.get_ts_varying_min_times().at_index(1)
assert min(t.time(u) for u in t.nodes()) < 0
with pytest.raises(ValueError, match="negative times"):
t.draw_svg(t.draw_svg(time_scale="log_time"))

def test_time_scale_time_and_max_time(self):
ts = msprime.simulate(5, recombination_rate=2, random_seed=2)
t = ts.first()
Expand All @@ -1727,16 +1764,40 @@ def test_time_scale_rank_and_max_time(self):
ts = msprime.simulate(5, recombination_rate=2, random_seed=2)
t = ts.first()
# The default should be the same as tree.
svg1 = t.draw_svg(max_time="tree", time_scale="rank")
svg1 = t.draw_svg(max_time="tree", time_scale="rank", y_axis=True)
self.verify_basic_svg(svg1)
svg2 = t.draw_svg(time_scale="rank")
svg2 = t.draw_svg(time_scale="rank", y_axis=True)
assert svg1 == svg2
svg3 = t.draw_svg(max_time="ts", time_scale="rank")
svg3 = t.draw_svg(max_time="ts", time_scale="rank", y_axis=True)
assert svg1 != svg3
self.verify_basic_svg(svg3)
# Numeric max time not supported for rank scale.
with pytest.raises(ValueError):
t.draw_svg(max_time=2, time_scale="rank")
t.draw_svg(max_time=2, time_scale="rank", y_axis=True)

def test_min_tree_time(self):
ts = self.get_ts_varying_min_times()
t = ts.first()
# The default should be the same as tree.
svg1 = t.draw_svg(min_time="tree", y_axis=True)
self.verify_basic_svg(svg1)
svg2 = t.draw_svg(y_axis=True)
assert svg1 == svg2
svg3 = t.draw_svg(min_time="ts", y_axis=True)
assert svg1 != svg3
svg4 = t.draw_svg(min_time=min(ts.tables.nodes.time), y_axis=True)
assert svg3 == svg4

def test_min_ts_time(self):
ts = self.get_ts_varying_min_times()
svg1 = ts.draw_svg(y_axis=True)
self.verify_basic_svg(svg1, width=200 * ts.num_trees)
svg2 = ts.draw_svg(min_time="ts", y_axis=True)
assert svg1 == svg2
with pytest.raises(ValueError, match="vary in timescale"):
ts.draw_svg(min_time="tree", y_axis=True)
svg3 = ts.draw_svg(min_time=min(ts.tables.nodes.time), y_axis=True)
assert svg2 == svg3

#
# TODO: update the tests below here to check the new SVG based interface.
Expand Down Expand Up @@ -1894,6 +1955,42 @@ def test_max_time(self):
snippet2 = svg2[svg2.rfind("edge", 0, str_pos) : str_pos]
assert snippet1 == snippet2

def test_min_time(self):
nodes = io.StringIO(
"""\
id is_sample time
0 0 -1.11
1 1 2.22
2 1 2.22
3 0 3.33
4 0 4.44
5 0 5.55
"""
)
edges = io.StringIO(
"""\
left right parent child
0 1 5 2
0 1 5 3
1 2 4 2
1 2 4 3
0 1 3 0
0 2 3 1
"""
)
ts = tskit.load_text(nodes, edges, strict=False)
svg1a = ts.at_index(0).draw_svg(y_axis=True)
svg1b = ts.at_index(0).draw_svg(y_axis=True, min_time="ts")
svg2a = ts.at_index(1).draw_svg(y_axis=True)
svg2b = ts.at_index(1).draw_svg(y_axis=True, min_time="ts")
# axis should start at -1.11
assert svg1a == svg1b
assert ">-1.11<" in svg1a
# 2nd tree should be different depending on whether min_time is "tree" or "ts"
assert svg2a != svg2b
assert ">-1.11<" not in svg2a
assert ">-1.11<" not in svg2b

def test_draw_sized_tree(self):
tree = self.get_binary_tree()
svg = tree.draw_svg(size=(600, 400))
Expand Down Expand Up @@ -1987,7 +2084,7 @@ def test_x_axis(self):
assert svg_no_css.count("y-axis") == 0

def test_y_axis(self):
tree = msprime.simulate(4, random_seed=2).first()
tree = self.get_simple_ts().first()
for hscale, label in [
(None, "Time"),
("time", "Time"),
Expand Down
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