def test_import(self, tree, tmpdir):
"""Test import of frequencies JSON that was exported from a frequencies instance.
"""
start_date = 2015.5
end_date = 2018.5
kde_frequencies = TreeKdeFrequencies(start_date=start_date,
end_date=end_date)
frequencies = kde_frequencies.estimate(tree)
frequencies_json = kde_frequencies.to_json()
# Try to dump exported JSON to disk.
tmp_fh = tmpdir.mkdir("json").join("frequencies.json")
fh = tmp_fh.open(mode="w")
json.dump(frequencies_json, fh)
fh.close()
assert tmp_fh.check()
# Import frequencies from existing tree and JSON.
fh = tmp_fh.open()
new_frequencies_json = json.load(fh)
fh.close()
new_kde_frequencies = TreeKdeFrequencies.from_json(
new_frequencies_json)
assert np.array_equal(kde_frequencies.pivots,
new_kde_frequencies.pivots)
# Get the first non-root key (root clade is number 0) and should be first in the sorted list of keys.
key = sorted(kde_frequencies.frequencies.keys())[1]
assert np.array_equal(kde_frequencies.frequencies[key],
new_kde_frequencies.frequencies[key])
def test_export_without_frequencies(self):
"""Test frequencies export to JSON when frequencies have *not* been estimated.
"""
kde_frequencies = TreeKdeFrequencies()
frequencies_json = kde_frequencies.to_json()
assert "params" in frequencies_json
assert kde_frequencies.pivot_frequency == frequencies_json["params"]["pivot_frequency"]
assert "node_filters" in frequencies_json["params"]
assert "data" not in frequencies_json
def test_import_without_frequencies(self):
"""Test import of frequencies JSON that was exported from a frequencies instance without frequency values.
"""
kde_frequencies = TreeKdeFrequencies()
frequencies_json = kde_frequencies.to_json()
# Import frequencies from existing tree and JSON.
new_kde_frequencies = TreeKdeFrequencies.from_json(frequencies_json)
assert kde_frequencies.pivot_frequency == new_kde_frequencies.pivot_frequency
assert not hasattr(new_kde_frequencies, "frequencies")
def test_export_without_frequencies(self):
"""Test frequencies export to JSON when frequencies have *not* been estimated.
"""
kde_frequencies = TreeKdeFrequencies()
frequencies_json = kde_frequencies.to_json()
assert "params" in frequencies_json
assert kde_frequencies.pivot_frequency == frequencies_json["params"][
"pivot_frequency"]
assert "node_filters" in frequencies_json["params"]
assert "data" not in frequencies_json
def test_import_without_frequencies(self):
"""Test import of frequencies JSON that was exported from a frequencies instance without frequency values.
"""
kde_frequencies = TreeKdeFrequencies()
frequencies_json = kde_frequencies.to_json()
# Import frequencies from existing tree and JSON.
new_kde_frequencies = TreeKdeFrequencies.from_json(frequencies_json)
assert kde_frequencies.pivot_frequency == new_kde_frequencies.pivot_frequency
assert not hasattr(new_kde_frequencies, "frequencies")
def test_export_with_frequencies(self, tree):
"""Test frequencies export to JSON when frequencies have been estimated.
"""
kde_frequencies = TreeKdeFrequencies()
frequencies = kde_frequencies.estimate(tree)
frequencies_json = kde_frequencies.to_json()
assert "params" in frequencies_json
assert kde_frequencies.pivot_frequency == frequencies_json["params"]["pivot_frequency"]
assert kde_frequencies.start_date == frequencies_json["params"]["start_date"]
assert kde_frequencies.end_date == frequencies_json["params"]["end_date"]
assert "data" in frequencies_json
assert "pivots" in frequencies_json["data"]
assert "frequencies" in frequencies_json["data"]
def test_export_with_frequencies(self, tree):
"""Test frequencies export to JSON when frequencies have been estimated.
"""
kde_frequencies = TreeKdeFrequencies()
frequencies = kde_frequencies.estimate(tree)
frequencies_json = kde_frequencies.to_json()
assert "params" in frequencies_json
assert kde_frequencies.pivot_frequency == frequencies_json["params"][
"pivot_frequency"]
assert kde_frequencies.start_date == frequencies_json["params"][
"start_date"]
assert kde_frequencies.end_date == frequencies_json["params"][
"end_date"]
assert "data" in frequencies_json
assert "pivots" in frequencies_json["data"]
assert "frequencies" in frequencies_json["data"]
def test_import(self, tree, tmpdir):
"""Test import of frequencies JSON that was exported from a frequencies instance.
"""
start_date = 2015.5
end_date = 2018.5
kde_frequencies = TreeKdeFrequencies(
start_date=start_date,
end_date=end_date
)
frequencies = kde_frequencies.estimate(tree)
frequencies_json = kde_frequencies.to_json()
# Try to dump exported JSON to disk.
tmp_fh = tmpdir.mkdir("json").join("frequencies.json")
fh = tmp_fh.open(mode="w")
json.dump(frequencies_json, fh)
fh.close()
assert tmp_fh.check()
# Import frequencies from existing tree and JSON.
fh = tmp_fh.open()
new_frequencies_json = json.load(fh)
fh.close()
new_kde_frequencies = TreeKdeFrequencies.from_json(new_frequencies_json)
assert np.array_equal(
kde_frequencies.pivots,
new_kde_frequencies.pivots
)
# Get the first non-root key (root clade is number 0) and should be first in the sorted list of keys.
key = sorted(kde_frequencies.frequencies.keys())[1]
assert np.array_equal(
kde_frequencies.frequencies[key],
new_kde_frequencies.frequencies[key]
)