def test_parameter_to_csv(tmpdir):
csv_path = tmpdir.join("parameters.csv")
params = ParameterGroup.from_yaml("""
b:
- ["1", 0.25, {vary: false, min: 0, max: 8}]
- ["2", 0.75, {expr: '1 - $b.1', non-negative: true}]
rates:
- ["total", 2]
- ["branch1", {expr: '$rates.total * $b.1'}]
- ["branch2", {expr: '$rates.total * $b.2'}]
""")
params.to_csv(csv_path)
with open(csv_path) as f:
print(f.read())
params_from_csv = ParameterGroup.from_csv(csv_path)
for label, p in params.all():
assert params_from_csv.has(label)
p_from_csv = params_from_csv.get(label)
assert p.label == p_from_csv.label
assert p.value == p_from_csv.value
assert p.minimum == p_from_csv.minimum
assert p.maximum == p_from_csv.maximum
assert p.vary == p_from_csv.vary
assert p.non_negative == p_from_csv.non_negative
assert p.expression == p_from_csv.expression
def test_param_group_from_csv(tmpdir):
csv_path = tmpdir.join("parameters.csv")
with open(csv_path, "w") as f:
f.write(TEST_CSV)
params = ParameterGroup.from_csv(csv_path)
assert "rates" in params
assert params.has("rates.k1")
p = params.get("rates.k1")
assert p.label == "k1"
assert p.value == 0.05
assert p.minimum == 0
assert p.maximum == 5
assert p.vary
assert p.non_negative
assert p.expression is None
assert params.has("rates.k2")
p = params.get("rates.k2")
assert p.label == "k2"
assert p.value == params.get("rates.k1") * 2
assert p.minimum == -np.inf
assert p.maximum == np.inf
assert not p.vary
assert not p.non_negative
assert p.expression == "$rates.k1 * 2"
assert params.has("rates.k3")
p = params.get("rates.k3")
assert p.label == "k3"
assert p.value == 2.311
assert p.minimum == -np.inf
assert p.maximum == np.inf
assert p.vary
assert p.non_negative
assert p.expression is None
assert "pen" in params
assert "eq" in params["pen"]
assert params.has("pen.eq.1")
p = params.get("pen.eq.1")
assert p.label == "1"
assert p.value == 1.0
assert p.minimum == -np.inf
assert p.maximum == np.inf
assert not p.vary
assert not p.non_negative
assert p.expression is None