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Alternate sbmlmath testing #241

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merged 5 commits into from
Sep 11, 2023
Merged

Alternate sbmlmath testing #241

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d69e3e3
Add flag for installing sbmlmath
cthoyt Sep 11, 2023
afad326
Update setup.cfg
cthoyt Sep 11, 2023
599c062
Do not ignore the rest of the unit tests that require sbmlmath
nanglo123 Sep 11, 2023
68a5f13
Update pyproject.toml
cthoyt Sep 11, 2023
a22184f
Update tox.ini
cthoyt Sep 11, 2023
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1 change: 1 addition & 0 deletions setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ install_requires =
typing_extensions
networkx
tqdm
sbmlmath; python_version >= "3.10"

zip_safe = false
include_package_data = True
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25 changes: 17 additions & 8 deletions tests/test_modeling/test_askenet_ops.py
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Original file line number Diff line number Diff line change
@@ -1,12 +1,21 @@
import unittest
import requests
import pytest
from copy import deepcopy as _d
from mira.modeling.askenet.ops import *
from sympy import *
from mira.metamodel.io import mathml_to_expression
from mira.metamodel.templates import Concept

try:
import sbmlmath
except ImportError:
sbmlmath_available = False
else:
sbmlmath_available = True


SBMLMATH_REQUIRED = unittest.skipUnless(sbmlmath_available, reason="SBMLMath package is not available")


class TestAskenetOperations(unittest.TestCase):
"""A test case for operations on template models."""
Expand Down Expand Up @@ -188,7 +197,7 @@ def test_remove_observable_or_parameter(self):

self.assertEqual(old_obs['id'], new_obs['id'])

@pytest.mark.sbmlmath
@SBMLMATH_REQUIRED
def test_add_observable(self):
amr = _d(self.sir_amr)
new_id = 'testinf'
Expand All @@ -207,7 +216,7 @@ def test_add_observable(self):
self.assertEqual(xml_expression, new_observable_dict[new_id]['expression_mathml'])
self.assertEqual(sstr(mathml_to_expression(xml_expression)), new_observable_dict[new_id]['expression'])

@pytest.mark.sbmlmath
@SBMLMATH_REQUIRED
def test_replace_parameter_id(self):
old_id = 'beta'
new_id = 'TEST'
Expand Down Expand Up @@ -311,7 +320,7 @@ def test_remove_transition(self):
for new_transition in new_model_transition:
self.assertNotEquals(removed_transition, new_transition['id'])

@pytest.mark.sbmlmath
@SBMLMATH_REQUIRED
def test_add_transition(self):
test_subject = Concept(name="test_subject", identifiers={"ido": "0000511"})
test_outcome = Concept(name="test_outcome", identifiers={"ido": "0000592"})
Expand Down Expand Up @@ -404,7 +413,7 @@ def test_add_transition(self):
natural_degradation_rates_dict[new_transition_id]['expression'])
self.assertIn(test_subject.name, natural_degradation_states_dict)

@pytest.mark.sbmlmath
@SBMLMATH_REQUIRED
def test_replace_rate_law_sympy(self):
transition_id = 'inf'
target_expression_xml_str = '<apply><plus/><ci>X</ci><cn>8</cn></apply>'
Expand All @@ -419,7 +428,7 @@ def test_replace_rate_law_sympy(self):
self.assertEqual(sstr(target_expression_sympy), new_rate['expression'])
self.assertEqual(target_expression_xml_str, new_rate['expression_mathml'])

@pytest.mark.sbmlmath
@SBMLMATH_REQUIRED
def test_replace_rate_law_mathml(self):
amr = _d(self.sir_amr)
transition_id = 'inf'
Expand All @@ -435,7 +444,7 @@ def test_replace_rate_law_mathml(self):
self.assertEqual(sstr(target_expression_sympy), new_rate['expression'])
self.assertEqual(target_expression_xml_str, new_rate['expression_mathml'])

@pytest.mark.sbmlmath
@SBMLMATH_REQUIRED
# Following 2 unit tests only test for replacing expressions in observables, not initials
def test_replace_observable_expression_sympy(self):
object_id = 'noninf'
Expand All @@ -449,7 +458,7 @@ def test_replace_observable_expression_sympy(self):
self.assertEqual(sstr(target_expression_sympy), new_obs['expression'])
self.assertEqual(target_expression_xml_str, new_obs['expression_mathml'])

@pytest.mark.sbmlmath
@SBMLMATH_REQUIRED
def test_replace_observable_expression_mathml(self):
object_id = 'noninf'
amr = _d(self.sir_amr)
Expand Down
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