Patch for SBML compatible units (for PR #320)

.github/workflows/test.yml

@@ -20,7 +20,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install pytest pytest-cov python-libsbml
-      - name: Tnstall biocrnpyler
+      - name: Install biocrnpyler
         run: pip install -e .
       - name: Test biocrnpyler
         run: pytest --cov biocrnpyler

Tests/Unit/test_chemicalReactionNetwork.py

@@ -228,7 +228,7 @@ def test_initial_condition_vector(self):
     def test_get_all_species_containing(self):
         # test that the species arument must be Species object
         with self.assertRaisesRegex(
-            ValueError, 'species argument must be an instance of Species!'
+            ValueError, 'species argument must be an instance of Species'
         ):
             self.crn.get_all_species_containing(species=self.species_list)
 

Tests/Unit/test_compartment.py

@@ -118,7 +118,6 @@ def test_compartment_setter(self):
         s1 = Species('S1', compartment=comp1)
         mixture_1 = Mixture(species=[s1])
         crn_1 = mixture_1.compile_crn()
-        crn_1.write_sbml_file('test_compartment_setter_1.xml')
         # change compartment
         s1.compartment = comp2
         mixture_2 = Mixture(species=[s1])

Tests/Unit/test_component_basic.py

@@ -11,7 +11,11 @@ def test_enzyme():
     products = 'P1'
     enzyme = 'E1'
 
-    e = Enzyme(enzyme=enzyme, substrates=substrates, products=products)
+    e = Enzyme(
+        enzyme=enzyme, substrates=substrates, products=products,
+    )
+    e.default_mechanism=None  # override failsafe
+
     assert any([s.name == 'S1' for s in e.substrates])
     assert any([p.name == 'P1' for p in e.products])
     assert enzyme == e.enzyme.name

Tests/Unit/test_component_membrane.py

@@ -21,6 +21,7 @@ def test_DiffusibleMolecule():
 
     assert dm.get_species().name == 'DP'
 
+    dm.default_mechanism = None  # override failsafe
     with pytest.raises(
         KeyError,
         match='Unable to find mechanism of type diffusion in Component',
@@ -46,6 +47,7 @@ def test_IntegralMembraneProtein():
 
     assert imp.get_species().name == 'MP1'
 
+    imp.default_mechanism = None  # override failsafe
     with pytest.raises(
         KeyError,
         match='Unable to find mechanism of type membrane_insertion in Component',
@@ -70,6 +72,7 @@ def test_MembraneChannel():
 
     assert mc.get_species().name == 'IMP1'
 
+    mc.default_mechanism = None  # override failsafe
     with pytest.raises(
         KeyError,
         match='Unable to find mechanism of type transport in Component',
@@ -94,6 +97,7 @@ def test_MembranePump():
 
     assert mp.get_species().name == 'MPump1'
 
+    mp.default_mechanism = None  # override failsafe
     with pytest.raises(
         KeyError,
         match='Unable to find mechanism of type transport in Component',
@@ -125,6 +129,7 @@ def test_MembraneSensor():
 
     assert ms.get_species().name == 'MSensor1'
 
+    ms.default_mechanism = None  # override failsafe
     with pytest.raises(
         KeyError,
         match='Unable to find mechanism of type membrane_sensor in Component',

Tests/Unit/test_parameter.py

@@ -516,7 +516,7 @@ def test_find_parameter(self):
         )
 
 
-def test_findpath():
+def test_findpath(tmp_path):
     import os
     import platform
 
@@ -530,21 +530,32 @@ def test_findpath():
         bcp.find_file_in_bcp_path('mechanisms/txtl_parameters.tsv')
     )
 
-    # Make sure we can find files in current directory
-    assert bcp.find_file_in_bcp_path('__testfile__.tsv') is None
-    open('__testfile__.tsv', 'w')
-    assert os.path.exists(bcp.find_file_in_bcp_path('__testfile__.tsv'))
-    os.remove('__testfile__.tsv')
-
-    # Make sure we can find files in the path
-    open('../__testfile__.tsv', 'w')
-    assert bcp.find_file_in_bcp_path('__testfile__.tsv') is None
-    if platform.system() == 'Windows':
-        os.environ['BCP_PATH'] = '/tmp;.;..'
-    else:
-        os.environ['BCP_PATH'] = '/tmp:.:..'
-    assert os.path.exists(bcp.find_file_in_bcp_path('__testfile__.tsv'))
-    os.remove('../__testfile__.tsv')
+    prev_cwd = os.getcwd()
+    prev_bcp_path = os.environ.get('BCP_PATH')
+    child_dir = tmp_path / 'child'
+    child_dir.mkdir()
+    os.chdir(child_dir)
+    try:
+        # Make sure we can find files in current directory
+        assert bcp.find_file_in_bcp_path('__testfile__.tsv') is None
+        (child_dir / '__testfile__.tsv').write_text('')
+        assert os.path.exists(bcp.find_file_in_bcp_path('__testfile__.tsv'))
+        os.remove(child_dir / '__testfile__.tsv')
+
+        # Make sure we can find files in the path
+        (tmp_path / '__testfile__.tsv').write_text('')
+        assert bcp.find_file_in_bcp_path('__testfile__.tsv') is None
+        if platform.system() == 'Windows':
+            os.environ['BCP_PATH'] = f'/tmp;.;{tmp_path}'
+        else:
+            os.environ['BCP_PATH'] = f'/tmp:.:{tmp_path}'
+        assert os.path.exists(bcp.find_file_in_bcp_path('__testfile__.tsv'))
+    finally:
+        os.chdir(prev_cwd)
+        if prev_bcp_path is None:
+            os.environ.pop('BCP_PATH', None)
+        else:
+            os.environ['BCP_PATH'] = prev_bcp_path
 
 
 def test_parameter_ordering():

Tests/Unit/test_sbml.py

@@ -359,6 +359,36 @@ def test_generate_sbml_model():
     assert validate_sbml(document) == 0
 
 
+def test_generate_sbml_model_writes_units_from_biocrnpyler():
+    compartment = Compartment('cell', size=1, unit='uL')
+    s1 = Species('S1', compartment=compartment)
+    s2 = Species('S2', compartment=compartment)
+    kf = ParameterEntry('k', 0.1, unit='/sec')
+    x0 = ParameterEntry('S1_0', 1.0, unit='uM')
+    rxn = Reaction.from_massaction(inputs=[s1], outputs=[s2], k_forward=kf)
+    crn = ChemicalReactionNetwork(
+        species=[s1, s2],
+        reactions=[rxn],
+        initial_concentration_dict={s1: x0},
+    )
+
+    document, model = crn.generate_sbml_model()
+    assert validate_sbml(document) == 0
+
+    sbml_compartment = model.getCompartment('cell')
+    assert sbml_compartment.getUnits() == 'uL'
+
+    sbml_species = model.getSpecies(0)
+    assert sbml_species.getSubstanceUnits() == 'pmol'
+    assert sbml_species.getInitialConcentration() == 1.0
+
+    sbml_parameter = model.getListOfParameters()[0]
+    assert sbml_parameter.getUnits() == 'per_sec'
+
+    unit_defs = {ud.getId() for ud in model.getListOfUnitDefinitions()}
+    assert {'uL', 'pmol', 'per_sec'}.issubset(unit_defs)
+
+
 def test_generate_sbml_model_parameter_names():
     s1 = Species('S1')
     s2 = Species('S2')
@@ -518,11 +548,8 @@ def check(value, message):
         global_param = _create_global_parameter(
             model, 'k_global', value=10, p_unit=24
         )
-    with pytest.warns(
-        Warning,
-        match="The string identifier for the unit 1_s is not supported by "
-        "BioCRNpyler. Add this to the dictionary in biocrnpyler/units.py "
-        "if you want this unit",
+    with pytest.raises(
+        ValueError, match="Unsupported SBML unit '1_s'"
     ):
         global_param = _create_global_parameter(
             model, 'k_global', value=10, p_unit='1_s'

biocrnpyler/__init__.py

@@ -11,6 +11,12 @@
 
 # All utilities
 from .utils import *
+from .utils.plotting import (
+    plot_all_species_containing as plot_all_species_containing,
+)
+from .utils.plotting import (
+    plot_gene_expression_data as plot_gene_expression_data,
+)
 
 try:
     from ._version import version as __version__

biocrnpyler/components/basic.py

@@ -6,6 +6,9 @@
 from ..core.component import Component
 from ..core.reaction import Reaction
 from ..core.species import Complex, Species
+from ..mechanisms.binding import One_Step_Binding
+from ..mechanisms.enzyme import MichaelisMenten
+from ..mechanisms.metabolite import OneStepPathway
 
 
 class DNA(Component):
@@ -402,7 +405,17 @@ def __init__(
                 else:
                     self.products.append(self.set_species(p))
 
-        Component.__init__(self=self, name=name, **kwargs)
+        if precursors is not None or products is not None:
+            default_mechanism = OneStepPathway()
+        else:
+            default_mechanism = None
+
+        Component.__init__(
+            self=self,
+            name=name,
+            default_mechanism=default_mechanism,
+            **kwargs,
+        )
 
     def get_species(self) -> Species:
         """Get the metabolite species.
@@ -602,7 +615,12 @@ def __init__(
         if name is None:
             name = self.species.name
 
-        Component.__init__(self=self, name=name, **kwargs)
+        Component.__init__(
+            self=self,
+            name=name,
+            default_mechanism=One_Step_Binding(),
+            **kwargs,
+        )
 
     def get_species(self) -> List[Species]:
         """Get the complex species.
@@ -773,7 +791,12 @@ def __init__(
         self.substrates = substrates
         self.products = products
 
-        Component.__init__(self=self, name=self.enzyme.name, **kwargs)
+        Component.__init__(
+            self=self,
+            name=self.enzyme.name,
+            default_mechanism=MichaelisMenten(),
+            **kwargs,
+        )
 
     @property
     def substrates(self) -> List:

biocrnpyler/components/combinatorial_conformation.py

@@ -140,8 +140,12 @@ def __init__(
 
         if name is None:
             name = str(self.internal_polymer.name)
-        Component.__init__(self, name=name, **kwargs)
-        self.add_mechanism(One_Step_Reversible_Conformation_Change())
+        Component.__init__(
+            self,
+            name=name,
+            default_mechanism=One_Step_Reversible_Conformation_Change(),
+            **kwargs,
+        )
 
     # Helper function to assert the correct class type
     def _assert_conformation(self, states, input_name='states'):