updated parameter processing

.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/Combinatorial/test_construct_combinatorially.py

@@ -185,6 +185,7 @@ def test_combinatorial_DNAconstruct_in_Mixtures():
         for mclass, args in mixture_classes:
             # create the Mixture with parameters
             args['parameters'] = dict(parameters)
+            args['parameter_file'] = None
             m = mclass(**args)
 
             # Promoters and terminators are instances
@@ -221,6 +222,7 @@ def test_combinatorial_RNAconstruct_in_Mixtures():
         for mclass, args in mixture_classes:
             # create the Mixture with parameters
             args['parameters'] = dict(parameters)
+            args['parameter_file'] = None
             m = mclass(**args)
 
             # RBSs and CDSs are instances
@@ -252,6 +254,7 @@ def test_combinatorial_DNAconstruct_RNAconstruct_in_Mixtures():
         for mclass, args in mixture_classes:
             # create the Mixture with parameters
             args['parameters'] = dict(parameters)
+            args['parameter_file'] = None
             m = mclass(**args)
 
             # Promoters and terminators are instances

Tests/Combinatorial/test_mixtures_and_components_combinatorially.py

@@ -198,8 +198,12 @@ def setUp(self) -> None:
         self.parameters = {
             'kb': 1.0,
             'ku': 1.0,
+            'kb_ntps': 1.0,
+            'ku_ntps': 1.0,
             'ktx': 1.0,
             'ktl': 1.0,
+            'kb_fuel': 1.0,
+            'ku_fuel': 1.0,
             'kdeg': 1.0,
             'kdil': 1.0,
             'kexpress': 1.0,

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])
@@ -135,7 +134,7 @@ def test_compartment_in_special_mixtures(self):
         )
         E = EnergyTxTlExtract(
             components=[activatable_assembly],
-            parameter_file='examples/Specialized Tutorials/txtl_toolbox_parameters.txt',
+            parameter_file='mixtures/extract_parameters.tsv',
         )
         CRN_1 = E.compile_crn()  # compile CRN
 

Tests/Unit/test_parameter.py

@@ -123,7 +123,7 @@ def test_parameter_entry(self):
                 parameter_value=1.0,
                 parameter_key={'part_id': 'id'},
                 parameter_info={'comment': 'comment', 'unit': 'M'},
-                unit='m',
+                unit='uM',
             )
 
         # Invalid keys
@@ -516,7 +516,7 @@ def test_find_parameter(self):
         )
 
 
-def test_findpath():
+def test_findpath(tmp_path):
     import os
     import platform
 
@@ -527,21 +527,180 @@ def test_findpath():
 
     # Make sure that files in package can be found
     assert os.path.exists(
-        bcp.find_file_in_bcp_path('components/tetr_parameters.tsv')
+        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():
+    import biocrnpyler as bcp
+
+    # Create the components for testing
+    TetR = bcp.Protein('TetR')
+    aTc = bcp.Species('aTc')
+    TetR_inactive=bcp.ChemicalComplex([TetR.species, aTc])
+    ptet = bcp.RegulatedPromoter('ptet', TetR)
+    dna_GFP = bcp.DNAassembly(
+        'GFP', promoter=ptet, rbs='RBS', protein='GFP')
+
+    # Default case: make sure we can compile with no additional paramters
+    default_mixture = bcp.BasicPURE(
+        'default', components=[dna_GFP, TetR_inactive])
+    default_crn = default_mixture.compile_crn()
+
+    # Find the binding reactions of TetR to DNA and aTc
+    aTc_TetR_index = dna_TetR_index = -1
+    for i, reaction in enumerate(default_crn.reactions):
+        if not isinstance(reaction.propensity_type, bcp.MassAction):
+            continue
+
+        inputs = [input.species for input in reaction.inputs]
+
+        # Find the binding of aTc to TetR
+        if aTc in inputs and TetR.species in inputs:
+            aTc_TetR_index = i
+
+        # Find the binding of TetR to DNA
+        if dna_GFP.species in inputs and TetR.species in inputs:
+            dna_TetR_index = i
+
+    assert aTc_TetR_index != -1 and dna_TetR_index != -1
+    assert default_crn.reactions[
+        dna_TetR_index].propensity_type.k_forward != 1
+    assert default_crn.reactions[
+        aTc_TetR_index].propensity_type.k_forward != 1
+
+    # Rebuild using given parameters
+    baseline_parameters = {
+        ('binding', None, 'kb'): 1,
+        ('binding', None, 'ku'): 0.1,
+        ('binding', None, 'cooperativity'): 2,
+    }
+    TetR_inactive=bcp.ChemicalComplex(
+        [TetR.species, aTc], parameters=baseline_parameters)
+    dna_GFP = bcp.DNAassembly(
+        'GFP', promoter=ptet, rbs='RBS', protein='GFP',
+        parameters=baseline_parameters)
+    baseline_mixture = bcp.BasicPURE(
+        'baseline', components=[dna_GFP, TetR_inactive])
+    baseline_crn = baseline_mixture.compile_crn()
+    assert baseline_crn.reactions[
+        dna_TetR_index].propensity_type.k_forward == 1
+    assert baseline_crn.reactions[
+        aTc_TetR_index].propensity_type.k_forward == 1
+
+    # Override using mechanism subtypes
+    mechtype_parameters = baseline_parameters | {
+        ('binding', 'dna_protein', 'kb'): 2,
+        ('binding', 'chemical_complex', 'kb'): 3,
+    }
+    TetR_inactive=bcp.ChemicalComplex(
+        [TetR.species, aTc], parameters=mechtype_parameters)
+    dna_GFP = bcp.DNAassembly(
+        'GFP', promoter=ptet, rbs='RBS', protein='GFP',
+        parameters=mechtype_parameters)
+    mechtype_mixture = bcp.BasicPURE(
+        'mechtype', components=[dna_GFP, TetR_inactive])
+    mechtype_crn = mechtype_mixture.compile_crn()
+    assert mechtype_crn.reactions[
+        dna_TetR_index].propensity_type.k_forward == 2
+    assert mechtype_crn.reactions[
+        aTc_TetR_index].propensity_type.k_forward == 3
+
+    # Override using part IDs
+    partid_parameters = mechtype_parameters | {
+        ('binding', 'ptet_TetR', 'kb'): 4,
+        ('binding', 'aTc_protein_TetR', 'kb'): 5,
+    }
+    TetR_inactive=bcp.ChemicalComplex(
+        [TetR.species, aTc], parameters=partid_parameters)
+    dna_GFP = bcp.DNAassembly(
+        'GFP', promoter=ptet, rbs='RBS', protein='GFP',
+        parameters=partid_parameters)
+    partid_mixture = bcp.BasicPURE(
+        'partid', components=[dna_GFP, TetR_inactive])
+    partid_crn = partid_mixture.compile_crn()
+    assert partid_crn.reactions[
+        dna_TetR_index].propensity_type.k_forward == 4
+    assert partid_crn.reactions[
+        aTc_TetR_index].propensity_type.k_forward == 5
+
+    # Override using mechanism name
+    mechname_parameters = baseline_parameters | {
+        ('one_step_cooperative_binding', None, 'kb'): 6,
+        ('binding', 'chemical_complex', 'kb'): 7,
+    }
+    TetR_inactive=bcp.ChemicalComplex(
+        [TetR.species, aTc], parameters=mechname_parameters)
+    dna_GFP = bcp.DNAassembly(
+        'GFP', promoter=ptet, rbs='RBS', protein='GFP',
+        parameters=mechname_parameters)
+    mechname_mixture = bcp.BasicPURE(
+        'mechname', components=[dna_GFP, TetR_inactive])
+    mechname_crn = mechname_mixture.compile_crn()
+    assert mechname_crn.reactions[
+        dna_TetR_index].propensity_type.k_forward == 6
+    assert mechname_crn.reactions[
+        aTc_TetR_index].propensity_type.k_forward == 7
+
+    # Override in mixture instead of components
+    mixture_parameters = baseline_parameters | {
+        ('one_step_cooperative_binding', None, 'kb'): 8,
+        ('binding', 'chemical_complex', 'kb'): 9,
+    }
+    TetR_inactive=bcp.ChemicalComplex([TetR.species, aTc])
+    dna_GFP = bcp.DNAassembly(
+        'GFP', promoter=ptet, rbs='RBS', protein='GFP')
+    mixture_mixture = bcp.BasicPURE(
+        'mixture', components=[dna_GFP, TetR_inactive],
+        parameters=mixture_parameters)
+    mixture_crn = mixture_mixture.compile_crn()
+    assert mixture_crn.reactions[
+        dna_TetR_index].propensity_type.k_forward == 8
+    assert mixture_crn.reactions[
+        aTc_TetR_index].propensity_type.k_forward == 9
+
+    # Override in components and not mixture
+    component_parameters = baseline_parameters | {
+        ('one_step_cooperative_binding', None, 'kb'): 10,
+        ('binding', 'chemical_complex', 'kb'): 11,
+    }
+    TetR_inactive=bcp.ChemicalComplex(
+        [TetR.species, aTc], parameters=component_parameters)
+    dna_GFP = bcp.DNAassembly(
+        'GFP', promoter=ptet, rbs='RBS', protein='GFP',
+        parameters=component_parameters)
+    mixture_mixture = bcp.BasicPURE(
+        'mixture', components=[dna_GFP, TetR_inactive],
+        parameters=mixture_parameters)
+    mixture_crn = mixture_mixture.compile_crn()
+    assert mixture_crn.reactions[
+        dna_TetR_index].propensity_type.k_forward == 10
+    assert mixture_crn.reactions[
+        aTc_TetR_index].propensity_type.k_forward == 11

Tests/Unit/test_plotting.py

@@ -228,7 +228,8 @@ def test_render_network_bokeh():
         ('rna_degradation_mm', None, 'kdeg'): 0.001,
         (None, None, 'cooperativity'): 2,
     }
-    txtl = bcp.TxTlExtract('mixture1', parameters=parameters)
+    txtl = bcp.TxTlExtract(
+        'mixture1', parameters=parameters, overwrite_parameters=True)
     dna = bcp.DNAassembly(
         'mydna',
         promoter=bcp.RegulatedPromoter('plac', ['laci']),

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'