update init for simple high level func

bio_compose/__init__.py

@@ -7,3 +7,36 @@
 with open(version_file_path, 'r') as f:
     __version__ = f.read().strip()
 
+
+def run_simulation(*args, **kwargs):
+    # TODO: implement this
+    pass
+
+
+def verify(*args, **kwargs):
+    import time
+    from bio_compose.verifier import Verifier
+
+    verifier = Verifier()
+    simulators = kwargs.get('simulators')
+    run_sbml = False
+    for arg in args:
+        if isinstance(arg, int):
+            run_sbml = True
+    submission = None
+    if run_sbml:
+        submission = verifier.verify_sbml(*args, **kwargs)
+    else:
+        submission = verifier.verify_omex(*args, **kwargs)
+    job_id = submission.get('job_id')
+    output = None
+    if job_id is not None:
+        while True:
+            verification_result = verifier.get_output(job_id=job_id)
+            status = verification_result['content']['status']
+            if not 'COMPLETED' in status:
+                time.sleep(1)
+            else:
+                output = verification_result
+                break
+    return output

tests/fixtures/sbml-core/BIOMD0000000001_url.xml.psc

@@ -0,0 +1,154 @@
+# Generated by PySCeS 1.2.2 (2024-09-03 15:15)
+
+# Keywords
+Description: Edelstein1996 - EPSP ACh event
+Modelname: BIOMD0000000001
+Output_In_Conc: True
+Species_In_Conc: True
+
+# GlobalUnitDefinitions
+UnitSubstance: mole, 1.0, 0, 1
+UnitVolume: litre, 1.0, 0, 1
+UnitTime: second, 1.0, 0, 1
+UnitLength: metre, 1.0, 0, 1
+UnitArea: metre, 1.0, 0, 2
+
+# Compartments
+Compartment: comp1, 1.0, 3 
+
+# Reactions
+React0@comp1:
+    B = BL
+    comp1*(kf_0*B-kr_0*BL)
+
+React1@comp1:
+    BL = BLL
+    comp1*(kf_1*BL-kr_1*BLL)
+
+React2@comp1:
+    BLL = ALL
+    comp1*(kf_2*BLL-kr_2*ALL)
+
+React3@comp1:
+    A = AL
+    comp1*(kf_3*A-kr_3*AL)
+
+React4@comp1:
+    AL = ALL
+    comp1*(kf_4*AL-kr_4*ALL)
+
+React5@comp1:
+    B = A
+    comp1*(kf_5*B-kr_5*A)
+
+React6@comp1:
+    BL = AL
+    comp1*(kf_6*BL-kr_6*AL)
+
+React7@comp1:
+    I = IL
+    comp1*(kf_7*I-kr_7*IL)
+
+React8@comp1:
+    IL = ILL
+    comp1*(kf_8*IL-kr_8*ILL)
+
+React9@comp1:
+    A = I
+    comp1*(kf_9*A-kr_9*I)
+
+React10@comp1:
+    AL = IL
+    comp1*(kf_10*AL-kr_10*IL)
+
+React11@comp1:
+    ALL = ILL
+    comp1*(kf_11*ALL-kr_11*ILL)
+
+React12@comp1:
+    D = DL
+    comp1*(kf_12*D-kr_12*DL)
+
+React13@comp1:
+    DL = DLL
+    comp1*(kf_13*DL-kr_13*DLL)
+
+React14@comp1:
+    I = D
+    comp1*(kf_14*I-kr_14*D)
+
+React15@comp1:
+    IL = DL
+    comp1*(kf_15*IL-kr_15*DL)
+
+React16@comp1:
+    ILL = DLL
+    comp1*(kf_16*ILL-kr_16*DLL)
+
+# Event definitions
+Event: RemovalACh, _TIME_ > t2, delay=0.0, priority=None, persistent=True {
+    kf_0 = 0
+    kf_3 = 0
+    kf_7 = 0
+    kf_12 = 0
+    kf_1 = 0
+    kf_4 = 0
+    kf_8 = 0
+    kf_13 = 0
+    }
+
+
+# Fixed species
+
+# Variable species
+BLL@comp1 = 0.0
+IL@comp1 = 0.0
+AL@comp1 = 0.0
+A@comp1 = 0.0
+BL@comp1 = 0.0
+B@comp1 = 1.66057788110262e-05
+DLL@comp1 = 0.0
+D@comp1 = 0.0
+ILL@comp1 = 0.0
+DL@comp1 = 0.0
+I@comp1 = 0.0
+ALL@comp1 = 0.0
+
+# Parameters
+kf_0 = 3000.0
+kr_0 = 8000.0
+kf_1 = 1500.0
+kr_1 = 16000.0
+kf_2 = 30000.0
+kr_2 = 700.0
+kf_3 = 3000.0
+kr_3 = 8.64
+kf_4 = 1500.0
+kr_4 = 17.28
+kf_5 = 0.54
+kr_5 = 10800.0
+kf_6 = 130.0
+kr_6 = 2740.0
+kf_7 = 3000.0
+kr_7 = 4.0
+kf_8 = 1500.0
+kr_8 = 8.0
+kf_9 = 19.7
+kr_9 = 3.74
+kf_10 = 19.85
+kr_10 = 1.74
+kf_11 = 20.0
+kr_11 = 0.81
+kf_12 = 3000.0
+kr_12 = 4.0
+kf_13 = 1500.0
+kr_13 = 8.0
+kf_14 = 0.05
+kr_14 = 0.0012
+kf_15 = 0.05
+kr_15 = 0.0012
+kf_16 = 0.05
+kr_16 = 0.0012
+t2 = 20.0
+
+