Release v0.11.1 (#244)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
         additional_dependencies: [toml]
 
   - repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.1.0
     hooks:
       - id: black
         additional_dependencies: [toml]

biomass/construction/reaction_rules.py

@@ -384,7 +384,6 @@ def _raise_exception(self, line_num: int, line: str) -> None:
             )
 
     def _process_pval_section(self, func_name: str, line_num: int, line: str, *args: str) -> None:
-
         param_values = line.split("|")[1].strip().split(",")
         if all("=" in pval for pval in param_values):
             for pval in param_values:
@@ -461,7 +460,6 @@ def _process_pval_section(self, func_name: str, line_num: int, line: str, *args:
             )
 
     def _process_ival_section(self, line_num: int, line: str) -> None:
-
         initial_values = line.split("|")[2].strip().split(",")
         for ival in initial_values:
             if ival.startswith("fixed "):

biomass/construction/template/observable.py

@@ -61,7 +61,6 @@ def simulate(self, x: list, y0: list, _perturbation: dict = {}):
         # unperturbed steady state
 
         for i, condition in enumerate(self.conditions):
-
             sol = solve_ode(self.diffeq, y0, self.t, tuple(x))
 
             if sol is None:

biomass/construction/template/viz.py

@@ -35,15 +35,12 @@ def __init__(self) -> None:
         self.sensitivity_options = SensitivityOptions(self.cm)
 
     def get_single_observable_options(self) -> List[SingleObservable]:
-
         return self.single_observable_options
 
     def get_multiple_observables_options(self) -> MultipleObservables:
-
         return self.multiple_observables_options
 
     def get_sensitivity_options(self) -> SensitivityOptions:
-
         return self.sensitivity_options
 
     @staticmethod

biomass/construction/text2model.py

@@ -505,7 +505,7 @@ def _update_observable(self) -> None:
                     for i, condition in enumerate(self.sim_conditions):
                         # Use ';' for adding description of each condition
                         if i == 0:
-                            lines[line_num + 1] = (
+                            lines[line_num] += (
                                 3 * self.indentation
                                 + f'if condition == \'{condition[0].strip(" ")}\':\n'
                                 + 4 * self.indentation
@@ -515,7 +515,7 @@ def _update_observable(self) -> None:
                                 + ("\n\n" if len(self.sim_conditions) == 1 else "")
                             )
                         else:
-                            lines[line_num + 1] += (
+                            lines[line_num] += (
                                 3 * self.indentation
                                 + f'elif condition == \'{condition[0].strip(" ")}\':\n'
                                 + 4 * self.indentation
@@ -526,8 +526,8 @@ def _update_observable(self) -> None:
                             )
                         # pa: parameters
                         # init: initial conditions
-                        lines[line_num + 1] = self._convert_names(
-                            line=lines[line_num + 1],
+                        lines[line_num] = self._convert_names(
+                            line=lines[line_num],
                             p=re.findall(r"p\[(.*?)\]", condition[1]),
                             init=re.findall(r"init\[(.*?)\]", condition[1]),
                         )

biomass/models/Nakakuki_Cell_2010/ode.py

@@ -28,7 +28,6 @@ def _get_ppMEK_slope(t, ligand) -> float:
 
     # Refined Model
     def diffeq(self, t, y, *x):
-
         v = self.flux(t, y, x)
 
         if self.perturbation:
@@ -104,7 +103,6 @@ def diffeq(self, t, y, *x):
 
 
 def param_values():
-
     x = [0] * C.NUM
 
     x[C.V1] = 0.34284837
@@ -228,7 +226,6 @@ def param_values():
 
 
 def initial_values():
-
     y0 = [0] * V.NUM
 
     y0[V.ERKc] = 9.60e02

biomass/models/Nakakuki_Cell_2010/viz.py

@@ -33,7 +33,6 @@ def __init__(self):
         self.sensitivity_options = SensitivityOptions(self.cm)
 
     def get_single_observable_options(self):
-
         for i, _ in enumerate(self.obs_names):
             self.single_observable_options[i].divided_by = 60  # sec. -> min.
             self.single_observable_options[i].xlim = (-5, 95)
@@ -98,7 +97,6 @@ def get_multiple_observables_options(self):
         return self.multiple_observables_options
 
     def get_sensitivity_options(self):
-
         return self.sensitivity_options
 
     @staticmethod

biomass/models/circadian_clock/viz.py

@@ -56,7 +56,6 @@ def get_multiple_observables_options(self):
         return self.multiple_observables_options
 
     def get_sensitivity_options(self):
-
         return self.sensitivity_options
 
     @staticmethod

biomass/models/g1s_transition/ode.py

@@ -9,7 +9,6 @@ def __init__(self, perturbation):
 
     # Refined Model
     def diffeq(self, t, y, *x):
-
         v = self.flux(t, y, x)
 
         if self.perturbation:
@@ -69,7 +68,6 @@ def diffeq(self, t, y, *x):
 
 
 def param_values():
-
     x = [0] * C.NUM
 
     ## CYCE SYNTHESISx[C.DEGRADATION AND P27 BINDING/DISSOCIATION:
@@ -111,7 +109,6 @@ def param_values():
 
 
 def initial_values():
-
     y0 = [0] * V.NUM
 
     y0[V.Cdh1dp] = 1.0

biomass/models/g1s_transition/viz.py

@@ -33,15 +33,12 @@ def __init__(self):
         self.sensitivity_options = SensitivityOptions(self.cm)
 
     def get_single_observable_options(self):
-
         return self.single_observable_options
 
     def get_multiple_observables_options(self):
-
         return self.multiple_observables_options
 
     def get_sensitivity_options(self):
-
         return self.sensitivity_options
 
     @staticmethod

biomass/models/insulin_signaling/ode.py

@@ -8,7 +8,6 @@ def __init__(self, perturbation):
         self.perturbation = perturbation
 
     def diffeq(self, t, y, *x):
-
         v = self.flux(t, y, x)
 
         if self.perturbation:

biomass/models/insulin_signaling/reaction_network.py

@@ -10,7 +10,6 @@ def __init__(self) -> None:
 
     @staticmethod
     def flux(t, y, x):
-
         v = {}
 
         v[1] = x[C.k1_synthesis] * (y[V.pro_IRcom] - y[V.IRcom])

biomass/models/insulin_signaling/viz.py

@@ -33,7 +33,6 @@ def __init__(self):
         self.sensitivity_options = SensitivityOptions(self.cm)
 
     def get_single_observable_options(self):
-
         for i, _ in enumerate(self.obs_names):
             self.single_observable_options[i].xticks = [120 * i for i in range(5)]
             self.single_observable_options[i].xlabel = "time (min)"
@@ -42,11 +41,9 @@ def get_single_observable_options(self):
         return self.single_observable_options
 
     def get_multiple_observables_options(self):
-
         return self.multiple_observables_options
 
     def get_sensitivity_options(self):
-
         return self.sensitivity_options
 
     @staticmethod

biomass/models/mapk_cascade/reaction_network.py

@@ -12,7 +12,6 @@ def __init__(self) -> None:
 
     @staticmethod
     def flux(t, y, x) -> dict:
-
         v = {}
         v[1] = (
             x[C.V1]

biomass/models/mapk_cascade/viz.py

@@ -67,7 +67,6 @@ def get_multiple_observables_options(self):
         return self.multiple_observables_options
 
     def get_sensitivity_options(self):
-
         return self.sensitivity_options
 
     @staticmethod

biomass/models/nfkb_pathway/viz.py

@@ -41,11 +41,9 @@ def get_single_observable_options(self):
         return self.single_observable_options
 
     def get_multiple_observables_options(self):
-
         return self.multiple_observables_options
 
     def get_sensitivity_options(self):
-
         return self.sensitivity_options
 
     @staticmethod

biomass/models/pan_rtk/ode.py

@@ -9,7 +9,6 @@ def __init__(self, perturbation):
 
     # Refined Model
     def diffeq(self, t, y, *x):
-
         v = self.flux(t, y, x)
 
         if self.perturbation:
@@ -113,7 +112,6 @@ def diffeq(self, t, y, *x):
 
 
 def param_values():
-
     x = [0] * C.NUM
 
     x[C.AKT_activation_pEGFR] = 1.00000000000008e-5
@@ -586,7 +584,6 @@ def param_values():
 
 
 def initial_values():
-
     y0 = [0] * V.NUM
 
     y0[V.dose_EGF] = 0.0

biomass/models/pan_rtk/viz.py

@@ -33,15 +33,12 @@ def __init__(self):
         self.sensitivity_options = SensitivityOptions(self.cm)
 
     def get_single_observable_options(self):
-
         return self.single_observable_options
 
     def get_multiple_observables_options(self):
-
         return self.multiple_observables_options
 
     def get_sensitivity_options(self):
-
         return self.sensitivity_options
 
     @staticmethod

biomass/models/prolif_quies/ode.py

@@ -9,12 +9,10 @@ def __init__(self, perturbation):
 
     @staticmethod
     def _heaviside(x):
-
         return 1 * (x > 0)
 
     # Refined Model
     def diffeq(self, t, y, *x):
-
         v = self.flux(t, y, x)
 
         if self.perturbation:
@@ -134,7 +132,6 @@ def diffeq(self, t, y, *x):
 
 
 def param_values():
-
     x = [0] * C.NUM
 
     x[C.Bg] = 0.05
@@ -196,7 +193,6 @@ def param_values():
 
 
 def initial_values():
-
     y0 = [0] * V.NUM
 
     y0[V.tP21] = 0.6

biomass/models/prolif_quies/viz.py

@@ -33,15 +33,12 @@ def __init__(self):
         self.sensitivity_options = SensitivityOptions(self.cm)
 
     def get_single_observable_options(self):
-
         return self.single_observable_options
 
     def get_multiple_observables_options(self):
-
         return self.multiple_observables_options
 
     def get_sensitivity_options(self):
-
         return self.sensitivity_options
 
     @staticmethod

biomass/models/tgfb_smad/ode.py

@@ -8,7 +8,6 @@ def __init__(self, perturbation):
         self.perturbation = perturbation
 
     def diffeq(self, t, y, *x):
-
         v = self.flux(t, y, x)
 
         if self.perturbation:

biomass/models/tgfb_smad/reaction_network.py

@@ -10,7 +10,6 @@ def __init__(self) -> None:
 
     @staticmethod
     def flux(t, y, x) -> dict:
-
         v = {}
 
         v[1] = y[V.Rec] * x[C.Rec_act] * y[V.TGFb]

biomass/models/tgfb_smad/viz.py

@@ -33,19 +33,16 @@ def __init__(self):
         self.sensitivity_options = SensitivityOptions(self.cm)
 
     def get_single_observable_options(self):
-
         for i, _ in enumerate(self.obs_names):
             self.single_observable_options[i].xticks = [200 * i for i in range(4)]
             self.single_observable_options[i].xlabel = "time (min)"
 
         return self.single_observable_options
 
     def get_multiple_observables_options(self):
-
         return self.multiple_observables_options
 
     def get_sensitivity_options(self):
-
         return self.sensitivity_options
 
     @staticmethod

biomass/version.py

@@ -1,2 +1,2 @@
 """BioMASS library version"""
-__version__ = "0.11.0"
+__version__ = "0.11.1"