Merge pull request #295 from gyorilab/regnet_initial

Allow floats in regnet initials
gyorilab · Feb 27, 2024 · 516ce1c · 516ce1c
2 parents 34f6383 + f3441bc
commit 516ce1c
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Showing 3 changed files with 20 additions and 15 deletions.
diff --git a/mira/modeling/amr/regnet.py b/mira/modeling/amr/regnet.py
@@ -9,7 +9,7 @@
 import json
 import logging
 from copy import deepcopy
-from typing import Dict, List, Optional
+from typing import Dict, List, Optional, Union
 
 import sympy
 from pydantic import BaseModel, Field
@@ -66,9 +66,14 @@ def __init__(self, model: Model):
  }
  initial = var.data.get('expression')
  if initial is not None:
- if isinstance(initial, float):
- initial = safe_parse_expr(str(initial))
- state_data['initial'] = str(initial)
+ # Here, initial is a SympyExprStr, and if its
+ # value is a float, we export it as a float,
+ # otherwise we export it as a string
+ try:
+ initial_float = float(initial.args[0])
+ state_data['initial'] = initial_float
+ except TypeError:
+ state_data['initial'] = str(initial)
  self.states.append(state_data)
  self._states_by_id[name] = state_data
 
@@ -315,7 +320,7 @@ def template_model_to_regnet_json(tm: TemplateModel):
 
 
 class Initial(BaseModel):
- expression: str
+ expression: Union[str, float]
  expression_mathml: str
 
 

diff --git a/notebooks/hackathon_2024.02/scenario4/scenario4_4spec_regnet.json b/notebooks/hackathon_2024.02/scenario4/scenario4_4spec_regnet.json
@@ -17,7 +17,7 @@
  "species": "1"
  }
  },
- "initial": "0.51",
+ "initial": 0.51,
  "rate_constant": "r_0",
  "sign": true
  },
@@ -30,7 +30,7 @@
  "species": "2"
  }
  },
- "initial": "0.39",
+ "initial": 0.39,
  "rate_constant": "r_1",
  "sign": true
  },
@@ -43,7 +43,7 @@
  "species": "3"
  }
  },
- "initial": "0.88",
+ "initial": 0.88,
  "rate_constant": "r_2",
  "sign": true
  },
@@ -56,7 +56,7 @@
  "species": "4"
  }
  },
- "initial": "0.4",
+ "initial": 0.4,
  "rate_constant": "r_3",
  "sign": true
  }

diff --git a/notebooks/hackathon_2024.02/scenario4/scenario4_6spec_regnet.json b/notebooks/hackathon_2024.02/scenario4/scenario4_6spec_regnet.json
@@ -17,7 +17,7 @@
  "species": "1"
  }
  },
- "initial": "0.51",
+ "initial": 0.51,
  "rate_constant": "r_0",
  "sign": true
  },
@@ -30,7 +30,7 @@
  "species": "2"
  }
  },
- "initial": "0.39",
+ "initial": 0.39,
  "rate_constant": "r_1",
  "sign": true
  },
@@ -43,7 +43,7 @@
  "species": "3"
  }
  },
- "initial": "0.88",
+ "initial": 0.88,
  "rate_constant": "r_2",
  "sign": true
  },
@@ -56,7 +56,7 @@
  "species": "4"
  }
  },
- "initial": "0.4",
+ "initial": 0.4,
  "rate_constant": "r_3",
  "sign": true
  },
@@ -69,7 +69,7 @@
  "species": "5"
  }
  },
- "initial": "0.2",
+ "initial": 0.2,
  "rate_constant": "r_4",
  "sign": true
  },
@@ -82,7 +82,7 @@
  "species": "6"
  }
  },
- "initial": "0.8",
+ "initial": 0.8,
  "rate_constant": "r_5",
  "sign": true
  }