def simulate() replaces VcmlSpatialSimulation object

Author: jcschaff

pyvcell/vcml/__init__.py

@@ -38,6 +38,7 @@
     write_vcml_file,
 )
 from pyvcell.vcml.vcml_reader import VcmlReader
+from pyvcell.vcml.vcml_simulation import simulate
 from pyvcell.vcml.vcml_writer import VcmlWriter
 from pyvcell.vcml.workspace import get_workspace_dir, set_workspace_dir
 
@@ -82,4 +83,5 @@
     "load_antimony_file",
     "get_workspace_dir",
     "set_workspace_dir",
+    "simulate",
 ]

pyvcell/vcml/vcml_simulation.py

@@ -1,67 +1,48 @@
 import os
-import shutil
 import tempfile
 from pathlib import Path
 
 from libvcell import vcml_to_finite_volume_input
 
 from pyvcell._internal.solvers.fvsolver import solve as fvsolve
 from pyvcell.sim_results.result import Result
-from pyvcell.vcml import to_vcml_str
 from pyvcell.vcml.field import Field
-from pyvcell.vcml.models import Biomodel
-
-
-class VcmlSpatialSimulation:
-    bio_model: Biomodel
-    fields: list[Field] | None
-    out_dir: Path
-
-    def __init__(
-        self,
-        bio_model: Biomodel,
-        out_dir: Path | str | None = None,
-        fields: list[Field] | None = None,
-    ):
-        self.bio_model = bio_model
-        self.fields = fields
-        if out_dir is None:
-            self.out_dir = Path(tempfile.mkdtemp(prefix="out_dir_"))
-        else:
-            self.out_dir = out_dir if isinstance(out_dir, Path) else Path(out_dir)
-
-    def run(self, simulation_name: str) -> Result:
-        vcml: str = to_vcml_str(bio_model=self.bio_model)
-
-        # check if fields are provided, if yes, write them to the output directory
-        if self.fields:
-            for field in self.fields:
-                fd_path = self.out_dir / field.create_template_filename()
-                field.write(file_path=fd_path)
-
-        success, error_message = vcml_to_finite_volume_input(
-            vcml_content=vcml, simulation_name=simulation_name, output_dir_path=self.out_dir
-        )
-
-        if not success:
-            raise ValueError(f"Failed to get solver input files: {error_message}")
-
-        # identify sim_id and job_id from the solver input files
-        files: list[str] = os.listdir(self.out_dir)
-        fv_input_file: Path | None = next((self.out_dir / file for file in files if file.endswith(".fvinput")), None)
-        vcg_input_file: Path | None = next((self.out_dir / file for file in files if file.endswith(".vcg")), None)
-        if fv_input_file is None or vcg_input_file is None:
-            raise ValueError(".fvinput file or .vcg file not found")
-        sim_id = int(fv_input_file.name.split("_")[1])
-        job_id = int(fv_input_file.name.split("_")[2])
-
-        # run the simulation
-        ret_code = fvsolve(input_file=fv_input_file, vcg_file=vcg_input_file, output_dir=self.out_dir)
-        if ret_code != 0:
-            raise ValueError(f"Error in solve: {ret_code}")
-
-        # return the result
-        return Result(solver_output_dir=self.out_dir, sim_id=sim_id, job_id=job_id)
-
-    def cleanup(self) -> None:
-        shutil.rmtree(self.out_dir)
+from pyvcell.vcml.models import Biomodel, Simulation
+from pyvcell.vcml.utils import to_vcml_str
+from pyvcell.vcml.workspace import get_workspace_dir
+
+
+def simulate(biomodel: Biomodel, simulation: Simulation | str, fields: list[Field] | None = None) -> Result:
+    vcml: str = to_vcml_str(bio_model=biomodel)
+    out_dir = Path(tempfile.mkdtemp(prefix="out_dir_", dir=get_workspace_dir()))
+
+    # check if fields are provided, if yes, write them to the output directory
+    if fields:
+        for field in fields:
+            fd_path = out_dir / field.create_template_filename()
+            field.write(file_path=fd_path)
+
+    simulation_name = simulation if isinstance(simulation, str) else simulation.name
+    success, error_message = vcml_to_finite_volume_input(
+        vcml_content=vcml, simulation_name=simulation_name, output_dir_path=out_dir
+    )
+
+    if not success:
+        raise ValueError(f"Failed to get solver input files: {error_message}")
+
+    # identify sim_id and job_id from the solver input files
+    files: list[str] = os.listdir(out_dir)
+    fv_input_file: Path | None = next((out_dir / file for file in files if file.endswith(".fvinput")), None)
+    vcg_input_file: Path | None = next((out_dir / file for file in files if file.endswith(".vcg")), None)
+    if fv_input_file is None or vcg_input_file is None:
+        raise ValueError(".fvinput file or .vcg file not found")
+    sim_id = int(fv_input_file.name.split("_")[1])
+    job_id = int(fv_input_file.name.split("_")[2])
+
+    # run the simulation
+    ret_code = fvsolve(input_file=fv_input_file, vcg_file=vcg_input_file, output_dir=out_dir)
+    if ret_code != 0:
+        raise ValueError(f"Error in solve: {ret_code}")
+
+    # return the result
+    return Result(solver_output_dir=out_dir, sim_id=sim_id, job_id=job_id)