Merge pull request #22 from virtualcell/sysbio-course-3

upgrade fvsolver and regenerate math before solving

Author: jcschaff

poetry.lock

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyvcell"
-version = "0.1.12"
+version = "0.1.13"
 description = "This is the python wrapper for vcell modeling and simulation"
 authors = ["Jim Schaff <[email protected]>"]
 repository = "https://github.com/virtualcell/pyvcell"
@@ -18,7 +18,7 @@ h5py = "^3.11.0"
 numpy = ">=1.26.4,<3.0"
 orjson = "^3.10.3"
 vtk = "^9.3.1"
-pyvcell-fvsolver = "^0.1.0"
+pyvcell-fvsolver = "^0.1.1"
 typer = ">=0.12.3,<1.0.0"
 pydantic = "^2.10.5"
 requests-oauth2client = "^1.6.0"

pyproject.toml

@@ -1,8 +1,3 @@
-import logging
-import tempfile
-from os import PathLike
-from pathlib import Path
-
 from pyvcell.vcml.models import (
     Application,
     Biomodel,
@@ -26,6 +21,22 @@
     SurfaceClass,
     VCMLDocument,
 )
+from pyvcell.vcml.utils import (
+    field_data_refs,
+    load_antimony_file,
+    load_antimony_str,
+    load_sbml_file,
+    load_sbml_str,
+    load_vcml_file,
+    load_vcml_str,
+    to_antimony_str,
+    to_sbml_str,
+    to_vcml_str,
+    update_biomodel,
+    write_antimony_file,
+    write_sbml_file,
+    write_vcml_file,
+)
 from pyvcell.vcml.vcml_reader import VcmlReader
 from pyvcell.vcml.vcml_writer import VcmlWriter
 
@@ -54,139 +65,18 @@
     "BoundaryType",
     "Application",
     "Simulation",
+    "update_biomodel",
+    "field_data_refs",
+    "to_vcml_str",
+    "to_sbml_str",
+    "to_antimony_str",
+    "load_vcml_str",
+    "load_sbml_str",
+    "load_antimony_str",
+    "write_vcml_file",
+    "write_sbml_file",
+    "write_antimony_file",
+    "load_vcml_file",
+    "load_sbml_file",
+    "load_antimony_file",
 ]
-
-
-def load_antimony_str(antimony_str: str) -> Biomodel:
-    import antimony  # type: ignore[import-untyped]
-
-    antimony_success = antimony.loadAntimonyString(antimony_str)
-    if antimony_success != -1:
-        sbml_str = antimony.getSBMLString()
-        sbml_str = sbml_str.replace("sboTerm", "metaid")
-        logging.info(f"Hack - introduced a metaid in place of sboTerm to SBML string:\n{sbml_str}")
-        return load_sbml_str(sbml_str)
-    else:
-        raise ValueError("Error loading model:", antimony.getLastError())
-
-
-def load_antimony_file(antimony_file: PathLike[str] | str) -> Biomodel:
-    import antimony  # ignore
-
-    antimony_success = antimony.loadAntimonyFile(antimony_file)
-    if antimony_success != -1:
-        sbml_str = antimony.getSBMLString()
-        return load_sbml_str(sbml_str)
-    else:
-        raise ValueError("Error loading model:", antimony.getLastError())
-
-
-def to_antimony_str(
-    bio_model: Biomodel, application_name: str | None = None, round_trip_validation: bool = True
-) -> str:
-    sbml_str = to_sbml_str(bio_model, application_name, round_trip_validation=round_trip_validation)
-    import antimony
-
-    antimony_success = antimony.loadSBMLString(sbml_str)
-    if antimony_success != -1:
-        antimony_str = str(antimony.getAntimonyString())
-        return antimony_str
-    else:
-        raise ValueError("Error converting SBML to Antimony:", antimony.getLastError())
-
-
-def write_antimony_file(bio_model: Biomodel, antimony_file: PathLike[str] | str) -> None:
-    antimony_str = to_antimony_str(bio_model)
-    with open(antimony_file, "w") as f:
-        f.write(antimony_str)
-
-
-def load_vcml_str(vcml_str: str) -> Biomodel:
-    return VcmlReader.biomodel_from_str(vcml_str)
-
-
-def load_vcml_file(vcml_file: PathLike[str] | str) -> Biomodel:
-    return VcmlReader.biomodel_from_file(vcml_file)
-
-
-def to_vcml_str(bio_model: Biomodel) -> str:
-    vcml_document = VCMLDocument(biomodel=bio_model)
-    vcml_str: str = VcmlWriter().write_vcml(document=vcml_document)
-    return vcml_str
-
-
-def write_vcml_file(bio_model: Biomodel, vcml_file: PathLike[str] | str) -> None:
-    vcml_document = VCMLDocument(biomodel=bio_model)
-    VcmlWriter.write_to_file(vcml_document=vcml_document, file_path=vcml_file)
-
-
-def load_sbml_str(sbml_str: str) -> Biomodel:
-    import libvcell
-
-    with tempfile.TemporaryDirectory() as tempdir:
-        vcml_path = Path(tempdir) / "model.vcml"
-        vc_success, vc_errmsg = libvcell.sbml_to_vcml(sbml_content=sbml_str, vcml_file_path=vcml_path)
-        if vc_success:
-            return VcmlReader.biomodel_from_file(vcml_path=vcml_path)
-        else:
-            raise ValueError("Error loading model:", vc_errmsg)
-
-
-def load_sbml_file(sbml_file: PathLike[str] | str) -> Biomodel:
-    import libvcell
-
-    with tempfile.TemporaryDirectory() as tempdir:
-        with open(sbml_file) as f:
-            sbml_str = f.read()
-        vcml_path = Path(tempdir) / "model.vcml"
-        vc_success, vc_errmsg = libvcell.sbml_to_vcml(sbml_content=sbml_str, vcml_file_path=vcml_path)
-        if vc_success:
-            return VcmlReader.biomodel_from_file(vcml_path=vcml_path)
-        else:
-            raise ValueError("Error loading model:", vc_errmsg)
-
-
-def to_sbml_str(bio_model: Biomodel, application_name: str | None = None, round_trip_validation: bool = True) -> str:
-    import libvcell
-
-    if application_name is None:
-        if len(bio_model.applications) == 0:
-            raise ValueError("sbml export from biomodel needs a biomodel application")
-        if len(bio_model.applications) > 1:
-            raise ValueError("Application must have exactly one application")
-        application_name = bio_model.applications[0].name
-    elif application_name not in [app.name for app in bio_model.applications]:
-        raise ValueError(f"Application '{application_name}' not found in biomodel")
-    vcml_document = VCMLDocument(biomodel=bio_model)
-    vcml_str: str = VcmlWriter().write_vcml(document=vcml_document)
-    with tempfile.TemporaryDirectory() as tempdir:
-        sbml_path = Path(tempdir) / "model.sbml"
-        success, msg = libvcell.vcml_to_sbml(
-            vcml_content=vcml_str,
-            application_name=application_name,
-            sbml_file_path=sbml_path,
-            round_trip_validation=round_trip_validation,
-        )
-        if not success:
-            raise ValueError("Error converting VCML to SBML:", msg)
-        with open(sbml_path) as f:
-            sbml_str = f.read()
-        return sbml_str
-
-
-def write_sbml_file(
-    bio_model: Biomodel,
-    sbml_file: PathLike[str] | str,
-    application_name: str | None = None,
-    round_trip_validation: bool = True,
-) -> None:
-    sbml_str = to_sbml_str(bio_model, application_name, round_trip_validation)
-    with open(sbml_file, "w") as f:
-        f.write(sbml_str)
-
-
-def refresh_biomodel(bio_model: Biomodel) -> Biomodel:
-    with tempfile.TemporaryDirectory() as tempdir:
-        vcml_path = Path(tempdir) / "model.vcml"
-        write_vcml_file(bio_model=bio_model, vcml_file=vcml_path)
-        return VcmlReader.biomodel_from_file(vcml_path=vcml_path)