Add script for converting ode2cellml

src/gotranx/cli/__init__.py

@@ -214,6 +214,60 @@ def cellml2ode(
     _main(fname=fname, outname=outname, verbose=verbose)
 
 
+@app.command()
+def ode2cellml(
+    fname: typing.Optional[Path] = typer.Argument(
+        None,
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        writable=False,
+        readable=True,
+        resolve_path=True,
+    ),
+    outname: typing.Optional[str] = typer.Option(
+        None,
+        "-o",
+        "--outname",
+        help="Output name",
+    ),
+    version: bool = typer.Option(
+        None,
+        "--version",
+        callback=version_callback,
+        is_eager=True,
+        help="Show version",
+    ),
+    license: bool = typer.Option(
+        None,
+        "--license",
+        callback=license_callback,
+        is_eager=True,
+        help="Show license",
+    ),
+    config: typing.Optional[Path] = typer.Option(
+        None,
+        "--config",
+        help="Read configuration options from a configuration file",
+    ),
+    verbose: bool = typer.Option(
+        False,
+        "--verbose",
+        "-v",
+        help="Verbose output",
+    ),
+):
+    if fname is None:
+        return typer.echo("No file specified")
+
+    config_data = utils.read_config(config)
+    verbose = config_data.get("verbose", verbose)
+
+    from .ode2cellml import main as _main
+
+    _main(fname=fname, outname=outname, verbose=verbose)
+
+
 @app.command()
 def ode2py(
     fname: typing.Optional[Path] = typer.Argument(

src/gotranx/cli/ode2cellml.py

@@ -0,0 +1,27 @@
+from __future__ import annotations
+from pathlib import Path
+import logging
+import structlog
+
+from ..myokit import gotran_to_cellml
+from ..load import load_ode
+
+logger = structlog.get_logger()
+
+
+def main(
+    fname: Path,
+    outname: str | None = None,
+    verbose: bool = False,
+) -> None:
+    loglevel = logging.DEBUG if verbose else logging.INFO
+    structlog.configure(
+        wrapper_class=structlog.make_filtering_bound_logger(loglevel),
+    )
+    assert fname.suffix in ".ode", f"File {fname} must be an ode file"
+    assert fname.exists(), f"File {fname} does not exist"
+    ode = load_ode(fname)
+    logger.info(f"Converting {fname} to CellML")
+    cellml_file = fname.with_suffix(".cellml") if outname is None else Path(outname)
+    gotran_to_cellml(ode, filename=cellml_file)
+    logger.info(f"Wrote {cellml_file}")