add timecourses.py

petab/timecourses.py

@@ -0,0 +1,65 @@
+"""Functions operating on the PEtab timecouse table."""
+
+from pathlib import Path
+from typing import TypeVar
+
+import pandas as pd
+
+from . import lint
+from .C import TIMECOURSE_ID, TIMECOURSE_NAME, TIMECOURSE
+
+
+__all__ = [
+    "get_timecourse_df",
+    "write_timecourse_df",
+]
+
+
+def get_timecourse_df(timecourse_file: str | Path | None) -> pd.DataFrame:
+    """Read the provided timecourse file into a ``pandas.Dataframe``.
+
+    Arguments:
+        timecourse_file:
+            Location of PEtab timecourse file, or a ``pandas.Dataframe``.
+
+    Returns:
+        The timecourses dataframe.
+    """
+    if timecourse_file is None:
+        return timecourse_file
+
+    if isinstance(timecourse_file, (str, Path)):
+        timecourse_file = pd.read_csv(
+            timecourse_file,
+            sep='\t',
+            float_precision='round_trip',
+        )
+
+    lint.assert_no_leading_trailing_whitespace(
+        timecourse_file.columns.values, TIMECOURSE
+    )
+
+    if not isinstance(timecourse_file.index, pd.RangeIndex):
+        timecourse_file.reset_index(inplace=True)
+
+    try:
+        timecourse_file.set_index([TIMECOURSE_ID], inplace=True)
+    except KeyError:
+        raise KeyError(
+            f'Timecourse table missing mandatory field {TIMECOURSE_ID}.')
+
+    return timecourse_file
+
+
+def write_timecourse_df(df: pd.DataFrame, filename: str | Path) -> None:
+    """Write the provided PEtab timecourse table to disk.
+
+    Arguments:
+        df:
+            The PEtab timecourse table.
+        filename:
+            The table will be written to this location.
+    """
+    df.to_csv(filename, sep='\t', index=True)
+
+