Merge pull request #136 from tjgalvin/dumpfield

Dumping field options to yaml file

flint/options.py

@@ -9,6 +9,10 @@
 from pathlib import Path
 from typing import Collection, List, NamedTuple, Optional, Union
 
+import yaml
+
+from flint.logging import logger
+
 
 class BandpassOptions(NamedTuple):
     """Container that reoresents the flint related options that
@@ -114,6 +118,41 @@ class FieldOptions(NamedTuple):
     """Rename MSs throught rounds of imaging and self-cal instead of creating copies. This will delete data-columns throughout. """
 
 
+def dump_field_options_to_yaml(
+    output_path: Path, field_options: FieldOptions, overwrite: bool = False
+) -> Path:
+    """Dump the supplied instance of `FieldOptions` to a yaml file
+    for record keeping.
+
+    The parent directory of the `output_path` will be created if it
+    does not already exist.
+
+    Args:
+        output_path (Path): Path of the output file.
+        field_options (FieldOptions): The `FieldOptions` class to write.
+        overwrite (bool, optional): Overwrite the file if it exists. Defaults to False.
+
+    Raises:
+        FileExistsError: Raise if `output_path` already exists and `overwrite` is `False`
+
+    Returns:
+        Path: Output path written to.
+    """
+
+    logger.info(f"Writing field_options to {output_path}")
+
+    if not overwrite and output_path.exists():
+        raise FileExistsError(f"{output_path=} exists. ")
+
+    # Create the directory just in case
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+
+    with open(output_path, "w") as out_file:
+        yaml.dump(data=field_options, stream=out_file, sort_keys=False)
+
+    return output_path
+
+
 # TODO: Perhaps move these to flint.naming, and can be built up
 # based on rules, e.g. imager used, source finder etc.
 DEFAULT_TAR_RE_PATTERNS = (

flint/prefect/flows/continuum_pipeline.py

@@ -23,10 +23,11 @@
 from flint.ms import find_mss
 from flint.naming import (
     CASDANameComponents,
+    add_timestamp_to_path,
     extract_components_from_name,
     get_sbid_from_path,
 )
-from flint.options import FieldOptions
+from flint.options import FieldOptions, dump_field_options_to_yaml
 from flint.prefect.clusters import get_dask_runner
 from flint.prefect.common.imaging import (
     _create_convol_linmos_images,
@@ -153,6 +154,13 @@ def process_science_fields(
         science_path=science_path, split_path=split_path, check_exists=True
     )
 
+    dump_field_options_to_yaml(
+        output_path=add_timestamp_to_path(
+            input_path=output_split_science_path / "field_options.yaml"
+        ),
+        field_optios=field_options,
+    )
+
     archive_wait_for: List[Any] = []
 
     strategy = _load_and_copy_strategy(

tests/test_options.py

@@ -5,10 +5,35 @@
 
 from pathlib import Path
 
-from flint.options import FieldOptions
+import pytest
+
+from flint.options import FieldOptions, dump_field_options_to_yaml
 from flint.prefect.flows.continuum_pipeline import get_parser
 
 
+def test_dump_field_options_to_yaml(tmpdir):
+    """See if the field options file can be dumped to an output directory"""
+    tmpdir = Path(tmpdir)
+
+    field_options = FieldOptions(
+        flagger_container=Path("a"), calibrate_container=Path("b")
+    )
+
+    assert not (tmpdir / "Jack").exists()
+
+    path_1 = tmpdir / "field_options.yaml"
+    path_2 = tmpdir / "Jack" / "Sparrow" / "field_options.yaml"
+
+    for path in (path_1, path_2):
+        output_path = dump_field_options_to_yaml(
+            output_path=path, field_options=field_options
+        )
+        assert output_path.exists()
+
+    with pytest.raises(FileExistsError):
+        dump_field_options_to_yaml(output_path=path_2, field_options=field_options)
+
+
 def test_config_field_options(tmpdir):
     output_file = f"{tmpdir}/example.config"
     contents = """--holofile /scratch3/projects/spiceracs/RACS_Low2_Holography/akpb.iquv.square_6x6.63.887MHz.SB39549.cube.fits