Switch to using the datamodel protocol

docs/source/model_library.rst

@@ -4,7 +4,7 @@ Model Library
 =============
 
 `~stpipe.library.AbstractModelLibrary` is a container designed to allow efficient processing of
-collections of `~stpipe.datamodel.AbstractDataModel` instances created from an association.
+collections of `~stpipe.protocols.DataModel` instances created from an association.
 
 `~stpipe.library.AbstractModelLibrary` is an ordered collection (like a `list`) but provides:
 
@@ -234,8 +234,8 @@ allowing the `~stpipe.step.Step` to generate an :ref:`library_on_disk`
 
 ``Step.process`` can extend the above pattern to
 support additional inputs (for example a single
-`~stpipe.datamodel.AbstractDataModel` or filename containing
-a `~stpipe.datamodel.AbstractDataModel`) to allow more
+`~stpipe.protocols.DataModel` or filename containing
+a `~stpipe.protocols.DataModel`) to allow more
 flexible data processings, although some consideration
 should be given to how to handle input that does not
 contain association metadata. Does it make sense
@@ -252,9 +252,9 @@ Isolated Processing
 
 Let's say we have a `~stpipe.step.Step`, ``flux_calibration``
 that performs an operation that is only concerned with the data
-for a single `~stpipe.datamodel.AbstractDataModel` at a time.
+for a single `~stpipe.protocols.DataModel` at a time.
 This step applies a function ``calibrate_model_flux`` that
-accepts a single `~stpipe.datamodel.AbstractDataModel` and index as an input.
+accepts a single `~stpipe.protocols.DataModel` and index as an input.
 Its ``Step.process`` function can make good use of
 `~stpipe.library.AbstractModelLibrary.map_function` to apply
 this method to each model in the library.

src/stpipe/config_parser.py

@@ -21,7 +21,7 @@
 
 from . import utilities
 from .config import StepConfig
-from .datamodel import AbstractDataModel
+from .protocols import DataModel
 from .utilities import _not_set
 
 # Configure logger
@@ -82,7 +82,7 @@ def _output_file_check(path):
 
 def _is_datamodel(value):
     """Verify that value is a DataModel."""
-    if isinstance(value, AbstractDataModel):
+    if isinstance(value, DataModel):
         return value
 
     raise VdtTypeError(value)
@@ -92,7 +92,7 @@ def _is_string_or_datamodel(value):
     """Verify that value is either a string (nominally a reference file path)
     or a DataModel (possibly one with no corresponding file.)
     """
-    if isinstance(value, AbstractDataModel):
+    if isinstance(value, DataModel):
         return value
 
     if isinstance(value, str):

src/stpipe/library.py

@@ -10,7 +10,7 @@
 
 import asdf
 
-from .datamodel import AbstractDataModel
+from .protocols import DataModel
 
 __all__ = [
     "LibraryError",
@@ -771,7 +771,7 @@ def _model_to_filename(self, model):
         return model_filename
 
     def _to_group_id(self, model_or_filename, index):
-        if isinstance(model_or_filename, AbstractDataModel):
+        if isinstance(model_or_filename, DataModel):
             getter = self._model_to_group_id
         else:
             getter = self._filename_to_group_id

src/stpipe/pipeline.py

@@ -151,7 +151,7 @@ def get_config_from_reference(cls, dataset, disable=None, crds_observatory=None)
             Either a class or instance of a class derived
             from `Step`.
 
-        dataset : `stpipe.datamodel.AbstractDataModel`
+        dataset : `stpipe.protocols.DataModel`
             A model of the input file.  Metadata on this input file will
             be used by the CRDS "bestref" algorithm to obtain a reference
             file.

src/stpipe/step.py

@@ -33,9 +33,9 @@
     DISCOURAGED_TYPES = None
 
 from . import config, config_parser, crds_client, log, utilities
-from .datamodel import AbstractDataModel
 from .format_template import FormatTemplate
 from .library import AbstractModelLibrary
+from .protocols import DataModel
 from .utilities import _not_set
 
 
@@ -398,7 +398,7 @@ def _check_args(self, args, discouraged_types, msg):
         for i, arg in enumerate(args):
             if isinstance(arg, discouraged_types):
                 self.log.error(
-                    "%s %s object.  Use an instance of AbstractDataModel instead.",
+                    "%s %s object.  Use an instance of DataModel instead.",
                     msg,
                     i,
                 )
@@ -492,7 +492,7 @@ def run(self, *args):
                                         e,
                                     )
                                 library.shelve(model, i)
-                    elif isinstance(args[0], AbstractDataModel):
+                    elif isinstance(args[0], DataModel):
                         if self.class_alias is not None:
                             if isinstance(args[0], Sequence):
                                 for model in args[0]:
@@ -506,7 +506,7 @@ def run(self, *args):
                                             "header: %s",
                                             e,
                                         )
-                            elif isinstance(args[0], AbstractDataModel):
+                            elif isinstance(args[0], DataModel):
                                 try:
                                     args[0][
                                         f"meta.cal_step.{self.class_alias}"
@@ -567,9 +567,7 @@ def run(self, *args):
                     for idx, result in enumerate(results_to_save):
                         if len(results_to_save) <= 1:
                             idx = None
-                        if isinstance(
-                            result, (AbstractDataModel | AbstractModelLibrary)
-                        ):
+                        if isinstance(result, (DataModel | AbstractModelLibrary)):
                             self.save_model(result, idx=idx)
                         elif hasattr(result, "save"):
                             try:
@@ -609,7 +607,7 @@ def finalize_result(self, result, reference_files_used):
 
         Parameters
         ----------
-        result : a datamodel that is an instance of AbstractDataModel or
+        result : a datamodel that is an instance of DataModel or
                  collections.abc.Sequence
                  One step result (potentially of many).
 
@@ -780,7 +778,7 @@ def get_ref_override(self, reference_file_type):
         """
         override_name = crds_client.get_override_name(reference_file_type)
         path = getattr(self, override_name, None)
-        if isinstance(path, AbstractDataModel):
+        if isinstance(path, DataModel):
             return path
 
         return abspath(path) if path and path != "N/A" else path
@@ -795,7 +793,7 @@ def get_reference_file(self, input_file, reference_file_type):
 
         Parameters
         ----------
-        input_file : a datamodel that is an instance of AbstractDataModel
+        input_file : a datamodel that is an instance of DataModel
             A model of the input file.  Metadata on this input file
             will be used by the CRDS "bestref" algorithm to obtain a
             reference file.
@@ -810,7 +808,7 @@ def get_reference_file(self, input_file, reference_file_type):
         """
         override = self.get_ref_override(reference_file_type)
         if override is not None:
-            if isinstance(override, AbstractDataModel):
+            if isinstance(override, DataModel):
                 self._reference_files_used.append(
                     (reference_file_type, override.override_handle)
                 )
@@ -846,7 +844,7 @@ def get_config_from_reference(cls, dataset, disable=None, crds_observatory=None)
         cls : stpipe.Step
             Either a class or instance of a class derived
             from `Step`.
-        dataset : A datamodel that is an instance of AbstractDataModel
+        dataset : A datamodel that is an instance of DataModel
             A model of the input file.  Metadata on this input file will
             be used by the CRDS "bestref" algorithm to obtain a reference
             file.
@@ -874,7 +872,7 @@ def get_config_from_reference(cls, dataset, disable=None, crds_observatory=None)
             if crds_observatory is None:
                 raise ValueError("Need a valid name for crds_observatory.")
         else:
-            # If the dataset is not an operable instance of AbstractDataModel,
+            # If the dataset is not an operable instance of DataModel,
             # log as such and return an empty config object
             try:
                 with cls._datamodels_open(dataset, asn_n_members=1) as model:
@@ -884,7 +882,7 @@ def get_config_from_reference(cls, dataset, disable=None, crds_observatory=None)
                     crds_parameters = model.get_crds_parameters()
                     crds_observatory = model.crds_observatory
             except (OSError, TypeError, ValueError):
-                logger.warning("Input dataset is not an instance of AbstractDataModel.")
+                logger.warning("Input dataset is not an instance of DataModel.")
                 disable = True
 
         # Check if retrieval should be attempted.
@@ -930,7 +928,7 @@ def set_primary_input(self, obj, exclusive=True):
 
         Parameters
         ----------
-        obj : str, pathlib.Path, or instance of AbstractDataModel
+        obj : str, pathlib.Path, or instance of DataModel
             The object to base the name on. If a datamodel,
             use Datamodel.meta.filename.
 
@@ -945,7 +943,7 @@ def set_primary_input(self, obj, exclusive=True):
         if not exclusive or parent_input_filename is None:
             if isinstance(obj, str | Path):
                 self._input_filename = str(obj)
-            elif isinstance(obj, AbstractDataModel):
+            elif isinstance(obj, DataModel):
                 try:
                     self._input_filename = obj.meta.filename
                 except AttributeError:
@@ -967,7 +965,7 @@ def save_model(
 
         Parameters
         ----------
-        model : a instance of AbstractDataModel
+        model : a instance of DataModel
             The model to save.
 
         suffix : str
@@ -1166,7 +1164,7 @@ def open_model(self, init, **kwargs):
 
         Returns
         -------
-        datamodel : instance of AbstractDataModel
+        datamodel : instance of DataModel
             Object opened as a datamodel
         """
         # Use the parent method if available, since this step

src/stpipe/subproc.py

@@ -1,7 +1,7 @@
 import os
 import subprocess
 
-from .datamodel import AbstractDataModel
+from .protocols import DataModel
 from .step import Step
 
 
@@ -28,7 +28,7 @@ class SystemCall(Step):
     def process(self, *args):
         newargs = []
         for i, arg in enumerate(args):
-            if isinstance(arg, AbstractDataModel):
+            if isinstance(arg, DataModel):
                 filename = f"{self.qualified_name}.{i:04d}.{self.output_ext}"
                 arg.save(filename)
                 newargs.append(filename)