Deprecate experimental result data sources.

src/citrine/__version__.py

@@ -1 +1 @@
-__version__ = "4.0.3"
+__version__ = "4.1.0"

src/citrine/informatics/data_sources.py

@@ -2,6 +2,8 @@
 from abc import abstractmethod
 from uuid import UUID
 
+from deprecation import deprecated
+
 from citrine._serialization import properties
 from citrine._serialization.polymorphic_serializable import PolymorphicSerializable
 from citrine._serialization.serializable import Serializable
@@ -115,7 +117,7 @@ def from_gemtable(cls, table: GemTable) -> "GemTableDataSource":
 
 
 class ExperimentDataSourceRef(Serializable['ExperimentDataSourceRef'], DataSource):
-    """A reference to a data source based on an experiment result hosted on the data platform.
+    """[DEPRECATED] A reference to a data source based on an experiment result on the platform.
 
     Parameters
     ----------
@@ -129,6 +131,10 @@ class ExperimentDataSourceRef(Serializable['ExperimentDataSourceRef'], DataSourc
 
     _data_source_type = "experiments"
 
+    @deprecated(deprecated_in="4.1.0", removed_in="5.0.0",
+                details="Replaced by creating materials from candidates on the platform. "
+                        "Alternatively, you may convert the candidate into a collection of GEMD "
+                        "objects manually.")
     def __init__(self, *, datasource_id: UUID):
         self.datasource_id: UUID = datasource_id
 

src/citrine/informatics/experiment_values.py

@@ -1,3 +1,5 @@
+from deprecation import deprecated
+
 from citrine._serialization.serializable import Serializable
 from citrine._serialization.polymorphic_serializable import PolymorphicSerializable
 from citrine._serialization import properties
@@ -14,11 +16,18 @@
 
 
 class ExperimentValue(PolymorphicSerializable['ExperimentValue']):
-    """An container for experiment values.
+    """[DEPRECATED] An container for experiment values.
 
     Abstract type that returns the proper type given a serialized dict.
     """
 
+    @classmethod
+    @deprecated(deprecated_in="4.1.0", removed_in="5.0.0",
+                details="Replaced by creating materials from candidates.")
+    def build(cls, data: dict) -> 'ExperimentValue':
+        """Build the underlying type."""
+        return super().build(data)
+
     @classmethod
     def get_type(cls, data) -> type[Serializable]:
         """Return the subtype."""
@@ -67,62 +76,74 @@ def _equals(self, other, attrs) -> bool:
 
 
 class RealExperimentValue(Serializable['RealExperimentValue'], ExperimentValue):
-    """A floating point experiment result."""
+    """[DEPRECATED] A floating point experiment result."""
 
     value = properties.Float('value')
     typ = properties.String('type', default='RealValue', deserializable=False)
 
+    @deprecated(deprecated_in="4.1.0", removed_in="5.0.0",
+                details="Replaced by creating materials from candidates.")
     def __init__(self, value: float):
         self.value = value
 
 
 class IntegerExperimentValue(Serializable['IntegerExperimentValue'], ExperimentValue):
-    """An integer value experiment result."""
+    """[DEPRECATED] An integer value experiment result."""
 
     value = properties.Integer('value')
     typ = properties.String('type', default='IntegerValue', deserializable=False)
 
+    @deprecated(deprecated_in="4.1.0", removed_in="5.0.0",
+                details="Replaced by creating materials from candidates.")
     def __init__(self, value: int):
         self.value = value
 
 
 class CategoricalExperimentValue(Serializable['CategoricalExperimentValue'], ExperimentValue):
-    """An experiment result with a categorical value."""
+    """[DEPRECATED] An experiment result with a categorical value."""
 
     value = properties.String('value')
     typ = properties.String('type', default='CategoricalValue', deserializable=False)
 
+    @deprecated(deprecated_in="4.1.0", removed_in="5.0.0",
+                details="Replaced by creating materials from candidates.")
     def __init__(self, value: str):
         self.value = value
 
 
 class MixtureExperimentValue(Serializable['MixtureExperimentValue'], ExperimentValue):
-    """An experiment result mapping ingredients and labels to real values."""
+    """[DEPRECATED] An experiment result mapping ingredients and labels to real values."""
 
     value = properties.Mapping(properties.String, properties.Float, 'value')
     typ = properties.String('type', default='MixtureValue', deserializable=False)
 
+    @deprecated(deprecated_in="4.1.0", removed_in="5.0.0",
+                details="Replaced by creating materials from candidates.")
     def __init__(self, value: dict[str, float]):
         self.value = value
 
 
 class ChemicalFormulaExperimentValue(Serializable['ChemicalFormulaExperimentValue'],
                                      ExperimentValue):
-    """Experiment value for a chemical formula."""
+    """[DEPRECATED] Experiment value for a chemical formula."""
 
     value = properties.String('value')
     typ = properties.String('type', default='InorganicValue', deserializable=False)
 
+    @deprecated(deprecated_in="4.1.0", removed_in="5.0.0",
+                details="Replaced by creating materials from candidates.")
     def __init__(self, value: str):
         self.value = value
 
 
 class MolecularStructureExperimentValue(Serializable['MolecularStructureExperimentValue'],
                                         ExperimentValue):
-    """Experiment value for a molecular structure."""
+    """[DEPRECATED] Experiment value for a molecular structure."""
 
     value = properties.String('value')
     typ = properties.String('type', default='OrganicValue', deserializable=False)
 
+    @deprecated(deprecated_in="4.1.0", removed_in="5.0.0",
+                details="Replaced by creating materials from candidates.")
     def __init__(self, value: str):
         self.value = value

src/citrine/informatics/predictors/graph_predictor.py

@@ -48,8 +48,6 @@ class GraphPredictor(VersionedEngineResource['GraphPredictor'], AsynchronousObje
     description = properties.Optional(properties.String(), 'data.description')
     predictors = properties.List(properties.Object(PredictorNode), 'data.instance.predictors')
 
-    # the default seems to be defined in instances, not the class itself
-    # this is tested in test_graph_default_training_data
     training_data = properties.List(
         properties.Object(DataSource), 'data.instance.training_data', default=[]
     )

src/citrine/resources/experiment_datasource.py

@@ -5,6 +5,8 @@
 from io import StringIO
 from uuid import UUID
 
+from deprecation import deprecated
+
 from citrine._rest.collection import Collection
 from citrine._serialization import properties
 from citrine._serialization.serializable import Serializable
@@ -32,6 +34,8 @@ class CandidateExperimentSnapshot(Serializable['CandidateExperimentSnapshot']):
                                    'overrides')
     """:dict[str, ExperimentValue]: dictionary of candidate material variable overrides"""
 
+    @deprecated(deprecated_in="4.1.0", removed_in="5.0.0",
+                details="Replaced by creating materials from candidates.")
     def __init__(self, *args, **kwargs):
         """Candidate experiment snapshots are not directly instantiated by the user."""
         pass  # pragma: no cover
@@ -58,6 +62,8 @@ class ExperimentDataSource(Serializable['ExperimentDataSource']):
     create_time = properties.Datetime('metadata.created.time', serializable=False)
     """:datetime: date and time at which this data source was created"""
 
+    @deprecated(deprecated_in="4.1.0", removed_in="5.0.0",
+                details="Replaced by creating materials from candidates.")
     def __init__(self, *args, **kwargs):
         """Experiment data sources are not directly instantiated by the user."""
         pass  # pragma: no cover
@@ -86,13 +92,17 @@ def read(self) -> str:
 
 
 class ExperimentDataSourceCollection(Collection[ExperimentDataSource]):
-    """Represents the collection of all experiment data sources associated with a project."""
+    """[DEPRECATED] The collection of all experiment data sources associated with a project."""
 
     _path_template = 'projects/{project_id}/candidate-experiment-datasources'
     _individual_key = None
     _resource = ExperimentDataSource
     _collection_key = 'response'
 
+    @deprecated(deprecated_in="4.1.0", removed_in="5.0.0",
+                details="Replaced by creating materials from candidates on the platform. "
+                        "Alternatively, you may convert the candidate into a collection of GEMD "
+                        "objects manually.")
     def __init__(self, project_id: UUID, session: Session):
         self.project_id = project_id
         self.session: Session = session

src/citrine/resources/predictor.py

@@ -1,4 +1,5 @@
 """Resources that represent collections of predictors."""
+import warnings
 from collections.abc import Iterable
 from functools import partial
 from typing import Any
@@ -11,7 +12,7 @@
 from citrine._rest.paginator import Paginator
 from citrine._serialization import properties
 from citrine._session import Session
-from citrine.informatics.data_sources import DataSource
+from citrine.informatics.data_sources import DataSource, ExperimentDataSourceRef
 from citrine.informatics.design_candidate import HierarchicalDesignMaterial
 from citrine.informatics.predictors import GraphPredictor
 from citrine.resources.status_detail import StatusDetail
@@ -107,6 +108,16 @@ def _page_fetcher(self, *, uid: UUID | str, **additional_params):
         }
         return partial(self._fetch_page, **fetcher_params)
 
+    def _check_data_sources(self, predictor: GraphPredictor):
+        for data_source in predictor.training_data:
+            print(data_source)
+            if isinstance(data_source, ExperimentDataSourceRef):
+                warnings.warn("This predictor contains an experiment result, which is being "
+                              "replaced by creating materials from candidates on the platform. "
+                              "Alternatively, you may convert the candidate into a collection of "
+                              "GEMD objects manually.",
+                              DeprecationWarning)
+
     def build(self, data: dict) -> GraphPredictor:
         """Build an individual Predictor."""
         predictor: GraphPredictor = GraphPredictor.build(data)
@@ -120,7 +131,9 @@ def get(self,
             version: int | str = MOST_RECENT_VER) -> GraphPredictor:
         path = self._construct_path(uid, version)
         entity = self.session.get_resource(path, version=self._api_version)
-        return self.build(entity)
+        predictor = self.build(entity)
+        self._check_data_sources(predictor)
+        return predictor
 
     def get_featurized_training_data(
             self,

tests/informatics/test_data_source.py

@@ -15,12 +15,16 @@
 @pytest.fixture(params=[
     GemTableDataSource(table_id=uuid.uuid4(), table_version=1),
     GemTableDataSource(table_id=uuid.uuid4(), table_version="2"),
-    ExperimentDataSourceRef(datasource_id=uuid.uuid4()),
     SnapshotDataSource(snapshot_id=uuid.uuid4())
 ])
 def data_source(request):
     return request.param
 
+@pytest.fixture
+def deprecated_data_source():
+    with pytest.deprecated_call():
+        return ExperimentDataSourceRef(datasource_id=uuid.uuid4())
+
 
 def test_deser_from_parent(data_source):
     # Serialize and deserialize the descriptors, making sure they are round-trip serializable
@@ -29,6 +33,13 @@ def test_deser_from_parent(data_source):
     assert data_source == data_source_deserialized
 
 
+def test_deser_from_parent_deprecated(deprecated_data_source):
+    # Serialize and deserialize the descriptors, making sure they are round-trip serializable
+    data = deprecated_data_source.dump()
+    data_source_deserialized = DataSource.build(data)
+    assert deprecated_data_source == data_source_deserialized
+
+
 def test_invalid_eq(data_source):
     other = None
     assert not data_source == other
@@ -42,6 +53,10 @@ def test_invalid_deser():
         DataSource.build({"type": "foo"})
 
 
+def test_deprecated_data_source_id(deprecated_data_source):
+    with pytest.deprecated_call():
+        assert deprecated_data_source == DataSource.from_data_source_id(deprecated_data_source.to_data_source_id())
+
 def test_data_source_id(data_source):
     assert data_source == DataSource.from_data_source_id(data_source.to_data_source_id())
 

tests/informatics/test_experiment_values.py

@@ -12,21 +12,24 @@
 
 
 @pytest.fixture(params=[
-    CategoricalExperimentValue("categorical"),
-    ChemicalFormulaExperimentValue("(Ca)1(O)3(Si)1"),
-    IntegerExperimentValue(7),
-    MixtureExperimentValue({"ingredient1": 0.3, "ingredient2": 0.7}),
-    MolecularStructureExperimentValue("CC1(CC(CC(N1)(C)C)NCCCCCCNC2CC(NC(C2)(C)C)(C)C)C.C1COCCN1C2=NC(=NC(=N2)Cl)Cl"),
-    RealExperimentValue(3.5)
+    (CategoricalExperimentValue, ("categorical", )),
+    (ChemicalFormulaExperimentValue, ("(Ca)1(O)3(Si)1",)),
+    (IntegerExperimentValue, (7,)),
+    (MixtureExperimentValue, ({"ingredient1": 0.3, "ingredient2": 0.7},)),
+    (MolecularStructureExperimentValue, ("CC1(CC(CC(N1)(C)C)NCCCCCCNC2CC(NC(C2)(C)C)(C)C)C.C1COCCN1C2=NC(=NC(=N2)Cl)Cl",)),
+    (RealExperimentValue, (3.5,))
 ])
 def experiment_value(request):
-    return request.param
+    cls, args = request.param
+    with pytest.deprecated_call():
+        return cls(*args)
 
 
 def test_deser_from_parent(experiment_value):
     # Serialize and deserialize the experiment values, making sure they are round-trip serializable
     data = experiment_value.dump()
-    experiment_value_deserialized = ExperimentValue.build(data)
+    with pytest.deprecated_call():
+        experiment_value_deserialized = ExperimentValue.build(data)
     assert experiment_value == experiment_value_deserialized
 
 

tests/resources/test_branch.py

@@ -537,7 +537,9 @@ def test_experiment_datasource(session, collection):
     session.set_response({'response': [erds]})
 
     # When / Then
-    assert branch.experiment_datasource is not None
+    with pytest.deprecated_call():
+        assert branch.experiment_datasource is not None
+
     assert session.calls == [
         FakeCall(method='GET', path=erds_path, params={'branch': str(branch.uid), 'version': LATEST_VER, 'per_page': 100, 'page': 1})
     ]
@@ -550,7 +552,9 @@ def test_no_experiment_datasource(session, collection):
     session.set_response({'response': []})
 
     # When / Then
-    assert branch.experiment_datasource is None
+    with pytest.deprecated_call():
+        assert branch.experiment_datasource is None
+
     assert session.calls == [
         FakeCall(method='GET', path=erds_path, params={'branch': str(branch.uid), 'version': LATEST_VER, 'per_page': 100, 'page': 1})
     ]

tests/resources/test_experiment_datasource.py

@@ -23,7 +23,8 @@ def session():
 
 @pytest.fixture
 def collection(session) -> ExperimentDataSourceCollection:
-    return ExperimentDataSourceCollection(uuid.uuid4(), session)
+    with pytest.deprecated_call():
+        return ExperimentDataSourceCollection(uuid.uuid4(), session)
 
 
 @pytest.fixture

tests/resources/test_predictor.py

@@ -5,7 +5,7 @@
 from copy import deepcopy
 
 from citrine.exceptions import BadRequest, Conflict, ModuleRegistrationFailedException, NotFound
-from citrine.informatics.data_sources import GemTableDataSource
+from citrine.informatics.data_sources import ExperimentDataSourceRef, GemTableDataSource
 from citrine.informatics.descriptors import RealDescriptor
 from citrine.informatics.predictors import (
     AutoMLPredictor,
@@ -754,3 +754,20 @@ def test_rename_description_only(valid_graph_predictor_data):
     versions_path = _PredictorVersionCollection._path_template.format(project_id=pc.project_id, uid=pred_id)
     expected_payload = {"name": None, "description": new_description}
     assert session.calls == [FakeCall(method="PUT", path=f"{versions_path}/{pred_version}/rename", json=expected_payload)]
+
+
+def test_get_predictor_with_experiment_data_source_deprecated(valid_graph_predictor_data):
+    # Given
+    session = FakeSession()
+    pc = PredictorCollection(uuid.uuid4(), session)
+
+    with pytest.deprecated_call():
+        erds = ExperimentDataSourceRef(datasource_id=uuid.uuid4())
+    entity = deepcopy(valid_graph_predictor_data)
+    entity["data"]["instance"]["training_data"] = [erds.dump()]
+
+    session.set_responses(entity)
+
+    # When
+    with pytest.deprecated_call():
+        pc.get(uuid.uuid4())