Remove deprecated code (#508)

Author: cthoyt

src/pyobo/api/embedding.py

@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 import tempfile
-import warnings
 from pathlib import Path
 from typing import TYPE_CHECKING, Any, Literal, cast
 
@@ -28,22 +27,11 @@
 __all__ = [
     "get_graph_embeddings_df",
     "get_text_embedding",
-    "get_text_embedding_model",
     "get_text_embedding_similarity",
     "get_text_embeddings_df",
 ]
 
 
-def get_text_embedding_model() -> sentence_transformers.SentenceTransformer:
-    """Get the default text embedding model."""
-    warnings.warn(
-        "get_text_embedding_model() is deprecated, use pystow.get_sentence_transfomer() directly",
-        DeprecationWarning,
-        stacklevel=2,
-    )
-    return get_sentence_transformer()
-
-
 def _get_text(
     reference: str | curies.Reference | curies.ReferenceTuple,
     /,

src/pyobo/cli/database.py

@@ -1,7 +1,6 @@
 """CLI for PyOBO Database Generation."""
 
 import logging
-import warnings
 from collections.abc import Callable, Iterable
 from pathlib import Path
 from typing import ParamSpec, TypeVar
@@ -383,29 +382,6 @@ def properties(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs])
         update_zenodo(PROPERTIES_RECORD, paths)
 
 
-@database_annotate
-def xrefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
-    """Make the prefix-identifier-xref dump."""
-    from .database_utils import _iter_xrefs
-    from ..getters import db_output_helper
-
-    warnings.warn("Use pyobo.database.mappings instead", DeprecationWarning, stacklevel=2)
-    with logging_redirect_tqdm():
-        it = _iter_xrefs(**kwargs)
-        paths = db_output_helper(
-            it,
-            "xrefs",
-            ("prefix", "identifier", "xref_prefix", "xref_identifier", "provenance"),
-            summary_detailed=(0, 2),  # second column corresponds to xref prefix
-            directory=directory,
-        )
-    if zenodo:
-        from zenodo_client import update_zenodo
-
-        # see https://zenodo.org/record/4021477
-        update_zenodo(JAVERT_RECORD, paths)
-
-
 @database_annotate
 def mappings(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the SSSOM dump."""
@@ -421,14 +397,18 @@ def mappings(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
     ]
     with logging_redirect_tqdm():
         it = _iter_mappings(**kwargs)
-        db_output_helper(
+        paths = db_output_helper(
             it,
             "mappings",
             columns,
             directory=directory,
         )
     if zenodo:
-        raise NotImplementedError("need to do initial manual upload of SSSOM build")
+        from zenodo_client import update_zenodo
+
+        # TODO might not work because file paths for old xrefs were different
+        # see https://zenodo.org/record/4021477
+        update_zenodo(JAVERT_RECORD, paths)
 
 
 if __name__ == "__main__":

src/pyobo/cli/database_utils.py

@@ -4,7 +4,6 @@
 
 import gzip
 import logging
-import warnings
 from collections.abc import Iterable
 from typing import cast
 
@@ -22,7 +21,6 @@
     get_properties_df,
     get_relations_df,
     get_typedef_df,
-    get_xrefs_df,
 )
 from ..constants import IterHelperHelperDict
 from ..getters import iter_helper, iter_helper_helper
@@ -132,19 +130,6 @@ def _iter_properties(**kwargs: Unpack[IterHelperHelperDict]) -> Iterable[tuple[s
                 yield cast(tuple[str, str, str, str], (prefix, *t))
 
 
-def _iter_xrefs(
-    **kwargs: Unpack[IterHelperHelperDict],
-) -> Iterable[tuple[str, str, str, str, str]]:
-    warnings.warn(f"use {_iter_mappings.__name__} instead", DeprecationWarning, stacklevel=2)
-    it = iter_helper_helper(get_xrefs_df, **kwargs)
-    for prefix, df in it:
-        df.dropna(inplace=True)
-        for row in df.values:
-            if any(not element for element in row):
-                continue
-            yield cast(tuple[str, str, str, str, str], (prefix, *row, prefix))
-
-
 def _iter_mappings(
     **kwargs: Unpack[IterHelperHelperDict],
 ) -> Iterable[tuple[str, str, str, str, str]]:

src/pyobo/struct/obo/reader.py

@@ -112,6 +112,7 @@ def _read_obo(
     return obonet.read_obo(
         tqdm(lines, disable=not use_tqdm, **tqdm_kwargs),
         ignore_obsolete=ignore_obsolete,
+        # TODO add include_clauses=True to get trailing modifiers
     )
 
 

src/pyobo/struct/struct_utils.py

@@ -5,7 +5,6 @@
 import datetime
 import itertools as itt
 import logging
-import warnings
 from abc import ABC, abstractmethod
 from collections import defaultdict
 from collections.abc import Iterable, Mapping, Sequence
@@ -882,16 +881,6 @@ def append_definition_xref(self, reference: ReferenceHint) -> Self:
         )
         return self
 
-    def append_provenance(
-        self,
-        reference: Reference,
-        *,
-        annotations: Iterable[Annotation] | None = None,
-    ) -> Self:
-        """Append a creative work that mentions this term."""
-        warnings.warn("use append_mentioned_by instead", DeprecationWarning, stacklevel=2)
-        return self.append_mentioned_by(reference, annotations=annotations)
-
     def append_mentioned_by(
         self,
         reference: Reference,

tests/test_api.py

@@ -93,7 +93,7 @@ def test_get_primary_errors(self) -> None:
     @mock_id_names_mapping
     def test_get_primary(self, _: Any, __: Any) -> None:
         """Test upgrading an obsolete identifier."""
-        primary_id = get_primary_identifier("go", "0001071")
+        primary_id = get_primary_identifier("go:0001071")
         self.assertIsNotNone(primary_id)
         self.assertEqual("0003700", primary_id)
         self.assertIsNone(get_name(ReferenceTuple("go", "0001071"), upgrade_identifier=False))