Remove the deprecated load_*/save_* aliases

docs/guides/compound_identifiers.rst

@@ -80,7 +80,7 @@ Look Them Up
 ###############
 
 The `ORD Reaction Editor <https://app.open-reaction-database.org/>`__ has a look up function which can
-be used to add chemicals by name. The `name_resolve function <https://docs.open-reaction-database.org/en/latest/ord_schema/ord_schema.html#ord_schema.resolvers.name_resolve>`__
+be used to add chemicals by name. The `resolve_name function <https://docs.open-reaction-database.org/en/latest/ord_schema/ord_schema.html#ord_schema.resolvers.resolve_name>`__
 uses the PubChem and OPSIN APIs to look up names and returns a SMILES string when it is available.
 
 For looking up identifiers of organic compounds the following online services can be useful:
@@ -97,7 +97,7 @@ For looking up identifiers of organic compounds the following online services ca
   websites will also report the SMILES in this style. Please refer to :ref:`dative-bonding` below for a recommended 
   workflow for generating SMILES strings which include dative bonding.
 
-Lists of names can be programmatically looked up using the ORD `name_resolve function <https://docs.open-reaction-database.org/en/latest/ord_schema/ord_schema.html#ord_schema.resolvers.name_resolve>`__
+Lists of names can be programmatically looked up using the ORD `resolve_name function <https://docs.open-reaction-database.org/en/latest/ord_schema/ord_schema.html#ord_schema.resolvers.resolve_name>`__
 in Python.
 
 

docs/guides/templates.rst

@@ -26,7 +26,7 @@ Step 1: Create a template reaction
 
         See the Python examples `here <https://docs.open-reaction-database.org/en/latest/schema.html#jupyter-colab>`_ 
         for how to construct reactions programmatically. After creating a template reaction,
-        save it as a pbtxt file using `message_helpers.write_message <https://docs.open-reaction-database.org/en/latest/ord_schema/ord_schema.html#module-ord_schema.message_helpers>`_.
+        save it as a pbtxt file using `message_helpers.save_message <https://docs.open-reaction-database.org/en/latest/ord_schema/ord_schema.html#module-ord_schema.message_helpers>`_.
 
 Here's an `example reaction <https://gist.github.com/skearnes/1e822a599c07df924f7320352103865b#file-reaction-pbtxt>`_.
 

ord_schema/message_helpers.py

@@ -36,7 +36,7 @@
 
 import ord_schema
 from ord_schema import atomic_io, units
-from ord_schema.proto import dataset_pb2, reaction_pb2
+from ord_schema.proto import reaction_pb2
 
 _COMPOUND_IDENTIFIER_LOADERS = {
     reaction_pb2.CompoundIdentifier.SMILES: Chem.MolFromSmiles,
@@ -1086,32 +1086,3 @@ def parse_doi(doi: str) -> str:
     if not match:
         raise ValueError(f"could not parse DOI: {doi}")
     return match.group(1)
-
-
-# Deprecated aliases, kept for backwards compatibility after the load_*/save_*
-# rename. Remove in a future minor release.
-def write_message(
-    message: ord_schema.Message, filename: str | os.PathLike[str]
-) -> None:
-    """Deprecated alias for :func:`save_message`."""
-    warnings.warn(
-        "message_helpers.write_message is deprecated; use save_message instead.",
-        DeprecationWarning,
-        stacklevel=2,
-    )
-    return save_message(message, filename)
-
-
-def write_dataset(
-    dataset: dataset_pb2.Dataset, filename: str | os.PathLike[str]
-) -> None:
-    """Deprecated alias for :func:`ord_schema.datasets.save_dataset`."""
-    from ord_schema import datasets  # noqa: PLC0415
-
-    warnings.warn(
-        "message_helpers.write_dataset is deprecated; "
-        "use ord_schema.datasets.save_dataset instead.",
-        DeprecationWarning,
-        stacklevel=2,
-    )
-    datasets.save_dataset(dataset, filename)

ord_schema/parquet.py

@@ -32,7 +32,6 @@
 import os
 import pathlib
 import tempfile
-import warnings
 from collections.abc import Iterable, Iterator
 from types import TracebackType
 from typing import Self
@@ -545,65 +544,3 @@ def _get(key: str) -> str | None:
     if dataset_id:
         dataset.dataset_id = dataset_id
     return dataset
-
-
-# Deprecated aliases, kept for backwards compatibility after the load_*/save_*
-# rename. Remove in a future minor release.
-def write_dataset(
-    dataset: dataset_pb2.Dataset,
-    path: str | os.PathLike[str],
-    *,
-    compression: str = "zstd",
-    row_group_size: int = 1000,
-) -> None:
-    """Deprecated alias for :func:`save_dataset`."""
-    warnings.warn(
-        "parquet.write_dataset is deprecated; use save_dataset instead.",
-        DeprecationWarning,
-        stacklevel=2,
-    )
-    return save_dataset(
-        dataset, path, compression=compression, row_group_size=row_group_size
-    )
-
-
-def read_dataset(path: str | os.PathLike[str]) -> dataset_pb2.Dataset:
-    """Deprecated alias for :func:`load_dataset`."""
-    warnings.warn(
-        "parquet.read_dataset is deprecated; use load_dataset instead.",
-        DeprecationWarning,
-        stacklevel=2,
-    )
-    return load_dataset(path)
-
-
-def read_metadata(path: str | os.PathLike[str]) -> dataset_pb2.Dataset:
-    """Deprecated alias for :func:`load_metadata`."""
-    warnings.warn(
-        "parquet.read_metadata is deprecated; use load_metadata instead.",
-        DeprecationWarning,
-        stacklevel=2,
-    )
-    return load_metadata(path)
-
-
-def read_footer(path: str | os.PathLike[str]) -> ParquetFooter:
-    """Deprecated alias for :func:`load_footer`."""
-    warnings.warn(
-        "parquet.read_footer is deprecated; use load_footer instead.",
-        DeprecationWarning,
-        stacklevel=2,
-    )
-    return load_footer(path)
-
-
-def read_reaction(
-    path: str | os.PathLike[str], reaction_id: str
-) -> reaction_pb2.Reaction:
-    """Deprecated alias for :func:`load_reaction`."""
-    warnings.warn(
-        "parquet.read_reaction is deprecated; use load_reaction instead.",
-        DeprecationWarning,
-        stacklevel=2,
-    )
-    return load_reaction(path, reaction_id)

ord_schema/resolvers.py

@@ -17,7 +17,6 @@
 import urllib.error
 import urllib.parse
 import urllib.request
-import warnings
 
 from rdkit import Chem
 
@@ -213,13 +212,3 @@ def resolve_input(input_string: str) -> reaction_pb2.ReactionInput:
     "NCI/CADD CIR": _cactus_resolve,
     "OPSIN": _opsin_resolve,
 }
-
-
-def name_resolve(*args: str, **kwargs: str) -> tuple[str, str]:
-    """Deprecated alias for :func:`resolve_name`."""
-    warnings.warn(
-        "resolvers.name_resolve is deprecated; use resolve_name instead.",
-        DeprecationWarning,
-        stacklevel=2,
-    )
-    return resolve_name(*args, **kwargs)

ord_schema/scripts/build_dataset.py

@@ -31,9 +31,8 @@ def parse_args(argv: list[str] | None = None) -> argparse.Namespace:
     parser = argparse.ArgumentParser(description="Build a Dataset from Reaction protos")
     parser.add_argument(
         "--input_pattern",
-        "--input",
         required=True,
-        help="Input pattern for Reaction protos (--input is a deprecated alias)",
+        help="Input pattern for Reaction protos",
     )
     parser.add_argument(
         "--output", required=True, help="Output Dataset filename (*.pbtxt)"

ord_schema/scripts/validate_dataset.py

@@ -103,9 +103,8 @@ def parse_args(argv: list[str] | None = None) -> argparse.Namespace:
     parser = argparse.ArgumentParser(description="Validate Dataset protocol buffers")
     parser.add_argument(
         "--input_pattern",
-        "--input",
         required=True,
-        help="Input pattern for Dataset protos (--input is a deprecated alias)",
+        help="Input pattern for Dataset protos",
     )
     parser.add_argument("--filter", default=None, help="Regex filename filter")
     parser.add_argument(

ord_schema/templating.py

@@ -20,7 +20,6 @@
 
 import pathlib
 import re
-import warnings
 from collections.abc import Mapping
 from typing import BinaryIO
 
@@ -176,17 +175,3 @@ def generate_dataset(
         reactions.append(reaction)
 
     return dataset_pb2.Dataset(name=name, description=description, reactions=reactions)
-
-
-# Deprecated alias, kept for backwards compatibility after the load_*/save_*
-# rename. Remove in a future minor release.
-def read_spreadsheet(
-    file_name_or_buffer: str | BinaryIO, suffix: str | None = None
-) -> pd.DataFrame:
-    """Deprecated alias for :func:`load_spreadsheet`."""
-    warnings.warn(
-        "templating.read_spreadsheet is deprecated; use load_spreadsheet instead.",
-        DeprecationWarning,
-        stacklevel=2,
-    )
-    return load_spreadsheet(file_name_or_buffer, suffix)