refactor!: drop num_processes and num_threads kwargs

Both were deprecated in the previous commit ('refactor: add
num_workers/use_threads to process_single_position'), with shims that
forwarded their values to num_workers. Drop the shims now — anything
still passing num_processes / num_threads gets a TypeError pointing at
the right argument name, which is more useful than a silent
DeprecationWarning that callers may never see (Python suppresses
DeprecationWarning raised from package code under the default filter).

Removes the corresponding regression test
(test_process_single_position_legacy_kwargs_deprecated) and the
unused 'warnings' import.

BREAKING CHANGE: callers of process_single_position must use
num_workers (and, optionally, use_threads) instead of num_processes /
num_threads.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: ieivanov

src/iohub/ngff/utils.py

@@ -4,7 +4,6 @@
 import itertools
 import multiprocessing as mp
 import os
-import warnings
 from collections import defaultdict
 from collections.abc import Callable, Sequence
 from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor, as_completed
@@ -305,8 +304,6 @@ def process_single_position(
     output_time_indices: list[int] | None = None,
     num_workers: int = 1,
     use_threads: bool = False,
-    num_processes: int | None = None,
-    num_threads: int | None = None,
     **kwargs,
 ) -> None:
     """
@@ -354,34 +351,13 @@ def process_single_position(
         If True, parallelize across threads via ``ThreadPoolExecutor``;
         otherwise spawn worker processes via ``ProcessPoolExecutor``.
         Defaults to False.
-    num_processes : int, optional
-        Deprecated. Use ``num_workers`` instead. When set, its value is
-        forwarded to ``num_workers``.
-    num_threads : int, optional
-        Deprecated. Use ``num_workers`` (and ``use_threads=True``) instead.
-        When set, its value is forwarded to ``num_workers``.
     kwargs : dict, optional
         Additional arguments to pass to the function.
         A dictionary with key "extra_metadata"
         can be passed to be stored at a FOV level,
         e.g.,
         kwargs={"extra_metadata": {"Temperature": 37.5, "CO2_level": 0.5}}.
     """
-    if num_processes is not None:
-        warnings.warn(
-            "num_processes is deprecated; use num_workers instead.",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-        num_workers = num_processes
-    if num_threads is not None:
-        warnings.warn(
-            "num_threads is deprecated; use num_workers "
-            "(with use_threads=True for a thread pool) instead.",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-        num_workers = num_threads
     click.echo(f"Function to be applied: \t{func}")
     click.echo(f"Input data path:\t{input_position_path}")
     click.echo(f"Output data path:\t{output_position_path}")

tests/ngff/test_ngff_utils.py

@@ -825,32 +825,6 @@ def test_available_cpus_honours_slurm_env(monkeypatch, env, expected_min, expect
         assert n == expected_max
 
 
-@pytest.mark.parametrize("legacy_kwarg", ["num_processes", "num_threads"])
-def test_process_single_position_legacy_kwargs_deprecated(tmp_path, legacy_kwarg):
-    """`num_processes` and `num_threads` emit DeprecationWarning and forward to `num_workers`."""
-    shape = (1, 1, 2, 4, 4)
-    position_key = ("A", "1", "0")
-    input_store = tmp_path / "input.zarr"
-    output_store = tmp_path / "output.zarr"
-    for store in (input_store, output_store):
-        create_empty_plate(
-            store_path=store,
-            position_keys=[position_key],
-            channel_names=["c0"],
-            shape=shape,
-        )
-    populate_store(input_store, [position_key], shape, np.float32)
-
-    with pytest.warns(DeprecationWarning, match=f"{legacy_kwarg} is deprecated"):
-        process_single_position(
-            func=dummy_transform,
-            input_position_path=input_store / Path(*position_key),
-            output_position_path=output_store / Path(*position_key),
-            constant=1,
-            **{legacy_kwarg: 2},
-        )
-
-
 # -- Explicit tests for version-specific chunk/shard defaults -----------------
 #
 # The hypothesis-based test_create_empty_plate exercises many parameter