chore!: remove old positional compat

docs/release-notes/3984.chore.md

@@ -0,0 +1 @@
+Remove compatibility helper for passing parameters positionally {smaller}`P Angerer`

pyproject.toml

@@ -55,7 +55,6 @@ dependencies = [
     "fast-array-utils[accel,sparse]>=1.2.1",
     "h5py>=3.11",
     "joblib",
-    "legacy-api-wrap>=1.5",                     # for positional API deprecations
     "matplotlib>=3.9",
     "natsort",
     "networkx>=2.8.8",
@@ -214,7 +213,6 @@ lint.pylint.max-args = 10
 lint.pylint.max-positional-args = 5
 
 [tool.ruff.lint.flake8-tidy-imports.banned-api]
-"legacy_api_wrap.legacy_api".msg = "Use scanpy._compat.old_positionals instead"
 "numba.jit".msg = "Use `scanpy._compat.njit` instead"
 "numba.njit".msg = "Use `scanpy._compat.njit` instead"
 "numpy.bool".msg = "Use `np.bool_` instead for numpy>=1.24<2 compatibility"

src/scanpy/_compat.py

@@ -7,7 +7,6 @@
 from pathlib import Path
 from typing import TYPE_CHECKING, Literal, cast, overload
 
-import legacy_api_wrap
 from packaging.version import Version
 from scipy import sparse
 
@@ -26,7 +25,6 @@
     "deprecated",
     "fullname",
     "njit",
-    "old_positionals",
     "pkg_metadata",
     "pkg_version",
     "warn",
@@ -79,17 +77,7 @@ def pkg_version(package: str) -> Version:
 
 
 # File prefixes for us and decorators we use
-_FILE_PREFIXES: tuple[str, ...] = (
-    str(Path(__file__).parent),
-    str(Path(legacy_api_wrap.__file__).parent),
-)
-
-
-old_positionals = partial(
-    legacy_api_wrap.legacy_api,  # noqa: TID251
-    category=FutureWarning,
-    skip_file_prefixes=_FILE_PREFIXES,
-)
+_FILE_PREFIXES: tuple[str, ...] = (str(Path(__file__).parent),)
 
 
 # we’re not using _FILE_PREFIXES here,

src/scanpy/_settings/__init__.py

@@ -8,7 +8,7 @@
 from typing import TYPE_CHECKING, Literal, get_args
 
 from .. import logging
-from .._compat import deprecated, old_positionals
+from .._compat import deprecated
 from .._singleton import SingletonMeta, documenting
 from ..logging import _RootLogger, _set_log_file, _set_log_level
 from .verbosity import Verbosity
@@ -334,20 +334,6 @@ def categories_to_ignore(cls, categories_to_ignore: Iterable[str]) -> None:
     def set_figure_params(cls, *args, **kwargs) -> None:
         cls._set_figure_params(*args, **kwargs)
 
-    @old_positionals(
-        "scanpy",
-        "dpi",
-        "dpi_save",
-        "frameon",
-        "vector_friendly",
-        "fontsize",
-        "figsize",
-        "color_map",
-        "format",
-        "facecolor",
-        "transparent",
-        "ipython_format",
-    )
     def _set_figure_params(  # noqa: PLR0913
         cls,
         *,

src/scanpy/datasets/_datasets.py

@@ -9,7 +9,7 @@
 from anndata import AnnData, OldFormatWarning
 
 from .. import _utils
-from .._compat import deprecated, old_positionals
+from .._compat import deprecated
 from .._settings import settings
 from .._utils._doctests import doctest_internet, doctest_needs
 from ..readwrite import read, read_h5ad, read_visium
@@ -54,9 +54,6 @@
 HERE = Path(__file__).parent
 
 
-@old_positionals(
-    "n_variables", "n_centers", "cluster_std", "n_observations", "random_state"
-)
 def blobs(
     *,
     n_variables: int = 11,

src/scanpy/external/exporting.py

@@ -14,7 +14,6 @@
 from fast_array_utils.stats import mean_var
 from pandas.api.types import CategoricalDtype
 
-from .._compat import old_positionals
 from .._utils import NeighborsView
 
 if TYPE_CHECKING:
@@ -25,14 +24,6 @@
 __all__ = ["cellbrowser", "spring_project"]
 
 
-@old_positionals(
-    "subplot_name",
-    "cell_groupings",
-    "custom_color_tracks",
-    "total_counts_key",
-    "neighbors_key",
-    "overwrite",
-)
 def spring_project(  # noqa: PLR0912, PLR0915
     adata: AnnData,
     project_dir: Path | str,
@@ -472,16 +463,6 @@ def _export_paga_to_spring(adata, paga_coords, outpath) -> None:
     Path(outpath).write_text(json.dumps(paga_data, indent=4))
 
 
-@old_positionals(
-    "embedding_keys",
-    "annot_keys",
-    "cluster_field",
-    "nb_marker",
-    "skip_matrix",
-    "html_dir",
-    "port",
-    "do_debug",
-)
 def cellbrowser(  # noqa: PLR0913
     adata: AnnData,
     data_dir: Path | str,

src/scanpy/external/pl.py

@@ -8,7 +8,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-from .._compat import deprecated, old_positionals
+from .._compat import deprecated
 from .._utils import _doc_params
 from .._utils._doctests import doctest_needs
 from ..plotting import _scrublet, _utils, embedding
@@ -162,7 +162,6 @@ def harmony_timeseries(
     return axes
 
 
-@old_positionals("c", "cmap", "linewidth", "edgecolor", "axes", "colorbar", "s")
 def sam(
     adata: AnnData,
     projection: str | np.ndarray = "X_umap",
@@ -257,17 +256,6 @@ def sam(
     return axes
 
 
-@old_positionals(
-    "no_bins",
-    "smoothing_factor",
-    "min_delta",
-    "show_variance",
-    "figsize",
-    "return_fig",
-    "show",
-    "save",
-    "ax",
-)
 @_doc_params(show_save_ax=doc_show_save_ax)
 def wishbone_marker_trajectory(  # noqa: PLR0913
     adata: AnnData,

src/scanpy/external/pp/_bbknn.py

@@ -2,7 +2,6 @@
 
 from typing import TYPE_CHECKING
 
-from ..._compat import old_positionals
 from ..._utils._doctests import doctest_needs
 
 if TYPE_CHECKING:
@@ -12,7 +11,6 @@
     from sklearn.metrics import DistanceMetric
 
 
-@old_positionals("batch_key", "use_rep", "approx", "use_annoy", "metric", "copy")
 @doctest_needs("bbknn")
 def bbknn(  # noqa: PLR0913
     adata: AnnData,

src/scanpy/external/pp/_dca.py

@@ -3,8 +3,6 @@
 from types import MappingProxyType
 from typing import TYPE_CHECKING
 
-from ..._compat import old_positionals
-
 if TYPE_CHECKING:
     from collections.abc import Mapping, Sequence
     from typing import Any, Literal
@@ -16,31 +14,6 @@
     type _AEType = Literal["zinb-conddisp", "zinb", "nb-conddisp", "nb"]
 
 
-@old_positionals(
-    "ae_type",
-    "normalize_per_cell",
-    "scale",
-    "log1p",
-    "hidden_size",
-    "hidden_dropout",
-    "batchnorm",
-    "activation",
-    "init",
-    "network_kwds",
-    "epochs",
-    "reduce_lr",
-    "early_stop",
-    "batch_size",
-    "optimizer",
-    "random_state",
-    "threads",
-    "learning_rate",
-    "verbose",
-    "training_kwds",
-    "return_model",
-    "return_info",
-    "copy",
-)
 def dca(  # noqa: PLR0913
     adata: AnnData,
     mode: Literal["denoise", "latent"] = "denoise",

src/scanpy/external/pp/_harmony_integrate.py

@@ -6,7 +6,6 @@
 
 import numpy as np
 
-from ..._compat import old_positionals
 from ..._utils._doctests import doctest_needs
 
 if TYPE_CHECKING:
@@ -15,7 +14,6 @@
     from anndata import AnnData
 
 
-@old_positionals("basis", "adjusted_basis")
 @doctest_needs("harmonypy")
 def harmony_integrate(
     adata: AnnData,

src/scanpy/external/pp/_hashsolo.py

@@ -37,7 +37,6 @@
 import pandas as pd
 from scipy.stats import norm
 
-from ..._compat import old_positionals
 from ..._utils import check_nonnegative_integers
 from ..._utils._doctests import doctest_skip
 
@@ -292,9 +291,6 @@ def _calculate_bayes_rule(
     }
 
 
-@old_positionals(
-    "priors", "pre_existing_clusters", "number_of_noise_barcodes", "inplace"
-)
 @doctest_skip("Illustrative but not runnable doctest code")
 def hashsolo(
     adata: AnnData,

src/scanpy/external/pp/_scanorama_integrate.py

@@ -6,16 +6,12 @@
 
 import numpy as np
 
-from ..._compat import old_positionals
 from ..._utils._doctests import doctest_needs
 
 if TYPE_CHECKING:
     from anndata import AnnData
 
 
-@old_positionals(
-    "basis", "adjusted_basis", "knn", "sigma", "approx", "alpha", "batch_size"
-)
 @doctest_needs("scanorama")
 def scanorama_integrate(
     adata: AnnData,

src/scanpy/external/tl/_harmony_timeseries.py

@@ -8,14 +8,12 @@
 import pandas as pd
 
 from ... import logging as logg
-from ..._compat import old_positionals
 from ..._utils._doctests import doctest_needs
 
 if TYPE_CHECKING:
     from anndata import AnnData
 
 
-@old_positionals("n_neighbors", "n_components", "n_jobs", "copy")
 @doctest_needs("harmony")
 def harmony_timeseries(
     adata: AnnData,

src/scanpy/external/tl/_palantir.py

@@ -7,24 +7,12 @@
 import pandas as pd
 
 from ... import logging as logg
-from ..._compat import old_positionals
 from ..._utils._doctests import doctest_needs
 
 if TYPE_CHECKING:
     from anndata import AnnData
 
 
-@old_positionals(
-    "n_components",
-    "knn",
-    "alpha",
-    "use_adjacency_matrix",
-    "distances_key",
-    "n_eigs",
-    "impute_data",
-    "n_steps",
-    "copy",
-)
 @doctest_needs("palantir")
 def palantir(
     adata: AnnData,
@@ -254,16 +242,6 @@ def palantir(
     return adata if copy else None
 
 
-@old_positionals(
-    "ms_data",
-    "terminal_states",
-    "knn",
-    "num_waypoints",
-    "n_jobs",
-    "scale_components",
-    "use_early_cell_as_start",
-    "max_iterations",
-)
 def palantir_results(
     adata: AnnData,
     early_cell: str,

src/scanpy/external/tl/_phate.py

@@ -5,7 +5,6 @@
 from typing import TYPE_CHECKING
 
 from ... import logging as logg
-from ..._compat import old_positionals
 from ..._settings import settings
 from ..._utils._doctests import doctest_needs
 
@@ -17,21 +16,6 @@
     from ..._utils.random import _LegacyRandom
 
 
-@old_positionals(
-    "k",
-    "a",
-    "n_landmark",
-    "t",
-    "gamma",
-    "n_pca",
-    "knn_dist",
-    "mds_dist",
-    "mds",
-    "n_jobs",
-    "random_state",
-    "verbose",
-    "copy",
-)
 @doctest_needs("phate")
 def phate(  # noqa: PLR0913
     adata: AnnData,