From f11b6ba93edbdd763acd824cb176cb64a9a63e39 Mon Sep 17 00:00:00 2001 From: "Philipp A." Date: Thu, 21 Nov 2024 14:04:06 +0100 Subject: [PATCH 1/2] Use deprecation decorator --- pyproject.toml | 1 + src/scanpy/_compat.py | 13 ++++++++++ src/scanpy/plotting/_preprocessing.py | 3 ++- .../_deprecated/highly_variable_genes.py | 24 +++++++++---------- src/scanpy/preprocessing/_simple.py | 21 ++++++++-------- 5 files changed, 39 insertions(+), 23 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index cfb7ffd28a..324c4c4262 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -66,6 +66,7 @@ dependencies = [ "packaging>=21.3", "session-info", "legacy-api-wrap>=1.4", # for positional API deprecations + "typing-extensions; python_version < '3.13'", ] dynamic = ["version"] diff --git a/src/scanpy/_compat.py b/src/scanpy/_compat.py index dca6c84c4e..b97b1a8603 100644 --- a/src/scanpy/_compat.py +++ b/src/scanpy/_compat.py @@ -48,6 +48,10 @@ class ZappyArray: "fullname", "pkg_metadata", "pkg_version", + "old_positionals", + "deprecated", + "njit", + "_numba_threading_layer", ] @@ -102,6 +106,15 @@ def old_positionals(*old_positionals: str): return lambda func: func +if sys.version_info >= (3, 13): + from warnings import deprecated as _deprecated +else: + from typing_extensions import deprecated as _deprecated + + +deprecated = partial(_deprecated, category=FutureWarning) + + @overload def njit(fn: Callable[P, R], /) -> Callable[P, R]: ... @overload diff --git a/src/scanpy/plotting/_preprocessing.py b/src/scanpy/plotting/_preprocessing.py index e6c7808be1..b51688082e 100644 --- a/src/scanpy/plotting/_preprocessing.py +++ b/src/scanpy/plotting/_preprocessing.py @@ -6,7 +6,7 @@ from matplotlib import pyplot as plt from matplotlib import rcParams -from .._compat import old_positionals +from .._compat import deprecated, old_positionals from .._settings import settings from . import _utils @@ -103,6 +103,7 @@ def highly_variable_genes( # backwards compat +@deprecated("Use sc.pl.highly_variable_genes instead") @old_positionals("log", "show", "save") def filter_genes_dispersion( result: np.recarray, diff --git a/src/scanpy/preprocessing/_deprecated/highly_variable_genes.py b/src/scanpy/preprocessing/_deprecated/highly_variable_genes.py index f2c3ce971b..27e8f1f846 100644 --- a/src/scanpy/preprocessing/_deprecated/highly_variable_genes.py +++ b/src/scanpy/preprocessing/_deprecated/highly_variable_genes.py @@ -9,7 +9,7 @@ from scipy.sparse import issparse from ... import logging as logg -from ..._compat import old_positionals +from ..._compat import deprecated, old_positionals from .._distributed import materialize_as_ndarray from .._utils import _get_mean_var @@ -19,6 +19,7 @@ from scipy.sparse import spmatrix +@deprecated("Use sc.pp.highly_variable_genes instead") @old_positionals( "flavor", "min_disp", @@ -48,18 +49,17 @@ def filter_genes_dispersion( """\ Extract highly variable genes :cite:p:`Satija2015,Zheng2017`. - .. warning:: - .. deprecated:: 1.3.6 - Use :func:`~scanpy.pp.highly_variable_genes` - instead. The new function is equivalent to the present - function, except that + .. deprecated:: 1.3.6 - * the new function always expects logarithmized data - * `subset=False` in the new function, it suffices to - merely annotate the genes, tools like `pp.pca` will - detect the annotation - * you can now call: `sc.pl.highly_variable_genes(adata)` - * `copy` is replaced by `inplace` + Use :func:`~scanpy.pp.highly_variable_genes` instead. + The new function is equivalent to the present function, except that + + * the new function always expects logarithmized data + * `subset=False` in the new function, it suffices to + merely annotate the genes, tools like `pp.pca` will + detect the annotation + * you can now call: `sc.pl.highly_variable_genes(adata)` + * `copy` is replaced by `inplace` If trying out parameters, pass the data matrix instead of AnnData. diff --git a/src/scanpy/preprocessing/_simple.py b/src/scanpy/preprocessing/_simple.py index 01936414a5..eaf9648690 100644 --- a/src/scanpy/preprocessing/_simple.py +++ b/src/scanpy/preprocessing/_simple.py @@ -18,7 +18,7 @@ from sklearn.utils import check_array, sparsefuncs from .. import logging as logg -from .._compat import njit, old_positionals +from .._compat import deprecated, njit, old_positionals from .._settings import settings as sett from .._utils import ( _check_array_function_arguments, @@ -474,6 +474,7 @@ def sqrt( return X.sqrt() +@deprecated("Use sc.pp.normalize_total instead") @old_positionals( "counts_per_cell_after", "counts_per_cell", @@ -497,16 +498,16 @@ def normalize_per_cell( """\ Normalize total counts per cell. - .. warning:: - .. deprecated:: 1.3.7 - Use :func:`~scanpy.pp.normalize_total` instead. - The new function is equivalent to the present - function, except that + .. deprecated:: 1.3.7 - * the new function doesn't filter cells based on `min_counts`, - use :func:`~scanpy.pp.filter_cells` if filtering is needed. - * some arguments were renamed - * `copy` is replaced by `inplace` + Use :func:`~scanpy.pp.normalize_total` instead. + The new function is equivalent to the present + function, except that + + * the new function doesn't filter cells based on `min_counts`, + use :func:`~scanpy.pp.filter_cells` if filtering is needed. + * some arguments were renamed + * `copy` is replaced by `inplace` Normalize each cell by total counts over all genes, so that every cell has the same total count after normalization. From 735f00aaa8622fcc3c3c3fff872088d9f060b13c Mon Sep 17 00:00:00 2001 From: "Philipp A." Date: Thu, 21 Nov 2024 14:15:09 +0100 Subject: [PATCH 2/2] relnote --- docs/release-notes/3380.bugfix.md | 1 + 1 file changed, 1 insertion(+) create mode 100644 docs/release-notes/3380.bugfix.md diff --git a/docs/release-notes/3380.bugfix.md b/docs/release-notes/3380.bugfix.md new file mode 100644 index 0000000000..633ce346af --- /dev/null +++ b/docs/release-notes/3380.bugfix.md @@ -0,0 +1 @@ +Raise {exc}`FutureWarning` when calling deprecated {mod}`scanpy.pp` functions {smaller}`P Angerer`