Deprecate Napari (#738)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Giovanni Palla <25887487+giovp@users.noreply.github.com>
Co-authored-by: giovp <giov.pll@gmail.com>

docs/release/notes-1.3.1.rst

@@ -0,0 +1,17 @@
+Squidpy 1.3.1 (2023-10-09)
+==========================
+
+Miscellaneous
+-------------
+
+- Deprecated napari.
+  `@LLehner <https://github.com/LLehner>`__
+  `#738 <https://github.com/scverse/squidpy/pull/738>`__
+
+- Various fixes.
+  `@giovp <https://github.com/giovp>`__
+  `#756 <https://github.com/scverse/squidpy/pull/756>`__
+
+- Add cruft.json to comply with scverse cookiecutter template.
+  `@LLehner <https://github.com/LLehner>`__
+  `#756 <https://github.com/scverse/squidpy/pull/747>`__

src/squidpy/_utils.py

@@ -1,6 +1,9 @@
 """Spatial tools general utility functions."""
 from __future__ import annotations
 
+import functools
+import inspect
+import warnings
 from contextlib import contextmanager
 from enum import Enum
 from multiprocessing import Manager, cpu_count
@@ -262,3 +265,70 @@ def verbosity(level: int) -> Generator[None, None, None]:
         yield
     finally:
         sc.settings.verbosity = verbosity
+
+
+string_types = (bytes, str)
+
+
+def deprecated(reason: str) -> Any:
+    """
+    This is a decorator which can be used to mark functions
+    as deprecated. It will result in a warning being emitted
+    when the function is used.
+    """
+
+    if isinstance(reason, string_types):
+        # The @deprecated is used with a 'reason'.
+        #
+        # .. code-block:: python
+        #
+        #    @deprecated("please, use another function")
+        #    def old_function(x, y):
+        #      pass
+
+        def decorator(func1: Callable[..., Any]) -> Callable[..., Any]:
+            if inspect.isclass(func1):
+                fmt1 = "Call to deprecated class {name} ({reason})."
+            else:
+                fmt1 = "Call to deprecated function {name} ({reason})."
+
+            @functools.wraps(func1)
+            def new_func1(*args: Any, **kwargs: Any) -> Any:
+                warnings.simplefilter("always", DeprecationWarning)
+                warnings.warn(
+                    fmt1.format(name=func1.__name__, reason=reason), category=DeprecationWarning, stacklevel=2
+                )
+                warnings.simplefilter("default", DeprecationWarning)
+                return func1(*args, **kwargs)
+
+            return new_func1
+
+        return decorator
+
+    elif inspect.isclass(reason) or inspect.isfunction(reason):
+        # The @deprecated is used without any 'reason'.
+        #
+        # .. code-block:: python
+        #
+        #    @deprecated
+        #    def old_function(x, y):
+        #      pass
+
+        func2 = reason
+
+        if inspect.isclass(func2):
+            fmt2 = "Call to deprecated class {name}."
+        else:
+            fmt2 = "Call to deprecated function {name}."
+
+        @functools.wraps(func2)
+        def new_func2(*args: Any, **kwargs: Any) -> Any:
+            warnings.simplefilter("always", DeprecationWarning)
+            warnings.warn(fmt2.format(name=func2.__name__), category=DeprecationWarning, stacklevel=2)
+            warnings.simplefilter("default", DeprecationWarning)
+            return func2(*args, **kwargs)
+
+        return new_func2
+
+    else:
+        raise TypeError(repr(type(reason)))

src/squidpy/im/_container.py

@@ -1114,7 +1114,7 @@ def interactive(
         """
         from squidpy.pl import Interactive  # type: ignore[attr-defined]
 
-        return Interactive(  # type: ignore[return-value]
+        return Interactive(  # type: ignore[no-any-return]
             img=self,
             adata=adata,
             spatial_key=spatial_key,

src/squidpy/pl/_interactive/_widgets.py

@@ -6,6 +6,7 @@
 
 import numpy as np
 import pandas as pd
+from deprecated import deprecated
 from napari.layers import Points
 from PyQt5 import QtCore, QtWidgets
 from PyQt5.QtCore import Qt
@@ -341,6 +342,7 @@ def update_color(self) -> None:
         self._colorbar._colorbar._colorbar._update()
 
 
+@deprecated
 class RangeSlider(QRangeSlider):
     def __init__(self, *args: Any, layer: Points, colorbar: CBarWidget, **kwargs: Any):
         super().__init__(*args, **kwargs)

src/squidpy/pl/_interactive/interactive.py

@@ -10,7 +10,7 @@
 from scanpy import logging as logg
 
 from squidpy._docs import d
-from squidpy._utils import NDArrayA
+from squidpy._utils import NDArrayA, deprecated
 from squidpy.im import ImageContainer  # type: ignore[attr-defined]
 from squidpy.pl._utils import save_fig
 
@@ -36,6 +36,9 @@ class Interactive:
     %(_interactive.parameters)s
     """
 
+    @deprecated(
+        reason="The squidpy napari plugin is deprecated, please use https://github.com/scverse/napari-spatialdata",
+    )
     def __init__(self, img: ImageContainer, adata: AnnData, **kwargs: Any):
         if _error is not None:
             raise ImportError(f"Unable to import the interactive viewer. Reason `{_error}`.")