Remove external tests and deprecate sc.external

pyproject.toml

@@ -107,10 +107,7 @@ test-full = [
     "zappy",
     # additional tested algorithms
     "scanpy[louvain]",
-    "scanpy[magic]",
     "scanpy[skmisc]",
-    "scanpy[harmony]",
-    "scanpy[scanorama]",
     "scanpy[dask-ml]",
 ]
 doc = [
@@ -142,11 +139,7 @@ dev = [
 paga = [ "igraph" ]
 louvain = [ "igraph", "louvain>=0.6.0,!=0.6.2" ] # Louvain community detection
 leiden = [ "igraph>=0.10", "leidenalg>=0.9.0" ]  # Leiden community detection
-bbknn = [ "bbknn" ]                              # Batch balanced KNN (batch correction)
-magic = [ "magic-impute>=2.0" ]                  # MAGIC imputation method
 skmisc = [ "scikit-misc>=0.1.3" ]                # highly_variable_genes method 'seurat_v3'
-harmony = [ "harmonypy" ]                        # Harmony dataset integration
-scanorama = [ "scanorama" ]                      # Scanorama dataset integration
 scrublet = [ "scikit-image>=0.20" ]              # Doublet detection with automatic thresholds
 # Acceleration
 rapids = [ "cudf>=0.9", "cuml>=0.9", "cugraph>=0.9" ] # GPU accelerated calculation of neighbors

src/scanpy/__init__.py

@@ -45,7 +45,7 @@
     )
 from anndata import AnnData, concat
 
-from . import datasets, experimental, external, get, logging, metrics, queries
+from . import datasets, experimental, get, logging, metrics, queries
 from . import plotting as pl
 from . import preprocessing as pp
 from . import tools as tl
@@ -67,7 +67,6 @@
     "concat",
     "datasets",
     "experimental",
-    "external",
     "get",
     "logging",
     "metrics",
@@ -91,3 +90,12 @@
     "tl",
     "write",
 ]
+
+
+def __getattr__(name: str) -> object:
+    if name == "external":
+        from . import external
+
+        return external
+
+    raise AttributeError(name)

src/scanpy/external/__init__.py

@@ -3,11 +3,16 @@
 from __future__ import annotations
 
 import sys
+import warnings
 
 from .. import _utils
 from . import exporting, pl, pp, tl
 
+__all__: list[str] = ["exporting", "pl", "pp", "tl"]
+
 _utils.annotate_doc_types(sys.modules[__name__], "scanpy")
-del sys, _utils
 
-__all__ = ["exporting", "pl", "pp", "tl"]
+msg = "The `scanpy.external` module is deprecated and will be removed in a future version."
+warnings.warn(msg, DeprecationWarning, stacklevel=2)
+
+del msg, sys, _utils, warnings

tests/test_package_structure.py

@@ -27,10 +27,6 @@
     "sc.tl",
     "sc.pl",
     "sc.experimental.pp",
-    "sc.external.pp",
-    "sc.external.tl",
-    "sc.external.pl",
-    "sc.external.exporting",
     "sc.get",
     "sc.logging",
     # "sc.neighbors",  # Not documented
@@ -54,11 +50,19 @@
 
 
 @pytest.mark.xfail(reason="TODO: unclear if we want this to totally match, let’s see")
+@pytest.mark.filterwarnings("ignore::DeprecationWarning:scanpy.external")
 def test_descend_classes_and_funcs():
     funcs = set(descend_classes_and_funcs(scanpy, "scanpy"))
     assert {p.values[0] for p in api_functions} == funcs
 
 
+def test_external_is_deprecated() -> None:
+    with pytest.warns(DeprecationWarning, match=r"scanpy.external"):
+        import scanpy.external
+
+        importlib.reload(scanpy.external)
+
+
 @pytest.mark.filterwarnings("error::FutureWarning:.*Import anndata.*")
 def test_import_future_anndata_import_warning():
     import scanpy