From 142e6d02deeb14e5c71a7ae7d7dcced8cf73da97 Mon Sep 17 00:00:00 2001
From: Philipp A <flying-sheep@web.de>
Date: Mon, 23 Dec 2019 17:20:02 +0100
Subject: [PATCH] Deprecate square matrix slicing in .uns

---
 anndata/_core/anndata.py   | 15 +++++++++++++--
 anndata/tests/test_base.py |  5 ++++-
 docs/release_notes.rst     |  1 +
 3 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/anndata/_core/anndata.py b/anndata/_core/anndata.py
index 44bd077ba..ee3f6b166 100644
--- a/anndata/_core/anndata.py
+++ b/anndata/_core/anndata.py
@@ -1097,7 +1097,10 @@ def strings_to_categoricals(self, df: Optional[pd.DataFrame] = None):
 
     _sanitize = strings_to_categoricals  # backwards compat
 
-    def _slice_uns_sparse_matrices_inplace(self, uns: MutableMapping, oidx: Index1D):
+    def _slice_uns_sparse_matrices_inplace(
+        self, uns: MutableMapping, oidx: Index1D, keys: Tuple[str, ...] = ()
+    ):
+        # TODO: remove
         # slice sparse spatrices of n_obs × n_obs in self.uns
         if not (
             isinstance(oidx, slice)
@@ -1108,11 +1111,19 @@ def _slice_uns_sparse_matrices_inplace(self, uns: MutableMapping, oidx: Index1D)
             for k, v in uns.items():
                 # treat nested dicts
                 if isinstance(v, Mapping):
-                    self._slice_uns_sparse_matrices_inplace(v, oidx)
+                    self._slice_uns_sparse_matrices_inplace(v, oidx, (*keys, k))
                 if isinstance(v, sparse.spmatrix) and v.shape == (
                     self.n_obs,
                     self.n_obs,
                 ):
+                    path = "".join(f"['{key}']" for key in (*keys, k))
+                    warnings.warn(
+                        f"During AnnData slicing, found matrix at .obs{path} "
+                        "that happens to be dimensioned at n_obs×n_obs "
+                        f"({self.n_obs}×{self.n_obs}). "
+                        "This slicing behavior will soon go away.",
+                        DeprecationWarning,
+                    )
                     uns[k] = v.tocsc()[:, oidx].tocsr()[oidx, :]
 
     def _inplace_subset_var(self, index: Index1D):
diff --git a/anndata/tests/test_base.py b/anndata/tests/test_base.py
index b01d74907..fcdd8396f 100644
--- a/anndata/tests/test_base.py
+++ b/anndata/tests/test_base.py
@@ -235,7 +235,10 @@ def test_slicing_graphs():
         np.array([[1, 2], [3, 4], [5, 6]]),
         uns=dict(neighbors=dict(connectivities=sp.csr_matrix(np.ones((3, 3))))),
     )
-    adata_sub = adata[[0, 1], :]
+    with pytest.warns(
+        DeprecationWarning, match=r".obs\['neighbors'\]\['connectivities'\] .*(3×3)"
+    ):
+        adata_sub = adata[[0, 1], :]
     assert adata_sub.uns["neighbors"]["connectivities"].shape[0] == 2
     assert adata.uns["neighbors"]["connectivities"].shape[0] == 3
     assert adata_sub.copy().uns["neighbors"]["connectivities"].shape[0] == 2
diff --git a/docs/release_notes.rst b/docs/release_notes.rst
index 4e64c6d81..91dd9aaa1 100644
--- a/docs/release_notes.rst
+++ b/docs/release_notes.rst
@@ -10,6 +10,7 @@
    - :attr:`~anndata.AnnData.filename` and :attr:`~anndata.AnnData.isbacked` will be unified under a new name.
    - The types of :attr:`~anndata.AnnData.raw`, :attr:`~anndata.AnnData.layers`, :attr:`~anndata.AnnData.obsm`,
      :attr:`~anndata.AnnData.varm`, :attr:`~anndata.AnnData.obsp` and :attr:`~anndata.AnnData.varp` will be exported.
+   - Square matrices in :attr:`~anndata.AnnData.uns` will no longer be sliced (use `.{obs,var}p` instead).
 
 
 0.7rc1 :small:`December 23, 2019`