Remove plot test

Author: LLehner

tests/_images/Niches_cellcharter_niche.png

@@ -98,81 +98,3 @@ def test_niche_calc_utag(adata_seqfish: AnnData):
     else:
         raise AssertionError
 
-
-def test_niche_calc_cellcharter(adata_seqfish: AnnData):
-    """Check whether niche calculation using CellCharter approach works as intended."""
-
-    spatial_neighbors(adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS)
-    calculate_niche(adata_seqfish, groups=GROUPS, flavor="cellcharter", distance=3, n_components=5)
-    niches = adata_seqfish.obs["cellcharter_niche"]
-
-    assert niches.nunique() == 5
-    assert niches.isna().sum() == 0
-
-    adj = adata_seqfish.obsp[SPATIAL_CONNECTIVITIES_KEY]
-    adj_hop = _setdiag(adj, value=0)
-    assert adj_hop.shape == adj.shape
-    assert issparse(adj_hop)
-    assert isinstance(adj_hop, scipy.sparse.csr_matrix)
-
-    adj_visited = _setdiag(adj.copy(), 1)  # Track visited neighbors
-    adj_hop, adj_visited = _hop(adj_hop, adj, adj_visited)
-    assert adj_hop.shape == adj.shape
-    assert adj_hop.shape == adj_visited.shape
-
-    assert np.array(np.sum(adj, axis=1)).squeeze().max() == N_NEIGHBORS
-    adj_hop_norm = _normalize(adj_hop)
-    assert adj_hop_norm.shape == adj.shape
-
-    mean_aggr_matrix = _aggregate(adata_seqfish, adj_hop_norm, "mean")
-    assert mean_aggr_matrix.shape == adata_seqfish.X.shape
-    var_aggr_matrix = _aggregate(adata_seqfish, adj_hop_norm, "variance")
-    assert var_aggr_matrix.shape == adata_seqfish.X.shape
-
-    # TODO: add test for GMM
-
-
-class TestNiches(PlotTester, metaclass=PlotTesterMeta):
-    def test_plot_utag_niche(self, adata_seqfish: AnnData):
-        spatial_neighbors(adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS)
-        calculate_niche(adata_seqfish, flavor="utag", n_neighbors=N_NEIGHBORS, resolutions=0.5)
-
-        sq.pl.spatial_scatter(
-            adata_seqfish,
-            color="utag_niche_res=0.5",
-            shape=None,
-        )
-
-    def test_plot_neighborhood_niche(self, adata_seqfish: AnnData):
-        spatial_neighbors(adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS)
-
-        calculate_niche(
-            adata_seqfish,
-            groups=GROUPS,
-            flavor="neighborhood",
-            n_neighbors=N_NEIGHBORS,
-            resolutions=0.5,
-            min_niche_size=100,
-        )
-
-        sq.pl.spatial_scatter(
-            adata_seqfish,
-            color="nhood_niche_res=0.5",
-            shape=None,
-        )
-
-    def test_plot_cellcharter_niche(self, adata_seqfish: AnnData):
-        spatial_neighbors(adata_seqfish, coord_type="generic", delaunay=False, n_neighs=N_NEIGHBORS)
-        calculate_niche(
-            adata_seqfish,
-            groups=GROUPS,
-            flavor="cellcharter",
-            distance=3,
-            n_components=5,
-        )
-
-        sq.pl.spatial_scatter(
-            adata_seqfish,
-            color="cellcharter_niche",
-            shape=None,
-        )