Merge pull request #71 from dpeerlab/fix_tests

fix test req
dpeerlab · Oct 16, 2024 · 2ccf179 · 2ccf179
2 parents fb21342 + 0c34e1f
commit 2ccf179
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diff --git a/requirements.txt b/requirements.txt
@@ -1,9 +1,9 @@
 scanpy >= 1.10.0
 numpy >= 1.23.1
 anndata >= 0.10.6
-flax >= "0.8.2"
-optax >= "0.2.1"
-chex >= "0.1.81"
-tensorflow_probability >= "0.22.0"
-clu >= "0.0.11"
-tqdm >= "4.66.1"
+flax >= 0.8.2
+optax >= 0.2.1
+chex >= 0.1.81
+tensorflow_probability >= 0.22.0
+clu >= 0.0.11
+tqdm >= 4.66.1
diff --git a/scenvi/ENVI.py b/scenvi/ENVI.py
@@ -626,12 +626,12 @@ def latent_rep(self):
         :return: nothing, adds 'envi_latent' self.spatial_data.obsm and self.spatial_data.obsm
         """
 
-        self.spatial_data.obsm["envi_latent"] = self.encode(
+        self.spatial_data.obsm["envi_latent"] = np.asarray(self.encode(
             self.spatial_data.X, mode="spatial"
-        )
-        self.sc_data.obsm["envi_latent"] = self.encode(
+        ))
+        self.sc_data.obsm["envi_latent"] = np.asarray(self.encode(
             self.sc_data[:, self.spatial_data.var_names].X, mode="sc"
-        )
+        ))
 
     def impute_genes(self):
         """
@@ -657,9 +657,9 @@ def infer_niche_covet(self):
         :return: nothing, adds 'COVET_SQRT' and 'COVET' to self.sc_data.obsm
         """
 
-        self.sc_data.obsm["COVET_SQRT"] = self.decode_cov(
+        self.sc_data.obsm["COVET_SQRT"] = np.asarray(self.decode_cov(
             self.sc_data.obsm["envi_latent"]
-        )
+        ))
         self.sc_data.obsm["COVET"] = np.matmul(
             self.sc_data.obsm["COVET_SQRT"], self.sc_data.obsm["COVET_SQRT"]
         )