Merge pull request #251 from DendrouLab/sarah_scanpy_version

fix scanpy version

panpipes/python_scripts/plot_qc_spatial.py

@@ -144,7 +144,7 @@
 
     axs[2].set_title("Transcripts per FOV")
     sns.histplot(
-        spatial.obs.groupby("fov").sum()["total_counts"],
+        spatial.obs.groupby('fov')[['total_counts']].sum(),
         kde=False,
         ax=axs[2],
     )
@@ -160,8 +160,8 @@
     #plt.savefig("merfish_histo.png", dpi=300)
     plt.savefig(figdir + "/histograms."+sprefix +".png", dpi=300)  # Adjust dpi as needed
     plt.close()  # Close the figure to free up memory
-
-            
+     
+
 
 L.info("Done")
 

panpipes/python_scripts/run_cell2location.py

@@ -266,6 +266,8 @@
 cell2loc_plot_QC_reference(model_ref, figdir + "/QC_reference_reconstruction_accuracy.png", figdir + "/QC_reference_expression signatures_vs_avg_expression.png")
 
 # save model and update mudata
+if adata_sc.var.index.names[0] in adata_sc.var.columns: 
+	adata_sc.var.index.names = [None]
 mdata_singlecell.mod["rna"] = adata_sc
 mdata_singlecell.update()
 if save_models is True:
@@ -301,6 +303,8 @@
 
 
 # save model and update mudata
+if adata_st.var.index.names[0] in adata_st.var.columns: 
+	adata_st.var.index.names = [None]
 mdata_spatial.mod["spatial"] = adata_st
 mdata_spatial.update()
 if save_models is True: 

pyproject.toml

@@ -36,7 +36,7 @@ dependencies = [
     "pyyaml",
     "ruffus",
     "scanorama",
-    "scanpy>=1.9.1",
+    "scanpy",
     "leidenalg",
     "louvain",
     "scib",
@@ -62,6 +62,7 @@ spatial = [
     "jax==0.4.23",
     "jaxlib==0.4.23",
     "scvi-tools==1.0.4",
+    "scipy==1.12.0",
     "squidpy",
     "cell2location",
     "tangram-sc"