update lisi to allow anndata write

Author: ghar1821

src/metrics/lisi/script.py

@@ -8,12 +8,15 @@
 # Note: this section is auto-generated by viash at runtime. To edit it, make changes
 # in config.vsh.yaml and then run `viash config inject config.vsh.yaml`.
 par = {
-    "input_unintegrated": "resources_test/.../unintegrated.h5ad",
-    "input_integrated_split1": "resources_test/.../integrated_split1.h5ad",
-    "input_integrated_split2": "resources_test/.../integrated_split2.h5ad",
-    "output": "output.h5ad",
+    "input_unintegrated": "resources_test/task_cyto_batch_integration/mouse_spleen_flow_cytometry_subset/unintegrated.h5ad",
+    "input_integrated_split1": "resources_test/task_cyto_batch_integration/mouse_spleen_flow_cytometry_subset/output_split1.h5ad",
+    "input_integrated_split2": "resources_test/task_cyto_batch_integration/mouse_spleen_flow_cytometry_subset/output_split2.h5ad",
+    "output": "resources_test/task_cyto_batch_integration/mouse_spleen_flow_cytometry_subset/output_lisi.h5ad",
+}
+meta = {
+    "name": "lisi",
+    "resources_dir": "src/utils",
 }
-meta = {"name": "lisi"}
 ## VIASH END
 
 sys.path.append(meta["resources_dir"])
@@ -22,6 +25,9 @@
     subset_markers_tocorrect,
 )
 
+# TODO: no idea why the new anndata >= 0.11 needs this even if we don't write anything to obs?
+ad.settings.allow_write_nullable_strings = True
+
 print("Reading input files", flush=True)
 input_unintegrated = ad.read_h5ad(par["input_unintegrated"])
 input_integrated_split1 = ad.read_h5ad(par["input_integrated_split1"])
@@ -64,6 +70,15 @@
 uns_metric_ids = ["iLisi", "cLisi"]
 uns_metric_values = [ilisi, clisi]
 
+print("iLisi split 1:", ilisi_s1, flush=True)
+print("iLisi split 2:", ilisi_s2, flush=True)
+print("cLisi split 1:", clisi_s1, flush=True)
+print("cLisi split 2:", clisi_s2, flush=True)
+print("Mean iLisi:", ilisi, flush=True)
+print("Mean cLisi:", clisi, flush=True)
+print("Metric IDs:", uns_metric_ids, flush=True)
+print("Metric values:", uns_metric_values, flush=True)
+
 print("Write output AnnData to file", flush=True)
 output = ad.AnnData(
     uns={