Adjust components check in no_integration_batch (#23)

* Adjust components check in no_integration_batch

* Style no_integration_batch script

src/control_methods/no_integration_batch/script.py

@@ -1,41 +1,49 @@
 import sys
-import scanpy as sc
+
 import numpy as np
+import scanpy as sc
 
 ## VIASH START
 
 par = {
-    'input_dataset': 'resources_test/task_batch_integration/cxg_immune_cell_atlas/dataset.h5ad',
-    'output': 'output.h5ad',
+    "input_dataset": "resources_test/task_batch_integration/cxg_immune_cell_atlas/dataset.h5ad",
+    "output": "output.h5ad",
 }
 
-meta = {
-    'functionality': 'foo',
-    'config': 'bar'
-}
+meta = {"functionality": "foo", "config": "bar"}
 
 ## VIASH END
 
 sys.path.append(meta["resources_dir"])
 from read_anndata_partial import read_anndata
 
+print(f"====== No integration (batch) (scanpy v{sc.__version__}) ======", flush=True)
 
-print('Read input_dataset', flush=True)
+print("\n>>> Reading input files...", flush=True)
+print(f"Input dataset H5AD file: '{par['input_dataset']}'", flush=True)
 adata = read_anndata(
-    par['input_dataset'],
-    X='layers/normalized',
-    obs='obs',
-    var='var',
-    uns='uns'
+    par["input_dataset"], X="layers/normalized", obs="obs", var="var", uns="uns"
 )
 adata.var["highly_variable"] = adata.var["hvg"]
+print(adata, flush=True)
 
-print("Process dataset", flush=True)
+print("\n>>> Calculating PCA by batch...", flush=True)
 adata.obsm["X_emb"] = np.zeros((adata.shape[0], 50), dtype=float)
 for batch in adata.obs["batch"].unique():
     batch_idx = adata.obs["batch"] == batch
-    n_comps = min(50, np.sum(batch_idx))
-    solver = "full" if n_comps == np.sum(batch_idx) else "arpack"
+
+    if np.sum(batch_idx) <= 50:
+        n_comps = np.sum(batch_idx) - 1
+        solver = "full"
+        print(
+            f"Batch '{batch}' has 50 or less cells.",
+            f"Using the 'full' solver with {n_comps} components for this batch.",
+            flush=True,
+        )
+    else:
+        n_comps = 50
+        solver = "arpack"
+
     adata.obsm["X_emb"][batch_idx, :n_comps] = sc.tl.pca(
         adata[batch_idx].copy(),
         n_comps=n_comps,
@@ -44,6 +52,11 @@
         copy=True,
     ).obsm["X_pca"]
 
-print("Store outputs", flush=True)
-adata.uns['method_id'] = meta['name']
-adata.write_h5ad(par['output'], compression='gzip')
+adata.uns["method_id"] = meta["name"]
+print(adata, flush=True)
+
+print("\n>>> Writing output to file...", flush=True)
+print(f"Output H5AD file: '{par['output']}'", flush=True)
+adata.write_h5ad(par["output"], compression="gzip")
+
+print("\n>>> Done!", flush=True)