Debug test

docs/tutorial.md

@@ -203,10 +203,11 @@ Python to simulate some data under the coalescent with recombination, using
 
 import builtins
 import sys
-from Bio import bgzf
+import os
 import subprocess
-import numpy as np
 
+from Bio import bgzf
+import numpy as np
 import msprime
 import tsinfer
 
@@ -238,10 +239,9 @@ vcf_name = f"{name}.vcf.gz"
 with bgzf.open(vcf_name, "wt") as f:
     ts.write_vcf(f)
 subprocess.run(["tabix", vcf_name])
-ret = subprocess.run(
-    "python -m bio2zarr vcf2zarr convert --force".split() + [vcf_name, f"{name}.vcz"],
-    stderr = subprocess.DEVNULL if name == "notebook-simulation" else None
-)
+!python -m bio2zarr vcf2zarr convert --force {vcf_name} {name}.vcz
+assert os.path.exists(f"{name}.vcz")
+
 if ret.returncode == 0:
     print(f"Converted to {name}.vcz")
 ```
@@ -308,6 +308,7 @@ In practice this means we can keep such files lying around without taking up too
 Once we have our `.vcz` file created, running the inference is straightforward.
 
 ```{code-cell} ipython3
+import os
 # Infer & save a ts from the notebook simulation.
 ancestral_alleles = np.load(f"{name}-AA.npy")
 vdata = tsinfer.VariantData(f"{name}.vcz", ancestral_alleles)