Fixup documentation and add some info logging

Author: jeromekelleher

bio2zarr/tskit.py

@@ -28,7 +28,12 @@ def __init__(
         else:
             # input 'ts' is a path.
             self._path = ts
+            logger.info(f"Loading from {ts}")
             self.ts = tskit.load(ts)
+        logger.info(
+            f"Input has {self.ts.num_individuals} individuals and "
+            f"{self.ts.num_sites} sites"
+        )
 
         self.contig_id = contig_id if contig_id is not None else "1"
         self.isolated_as_missing = isolated_as_missing
@@ -42,6 +47,7 @@ def __init__(
         sample_ids = model_mapping.individuals_name
 
         self._num_samples = individuals_nodes.shape[0]
+        logger.info(f"Converting for {self._num_samples} samples")
         if self._num_samples < 1:
             raise ValueError("individuals_nodes must have at least one sample")
         self.max_ploidy = individuals_nodes.shape[1]
@@ -100,6 +106,7 @@ def iter_field(self, field_name, shape, start, stop):
     def iter_alleles_and_genotypes(self, start, stop, shape, num_alleles):
         # All genotypes in tskit are considered phased
         phased = np.ones(shape[:-1], dtype=bool)
+        logger.debug(f"Getting genotpes start={start} stop={stop}")
 
         for variant in self.ts.variants(
             isolated_as_missing=self.isolated_as_missing,

docs/tskit2zarr/python_api.md

@@ -12,13 +12,14 @@ This will convert the [tskit](https://tskit.dev) tree sequence stored
 at ``ts_path`` to VCF Zarr stored at ``vcz_path`` using 8 worker processes.
 The details of how we map from the
 tskit {ref}`tskit:sec_data_model` to VCF Zarr are taken care of by
-TreeSequence.map_to_vcf_model method, which is called with no
+{meth}`tskit.TreeSequence.map_to_vcf_model`
+method, which is called with no
 parameters by default if the ``model_mapping`` parameter to
 {func}`~bio2zarr.tskit.convert` is not specified.
 
 For more control over the properties of the output, for example
 to pick a specific subset of individuals, you can use
-TreeSequence.map_to_vcf_model
+{meth}`~tskit.TreeSequence.map_to_vcf_model`
 to return the required mapping:
 
 ```python