Override VariantData.from_tree_sequence

Fixes #915

Author: hyanwong

tests/test_variantdata.py

@@ -757,3 +757,9 @@ def test_empty_alleles_not_at_end(self, tmp_path):
         samples = tsinfer.VariantData(path, "variant_ancestral_allele")
         with pytest.raises(ValueError, match="Empty alleles must be at the end"):
             tsinfer.infer(samples)
+
+    def test_unimplemented_from_tree_sequence(self):
+        # NB we should reimplement something like this functionality.
+        # Requires e.g. https://github.com/tskit-dev/tsinfer/issues/924
+        with pytest.raises(NotImplementedError):
+            tsinfer.VariantData.from_tree_sequence(None)

tsinfer/formats.py

@@ -2785,6 +2785,10 @@ def _all_haplotypes(self, sites=None, recode_ancestral=None, samples_slice=None)
                 sample_index += 1
         assert sample_index == samples_slice[1]
 
+    @classmethod
+    def from_tree_sequence(*args, **kwargs):
+        raise NotImplementedError("This method is not implemented for VariantData")
+
 
 @attr.s(order=False, eq=False)
 class Ancestor: