fix: remove hail test context

Author: ameynert

divref/divref/main.py

@@ -8,6 +8,7 @@
 from divref.tools.compute_haplotype_statistics import compute_haplotype_statistics
 from divref.tools.compute_haplotypes import compute_haplotypes
 from divref.tools.compute_variation_ratios import compute_variation_ratios
+from divref.tools.create_fasta_and_index import create_fasta_and_index
 from divref.tools.create_gnomad_sites_vcf import create_gnomad_sites_vcf
 from divref.tools.extract_gnomad_afs import extract_gnomad_afs
 from divref.tools.extract_sample_metadata import extract_sample_metadata
@@ -17,6 +18,7 @@
     compute_haplotypes,
     compute_haplotype_statistics,
     compute_variation_ratios,
+    create_fasta_and_index,
     create_gnomad_sites_vcf,
     extract_gnomad_afs,
     extract_sample_metadata,

divref/divref/tools/create_fasta_and_index.py

@@ -7,7 +7,7 @@
 import hail as hl
 import polars
 
-from divref.haplotype import HailPath
+from divref.alias import HailPath
 from divref.haplotype import get_haplo_sequence
 from divref.haplotype import split_haplotypes
 

divref/tests/tools/test_create_fasta_and_index.py

@@ -3,11 +3,9 @@
 from typing import Any
 from unittest.mock import patch
 
-import pytest
+import hail as hl
 
-hl = pytest.importorskip("hail")
-
-from divref.haplotype import get_haplo_sequence  # noqa: E402
+from divref.haplotype import get_haplo_sequence
 
 
 def _create_variant(contig: str, position: int, ref: str, alt: str) -> Any:
@@ -55,7 +53,6 @@ def mock_get_sequence(
     return mock_get_sequence
 
 
-@pytest.mark.skip(reason="Requires a running Hail/Spark JVM context")
 def test_get_haplo_sequence_edge_cases() -> None:
     """Test get_haplo_sequence with SNPs, insertions, and deletions."""
     reference = "01234567891"