fix doctest imports

Author: nebfield

pgscatalog.core/src/pgscatalog/core/lib/_normalise.py

@@ -90,6 +90,7 @@ def check_duplicates(variants):
 def drop_hla(variants):
     """Drop HLA alleles from a list of ScoreVariants
 
+    >>> from .scorevariant import ScoreVariant
     >>> variant = ScoreVariant(**{"effect_allele": "A", "effect_weight": 5, "accession": "test", "row_nr": 0, "chr_name": "1", "chr_position": 1})
     >>> list(drop_hla([variant])) # doctest: +ELLIPSIS
     [ScoreVariant(..., effect_allele=Allele(allele='A', is_snp=True), ...
@@ -116,6 +117,7 @@ def drop_hla(variants):
 def assign_other_allele(variants):
     """Check if there's more than one possible other allele, remove if true
 
+    >>> from .scorevariant import ScoreVariant
     >>> variant = ScoreVariant(**{"chr_position": 1, "rsID": None, "chr_name": "1", "effect_allele": "A", "effect_weight": 5, "other_allele": "A", "row_nr": 0, "accession": "test"})
     >>> list(assign_other_allele([variant]))[0] # doctest: +ELLIPSIS
     ScoreVariant(..., effect_allele=Allele(allele='A', is_snp=True), other_allele=Allele(allele='A', is_snp=True), ...)
@@ -142,6 +144,7 @@ def remap_harmonised(variants, harmonised, target_build):
     In this case chr_name, chr_position, and other allele are missing.
     Perhaps authors submitted rsID and effect allele originally:
 
+    >>> from .scorevariant import ScoreVariant
     >>> variant = ScoreVariant(**{"chr_position": 1, "rsID": None, "chr_name": "2", "effect_allele": "A", "effect_weight": 5, "accession": "test", "hm_chr": "1", "hm_pos": 100, "hm_rsID": "testrsid", "hm_inferOtherAllele": "A", "row_nr": 0})
     >>> variant
     ScoreVariant(..., effect_allele=Allele(allele='A', is_snp=True), other_allele=None, ...
@@ -171,6 +174,7 @@ def check_effect_allele(variants, drop_missing=False):
     """
     Odd effect allele:
 
+    >>> from .scorevariant import ScoreVariant
     >>> variant = ScoreVariant(**{"effect_allele": "Z", "effect_weight": 5, "accession": "test", "row_nr": 0, "chr_name": "1", "chr_position": 1})
     >>> list(check_effect_allele([variant], drop_missing=True)) # doctest: +ELLIPSIS
     []