doctest fix

numpy 2.0 was different between local/action

repo_utils/run_doctests.py

@@ -33,4 +33,5 @@ def tester(module):
 fails += tester(msatovcf)
 fails += tester(af_calc)
 
+os.remove("log.txt")
 sys.exit(fails)

truvari/annotations/af_calc.py

@@ -157,7 +157,7 @@ def allele_freq_annos(entry, samples=None):
         >>> import pysam
         >>> v = pysam.VariantFile('repo_utils/test_files/variants/multi.vcf.gz')
         >>> truvari.allele_freq_annos(next(v))
-        {'AF': 0.5, 'MAF': 0.5, 'ExcHet': 1.0, 'HWE': 1.0, 'MAC': 1, 'AC': [1, 1], 'AN': 2, 'N_HEMI': 0, 'N_HOMREF': 0, 'N_HET': 1, 'N_HOMALT': 0, 'N_MISS': 2}
+        {'AF': 0.5, 'MAF': 0.5, 'ExcHet': np.float64(1.0), 'HWE': np.float64(1.0), 'MAC': 1, 'AC': [1, 1], 'AN': 2, 'N_HEMI': 0, 'N_HOMREF': 0, 'N_HET': 1, 'N_HOMALT': 0, 'N_MISS': 2}
     """
     if samples is None:
         samples = list(entry.samples.keys())

truvari/msatovcf.py

@@ -64,8 +64,7 @@ def aln_to_vars(chrom, start_pos, ref_seq, alt_seq, anchor_base):
 
         if ref_base == alt_base:  # No variant
             if cur_variant and is_ref:  # back to matching reference
-                for variant in decompose_variant(cur_variant):
-                    yield variant
+                yield from decompose_variant(cur_variant)
                 cur_variant = []
         else:
             if not cur_variant:
@@ -80,8 +79,7 @@ def aln_to_vars(chrom, start_pos, ref_seq, alt_seq, anchor_base):
             anchor_base = ref_base
     # End Zipping
     if cur_variant:
-        for variant in decompose_variant(cur_variant):
-            yield variant
+        yield from decompose_variant(cur_variant)
 
 def msa_to_vars(msa, chrom, ref_seq=None, start_pos=0, abs_anchor_base='N'):
     """

truvari/utils.py

@@ -336,8 +336,7 @@ def gz_hdlr(fn):
 
     def fh_hdlr(fn):
         with open(fn) as fh:
-            for line in fh:
-                yield line
+            yield from fh
 
     if in_fn.endswith('.gz'):
         return gz_hdlr(in_fn)