print lint rule (#791)

Author: bpblanken

pyproject.toml

@@ -41,7 +41,6 @@ ignore = [
     "FBT",   # flake-boolean-trap... disallows boolean args to functions... fixing this code will require refactors.
     "ANN",   # flake8-annotations is for typed code
     "DJ",    # django specific
-    "T20",   # forbids print, we print quite a bit
     "PYI",   # pyi is typing stub files
     "PT",    # pytest specific
     "PTH",   # pathlib is preferred, but we're not using it yet

v03_pipeline/bin/write_cached_reference_dataset_query_ht.py

@@ -2,6 +2,10 @@
 
 import hail as hl
 
+from v03_pipeline.lib.logger import get_logger
+
+logger = get_logger(__name__)
+
 
 class MatrixTableSampleSetError(Exception):
     def __init__(self, message, missing_samples):
@@ -42,15 +46,15 @@ def remap_sample_ids(
             f'All callset sample IDs:{mt.s.collect()}'
         )
         if ignore_missing_samples_when_remapping:
-            print(message)
+            logger.info(message)
         else:
             raise MatrixTableSampleSetError(message, missing_samples)
 
     mt = mt.annotate_cols(**project_remap_ht[mt.s])
     remap_expr = hl.if_else(hl.is_missing(mt.seqr_id), mt.s, mt.seqr_id)
     mt = mt.annotate_cols(seqr_id=remap_expr, vcf_id=mt.s)
     mt = mt.key_cols_by(s=mt.seqr_id)
-    print(f'Remapped {remap_count} sample ids...')
+    logger.info(f'Remapped {remap_count} sample ids...')
     return mt
 
 
@@ -77,9 +81,9 @@ def subset_samples(
         if (
             subset_count > anti_join_ht_count
         ) and ignore_missing_samples_when_subsetting:
-            print(message)
+            logger.info(message)
         else:
             raise MatrixTableSampleSetError(message, missing_samples)
-    print(f'Subsetted to {subset_count} sample ids')
+    logger.info(f'Subsetted to {subset_count} sample ids')
     mt = mt.semi_join_cols(sample_subset_ht)
     return mt.filter_rows(hl.agg.any(hl.is_defined(mt.GT)))