Bump black from 23.7.0 to 24.3.0

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/psf/black
-    rev: 23.7.0 # This should be kept in sync with the version in requirements-dev.in
+    rev: 24.3.0 # This should be kept in sync with the version in requirements-dev.in
     hooks:
       - id: black
         language_version: python3

gnomad/resources/grch37/gnomad_ld.py

@@ -21,9 +21,7 @@ def _ld_matrix_path(
             CURRENT_EXOME_RELEASE if data_type == "exomes" else CURRENT_GENOME_RELEASE
         )
     subdir = "sv/" if data_type == "genomes_snv_sv" else ""
-    return (
-        f'gs://gnomad-public-requester-pays/release/{version}/ld/{subdir}gnomad.{data_type}.r{version}.{pop}.{"common." if common_only else ""}{"adj." if adj else ""}ld.bm'
-    )
+    return f'gs://gnomad-public-requester-pays/release/{version}/ld/{subdir}gnomad.{data_type}.r{version}.{pop}.{"common." if common_only else ""}{"adj." if adj else ""}ld.bm'
 
 
 def _ld_index_path(
@@ -38,9 +36,7 @@ def _ld_index_path(
             CURRENT_EXOME_RELEASE if data_type == "exomes" else CURRENT_GENOME_RELEASE
         )
     subdir = "sv/" if data_type == "genomes_snv_sv" else ""
-    return (
-        f'gs://gnomad-public-requester-pays/release/{version}/ld/{subdir}gnomad.{data_type}.r{version}.{pop}.{"common." if common_only else ""}{"adj." if adj else ""}ld.variant_indices.ht'
-    )
+    return f'gs://gnomad-public-requester-pays/release/{version}/ld/{subdir}gnomad.{data_type}.r{version}.{pop}.{"common." if common_only else ""}{"adj." if adj else ""}ld.variant_indices.ht'
 
 
 def _ld_snv_sv_path(pop):
@@ -62,9 +58,7 @@ def _cross_pop_ld_scores_path(
         version = (
             CURRENT_EXOME_RELEASE if data_type == "exomes" else CURRENT_GENOME_RELEASE
         )
-    return (
-        f'gs://gnomad-public-requester-pays/release/{version}/ld/scores/gnomad.{data_type}.r{version}.{pop1}.{pop2}.{"adj." if adj else ""}ld_scores.ht'
-    )
+    return f'gs://gnomad-public-requester-pays/release/{version}/ld/scores/gnomad.{data_type}.r{version}.{pop1}.{pop2}.{"adj." if adj else ""}ld_scores.ht'
 
 
 def _ld_scores_path(
@@ -74,9 +68,7 @@ def _ld_scores_path(
         version = (
             CURRENT_EXOME_RELEASE if data_type == "exomes" else CURRENT_GENOME_RELEASE
         )
-    return (
-        f'gs://gnomad-public-requester-pays/release/{version}/ld/scores/gnomad.{data_type}.r{version}.{pop}.{"adj." if adj else ""}ld_scores.ht'
-    )
+    return f'gs://gnomad-public-requester-pays/release/{version}/ld/scores/gnomad.{data_type}.r{version}.{pop}.{"adj." if adj else ""}ld_scores.ht'
 
 
 def ld_matrix(pop: str) -> GnomadPublicBlockMatrixResource:

gnomad/sample_qc/filtering.py

@@ -251,7 +251,8 @@ def compute_stratified_metrics_filter(
         **{
             f"fail_{metric}": (
                 ht._qc_metrics[metric] <= metrics_stats_expr[metric].lower
-            ) | (ht._qc_metrics[metric] >= metrics_stats_expr[metric].upper)
+            )
+            | (ht._qc_metrics[metric] >= metrics_stats_expr[metric].upper)
             for metric in qc_metrics
         }
     )

gnomad/sample_qc/relatedness.py

@@ -411,7 +411,7 @@ def infer_families(
     """
 
     def group_parent_child_pairs_by_fam(
-        parent_child_pairs: Iterable[Tuple[str, str]]
+        parent_child_pairs: Iterable[Tuple[str, str]],
     ) -> List[List[Tuple[str, str]]]:
         """
         Group parent-child pairs into a list of families.

gnomad/utils/constraint.py

@@ -409,7 +409,7 @@ def annotate_mutation_type(
 
 
 def trimer_from_heptamer(
-    t: Union[hl.MatrixTable, hl.Table]
+    t: Union[hl.MatrixTable, hl.Table],
 ) -> Union[hl.MatrixTable, hl.Table]:
     """
     Trim heptamer context to create trimer context.
@@ -426,7 +426,7 @@ def trimer_from_heptamer(
 
 
 def collapse_strand(
-    t: Union[hl.Table, hl.MatrixTable]
+    t: Union[hl.Table, hl.MatrixTable],
 ) -> Union[hl.Table, hl.MatrixTable]:
     """
     Return the deduplicated context by collapsing DNA strands.

gnomad/utils/filtering.py

@@ -197,7 +197,7 @@ def filter_low_conf_regions(
 
 
 def filter_to_autosomes(
-    t: Union[hl.MatrixTable, hl.Table]
+    t: Union[hl.MatrixTable, hl.Table],
 ) -> Union[hl.MatrixTable, hl.Table]:
     """
     Filter the Table or MatrixTable to autosomes only.
@@ -470,7 +470,7 @@ def remove_fields_from_constant(
 
 
 def filter_x_nonpar(
-    t: Union[hl.Table, hl.MatrixTable]
+    t: Union[hl.Table, hl.MatrixTable],
 ) -> Union[hl.Table, hl.MatrixTable]:
     """
     Filter to loci that are in non-PAR regions on chromosome X.
@@ -496,7 +496,7 @@ def filter_x_nonpar(
 
 
 def filter_y_nonpar(
-    t: Union[hl.Table, hl.MatrixTable]
+    t: Union[hl.Table, hl.MatrixTable],
 ) -> Union[hl.Table, hl.MatrixTable]:
     """
     Filter to loci that are in non-PAR regions on chromosome Y.

gnomad/utils/liftover.py

@@ -27,7 +27,7 @@
 
 
 def get_liftover_genome(
-    t: Union[hl.MatrixTable, hl.Table]
+    t: Union[hl.MatrixTable, hl.Table],
 ) -> Tuple[hl.genetics.ReferenceGenome, hl.genetics.ReferenceGenome]:
     """
     Infer reference genome build of input data and assume destination reference genome build.

gnomad/utils/sparse_mt.py

@@ -869,7 +869,8 @@ def get_chr_dp_ann(chrom: str) -> hl.Table:
                     f"{chrom}_mean_dp": hl.agg.filter(
                         chr_mt.LGT.is_non_ref(),
                         hl.agg.sum(chr_mt.DP),
-                    ) / hl.agg.filter(chr_mt.LGT.is_non_ref(), hl.agg.count())
+                    )
+                    / hl.agg.filter(chr_mt.LGT.is_non_ref(), hl.agg.count())
                 }
             ).cols()
         else:
@@ -899,12 +900,10 @@ def get_chr_dp_ann(chrom: str) -> hl.Table:
 
     return ht.annotate(
         **{
-            f"{chr_x}_ploidy": ht[f"{chr_x}_mean_dp"] / (
-                ht[f"{normalization_contig}_mean_dp"] / 2
-            ),
-            f"{chr_y}_ploidy": ht[f"{chr_y}_mean_dp"] / (
-                ht[f"{normalization_contig}_mean_dp"] / 2
-            ),
+            f"{chr_x}_ploidy": ht[f"{chr_x}_mean_dp"]
+            / (ht[f"{normalization_contig}_mean_dp"] / 2),
+            f"{chr_y}_ploidy": ht[f"{chr_y}_mean_dp"]
+            / (ht[f"{normalization_contig}_mean_dp"] / 2),
         }
     )
 
@@ -1390,7 +1389,7 @@ def compute_allele_number_per_ref_site(
 
 
 def filter_ref_blocks(
-    t: Union[hl.MatrixTable, hl.Table]
+    t: Union[hl.MatrixTable, hl.Table],
 ) -> Union[hl.MatrixTable, hl.Table]:
     """
     Filter ref blocks out of the Table or MatrixTable.

gnomad/utils/transcript_annotation.py

@@ -1,4 +1,5 @@
 """Utils module containing generic functions that are useful for adding transcript expression-aware annotations."""
+
 import logging
 from typing import Callable, List, Optional, Tuple, Union
 

gnomad/utils/vep.py

@@ -544,18 +544,21 @@ def get_csq_from_struct(
                 "gene": element.gene_id,
                 "symbol": element.gene_symbol,
                 "symbol_source": element.gene_symbol_source,
-                "cdna_position": hl.str(element.cdna_start) + hl.if_else(
+                "cdna_position": hl.str(element.cdna_start)
+                + hl.if_else(
                     element.cdna_start == element.cdna_end,
                     "",
                     "-" + hl.str(element.cdna_end),
                 ),
-                "cds_position": hl.str(element.cds_start) + hl.if_else(
+                "cds_position": hl.str(element.cds_start)
+                + hl.if_else(
                     element.cds_start == element.cds_end,
                     "",
                     "-" + hl.str(element.cds_end),
                 ),
                 "mirna": hl.delimit(element.mirna, "&") if "mirna" in element else None,
-                "protein_position": hl.str(element.protein_start) + hl.if_else(
+                "protein_position": hl.str(element.protein_start)
+                + hl.if_else(
                     element.protein_start == element.protein_end,
                     "",
                     "-" + hl.str(element.protein_end),

requirements-dev.in

@@ -1,7 +1,7 @@
 # Used to create the requirements-dev.txt file
 # Note: `pip-compile requirements-dev.in` needs to be run before changes in requirements-dev.in are reflected in
 # requirements-dev.txt, which is used for GitHub Actions
-black==23.7.0 # This should be kept in sync with the version in .pre-commit-config.yaml
+black==24.3.0 # This should be kept in sync with the version in .pre-commit-config.yaml
 isort==5.12.0 # This should be kept in sync with the version in .pre-commit-config.yaml
 autopep8==2.0.2 # This should be kept in sync with the version in .pre-commit-config.yaml
 pre-commit

requirements-dev.txt

@@ -8,7 +8,7 @@ astroid==3.0.1
     # via pylint
 autopep8==2.0.2
     # via -r requirements-dev.in
-black==23.7.0
+black==24.3.0
     # via -r requirements-dev.in
 cfgv==3.4.0
     # via pre-commit