Update black to later version for both pre-commit and github action (…

…fixed to 23.10.1)

.github/workflows/black.yml

@@ -7,4 +7,4 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - uses: psf/black@stable
+      - uses: psf/black@23.10.1

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
         - --keep-unused-type-checking
         - --black-line-length=79
 
--   repo: https://github.com/python/black
-    rev: 22.3.0
+-   repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 23.10.1
     hooks:
     -   id: black

lib/Lineages_UPDATER.py

@@ -19,6 +19,7 @@
 #    print("Dependency `pango_aliasor` missing, please install using `pip install pango_aliasor`")
 #    raise e
 
+
 # In covSonar 1 we will copy the class from https://github.com/corneliusroemer/pango_aliasor/blob/main/src/pango_aliasor/aliasor.py
 # but for V.2 we will switch using the package to "pip install pango_aliasor"
 class Aliasor:

lib/sonardb.py

@@ -1606,7 +1606,6 @@ def iter_table(self, table, batch_size=1000):
 
     ## extra features
     def get_list_of_lineages(self, lineage):
-
         sql = (
             "SELECT DISTINCT lineage FROM genome WHERE lineage LIKE '" + lineage + "';"
         )
@@ -1719,7 +1718,6 @@ def match(
         count=False,
         frameshifts=0,
     ):
-
         # creating where condition
         where_clause = []
         where_vals = []

lib/sonartoVCF_v2.bak.py

@@ -113,7 +113,6 @@ def calculate_AC_AN(final_df):
 
 
 def create_vcf(rows_grouped, tmp_dirname, refdescr):
-
     process_id = str(getpid())
     # print(process_id+" Start")
     # iterate over each group

lib/sonartoVCF_v2.py

@@ -119,7 +119,6 @@ def calculate_AC_AN(final_df):
 
 
 def _check_variant_type(ref, alt):
-
     if len(ref) == len(alt) and len(alt) == 1:  # SNP
         return "SNP"
     elif len(ref) < len(alt) and len(alt) > 0:  # INS
@@ -191,7 +190,6 @@ def create_vcf(rows_grouped, tmp_dirname, refdescr):
                 # final_snp_df[group_name] = "." # init value
                 # final_indel_df[group_name] = "." # init value
                 for row in df_.itertuples():
-
                     _id = (
                         getattr(row, "ref")
                         + str(getattr(row, "start"))
@@ -208,7 +206,6 @@ def create_vcf(rows_grouped, tmp_dirname, refdescr):
                             index_start_postion
                         ]  # return scalar instead DF
                         if selected_row.ID == ".":  # A
-
                             final_snp_df.at[index_start_postion, "ID"] = _id
                             final_snp_df.at[index_start_postion, group_name] = "1"
                             final_snp_df.at[index_start_postion, "REF"] = getattr(
@@ -225,7 +222,6 @@ def create_vcf(rows_grouped, tmp_dirname, refdescr):
                             ):  # only one ID exists and just update GT of a sample
                                 final_snp_df.at[index_start_postion, group_name] = "1"
                             else:
-
                                 splited_final_id_list = selected_row.ID.split(";")
                                 totel_len = len(splited_final_id_list)
                                 for new_GT, splited_final_id in enumerate(
@@ -264,7 +260,6 @@ def create_vcf(rows_grouped, tmp_dirname, refdescr):
                     elif (
                         _type == "INS" or _type == "INDEL" or _type == "DEL"
                     ):  # C      or _type == 'DEL'
-
                         selected_row = final_indel_df[
                             (final_indel_df["POS"] == getattr(row, "start"))
                             & (final_indel_df["TYPE"] == _type)

sonar.py

@@ -1001,7 +1001,6 @@ def process_update_expressions(expr):
 
     # add
     if args.tool == "add":
-
         # sanity check
         if not args.file and not args.cache:
             sys.exit("nothing to add.")