style(acquisition): minor formatting fixes

Author: dshemetov

src/acquisition/ecdc/ecdc_db_update.py

@@ -156,15 +156,23 @@ def update_from_file(issue, date, dir, test_mode=False):
 def main():
     # args and usage
     parser = argparse.ArgumentParser()
+    # fmt: off
     parser.add_argument(
-        "--test", action="store_true", help="do dry run only, do not update the database"
+        "--test",
+        action="store_true",
+        help="do dry run only, do not update the database"
     )
     parser.add_argument(
-        "--file", type=str, help="load an existing zip file (otherwise fetch current data)"
+        "--file",
+        type=str,
+        help="load an existing zip file (otherwise fetch current data)"
     )
     parser.add_argument(
-        "--issue", type=int, help="issue of the file (e.g. 201740); used iff --file is given"
+        "--issue",
+        type=int,
+        help="issue of the file (e.g. 201740); used iff --file is given"
     )
+    # fmt: on
     args = parser.parse_args()
 
     if (args.file is None) != (args.issue is None):

src/acquisition/flusurv/flusurv_update.py

@@ -160,12 +160,19 @@ def update(issue, location_name, test_mode=False):
 def main():
     # args and usage
     parser = argparse.ArgumentParser()
+    # fmt: off
     parser.add_argument(
-        "location", help='location for which data should be scraped (e.g. "CA" or "all")'
+        "location",
+        help='location for which data should be scraped (e.g. "CA" or "all")'
     )
     parser.add_argument(
-        "--test", "-t", default=False, action="store_true", help="do not commit database changes"
+        "--test",
+        "-t",
+        default=False,
+        action="store_true",
+        help="do not commit database changes"
     )
+    # fmt: on
     args = parser.parse_args()
 
     # scrape current issue from the main page

src/acquisition/fluview/fluview_update.py

@@ -516,15 +516,23 @@ def update_from_file(issue, date, filename, test_mode=False):
 def main():
     # args and usage
     parser = argparse.ArgumentParser()
+    # fmt: off
     parser.add_argument(
-        "--test", action="store_true", help="do dry run only, do not update the database"
+        "--test",
+        action="store_true",
+        help="do dry run only, do not update the database"
     )
     parser.add_argument(
-        "--file", type=str, help="load an existing zip file (otherwise fetch current data)"
+        "--file",
+        type=str,
+        help="load an existing zip file (otherwise fetch current data)"
     )
     parser.add_argument(
-        "--issue", type=int, help="issue of the file (e.g. 201740); used iff --file is given"
+        "--issue",
+        type=int,
+        help="issue of the file (e.g. 201740); used iff --file is given"
     )
+    # fmt: on
     args = parser.parse_args()
 
     if (args.file is None) != (args.issue is None):

src/acquisition/ght/ght_update.py

@@ -330,9 +330,7 @@ def get_num_rows():
                         # print(' [%s|%s|%d] missing value' % (term, location, ew))
                     ew = flu.add_epiweeks(ew, 1)
                 if num_missing > 0:
-                    print(
-                        f" [{term}|{location}] missing {int(num_missing)}/{len(values)} value(s)"
-                    )
+                    print(f" [{term}|{location}] missing {int(num_missing)}/{len(values)} value(s)")
             except Exception as ex:
                 print(f" [{term}|{location}] caught exception (will NOT retry):", ex)
 
@@ -350,11 +348,41 @@ def main():
     # args and usage
     parser = argparse.ArgumentParser()
     # fmt: off
-    parser.add_argument("location", action="store", type=str, default=None, help="location(s) (ex: all; US; TX; CA,LA,WY)")
-    parser.add_argument("term", action="store", type=str, default=None, help='term/query/topic (ex: all; /m/0cycc; "flu fever")')
-    parser.add_argument("--first", "-f", default=None, type=int, help="first epiweek override")
-    parser.add_argument("--last", "-l", default=None, type=int, help="last epiweek override")
-    parser.add_argument("--country", "-c", default="US", type=str, help="location country (ex: US; BR)")
+    parser.add_argument(
+        "location",
+        action="store",
+        type=str,
+        default=None,
+        help="location(s) (ex: all; US; TX; CA,LA,WY)"
+    )
+    parser.add_argument(
+        "term",
+        action="store",
+        type=str,
+        default=None,
+        help='term/query/topic (ex: all; /m/0cycc; "flu fever")'
+    )
+    parser.add_argument(
+        "--first",
+        "-f",
+        default=None,
+        type=int,
+        help="first epiweek override"
+    )
+    parser.add_argument(
+        "--last",
+        "-l",
+        default=None,
+        type=int,
+        help="last epiweek override"
+    )
+    parser.add_argument(
+        "--country",
+        "-c",
+        default="US",
+        type=str,
+        help="location country (ex: US; BR)"
+    )
     # fmt: on
     args = parser.parse_args()
 

src/acquisition/ght/google_health_trends.py

@@ -116,19 +116,39 @@ def main():
     parser = argparse.ArgumentParser()
     # fmt: off
     parser.add_argument(
-        "apikey", action="store", type=str, default=None, help="API key"
+        "apikey",
+        action="store",
+        type=str,
+        default=None,
+        help="API key"
     )
     parser.add_argument(
-        "startweek", action="store", type=int, default=None, help="first week (ex: 201440)"
+        "startweek",
+        action="store",
+        type=int,
+        default=None,
+        help="first week (ex: 201440)"
     )
     parser.add_argument(
-        "endweek", action="store", type=int, default=None, help="last week (ex: 201520)"
+        "endweek",
+        action="store",
+        type=int,
+        default=None,
+        help="last week (ex: 201520)"
     )
     parser.add_argument(
-        "location", action="store", type=str, default=None, help="location (ex: US)"
+        "location",
+        action="store",
+        type=str,
+        default=None,
+        help="location (ex: US)"
     )
     parser.add_argument(
-        "term", action="store", type=str, default=None, help="term/query/topic (ex: /m/0cycc)"
+        "term",
+        action="store",
+        type=str,
+        default=None,
+        help="term/query/topic (ex: /m/0cycc)"
     )
     # fmt: on
     args = parser.parse_args()

src/acquisition/paho/paho_db_update.py

@@ -234,15 +234,23 @@ def update_from_file(issue, date, filename, test_mode=False):
 def main():
     # args and usage
     parser = argparse.ArgumentParser()
+    # fmt: off
     parser.add_argument(
-        "--test", action="store_true", help="do dry run only, do not update the database"
+        "--test",
+        action="store_true",
+        help="do dry run only, do not update the database"
     )
     parser.add_argument(
-        "--file", type=str, help="load an existing zip file (otherwise fetch current data)"
+        "--file",
+        type=str,
+        help="load an existing zip file (otherwise fetch current data)"
     )
     parser.add_argument(
-        "--issue", type=int, help="issue of the file (e.g. 201740); used iff --file is given"
+        "--issue",
+        type=int,
+        help="issue of the file (e.g. 201740); used iff --file is given"
     )
+    # fmt: on
     args = parser.parse_args()
 
     if (args.file is None) != (args.issue is None):

src/acquisition/quidel/quidel.py

@@ -140,7 +140,7 @@ def retrieve_excels(self):
         m.select("INBOX")  # here you a can choose a mail box like INBOX instead
         # use m.list() to get all the mailboxes
         # you could filter using the IMAP rules here (check https://www.example-code.com/csharp/imap-search-critera.asp)
-        _, items = m.search(None, "ALL")  
+        _, items = m.search(None, "ALL")
         items = items[0].split()  # getting the mails id
 
         # The emailids are ordered from past to now

src/acquisition/quidel/quidel_update.py

@@ -125,11 +125,39 @@ def main():
     # args and usage
     parser = argparse.ArgumentParser()
     # fmt: off
-    parser.add_argument("--location", action="store", type=str, default=None, help="location(s) (ex: all; any of hhs1-10)")
-    parser.add_argument("--first", "-f", default=None, type=int, help="first epiweek override")
-    parser.add_argument("--last", "-l", default=None, type=int, help="last epiweek override")
-    parser.add_argument("--force_update", "-u", action="store_true", help="force update db values")
-    parser.add_argument("--skip_email", "-s", action="store_true", help="skip email downloading step")
+    parser.add_argument(
+        "--location",
+        action="store",
+        type=str,
+        default=None,
+        help="location(s) (ex: all; any of hhs1-10)"
+    )
+    parser.add_argument(
+        "--first",
+        "-f",
+        default=None,
+        type=int,
+        help="first epiweek override"
+    )
+    parser.add_argument(
+        "--last",
+        "-l",
+        default=None,
+        type=int,
+        help="last epiweek override"
+    )
+    parser.add_argument(
+        "--force_update",
+        "-u",
+        action="store_true",
+        help="force update db values"
+    )
+    parser.add_argument(
+        "--skip_email",
+        "-s",
+        action="store_true",
+        help="skip email downloading step"
+    )
     # fmt: on
     args = parser.parse_args()
 

src/acquisition/twtr/healthtweets.py

@@ -216,12 +216,45 @@ def main():
     # args and usage
     parser = argparse.ArgumentParser()
     # fmt: off
-    parser.add_argument("username", action="store", type=str, help="healthtweets.org username")
-    parser.add_argument("password", action="store", type=str, help="healthtweets.org password")
-    parser.add_argument("state", action="store", type=str, choices=list(HealthTweets.STATE_CODES.keys()), help="U.S. state (ex: TX)")
-    parser.add_argument("date1", action="store", type=str, help="first date, inclusive (ex: 2015-01-01)")
-    parser.add_argument("date2", action="store", type=str, help="last date, inclusive (ex: 2015-01-01)")
-    parser.add_argument("-d", "--debug", action="store_const", const=True, default=False, help="enable debug mode")
+    parser.add_argument(
+        "username",
+        action="store",
+        type=str,
+        help="healthtweets.org username"
+    )
+    parser.add_argument(
+        "password",
+        action="store",
+        type=str,
+        help="healthtweets.org password"
+    )
+    parser.add_argument(
+        "state",
+        action="store",
+        type=str,
+        choices=list(HealthTweets.STATE_CODES.keys()),
+        help="U.S. state (ex: TX)"
+    )
+    parser.add_argument(
+        "date1",
+        action="store",
+        type=str,
+        help="first date, inclusive (ex: 2015-01-01)"
+    )
+    parser.add_argument(
+        "date2",
+        action="store",
+        type=str,
+        help="last date, inclusive (ex: 2015-01-01)"
+    )
+    parser.add_argument(
+        "-d",
+        "--debug", 
+        action="store_const",
+        const=True,
+        default=False,
+        help="enable debug mode"
+    )
     # fmt: on
     args = parser.parse_args()
 

src/acquisition/wiki/wiki_download.py

@@ -288,12 +288,51 @@ def main():
     # args and usage
     parser = argparse.ArgumentParser()
     # fmt: off
-    parser.add_argument("secret", type=str, help="hmac secret key")
-    parser.add_argument("-b", "--blimit", action="store", type=int, default=None, help="download limit, in bytes")
-    parser.add_argument("-j", "--jlimit", action="store", type=int, default=None, help="job limit")
-    parser.add_argument("-s", "--sleep", action="store", type=int, default=1, help="seconds to sleep between each job")
-    parser.add_argument("-t", "--type", action="store", type=int, default=0, help="type of job")
-    parser.add_argument("-d", "--debug", action="store_const", const=True, default=False, help="enable debug mode")
+    parser.add_argument(
+        "secret",
+        type=str,
+        help="hmac secret key"
+    )
+    parser.add_argument(
+        "-b",
+        "--blimit",
+        action="store",
+        type=int,
+        default=None,
+        help="download limit, in bytes"
+    )
+    parser.add_argument(
+        "-j",
+        "--jlimit",
+        action="store",
+        type=int,
+        default=None,
+        help="job limit"
+    )
+    parser.add_argument(
+        "-s",
+        "--sleep",
+        action="store",
+        type=int,
+        default=1,
+        help="seconds to sleep between each job"
+    )
+    parser.add_argument(
+        "-t",
+        "--type",
+        action="store",
+        type=int,
+        default=0,
+        help="type of job"
+    )
+    parser.add_argument(
+        "-d",
+        "--debug",
+        action="store_const",
+        const=True,
+        default=False,
+        help="enable debug mode"
+    )
     # fmt: on
     args = parser.parse_args()