Fix linting warnings. Improve Python style

seiscat/db.py

@@ -13,7 +13,6 @@
 import sqlite3
 import numpy as np
 from obspy import UTCDateTime
-from .utils import err_exit
 
 # Current supported DB version
 # Increment this number when changing the DB schema
@@ -26,15 +25,19 @@ def _get_db_connection(config, initdb=False):
 
  :param config: config object
  :return: database connection
+
+ :raises ValueError: if db_file is not set in config file
+ :raises FileNotFoundError: if database file does not exist
  """
  db_file = config.get('db_file', None)
  if db_file is None:
- err_exit('db_file not set in config file')
+ raise ValueError('db_file not set in config file')
  if not initdb:
  try:
- open(db_file, 'r')
- except FileNotFoundError:
- err_exit(f'Database file "{db_file}" not found.')
+ open(db_file, 'r', encoding='utf8')
+ except FileNotFoundError as e:
+ raise FileNotFoundError(
+ f'Database file "{db_file}" not found.') from e
  return sqlite3.connect(db_file)
 
 
@@ -44,6 +47,8 @@ def _check_db_version(cursor, config):
 
  :param cursor: database cursor
  :param config: config object
+
+ :raises ValueError: if db_file version is not supported
  """
  db_version = cursor.execute('PRAGMA user_version').fetchone()[0]
  db_file = config['db_file']
@@ -54,7 +59,7 @@ def _check_db_version(cursor, config):
  'Remove or rename your old database file, '
  'so that a new one can be created.'
  )
- err_exit(msg)
+ raise ValueError(msg)
 
 
 def _set_db_version(cursor):
@@ -63,7 +68,7 @@ def _set_db_version(cursor):
 
  :param cursor: database cursor
  """
- cursor.execute('PRAGMA user_version = {v:d}'.format(v=DB_VERSION))
+ cursor.execute(f'PRAGMA user_version = {DB_VERSION:d}')
 
 
 def check_db_exists(config, initdb):
@@ -72,26 +77,30 @@ def check_db_exists(config, initdb):
 
  :param config: config object
  :param initdb: if True, create new database file
+
+ :raises ValueError: if db_file is not set in config file
+ :raises RuntimeError: if user does not want to overwrite existing database
+ :raises FileNotFoundError: if database file does not exist
  """
  db_file = config.get('db_file', None)
  if db_file is None:
- err_exit('db_file not set in config file')
+ raise ValueError('db_file not set in config file')
  if initdb and os.path.exists(db_file):
  ans = input(
  f'"{db_file}" already exists. '
  'Do you want to overwrite it?\n'
  f'(Current database will be saved as "{db_file}.bak") [y/N] '
  )
  if ans not in ['y', 'Y']:
- err_exit('No database file created. Exiting.')
- else:
-  os.rename(
-  db_file, f'{db_file}.bak')
-  print(
-  f'Backup of "{db_file}" saved to '
-  f'"{db_file}.bak"')
+ raise RuntimeError(
+  'Existing database file will not be overwritten. Exiting.')
+ os.rename(
+ db_file, f'{db_file}.bak')
+ print(
+ f'Backup of "{db_file}" saved to '
+ f'"{db_file}.bak"')
  if not initdb and not os.path.exists(db_file):
- err_exit(
+ raise FileNotFoundError(
  f'Database file "{db_file}" does not exist.\n'
  'Run "seiscat initdb" first.'
  )
@@ -315,11 +324,14 @@ def replicate_event_in_db(config, eventid, version=1):
  :param config: config object
  :param eventid: event id of the original event
  :param version: version of the original event
+
+ :raises ValueError: if eventid/version is not found in database
  """
  fields, rows = read_fields_and_rows_from_db(
  config, eventid=eventid, version=version)
  if not rows:
- err_exit(f'Event {eventid} version {version} not found in database')
+ raise ValueError(
+ f'Event {eventid} version {version} not found in database')
  row = list(rows[0])
  # increment version
  ver_index = fields.index('ver')
@@ -380,15 +392,17 @@ def update_event_in_db(config, eventid, version, field, value):
  :param version: version of the event to update
  :param field: field to update
  :param value: new value
+
+ :raises ValueError: if field is not found in database
  """
  conn = _get_db_connection(config)
  c = conn.cursor()
  try:
  c.execute(
  f'UPDATE events SET {field} = ? WHERE evid = ? AND ver = ?',
  (value, eventid, version))
- except sqlite3.OperationalError:
- err_exit(f'Field "{field}" not found in database')
+ except sqlite3.OperationalError as e:
+ raise ValueError(f'Field "{field}" not found in database') from e
  # close database connection
  conn.commit()
  print(
@@ -405,14 +419,17 @@ def increment_event_in_db(config, eventid, version, field, value):
  :param version: version of the event to update
  :param field: field to update
  :param value: value to increment, must be a number
+
+ :raises ValueError: if field is not found in database,
+ or if value is not a number
  """
  conn = _get_db_connection(config)
  c = conn.cursor()
  # check if value is numeric
  try:
  value = float(value)
- except ValueError:
- err_exit(f'Value "{value}" is not a number')
+ except ValueError as e:
+ raise ValueError(f'Value "{value}" is not a number') from e
  # if value is an integer, convert it to int
  if value == int(value):
  value = int(value)
@@ -426,18 +443,18 @@ def increment_event_in_db(config, eventid, version, field, value):
  new_value = float(old_value) + value
  if new_value == int(new_value):
  new_value = int(new_value)
- except ValueError:
- err_exit(f'Field "{field}" is not a number')
- except sqlite3.OperationalError:
- err_exit(f'Field "{field}" not found in database')
+ except ValueError as e:
+ raise ValueError(f'Field "{field}" is not a number') from e
+ except sqlite3.OperationalError as e:
+ raise ValueError(f'Field "{field}" not found in database') from e
  # update database
  try:
  c.execute(
  f'UPDATE events SET {field} = ? '
  'WHERE evid = ? AND ver = ?',
  (new_value, eventid, version))
- except sqlite3.OperationalError:
- err_exit(f'Field "{field}" not found in database')
+ except sqlite3.OperationalError as e:
+ raise ValueError(f'Field "{field}" not found in database') from e
  # close database connection
  conn.commit()
  print(

seiscat/download_and_store.py

@@ -11,7 +11,7 @@
 """
 from .db import check_db_exists, write_catalog_to_db
 from .fdsnws import open_fdsn_connection, query_events
-from .utils import err_exit
+from .utils import ExceptionExit
 
 
 def download_and_store(config, initdb):
@@ -21,10 +21,11 @@ def download_and_store(config, initdb):
  :param config: config object
  :param initdb: if True, create new database file
  """
- check_db_exists(config, initdb)
- try:
+ with ExceptionExit():
+ check_db_exists(config, initdb)
+ with ExceptionExit(additional_msg='Error connecting to FDSN server'):
  client = open_fdsn_connection(config)
- except Exception as e:
- err_exit(e)
- cat = query_events(client, config, first_query=initdb)
- write_catalog_to_db(cat, config, initdb)
+ with ExceptionExit(additional_msg='Error querying FDSN server'):
+ cat = query_events(client, config, first_query=initdb)
+ with ExceptionExit(additional_msg='Error writing to database'):
+  write_catalog_to_db(cat, config, initdb)

seiscat/fdsnws.py

@@ -14,7 +14,6 @@
 from obspy import Catalog
 from obspy.clients.fdsn import Client
 from obspy.clients.fdsn.header import FDSNNoDataException
-from .utils import err_exit
 
 
 def open_fdsn_connection(config):
@@ -194,10 +193,7 @@ def query_events(client, config, first_query=True):
  :returns: obspy Catalog object
  """
  print(f'Querying events from FDSN server "{config["fdsn_event_url"]}"...')
- try:
- cat = _query_box_or_circle(client, config, first_query=first_query)
- except Exception as e:
- err_exit(e)
+ cat = _query_box_or_circle(client, config, first_query=first_query)
  # see if there are additional queries to be done
  n = 1
  while True:
@@ -206,8 +202,6 @@ def query_events(client, config, first_query=True):
  client, config, suffix=f'_{n}', first_query=first_query)
  except InvalidQuery:
  break
- except Exception as e:
- err_exit(e)
  cat += _cat
  n += 1
  print(f'Found {len(cat)} events.')

seiscat/parse_arguments.py

@@ -13,7 +13,6 @@
 import argparse
 import argcomplete
 from ._version import get_versions
-_db_cursor = None
 
 
 def _get_db_cursor(configfile):
@@ -24,7 +23,7 @@ def _get_db_cursor(configfile):
  :return: cursor to the database
  """
  try:
- fp = open(configfile, 'r')
+ fp = open(configfile, 'r', encoding='utf-8')
  except FileNotFoundError:
  return None
  try:
@@ -34,15 +33,16 @@ def _get_db_cursor(configfile):
  except IndexError:
  db_file = 'seiscat.sqlite'
  try:
- open(db_file, 'r')
+ open(db_file, 'r', encoding='utf-8')
  except FileNotFoundError:
  return None
+ # pylint: disable=import-outside-toplevel
  import sqlite3 # lazy import to speed up startup time
  conn = sqlite3.connect(db_file)
  return conn.cursor()
 
 
-def _evid_completer(prefix, parsed_args, **kwargs):
+def _evid_completer(prefix, parsed_args, **_kwargs):
  """
  Completer for event IDs.
 
@@ -51,15 +51,15 @@ def _evid_completer(prefix, parsed_args, **kwargs):
  :param kwargs: keyword arguments
  :return: list of event IDs
  """
- global _db_cursor
- if _db_cursor is None:
- _db_cursor = _get_db_cursor(parsed_args.configfile)
- if _db_cursor is None:
+ if _evid_completer.db_cursor is None:
+ _evid_completer.db_cursor = _get_db_cursor(parsed_args.configfile)
+ if _evid_completer.db_cursor is None:
  return []
- _db_cursor.execute(
+ _evid_completer.db_cursor.execute(
  'SELECT evid FROM events WHERE evid LIKE ?', (f'{prefix}%',)
  )
- return [row[0] for row in _db_cursor.fetchall()]
+ return [row[0] for row in _evid_completer.db_cursor.fetchall()]
+_evid_completer.db_cursor = None # noqa: E305
 
 
 def parse_arguments():

seiscat/scripts/seiscat.py

@@ -13,6 +13,7 @@
 """
 import sys
 # NOTE: other modules are lazy-imported to speed up startup time
+# pylint: disable=import-outside-toplevel, relative-beyond-top-level
 
 
 def run():

seiscat/utils.py

@@ -11,6 +11,7 @@
 """
 import os
 import sys
+import contextlib
 from .configobj import ConfigObj
 from .configobj.validate import Validator
 
@@ -26,6 +27,28 @@ def err_exit(msg):
  sys.exit(1)
 
 
+class ExceptionExit(contextlib.AbstractContextManager):
+ """
+ Context manager to exit when an exception is raised.
+ """
+
+ def __init__(self, additional_msg=None):
+ """
+ Initialize the context manager.
+
+ :param additional_msg: additional message to print
+ """
+ self.additional_msg = additional_msg
+
+ def __exit__(self, exc_type, exc_value, _traceback):
+ if exc_type:
+ if self.additional_msg is not None:
+ msg = f'{self.additional_msg}: {exc_value}'
+ else:
+ msg = exc_value
+ err_exit(msg)
+
+
 def parse_configspec():
  """
  Parse the configspec file.
@@ -86,13 +109,8 @@ def read_config(config_file, configspec=None):
  if configspec is None:
  kwargs.update(
  dict(interpolation=False, list_values=False, _inspec=True))
- try:
+ with ExceptionExit(additional_msg=f'Unable to read "{config_file}"'):
  config_obj = ConfigObj(config_file, **kwargs)
- except IOError as err:
- err_exit(err)
- except Exception as err:
- msg = f'Unable to read "{config_file}": {err}'
- err_exit(msg)
  for k, v in config_obj.items():
  if v == 'None':
  config_obj[k] = None