imports

jcvi/utils/__main__.py

@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 -*-
 """
-Assortment of utility scripts implementing recipes from Python cookbooks, such as iterators, sorters, range queries, etc. 
+Assortment of utility scripts implementing recipes from Python cookbooks, such as iterators, sorters, range queries, etc.
 """
 
-from jcvi.apps.base import dmain
+from ..apps.base import dmain
 
 
 if __name__ == "__main__":

jcvi/utils/aws.py

@@ -4,31 +4,35 @@
 """
 AWS-related methods.
 """
+import fnmatch
+import getpass
+import json
 import os
 import os.path as op
 import sys
-import fnmatch
-import boto3
-import json
-import logging
 import time
-import getpass
 
 from configparser import NoOptionError, NoSectionError
 from datetime import datetime
 from multiprocessing import Pool
+
+import boto3
+
 from botocore.exceptions import ClientError, ParamValidationError
 
-from jcvi.formats.base import BaseFile, SetFile, timestamp
-from jcvi.utils.console import console
-from jcvi.apps.base import (
-    OptionParser,
+from ..apps.base import (
     ActionDispatcher,
+    OptionParser,
     datafile,
     get_config,
+    logger,
     popen,
     sh,
 )
+from ..formats.base import BaseFile, SetFile, timestamp
+
+from .console import console
+
 
 AWS_CREDS_PATH = "%s/.aws/credentials" % (op.expanduser("~"),)
 
@@ -165,7 +169,7 @@ def start(args):
     # Make sure the instance id is empty
     instance_id = s.instance_id
     if instance_id != "":
-        logging.error("Instance exists {}".format(instance_id))
+        logger.error("Instance exists {}".format(instance_id))
         sys.exit(1)
 
     launch_spec = s.launch_spec
@@ -208,14 +212,14 @@ def start(args):
             if "InstanceId" in response["SpotInstanceRequests"][0]:
                 instance_id = response["SpotInstanceRequests"][0]["InstanceId"]
             else:
-                logging.debug("Waiting to be fulfilled ...")
+                logger.debug("Waiting to be fulfilled ...")
                 time.sleep(10)
 
     # Check if the instance is running
     print("Instance id {}".format(instance_id), file=sys.stderr)
     status = ""
     while status != "running":
-        logging.debug("Waiting instance to run ...")
+        logger.debug("Waiting instance to run ...")
         time.sleep(3)
         response = client.describe_instance_status(InstanceIds=[instance_id])
         if len(response["InstanceStatuses"]) > 0:
@@ -271,7 +275,7 @@ def stop(args):
     # Make sure the instance id is NOT empty
     instance_id = s.instance_id
     if instance_id == "":
-        logging.error("Cannot find instance_id {}".format(instance_id))
+        logger.error("Cannot find instance_id {}".format(instance_id))
         sys.exit(1)
 
     block_device_mappings = []
@@ -289,7 +293,7 @@ def stop(args):
 
     image_status = ""
     while image_status != "available":
-        logging.debug("Waiting for image to be ready")
+        logger.debug("Waiting for image to be ready")
         time.sleep(10)
         response = client.describe_images(ImageIds=[new_image_id])
         image_status = response["Images"][0]["State"]
@@ -488,7 +492,7 @@ def check_exists_s3(s3_store_obj_name: str, warn=False) -> bool:
     counts = int(popen(cmd).read())
     exists = counts != 0
     if exists and warn:
-        logging.debug("{} exists. Skipped.".format(s3_store_obj_name))
+        logger.debug("{} exists. Skipped.".format(s3_store_obj_name))
     return exists
 
 
@@ -577,7 +581,7 @@ def validate(args, config):
         )
     else:
         role_msg = ""
-    logging.info("Validating credentials for profile: %s %s" % (profile, role_msg))
+    logger.info("Validating credentials for profile: %s %s" % (profile, role_msg))
     reup_message = "Obtaining credentials for a new role or profile."
 
     try:
@@ -642,7 +646,7 @@ def validate(args, config):
             for option in required_options:
                 short_term[option] = config.get(profile, option)
         except NoOptionError:
-            logging.warning(
+            logger.warning(
                 "Your existing credentials are missing or invalid, "
                 "obtaining new credentials."
             )
@@ -654,12 +658,12 @@ def validate(args, config):
             current_role = None
 
         if args.force:
-            logging.info("Forcing refresh of credentials.")
+            logger.info("Forcing refresh of credentials.")
             force_refresh = True
         # There are not credentials for an assumed role,
         # but the user is trying to assume one
         elif current_role is None and args.assume_role:
-            logging.info(reup_message)
+            logger.info(reup_message)
             force_refresh = True
         # There are current credentials for a role and
         # the role arn being provided is the same.
@@ -676,12 +680,12 @@ def validate(args, config):
             and args.assume_role
             and current_role != args.assume_role
         ):
-            logging.info(reup_message)
+            logger.info(reup_message)
             force_refresh = True
         # There are credentials for a current role and no role arn is
         # being supplied
         elif current_role is not None and args.assume_role is None:
-            logging.info(reup_message)
+            logger.info(reup_message)
             force_refresh = True
 
     should_refresh = True
@@ -691,10 +695,10 @@ def validate(args, config):
         exp = datetime.strptime(config.get(profile, "expiration"), "%Y-%m-%d %H:%M:%S")
         diff = exp - datetime.utcnow()
         if diff.total_seconds() <= 0:
-            logging.info("Your credentials have expired, renewing.")
+            logger.info("Your credentials have expired, renewing.")
         else:
             should_refresh = False
-            logging.info(
+            logger.info(
                 "Your credentials are still valid for %s seconds"
                 " they will expire at %s" % (diff.total_seconds(), exp)
             )
@@ -714,7 +718,7 @@ def get_credentials(profile, args, config):
 
     if args.assume_role:
 
-        logging.info(
+        logger.info(
             "Assuming Role - Profile: %s, Role: %s, Duration: %s",
             profile,
             args.assume_role,
@@ -747,7 +751,7 @@ def get_credentials(profile, args, config):
             args.assume_role,
         )
     else:
-        logging.info(
+        logger.info(
             "Fetching Credentials - Profile: %s, Duration: %s", profile, args.duration
         )
         try:
@@ -790,15 +794,15 @@ def get_credentials(profile, args, config):
     with open(AWS_CREDS_PATH, "w") as configfile:
         config.write(configfile)
 
-    logging.info(
+    logger.info(
         "Success! Your credentials will expire in %s seconds at: %s"
         % (args.duration, response["Credentials"]["Expiration"])
     )
 
 
 def log_error_and_exit(message):
     """Log an error message and exit with error"""
-    logging.error(message)
+    logger.error(message)
     sys.exit(1)
 
 

jcvi/utils/cbook.py

@@ -6,10 +6,11 @@
 import os.path as op
 import re
 import sys
-import logging
 
 from collections import defaultdict
 
+from ..apps.base import logger
+
 
 def inspect(item, maxchar=80):
     """
@@ -37,7 +38,7 @@ def timed(*args, **kw):
         te = time.time()
 
         msg = "{0}{1} {2:.2f}s".format(func.__name__, args, te - ts)
-        logging.debug(msg)
+        logger.debug(msg)
 
         return result
 
@@ -149,7 +150,7 @@ def tofile(self, filename):
         for x in self.data:
             print(x, file=fw)
         fw.close()
-        logging.debug(
+        logger.debug(
             "Array of size {0} written to file `{1}`.".format(self.size, filename)
         )
 

jcvi/utils/db.py

@@ -5,13 +5,12 @@
 Connect to databases (Sybase, MySQL and PostgreSQL database backends)
 """
 import os.path as op
-import sys
-import logging
 import re
+import sys
 
-from jcvi.formats.base import must_open
-from jcvi.apps.base import OptionParser, ActionDispatcher, sh, getusername
-from jcvi.utils.cbook import AutoVivification
+from ..apps.base import ActionDispatcher, OptionParser, getusername, logger, sh
+from ..formats.base import must_open
+from ..utils.cbook import AutoVivification
 
 
 # set up valid database connection params
@@ -299,10 +298,8 @@ def query(args):
     else:
         for qry in qrys:
             if re.search(r"{\d+}", qry):
-                logging.error(
-                    "Query `{0}` contains placeholders, no datafile(s) specified".format(
-                        qry
-                    )
+                logger.error(
+                    "Query `%s` contains placeholders, no datafile(s) specified", qry
                 )
                 sys.exit()
             queries.add(qry)

jcvi/utils/range.py

@@ -11,6 +11,7 @@
 
 from collections import namedtuple, defaultdict
 from itertools import groupby
+
 from more_itertools import pairwise
 
 

jcvi/utils/taxonomy.py

@@ -28,7 +28,6 @@
 """
 import sys
 import time
-import logging
 
 from functools import lru_cache
 
@@ -40,7 +39,7 @@
 from ClientForm import ParseResponse
 from BeautifulSoup import BeautifulSoup
 
-from jcvi.apps.base import OptionParser, ActionDispatcher
+from ..apps.base import ActionDispatcher, OptionParser, logger
 
 
 URL = "http://itol.embl.de/other_trees.shtml"
@@ -65,8 +64,8 @@ def __init__(self, list_of_taxids):
                 response = urlopen(URL)
                 success = True
             except (URLError, HTTPError, RuntimeError) as e:
-                logging.error(e)
-                logging.debug("wait 5 seconds to reconnect...")
+                logger.error(e)
+                logger.debug("wait 5 seconds to reconnect...")
                 time.sleep(5)
 
         forms = ParseResponse(response, backwards_compat=False)

jcvi/utils/webcolors.py

@@ -8,12 +8,12 @@
 # Copyright © 2021 Haibao Tang. All rights reserved.
 #
 
-import logging
-
 import numpy as np
 
-from webcolors import CSS3_HEX_TO_NAMES, hex_to_rgb
 from skimage.color import rgb2lab, deltaE_cmc
+from webcolors import CSS3_HEX_TO_NAMES, hex_to_rgb
+
+from ..apps.base import logger
 
 
 def color_diff(rgb1, rgb2):
@@ -37,12 +37,12 @@ def closest_color(requested_color):
     """
     Find closest color name for the request RGB tuple.
     """
-    logging.disable(logging.DEBUG)
+    logger.disable(logger.DEBUG)
     colors = []
     for key, name in CSS3_HEX_TO_NAMES.items():
         diff = color_diff(hex_to_rgb(key), requested_color)
         colors.append((diff, name))
-    logging.disable(logging.NOTSET)
+    logger.disable(logger.NOTSET)
     _, min_color = min(colors)
 
     return min_color

jcvi/variation/__main__.py

@@ -4,7 +4,7 @@
 Set of scripts relating to variation studies such as imputation, phasing, SNP/CNV analysis, and other supporting routines
 """
 
-from jcvi.apps.base import dmain
+from ..apps.base import dmain
 
 
 if __name__ == "__main__":