use specific package level logger; update metadata (#1732)

reacnetgenerator/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2019, East China Normal University
+# Copyright 2018-2022, East China Normal University
 """
 ``reacnetgenerator``
 ====================
@@ -14,12 +14,11 @@
 """
 
 __date__ = '2018-03-11'
-__update__ = '2019-10-07'
 __author__ = 'Jinzhe Zeng'
 __email__ = 'jinzhe.zeng@rutgers.edu'
 __credits__ = ['Jinzhe Zeng', 'Tong Zhu',
                'Liqun Cao', 'Chih-Hao Chin', 'John ZH Zhang']
-__copyright__ = 'Copyright 2018-2019, East China Normal University'
+__copyright__ = 'Copyright 2018-2022, East China Normal University'
 
 import matplotlib as mpl
 mpl.use("svg")  # noqa

reacnetgenerator/_draw.py

@@ -18,7 +18,6 @@
 placement. Software: Practice and experince. 1991, 21(11),1129-1164.
 """
 
-import logging
 import math
 import traceback
 from io import StringIO
@@ -31,6 +30,7 @@
 import scour.scour
 
 from .utils import SCOUROPTIONS, SharedRNGData
+from ._logging import logger
 
 
 class _DrawNetwork(SharedRNGData):
@@ -73,8 +73,8 @@ def _draw(self, timeaxis=None):
                                    fixed=list(self.pos) if self.pos else None,
                                    k=self.k)
             if pos:
-                logging.info("The position of the species in the network is:")
-                logging.info(pos)
+                logger.info("The position of the species in the network is:")
+                logger.info(pos)
             for with_labels in ([True] if not self.nolabel else [True, False]):
                 nx.draw(
                     G, pos=pos, width=widths, node_size=self.node_size,
@@ -88,8 +88,7 @@ def _draw(self, timeaxis=None):
                         stringio.getvalue(), SCOUROPTIONS))
                 plt.close()
         except Exception as e:
-            logging.error(f"Error: cannot draw images. Details: {e}")
-            traceback.print_tb(e.__traceback__)
+            logger.exception(f"Error: cannot draw images. Details: {e}")
 
     def _readtable(self, filename):
         df = pd.read_csv(filename, sep=' ', index_col=0, header=0)
@@ -106,7 +105,7 @@ def _handlespecies(self, name):
         else:
             showname = dict([(u, u) for u in species])
         if species:
-            logging.info("Species are:")
+            logger.info("Species are:")
             for specname, n in showname.items():
-                logging.info("{} {}".format(n, specname))
+                logger.info("{} {}".format(n, specname))
         return species, showname

reacnetgenerator/_logging.py

@@ -4,6 +4,8 @@
 import logging
 import coloredlogs
 from ._version import __version__
+
+logger = logging.getLogger(__name__)
 coloredlogs.install(
-    fmt=f'%(asctime)s - ReacNetGen {__version__} - %(levelname)s: %(message)s',
-    level=logging.INFO, milliseconds=True)
+    fmt=f'%(asctime)s - ReacNetGenerator {__version__} - %(levelname)s: %(message)s',
+    level=logging.INFO, milliseconds=True, logger=logger)

reacnetgenerator/_reachtml.py

@@ -11,7 +11,6 @@
 """
 
 import json
-import logging
 import re
 import os
 from collections import defaultdict
@@ -20,6 +19,7 @@
 import scour.scour
 
 from .utils import SCOUROPTIONS, SharedRNGData
+from ._logging import logger
 
 
 class _HTMLResult(SharedRNGData):
@@ -39,7 +39,7 @@ def report(self):
         """Generate a web page to show the result."""
         self._readdata()
         self._generateresult()
-        logging.info(
+        logger.info(
             f"Report is generated. Please see {self.resultfilename} for more details.")
 
     def _re(self, smi):

reacnetgenerator/gui.py

@@ -14,18 +14,18 @@
 import webbrowser
 import base64
 import pkg_resources
-import logging
 from multiprocessing import cpu_count
 
 from . import ReacNetGenerator, __version__
+from ._logging import logger
 
 
 class GUI:
     """GUI class."""
 
     def __init__(self):
         """Init GUI class."""
-        logging.info(__doc__)
+        logger.info(__doc__)
         self._filename = ''
 
         self._top = tk.Tk()
@@ -109,10 +109,10 @@ def _run(self):
                     webbrowser.open_new(os.path.abspath(
                         reacnetgenerator.resultfilename))
             except Exception as e:
-                logging.error(e)
+                logger.exception(e)
                 tkmb.showerror("Error", e)
         else:
-            logging.error("File not exsit.")
+            logger.error("File not exsit.")
             tkmb.showerror("Error", "File not exsit.")
 
     def _openfiles(self):

reacnetgenerator/reacnetgen.py

@@ -41,7 +41,6 @@
 
 
 import gc
-import logging
 import os
 import time
 import itertools
@@ -50,7 +49,8 @@
 
 import numpy as np
 
-from . import __version__, __date__, __update__
+from . import __version__, __date__
+from ._logging import logger
 from ._detect import _Detect
 from ._draw import _DrawNetwork
 from ._mergeiso import _mergeISO 
@@ -119,8 +119,8 @@ class ReacNetGenerator:
 
     def __init__(self, **kwargs):
         """Init ReacNetGenerator."""
-        logging.info(__doc__)
-        logging.info(
+        logger.info(__doc__)
+        logger.info(
             f"Version: {__version__}  Creation date: {__date__}")
 
         # process kwargs
@@ -292,7 +292,7 @@ def _process(self, steps):
             # garbage collect
             gc.collect()
             timearray.append(time.perf_counter())
-            logging.info(
+            logger.info(
                 f"Step {i}: Done! Time consumed (s): {timearray[-1]-timearray[-2]:.3f} ({runstep})")
 
         # delete tempfile
@@ -304,5 +304,5 @@ def _process(self, steps):
                 except OSError:
                     pass
         # Summary
-        logging.info("====== Summary ======")
-        logging.info(f"Total time(s): {timearray[-1]-timearray[0]:.3f} s")
+        logger.info("====== Summary ======")
+        logger.info(f"Total time(s): {timearray[-1]-timearray[0]:.3f} s")

reacnetgenerator/utils.py

@@ -6,7 +6,6 @@
 import os
 import shutil
 import itertools
-import logging
 import pickle
 import hashlib
 import asyncio
@@ -19,6 +18,8 @@
 from requests.adapters import HTTPAdapter
 from tqdm import tqdm
 
+from ._logging import logger
+
 
 class WriteBuffer:
     """Store a buffer for writing files.
@@ -355,11 +356,11 @@ def checksha256(filename, sha256_check):
         for n in iter(lambda: f.readinto(mv), 0):
             h.update(mv[:n])
     sha256 = h.hexdigest()
-    logging.info(f"SHA256 of {filename}: {sha256}")
+    logger.info(f"SHA256 of {filename}: {sha256}")
     if sha256 in must_be_list(sha256_check):
         return True
-    logging.warning("SHA256 is not correct.")
-    logging.warning(open(filename).read())
+    logger.warning("SHA256 is not correct.")
+    logger.warning(open(filename).read())
     return False
 
 
@@ -389,13 +390,13 @@ async def download_file(urls, pathfilename, sha256):
 
     # from https://stackoverflow.com/questions/16694907
     for url in must_be_list(urls):
-        logging.info(f"Try to download {pathfilename} from {url}")
+        logger.info(f"Try to download {pathfilename} from {url}")
         with s.get(url, stream=True) as r, open(pathfilename, 'wb') as f:
             try:
                 shutil.copyfileobj(r.raw, f)
                 break
             except requests.exceptions.RequestException as e:
-                logging.warning(f"Request {pathfilename} Error.", exc_info=e)
+                logger.warning(f"Request {pathfilename} Error.", exc_info=e)
     else:
         raise RuntimeError(f"Cannot download {pathfilename}.")
 
@@ -441,7 +442,7 @@ def run_mp(nproc, **arg):
             yield item
             semaphore.release()
     except:
-        logging.exception("run_mp failed")
+        logger.exception("run_mp failed")
         pool.terminate()
         raise
     else: