New Logger new_release (#64)

* add loggin

* create log file in tmp path

* add logger file

* remove file and line description in log file

* fix stdout output to pass pytests

* added print function along with logging function; added the logging.exception function to catch the raise exception.

* logger fix to remove redundant prints

* fix handlers

* Refactored logger and cli

* Test -w x -d args

* Decoupled stdout from file log

* Use tempfile for log

* Fixed logic for delOutputFiles()

Co-authored-by: lkagami <[email protected]>

Acpype_API_Jupyter.ipynb

@@ -34,7 +34,7 @@
  "name": "stdout",
  "output_type": "stream",
  "text": [
- "2021.12.14\n"
+ "2021.12.24\n"
  ]
  },
  {
@@ -91,13 +91,6 @@
  "==> * Antechamber OK *\n",
  "==> * Parmchk OK *\n",
  "==> Executing Tleap...\n",
- "++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n",
- "Checking 'DMP'....\n",
- "Checking parameters for unit 'DMP'.\n",
- "Checking for bond parameters.\n",
- "Checking for angle parameters.\n",
- "Unit is OK.\n",
- "++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n",
  "==> * Tleap OK *\n",
  "==> Removing temporary files...\n"
  ]

acpype/__init__.py

@@ -1,4 +1,4 @@
 # from https://packaging.python.org/guides/single-sourcing-package-version/
 # using option 2
 # updated automatically via pre-commit git-hook
-__version__ = "2021.12.23"
+__version__ = "2021.12.24"

acpype/cli.py

@@ -55,31 +55,19 @@
 import time
 import os
 import sys
-from shutil import rmtree, which
+from shutil import rmtree
 from acpype.topol import MolTopol, ACTopol, header
 from acpype.parser_args import get_option_parser
-from acpype.utils import while_replace, elapsedTime
+from acpype.utils import while_replace, elapsedTime, set_for_pip
 from acpype.params import binaries
-
-
-def set_for_pip(binaries):
- # For pip package
- if which(binaries["ac_bin"]) is None:
- LOCAL_PATH = os.path.dirname(__file__)
- if sys.platform == "linux":
- os.environ["PATH"] += os.pathsep + LOCAL_PATH + "/amber21-11_linux/bin"
- os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_linux/"
- os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_linux/lib/"
- elif sys.platform == "darwin":
- os.environ["PATH"] += os.pathsep + LOCAL_PATH + "/amber21-11_os/bin"
- os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_os/"
- os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_os/lib/"
- os.environ["DYLD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_os/lib/"
+from acpype.logger import copy_log, set_logging_conf as logger
 
 
 def chk_py_ver():
  if sys.version_info < (3, 6):
- raise Exception("Sorry, you need python 3.6 or higher")
+ msg = "Sorry, you need python 3.6 or higher"
+ logger().exception(msg)
+ raise Exception(msg)
 
 
 def init_main(binaries=binaries, argv=None):
@@ -103,7 +91,13 @@ def init_main(binaries=binaries, argv=None):
  print(header)
  sys.exit(0)
 
- print(header)
+ level = 20
+ if not args.verboseless:
+ level = 100
+ if args.debug:
+ level = 10
+
+ logger(level).info(header)
 
  if not args.input:
  amb2gmxF = True
@@ -112,16 +106,16 @@ def init_main(binaries=binaries, argv=None):
  elif args.inpcrd or args.prmtop:
  parser.error("either '-i' or ('-p', '-x'), but not both")
 
- if args.debug:
-  texta = "Python Version %s" % sys.version
-  print("DEBUG: %s" % while_replace(texta))
+ logger(level).debug(f"CLI: {' '.join(argv)}")
+ texta = "Python Version %s" % sys.version
+ logger(level).debug(while_replace(texta))
 
  if args.direct and not amb2gmxF:
  parser.error("option -u is only meaningful in 'amb2gmx' mode (args '-p' and '-x')")
 
  try:
  if amb2gmxF:
- print("Converting Amber input files to Gromacs ...")
+ logger(level).info("Converting Amber input files to Gromacs ...")
  system = MolTopol(
  acFileXyz=args.inpcrd,
  acFileTop=args.prmtop,
@@ -138,6 +132,7 @@ def init_main(binaries=binaries, argv=None):
 
  system.printDebug("prmtop and inpcrd files parsed")
  system.writeGromacsTopolFiles()
+ copy_log(system)
  else:
  molecule = ACTopol(
  args.input,
@@ -165,11 +160,11 @@ def init_main(binaries=binaries, argv=None):
 
  molecule.createACTopol()
  molecule.createMolTopol()
-
+ copy_log(molecule)
  acpypeFailed = False
  except Exception:
  _exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
- print("ACPYPE FAILED: %s" % exceptionValue)
+ logger(level).error("ACPYPE FAILED: %s" % exceptionValue)
  if args.debug:
  traceback.print_tb(exceptionTraceback, file=sys.stdout)
  acpypeFailed = True
@@ -179,7 +174,7 @@ def init_main(binaries=binaries, argv=None):
  amsg = "less than a second"
  else:
  amsg = elapsedTime(execTime)
- print("Total time of execution: %s" % amsg)
+ logger(level).info("Total time of execution: %s" % amsg)
 
  if args.ipython:
  import IPython # pylint: disable=import-outside-toplevel
@@ -190,6 +185,7 @@ def init_main(binaries=binaries, argv=None):
  rmtree(molecule.tmpDir)
  except Exception:
  pass
+
  if acpypeFailed:
  sys.exit(19)
  try:

acpype/logger.py

@@ -0,0 +1,71 @@
+import os
+from shutil import move
+import sys
+import logging
+from tempfile import NamedTemporaryFile
+
+tmpLogFile = NamedTemporaryFile().name
+
+
+class LogFormatter(logging.Formatter):
+
+ """
+ Define log formatter
+ """
+
+ err_fmt = "ERROR: %(msg)s"
+ warn_fmt = "WARNING: %(msg)s"
+ dbg_fmt = "DEBUG: %(msg)s"
+ info_fmt = "%(msg)s"
+
+ def __init__(self):
+ super().__init__(fmt="%(levelno)d: %(msg)s", datefmt=None, style="%")
+
+ def format(self, record):
+
+ # Save the original format configured by the user
+ # when the logger formatter was instantiated
+ format_orig = self._style._fmt
+
+ # Replace the original format with one customized by logging level
+ if record.levelno == logging.DEBUG:
+ self._style._fmt = LogFormatter.dbg_fmt
+ elif record.levelno == logging.INFO:
+ self._style._fmt = LogFormatter.info_fmt
+ elif record.levelno == logging.ERROR:
+ self._style._fmt = LogFormatter.err_fmt
+ elif record.levelno == logging.WARNING:
+ self._style._fmt = LogFormatter.warn_fmt
+ # Call the original formatter class to do the grunt work
+ result = logging.Formatter.format(self, record)
+ # Restore the original format configured by the user
+ self._style._fmt = format_orig
+ return result
+
+
+def copy_log(molecule):
+ local_log = os.path.join(molecule.absHomeDir, "acpype.log")
+ if os.path.exists(local_log):
+ os.remove(local_log)
+ if os.path.exists(tmpLogFile):
+ move(tmpLogFile, local_log)
+
+
+def set_logging_conf(level=20):
+ # Setting logging configurations
+ logging.root.setLevel(0)
+ logger = logging.getLogger(__name__)
+ if logger.handlers:
+ logger.handlers.pop()
+
+ fmt = LogFormatter()
+ file_handler = logging.FileHandler(filename=tmpLogFile)
+ stdout_handler = logging.StreamHandler(sys.stdout)
+ file_handler.setLevel(logging.DEBUG)
+ stdout_handler.setLevel(level)
+ stdout_handler.setFormatter(fmt)
+ file_handler.setFormatter(fmt)
+ if not logger.handlers:
+ logger.addHandler(file_handler)
+ logger.addHandler(stdout_handler)
+ return logger

acpype/parser_args.py

@@ -100,6 +100,14 @@ def get_option_parser():
  dest="debug",
  help="for debugging purposes, keep any temporary file created (not allowed with arg -w)",
  )
+ group.add_argument(
+ "-w",
+ "--verboseless",
+ action="store_false",
+ default=True,
+ dest="verboseless",
+ help="print nothing (not allowed with arg -d)",
+ )
  parser.add_argument(
  "-o",
  "--outtop",
@@ -139,14 +147,6 @@ def get_option_parser():
  dest="ipython",
  help="start iPython interpreter",
  )
- group.add_argument(
- "-w",
- "--verboseless",
- action="store_false",
- default=True,
- dest="verboseless",
- help="print nothing (not allowed with arg -d)",
- )
  parser.add_argument(
  "-g",
  "--merge",