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",