Merge pull request #73 from leeping/rawstreamhandler

Handlers that do not add newline characters

geometric/log.ini

@@ -12,13 +12,13 @@ level=INFO
 handlers=stream_handler, file_handler
 
 [handler_stream_handler]
-class=StreamHandler
+class=geometric.nifty.RawStreamHandler
 level=INFO
 formatter=formatter
 args=(sys.stderr,)
 
 [handler_file_handler]
-class=FileHandler
+class=geometric.nifty.RawFileHandler
 level=INFO
 formatter=formatter
 args=('%(logfilename)s',)

geometric/logJson.ini

@@ -0,0 +1,22 @@
+[loggers]
+keys=root
+
+[handlers]
+keys=stream_handler
+
+[formatters]
+keys=formatter
+
+[logger_root]
+level=INFO
+handlers=stream_handler
+
+[handler_stream_handler]
+class=geometric.nifty.RawStreamHandler
+level=INFO
+formatter=formatter
+args=(sys.stderr,)
+
+[formatter_formatter]
+format=%(message)s
+#format=%(asctime)s %(name)-12s %(levelname)-8s %(message)s

geometric/nifty.py

@@ -50,34 +50,54 @@
 if "forcebalance" in __name__:
     # If this module is part of ForceBalance, use the package level logger
     from .output import *
-elif "geometric" in __name__:
-    # This ensures logging behavior is consistent with the rest of geomeTRIC
-    from logging import *
-    logger = getLogger(__name__)
-    logger.setLevel(INFO)
+    package="ForceBalance"
 else:
-    # Previous default behavior if FB package level loggers could not be imported
     from logging import *
+    # Define two handlers that don't print newline characters at the end of each line
     class RawStreamHandler(StreamHandler):
-        """Exactly like output.StreamHandler except it does no extra formatting
-        before sending logging messages to the stream. This is more compatible with
-        how output has been displayed in ForceBalance. Default stream has also been
-        changed from stderr to stdout"""
+        """
+        Exactly like StreamHandler, except no newline character is printed at the end of each message.
+        This is done in order to ensure functions in molecule.py and nifty.py work consistently
+        across multiple packages.
+        """
         def __init__(self, stream = sys.stdout):
             super(RawStreamHandler, self).__init__(stream)
 
         def emit(self, record):
             message = record.getMessage()
             self.stream.write(message)
             self.flush()
-    # logger=getLogger()
-    # logger.handlers = [RawStreamHandler(sys.stdout)]
-    # LPW: Daniel Smith suggested these changes to improve logger behavior
-    logger = getLogger("NiftyLogger")
-    logger.setLevel(INFO)
-    handler = RawStreamHandler()
-    logger.addHandler(handler)
 
+    class RawFileHandler(FileHandler):
+        """
+        Exactly like FileHandler, except no newline character is printed at the end of each message.
+        This is done in order to ensure functions in molecule.py and nifty.py work consistently
+        across multiple packages.
+        """
+        def __init__(self, *args, **kwargs):
+            super(RawFileHandler, self).__init__(*args, **kwargs)
+
+        def emit(self, record):
+            if self.stream is None:
+                self.stream = self._open()
+            message = record.getMessage()
+            self.stream.write(message)
+            self.flush()
+
+    if "geometric" in __name__:
+        # This ensures logging behavior is consistent with the rest of geomeTRIC
+        logger = getLogger(__name__)
+        logger.setLevel(INFO)
+        package="geomeTRIC"
+    else:
+        logger = getLogger("NiftyLogger")
+        logger.setLevel(INFO)
+        handler = RawStreamHandler()
+        logger.addHandler(handler)
+        if __name__ == "__main__":
+            package = "LPW-nifty.py"
+        else:
+            package = __name__.split('.')[0]
 
 try:
     import bz2
@@ -93,7 +113,6 @@ def emit(self, record):
     logger.warning("gzip module import failed (used in compressing or decompressing pickle files)\n")
     HaveGZ = False
 
-
 ## Boltzmann constant
 kb = 0.0083144100163
 ## Q-Chem to GMX unit conversion for energy
@@ -152,6 +171,7 @@ def pvec1d(vec1d, precision=1, format="e", loglevel=INFO):
     v2a = np.array(vec1d)
     for i in range(v2a.shape[0]):
         logger.log(loglevel, "%% .%i%s " % (precision, format) % v2a[i])
+    logger.log(loglevel, '\n')
 
 def astr(vec1d, precision=4):
     """ Write an array to a string so we can use it to key a dictionary. """
@@ -164,7 +184,9 @@ def pmat2d(mat2d, precision=1, format="e", loglevel=INFO):
     """
     m2a = np.array(mat2d)
     for i in range(m2a.shape[0]):
-        logger.log(loglevel, ' '.join(["%% .%i%s " % (precision, format) % m2a[i][j] for j in range(m2a[i].shape[0])]))
+        for j in range(m2a.shape[1]):
+            logger.log(loglevel, "%% .%i%s " % (precision, format) % m2a[i][j])
+        logger.log(loglevel, '\n')
 
 def grouper(iterable, n):
     """Collect data into fixed-length chunks or blocks"""
@@ -504,26 +526,26 @@ def monotonic_decreasing(arr, start=None, end=None, verbose=False):
         end = len(arr) - 1
     a0 = arr[start]
     idx = [start]
-    if verbose: logger.info("Starting @ %i : %.6f" % (start, arr[start]))
+    if verbose: logger.info("Starting @ %i : %.6f\n" % (start, arr[start]))
     if end > start:
         i = start+1
         while i < end:
             if arr[i] < a0:
                 a0 = arr[i]
                 idx.append(i)
-                if verbose: logger.info("Including  %i : %.6f" % (i, arr[i]))
+                if verbose: logger.info("Including  %i : %.6f\n" % (i, arr[i]))
             else:
-                if verbose: logger.info("Excluding  %i : %.6f" % (i, arr[i]))
+                if verbose: logger.info("Excluding  %i : %.6f\n" % (i, arr[i]))
             i += 1
     if end < start:
         i = start-1
         while i >= end:
             if arr[i] < a0:
                 a0 = arr[i]
                 idx.append(i)
-                if verbose: logger.info("Including  %i : %.6f" % (i, arr[i]))
+                if verbose: logger.info("Including  %i : %.6f\n" % (i, arr[i]))
             else:
-                if verbose: logger.info("Excluding  %i : %.6f" % (i, arr[i]))
+                if verbose: logger.info("Excluding  %i : %.6f\n" % (i, arr[i]))
             i -= 1
     return np.array(idx)
 
@@ -835,7 +857,7 @@ def getWQIds():
     global WQIDS
     return WQIDS
 
-def createWorkQueue(wq_port, debug=True, name='geomeTRIC'):
+def createWorkQueue(wq_port, debug=True, name=package):
     global WORK_QUEUE
     if debug:
         work_queue.set_debug_flag('all')
@@ -1083,7 +1105,7 @@ def listfiles(fnms=None, ext=None, err=False, dnm=None):
             raise RuntimeError
         answer = [fnms]
     elif fnms is not None:
-        logger.info(fnms)
+        logger.info(str(fnms))
         logger.error('First argument to listfiles must be a list, a string, or None')
         raise RuntimeError
     if answer == [] and ext is not None: