Whitespace cleanup

api_gen.py

@@ -1,24 +1,24 @@
 
 """
     Generate the lowest-level Cython bindings to HDF5.
-    
+
     In order to translate HDF5 errors to exceptions, the raw HDF5 API is
     wrapped with Cython "error wrappers".  These are cdef functions with
     the same names and signatures as their HDF5 equivalents, but implemented
     in the h5py.defs extension module.
-    
+
     The h5py.defs files (defs.pyx and defs.pxd), along with the "real" HDF5
     function definitions (_hdf5.pxd), are auto-generated by this script from
     api_functions.txt.  This file also contains annotations which indicate
     whether a function requires a certain minimum version of HDF5, an
     MPI-aware build of h5py, or special error handling.
-    
+
     This script is called automatically by the h5py build system when the
     output files are missing, or api_functions.txt has been updated.
-    
+
     See the Line class in this module for documentation of the format for
     api_functions.txt.
-        
+
     h5py/_hdf5.pxd:     Cython "extern" definitions for HDF5 functions
     h5py/defs.pxd:      Cython definitions for error wrappers
     h5py/defs.pyx:      Cython implementations of error wrappers
@@ -32,19 +32,19 @@ class Line(object):
 
     """
         Represents one line from the api_functions.txt file.
-        
+
         Exists to provide the following attributes:
-        
+
         mpi:        Bool indicating if MPI required
         error:      Bool indicating if special error handling required
         version:    None or a minimum-version tuple
         code:       String with function return type
         fname:      String with function name
         sig:        String with raw function signature
         args:       String with sequence of arguments to call function
-        
+
         Example:    MPI ERROR 1.8.12 int foo(char* a, size_t b)
-        
+
         .mpi:       True
         .error:     True
         .version:   (1, 8, 12)
@@ -53,7 +53,7 @@ class Line(object):
         .sig:       "char* a, size_t b"
         .args:      "a, b"
     """
-        
+
     PATTERN = re.compile("""(?P<mpi>(MPI)[ ]+)?
                             (?P<error>(ERROR)[ ]+)?
                             (?P<version>([0-9]+\.[0-9]+\.[0-9]+))?
@@ -69,19 +69,19 @@ class Line(object):
                              [ ]+[ *]*
                              (?P<param>[a-zA-Z_]+[a-zA-Z0-9_]*)
                              """, re.VERBOSE)
-                            
+
     def __init__(self, text):
         """ Break the line into pieces and populate object attributes.
-        
+
         text: A valid function line, with leading/trailing whitespace stripped.
         """
-        
+
         m = self.PATTERN.match(text)
         if m is None:
             raise ValueError("Invalid line encountered: {0}".format(text))
-            
+
         parts = m.groupdict()
-        
+
         self.mpi = parts['mpi'] is not None
         self.error = parts['error'] is not None
         self.version = parts['version']
@@ -141,14 +141,14 @@ def run(self):
         self.cython_imp.write(imp_preamble)
 
         for text in self.functions:
-        
+
             # Directive specifying a header file
             if not text.startswith(' ') and not text.startswith('#') and \
             len(text.strip()) > 0:
                 inc = text.split(':')[0]
                 self.raw_defs.write('cdef extern from "%s.h":\n' % inc)
                 continue
-            
+
             text = text.strip()
 
             # Whitespace or comment line
@@ -160,15 +160,15 @@ def run(self):
             self.write_raw_sig()
             self.write_cython_sig()
             self.write_cython_imp()
-    
+
         self.functions.close()
         self.cython_imp.close()
         self.cython_defs.close()
         self.raw_defs.close()
 
     def add_cython_if(self, block):
         """ Wrap a block of code in the required "IF" checks """
-        
+
         def wrapif(condition, code):
             code = code.replace('\n', '\n    ', code.count('\n')-1) # Yes, -1.
             code = "IF {0}:\n    {1}".format(condition, code)

docs_api/automod.py

@@ -49,11 +49,11 @@ def safe_replace(istr, expr, rpl):
 
 
 try:
-    class_exprs = dict( 
+    class_exprs = dict(
         (re.compile(class_base % x.replace(" ",r"\s"), re.VERBOSE), y) \
         for x, y in class_exprs.iteritems() )
 except AttributeError:
-    class_exprs = dict( 
+    class_exprs = dict(
         (re.compile(class_base % x.replace(" ",r"\s"), re.VERBOSE), y) \
         for x, y in class_exprs.items() )
 
@@ -98,7 +98,7 @@ def rpl(target, match):
 (?P<post>
   \W?                         # May have trailing punctuation
   (?:$|\s+)                   # Must be followed by whitespace or end of string
-)                      
+)
 """ % const_exclude, re.VERBOSE)
 
 def replace_constant(istr, current_module):
@@ -266,4 +266,3 @@ def getsig(docstring):
 
     spx.connect('autodoc-process-signature', proc_sig)
     spx.connect('autodoc-process-docstring', proc_doc)
-

examples/collective_io.py

@@ -1,5 +1,5 @@
 # This file is to test collective io in h5py
- 
+
 """
 Author:  Jialin Liu, [email protected]
 Date:    Nov 17, 2015
@@ -14,14 +14,14 @@
 import time
 import sys
 
-#"run as "mpirun -np 64 python-mpi collective_io.py 1 file.h5" 
+#"run as "mpirun -np 64 python-mpi collective_io.py 1 file.h5"
 #(1 is for collective write, other numbers for non-collective write)"
 
 colw=1 #default is collective write
 filename="parallel_test.hdf5"
 if len(sys.argv)>2:
-	colw = int(sys.argv[1])
-	filename=str(sys.argv[2])
+    colw = int(sys.argv[1])
+    filename=str(sys.argv[2])
 comm =MPI.COMM_WORLD
 nproc = comm.Get_size()
 f = h5py.File(filename, 'w', driver='mpio', comm=MPI.COMM_WORLD)
@@ -42,17 +42,17 @@
     end=start+length_last_rank
 temp=np.random.random((end-start,length_y))
 if colw==1:
-	with dset.collective:
-		dset[start:end,:] = temp
-else :
-	dset[start:end,:] = temp
+    with dset.collective:
+        dset[start:end,:] = temp
+else:
+    dset[start:end,:] = temp
 comm.Barrier()
 timeend=MPI.Wtime()
 if rank==0:
     if colw==1:
-    	print "collective write time %f" %(timeend-timestart)
-    else :
-	print "independent write time %f" %(timeend-timestart)
+        print "collective write time %f" %(timeend-timestart)
+    else:
+        print "independent write time %f" %(timeend-timestart)
     print "data size x: %d y: %d" %(length_x, length_y)
     print "file size ~%d GB" % (length_x*length_y/1024.0/1024.0/1024.0*8.0)
     print "number of processes %d" %nproc

examples/multiprocessing_example.py

@@ -85,7 +85,7 @@ def run_calculation():
     dset.attrs['YSTART'] = YSTART
     dset.attrs['XEXTENT'] = XEXTENT
     dset.attrs['YEXTENT'] = YEXTENT
-    
+
     result = pool.imap(compute_row, (x*xincr for x in xrange(NX)))
 
     for idx, arr in enumerate(result):
@@ -126,6 +126,3 @@ def visualize_file():
     else:
         print('Fractal found in "mandelbrot.hdf5". Delete file to re-run calculation.')
     visualize_file()
-
-
-

examples/swmr_inotify_example.py

@@ -2,19 +2,19 @@
 """
     Demonstrate the use of h5py in SWMR mode to monitor the growth of a dataset
     on nofication of file modifications.
-    
+
     This demo uses pyinotify as a wrapper of Linux inotify.
     https://pypi.python.org/pypi/pyinotify
-    
+
     Usage:
             swmr_inotify_example.py [FILENAME [DATASETNAME]]
-            
+
               FILENAME:    name of file to monitor. Default: swmr.h5
               DATASETNAME: name of dataset to monitor in DATAFILE. Default: data
-            
+
     This script will open the file in SWMR mode and monitor the shape of the
-    dataset on every write event (from inotify). If another application is 
-    concurrently writing data to the file, the writer must have have switched 
+    dataset on every write event (from inotify). If another application is
+    concurrently writing data to the file, the writer must have have switched
     the file into SWMR mode before this script can open the file.
 """
 import asyncore
@@ -34,25 +34,25 @@ def monitor_dataset(self, filename, datasetname):
         self.dset = self.f[datasetname]
 
         self.get_dset_shape()
-        
+
     def get_dset_shape(self):
         logging.debug("Refreshing dataset")
         self.dset.refresh()
-        
+
         logging.debug("Getting shape")
         shape = self.dset.shape
         logging.info("Read data shape: %s"%str(shape))
-        return shape        
-        
+        return shape
+
     def read_dataset(self, latest):
         logging.info("Reading out dataset [%d]"%latest)
         self.dset[latest:]
-                
+
     def process_IN_MODIFY(self, event):
         logging.debug("File modified!")
         shape = self.get_dset_shape()
         self.read_dataset(shape[0])
-                    
+
     def process_IN_CLOSE_WRITE(self, event):
         logging.info("File writer closed file")
         self.get_dset_shape()
@@ -62,7 +62,7 @@ def process_IN_CLOSE_WRITE(self, event):
 
 if __name__ == "__main__":
     logging.basicConfig(format='%(asctime)s  %(levelname)s\t%(message)s',level=logging.INFO)
-    
+
     file_name = "swmr.h5"
     if len(sys.argv) > 1:
         file_name = sys.argv[1]
@@ -72,7 +72,7 @@ def process_IN_CLOSE_WRITE(self, event):
 
 
     wm = pyinotify.WatchManager()  # Watch Manager
-    mask = pyinotify.IN_MODIFY | pyinotify.IN_CLOSE_WRITE 
+    mask = pyinotify.IN_MODIFY | pyinotify.IN_CLOSE_WRITE
     evh = EventHandler()
     evh.monitor_dataset( file_name, dataset_name )
 
@@ -82,4 +82,3 @@ def process_IN_CLOSE_WRITE(self, event):
     # Sit in this loop() until the file writer closes the file
     # or the user hits ctrl-c
     asyncore.loop()
-

examples/swmr_multiprocess.py

@@ -1,18 +1,18 @@
 """
-    Demonstrate the use of h5py in SWMR mode to write to a dataset (appending) 
+    Demonstrate the use of h5py in SWMR mode to write to a dataset (appending)
     from one process while monitoring the growing dataset from another process.
-    
+
     Usage:
             swmr_multiprocess.py [FILENAME [DATASETNAME]]
-            
+
               FILENAME:    name of file to monitor. Default: swmrmp.h5
               DATASETNAME: name of dataset to monitor in DATAFILE. Default: data
-            
+
     This script will start up two processes: a writer and a reader. The writer
     will open/create the file (FILENAME) in SWMR mode, create a dataset and start
     appending data to it. After each append the dataset is flushed and an event
-    sent to the reader process. Meanwhile the reader process will wait for events 
-    from the writer and when triggered it will refresh the dataset and read the 
+    sent to the reader process. Meanwhile the reader process will wait for events
+    from the writer and when triggered it will refresh the dataset and read the
     current shape of it.
 """
 
@@ -29,13 +29,13 @@ def __init__(self, event, fname, dsetname, timeout = 2.0):
         self._fname = fname
         self._dsetname = dsetname
         self._timeout = timeout
-        
+
     def run(self):
         self.log = logging.getLogger('reader')
         self.log.info("Waiting for initial event")
         assert self._event.wait( self._timeout )
         self._event.clear()
-        
+
         self.log.info("Opening file %s", self._fname)
         f = h5py.File(self._fname, 'r', libver='latest', swmr=True)
         assert f.swmr_mode
@@ -58,7 +58,7 @@ def __init__(self, event, fname, dsetname):
         self._event = event
         self._fname = fname
         self._dsetname = dsetname
-        
+
     def run(self):
         self.log = logging.getLogger('writer')
         self.log.info("Creating file %s", self._fname)
@@ -72,7 +72,7 @@ def run(self):
             f.swmr_mode = True
             assert f.swmr_mode
             self.log.debug("Sending initial event")
-            self._event.set()        
+            self._event.set()
 
             # Write loop
             for i in range(5):
@@ -85,7 +85,7 @@ def run(self):
                 self.log.debug("Flushing data")
                 dset.flush()
                 self.log.info("Sending event")
-                self._event.set()        
+                self._event.set()
         finally:
             f.close()
 
@@ -98,19 +98,17 @@ def run(self):
         fname = sys.argv[1]
     if len(sys.argv) > 2:
         dsetname = sys.argv[2]
-        
+
     event = Event()
     reader = SwmrReader(event, fname, dsetname)
     writer = SwmrWriter(event, fname, dsetname)
-    
+
     logging.info("Starting reader")
     reader.start()
     logging.info("Starting reader")
     writer.start()
-    
+
     logging.info("Waiting for writer to finish")
     writer.join()
     logging.info("Waiting for reader to finish")
     reader.join()
-
-