Accept file and path names to be pathlib objects

neo/io/baseio.py

@@ -97,7 +97,7 @@ class BaseIO:
     mode = 'file'  # or 'fake' or 'dir' or 'database'
 
     def __init__(self, filename=None, **kargs):
-        self.filename = filename
+        self.filename = str(filename)
         # create a logger for the IO class
         fullname = self.__class__.__module__ + '.' + self.__class__.__name__
         self.logger = logging.getLogger(fullname)

neo/io/igorproio.py

@@ -12,7 +12,7 @@
 """
 
 from warnings import warn
-import numpy as np
+import pathlib
 import quantities as pq
 from neo.io.baseio import BaseIO
 from neo.core import Block, Segment, AnalogSignal
@@ -66,28 +66,29 @@ def __init__(self, filename=None, parse_notes=None):
 
         """
         BaseIO.__init__(self)
-        assert any([filename.endswith('.%s' % x) for x in self.extensions]), \
+        filename = pathlib.Path(filename)
+        assert filename.suffix[1:] in self.extensions, \
             "Only the following extensions are supported: %s" % self.extensions
         self.filename = filename
-        self.extension = filename.split('.')[-1]
+        self.extension = filename.suffix[1:]
         self.parse_notes = parse_notes
         self._filesystem = None
 
     def read_block(self, lazy=False):
         assert not lazy, 'This IO does not support lazy mode'
 
-        block = Block(file_origin=self.filename)
+        block = Block(file_origin=str(self.filename))
         block.segments.append(self.read_segment(lazy=lazy))
         block.segments[-1].block = block
         return block
 
     def read_segment(self, lazy=False):
         assert not lazy, 'This IO does not support lazy mode'
-        segment = Segment(file_origin=self.filename)
+        segment = Segment(file_origin=str(self.filename))
 
         if self.extension == 'pxp':
             if not self._filesystem:
-                _, self.filesystem = pxp.load(self.filename)
+                _, self.filesystem = pxp.load(str(self.filename))
 
             def callback(dirpath, key, value):
                 if isinstance(value, WaveRecord):
@@ -109,7 +110,7 @@ def read_analogsignal(self, path=None, lazy=False):
             raise Exception("`igor` package not installed. "
                              "Try `pip install igor`")
         if self.extension == 'ibw':
-            data = bw.load(self.filename)
+            data = bw.load(str(self.filename))
             version = data['version']
             if version > 5:
                 raise IOError("Igor binary wave file format version {} "
@@ -118,7 +119,7 @@ def read_analogsignal(self, path=None, lazy=False):
             assert type(path) is str, \
                 "A colon-separated Igor-style path must be provided."
             if not self._filesystem:
-                _, self.filesystem = pxp.load(self.filename)
+                _, self.filesystem = pxp.load(str(self.filename))
                 path = path.split(':')
                 location = self.filesystem['root']
                 for element in path:
@@ -162,7 +163,7 @@ def _wave_to_analogsignal(self, content, dirpath):
 
         signal = AnalogSignal(signal, units=units, copy=False, t_start=t_start,
                               sampling_period=sampling_period, name=name,
-                              file_origin=self.filename, **annotations)
+                              file_origin=str(self.filename), **annotations)
         return signal
 
 

neo/io/nixio.py

@@ -175,7 +175,7 @@ def __init__(self, filename, mode="rw"):
         """
         check_nix_version()
         BaseIO.__init__(self, filename)
-        self.filename = filename
+        self.filename = str(filename)
         if mode == "ro":
             filemode = nix.FileMode.ReadOnly
         elif mode == "rw":

neo/rawio/axonarawio.py

@@ -22,7 +22,7 @@
 import numpy as np
 import os
 import re
-import contextlib
+import pathlib
 import datetime
 
 
@@ -66,10 +66,11 @@ class AxonaRawIO(BaseRawIO):
     def __init__(self, filename):
         BaseRawIO.__init__(self)
 
+        filename = pathlib.Path(filename)
         # We accept base filenames, .bin and .set extensions
-        self.filename = filename.replace('.bin', '').replace('.set', '')
-        self.bin_file = os.path.join(self.filename + '.bin')
-        self.set_file = os.path.join(self.filename + '.set')
+        self.filename = filename.with_suffix('')
+        self.bin_file = self.filename.with_suffix('.bin')
+        self.set_file = self.filename.with_suffix('.set')
         self.set_file_encoding = 'cp1252'
 
     def _source_name(self):

neo/rawio/blackrockrawio.py

@@ -132,7 +132,7 @@ def __init__(self, filename=None, nsx_override=None, nev_override=None,
         """
         BaseRawIO.__init__(self)
 
-        self.filename = filename
+        self.filename = str(filename)
 
         # remove extension from base _filenames
         for ext in self.extensions:

neo/rawio/elanrawio.py

@@ -22,9 +22,8 @@
 import numpy as np
 
 import datetime
-import os
 import re
-import io
+import pathlib
 
 
 class ElanRawIO(BaseRawIO):
@@ -33,13 +32,15 @@ class ElanRawIO(BaseRawIO):
 
     def __init__(self, filename=None, entfile=None, posfile=None):
         BaseRawIO.__init__(self)
-        self.filename = filename
+        self.filename = pathlib.Path(filename)
 
         # check whether ent and pos files are defined
+        # keep existing suffixes in the process of ent and pos filename
+        # generation
         if entfile is None:
-            entfile = self.filename + '.ent'
+            entfile = self.filename.with_suffix(self.filename.suffix + '.ent')
         if posfile is None:
-            posfile = self.filename + '.pos'
+            posfile = self.filename.with_suffix(self.filename.suffix + '.pos')
         self.entfile = entfile
         self.posfile = posfile
 

neo/rawio/nixrawio.py

@@ -42,7 +42,7 @@ class NIXRawIO(BaseRawIO):
     def __init__(self, filename=''):
         check_nix_version()
         BaseRawIO.__init__(self)
-        self.filename = filename
+        self.filename = str(filename)
 
     def _source_name(self):
         return self.filename

neo/rawio/tdtrawio.py

@@ -42,6 +42,7 @@ def __init__(self, dirname='', sortname=''):
         which uses the original online sort.
         """
         BaseRawIO.__init__(self)
+        dirname = str(dirname)
         if dirname.endswith('/'):
             dirname = dirname[:-1]
         self.dirname = dirname

neo/test/iotest/common_io_test.py

@@ -21,6 +21,7 @@
 import inspect
 from copy import copy
 import unittest
+import pathlib
 
 from neo.core import Block, Segment
 from neo.io.basefromrawio import BaseFromRaw
@@ -39,6 +40,7 @@
                                    close_object_safe, create_generic_io_object,
                                    create_generic_reader,
                                    create_generic_writer,
+                                   get_test_file_full_path,
                                    iter_generic_io_objects,
                                    iter_generic_readers, iter_read_objects,
                                    read_generic,
@@ -205,65 +207,6 @@ def generic_io_object(self, filename=None, return_path=False, clean=False):
                                         return_path=return_path,
                                         clean=clean)
 
-    def create_file_reader(self, filename=None, return_path=False,
-                           clean=False, target=None, readall=False):
-        '''
-        Create a function that can read from the specified filename.
-
-        If filename is None, create a filename (default).
-
-        If return_path is True, return the full path of the file along with
-        the reader function.  return reader, path.  Default is False.
-
-        If clean is True, try to delete existing versions of the file
-        before creating the io object.  Default is False.
-
-        If target is None, use the first supported_objects from ioobj
-        If target is False, use the 'read' method.
-        If target is the Block or Segment class, use read_block or
-        read_segment, respectively.
-        If target is a string, use 'read_'+target.
-
-        If readall is True, use the read_all_ method instead of the read_
-        method. Default is False.
-        '''
-        ioobj, path = self.generic_io_object(filename=filename,
-                                             return_path=True, clean=clean)
-
-        res = create_generic_reader(ioobj, target=target, readall=readall)
-
-        if return_path:
-            return res, path
-        return res
-
-    def create_file_writer(self, filename=None, return_path=False,
-                           clean=False, target=None):
-        '''
-        Create a function that can write from the specified filename.
-
-        If filename is None, create a filename (default).
-
-        If return_path is True, return the full path of the file along with
-        the writer function.  return writer, path.  Default is False.
-
-        If clean is True, try to delete existing versions of the file
-        before creating the io object.  Default is False.
-
-        If target is None, use the first supported_objects from ioobj
-        If target is False, use the 'write' method.
-        If target is the Block or Segment class, use write_block or
-        write_segment, respectively.
-        If target is a string, use 'write_'+target.
-        '''
-        ioobj, path = self.generic_io_object(filename=filename,
-                                             return_path=True, clean=clean)
-
-        res = create_generic_writer(ioobj, target=target)
-
-        if return_path:
-            return res, path
-        return res
-
     def read_file(self, filename=None, return_path=False, clean=False,
                   target=None, readall=False, lazy=False):
         '''
@@ -569,3 +512,14 @@ def test_create_group_across_segment(self):
                                 reader(lazy=self.ioclass.support_lazy, create_group_across_segment=case)
                         else:
                             reader(lazy=self.ioclass.support_lazy, create_group_across_segment=case)
+
+    def test__handle_pathlib_filename(self):
+        if self.files_to_test:
+            filename = get_test_file_full_path(self.ioclass, filename=self.files_to_test[0],
+                                               directory=self.local_test_dir)
+            pathlib_filename = pathlib.Path(filename)
+
+            if self.ioclass.mode == 'file':
+                self.ioclass(filename=pathlib_filename)
+            elif self.ioclass.mode == 'dir':
+                self.ioclass(dirname=pathlib_filename)

neo/test/iotest/tools.py

@@ -45,23 +45,16 @@ def cleanup_test_file(mode, path, directory=None):
             shutil.rmtree(path)
 
 
-def get_test_file_full_path(ioclass, filename=None,
-                            directory=None, clean=False):
+def get_test_file_full_path(ioclass, filename=None, directory=None, clean=False):
     """
     Get the full path for a file of the given filename.
 
     If filename is None, create a filename.
-
     If filename is a list, get the full path for each item in the list.
 
-    If return_path is True, also return the full path to the file.
-
     If directory is not None and path is not an absolute path already,
     use the file from the given directory.
 
-    If return_path is True, return the full path of the file along with
-    the io object.  return reader, path.  Default is False.
-
     If clean is True, try to delete existing versions of the file
     before creating the io object.  Default is False.
     """