Remove HAVE_XXXX from neo.io

Author: samuelgarcia

neo/io/igorproio.py

@@ -17,13 +17,6 @@
 from neo.io.baseio import BaseIO
 from neo.core import Block, Segment, AnalogSignal
 
-try:
-    import igor.binarywave as bw
-    import igor.packed as pxp
-    from igor.record.wave import WaveRecord
-    HAVE_IGOR = True
-except ImportError:
-    HAVE_IGOR = False
 
 
 class IgorIO(BaseIO):
@@ -83,6 +76,9 @@ def read_block(self, lazy=False):
         return block
 
     def read_segment(self, lazy=False):
+        import igor.packed as pxp
+        from igor.record.wave import WaveRecord
+
         assert not lazy, 'This IO does not support lazy mode'
         segment = Segment(file_origin=str(self.filename))
 
@@ -104,11 +100,11 @@ def callback(dirpath, key, value):
         return segment
 
     def read_analogsignal(self, path=None, lazy=False):
+        import igor.binarywave as bw
+        import igor.packed as pxp
+
         assert not lazy, 'This IO does not support lazy mode'
 
-        if not HAVE_IGOR:
-            raise Exception("`igor` package not installed. "
-                             "Try `pip install igor`")
         if self.extension == 'ibw':
             data = bw.load(str(self.filename))
             version = data['version']

neo/io/klustakwikio.py

@@ -21,14 +21,6 @@
 # note neo.core need only numpy and quantitie
 import numpy as np
 
-try:
-    import matplotlib.mlab as mlab
-except ImportError as err:
-    HAVE_MLAB = False
-    MLAB_ERR = err
-else:
-    HAVE_MLAB = True
-    MLAB_ERR = None
 
 # I need to subclass BaseIO
 from neo.io.baseio import BaseIO
@@ -105,8 +97,6 @@ def __init__(self, filename, sampling_rate=30000.):
         sampling_rate : in Hz, necessary because the KlustaKwik files
             stores data in samples.
         """
-        if not HAVE_MLAB:
-            raise MLAB_ERR
         BaseIO.__init__(self)
         # self.filename = os.path.normpath(filename)
         self.filename, self.basename = os.path.split(os.path.abspath(filename))

neo/io/kwikio.py

@@ -15,23 +15,6 @@
 import quantities as pq
 import os
 
-try:
-    from scipy import stats
-except ImportError as err:
-    HAVE_SCIPY = False
-    SCIPY_ERR = err
-else:
-    HAVE_SCIPY = True
-    SCIPY_ERR = None
-
-try:
-    from klusta import kwik
-except ImportError as err:
-    HAVE_KWIK = False
-    KWIK_ERR = err
-else:
-    HAVE_KWIK = True
-    KWIK_ERR = None
 
 # I need to subclass BaseIO
 from neo.io.baseio import BaseIO
@@ -77,8 +60,8 @@ def __init__(self, filename):
         Arguments:
             filename : the filename
         """
-        if not HAVE_KWIK:
-            raise KWIK_ERR
+        from klusta import kwik
+
         BaseIO.__init__(self)
         self.filename = os.path.abspath(filename)
         model = kwik.KwikModel(self.filename)  # TODO this group is loaded twice

neo/io/neomatlabio.py

@@ -18,23 +18,8 @@
 import numpy as np
 import quantities as pq
 
-# check scipy
-try:
-    from packaging.version import Version
-    import scipy.io
-    import scipy.version
-except ImportError as err:
-    HAVE_SCIPY = False
-    SCIPY_ERR = err
-else:
-    if Version(scipy.version.version) < Version('0.12.0'):
-        HAVE_SCIPY = False
-        SCIPY_ERR = ImportError("your scipy version is too old to support "
-                                + "MatlabIO, you need at least 0.12.0. "
-                                + "You have %s" % scipy.version.version)
-    else:
-        HAVE_SCIPY = True
-        SCIPY_ERR = None
+from packaging.version import Version
+
 
 from neo.io.baseio import BaseIO
 from neo.core import (Block, Segment, AnalogSignal, IrregularlySampledSignal,
@@ -212,8 +197,13 @@ def __init__(self, filename=None):
         Arguments:
             filename : the filename to read
         """
-        if not HAVE_SCIPY:
-            raise SCIPY_ERR
+        import scipy
+
+        if Version(scipy.version.version) < Version('0.12.0'):
+            raise ImportError("your scipy version is too old to support "
+                                    + "MatlabIO, you need at least 0.12.0. "
+                                    + "You have %s" % scipy.version.version)
+
         BaseIO.__init__(self)
         self.filename = filename
 
@@ -222,6 +212,7 @@ def read_block(self, lazy=False):
         Arguments:
 
         """
+        import scipy.io
         assert not lazy, 'Do not support lazy'
 
         d = scipy.io.loadmat(self.filename, struct_as_record=False,
@@ -241,7 +232,7 @@ def write_block(self, bl, **kargs):
         Arguments:
             bl: the block to b saved
         """
-
+        import scipy.io
         bl_struct = self.create_struct_from_obj(bl)
 
         for seg in bl.segments:

neo/io/nixio.py

@@ -39,13 +39,6 @@
 from ..io.proxyobjects import BaseProxy
 from ..version import version as neover
 
-try:
-    import nixio as nix
-
-    HAVE_NIX = True
-except ImportError:
-    HAVE_NIX = False
-
 
 datetime_types = (date, time, datetime)
 
@@ -121,16 +114,17 @@ def dt_from_nix(nixdt, annotype):
 
 
 def check_nix_version():
-    if not HAVE_NIX:
+    try:
+        import nixio
+    except ImportError:
         raise Exception(
             "Failed to import NIX. "
             "The NixIO requires the Python package for NIX "
             "(nixio on PyPi). Try `pip install nixio`."
-
         )
 
     # nixio version numbers have a 'v' prefix which breaks the comparison
-    nixverstr = nix.__version__.lstrip("v")
+    nixverstr = nixio.__version__.lstrip("v")
     try:
         nixver = Version(nixverstr)
     except ValueError:
@@ -174,25 +168,27 @@ def __init__(self, filename, mode="rw"):
         :param filename: Full path to the file
         """
         check_nix_version()
+        import nixio
+
         BaseIO.__init__(self, filename)
         self.filename = str(filename)
         if mode == "ro":
-            filemode = nix.FileMode.ReadOnly
+            filemode = nixio.FileMode.ReadOnly
         elif mode == "rw":
-            filemode = nix.FileMode.ReadWrite
+            filemode = nixio.FileMode.ReadWrite
         elif mode == "ow":
-            filemode = nix.FileMode.Overwrite
+            filemode = nixio.FileMode.Overwrite
         else:
             raise ValueError(f"Invalid mode specified '{mode}'. "
                              "Valid modes: 'ro' (ReadOnly)', 'rw' (ReadWrite),"
                              " 'ow' (Overwrite).")
-        self.nix_file = nix.File.open(self.filename, filemode)
+        self.nix_file = nixio.File.open(self.filename, filemode)
 
-        if self.nix_file.mode == nix.FileMode.ReadOnly:
+        if self.nix_file.mode == nixio.FileMode.ReadOnly:
             self._file_version = '0.5.2'
             if "neo" in self.nix_file.sections:
                 self._file_version = self.nix_file.sections["neo"]["version"]
-        elif self.nix_file.mode == nix.FileMode.ReadWrite:
+        elif self.nix_file.mode == nixio.FileMode.ReadWrite:
             if "neo" in self.nix_file.sections:
                 self._file_version = self.nix_file.sections["neo"]["version"]
             else:
@@ -1154,6 +1150,8 @@ def _write_spiketrain(self, spiketrain, nixblock, nixgroup):
         :param nixblock: NIX Block where the MultiTag will be created
         :param nixgroup: NIX Group where the MultiTag will be attached
         """
+        import nixio
+
         if "nix_name" in spiketrain.annotations:
             nix_name = spiketrain.annotations["nix_name"]
         else:
@@ -1208,7 +1206,7 @@ def _write_spiketrain(self, spiketrain, nixblock, nixgroup):
                                               data=wfdata)
             wfda.unit = wfunits
             wfda.metadata = nixmt.metadata.create_section(wfda.name, "neo.waveforms.metadata")
-            nixmt.create_feature(wfda, nix.LinkType.Indexed)
+            nixmt.create_feature(wfda, nixio.LinkType.Indexed)
             # TODO: Move time dimension first for PR #457
             # https://github.com/NeuralEnsemble/python-neo/pull/457
             wfda.append_set_dimension()
@@ -1234,6 +1232,7 @@ def _write_property(self, section, name, v):
         :param v: The value to write
         :return: The newly created property
         """
+        import nixio
 
         if isinstance(v, datetime_types):
             value, annotype = dt_to_nix(v)
@@ -1243,7 +1242,7 @@ def _write_property(self, section, name, v):
             if len(v):
                 section.create_property(name, v)
             else:
-                section.create_property(name, nix.DataType.String)
+                section.create_property(name, nixio.DataType.String)
         elif isinstance(v, bytes):
             section.create_property(name, v.decode())
         elif isinstance(v, Iterable):
@@ -1258,7 +1257,7 @@ def _write_property(self, section, name, v):
                 # NIX supports empty properties but dtype must be specified
                 # Defaulting to String and using definition to signify empty
                 # iterable as opposed to empty string
-                values = nix.DataType.String
+                values = nixio.DataType.String
                 definition = EMPTYANNOTATION
             else:
                 for item in v:
@@ -1303,6 +1302,8 @@ def _nix_attr_to_neo(nix_obj):
         Metadata: For properties that specify a 'unit', a Quantity object is
                   created.
         """
+        import nixio
+
         neo_attrs = dict()
         neo_attrs["nix_name"] = nix_obj.name
         neo_attrs["description"] = stringify(nix_obj.definition)
@@ -1312,7 +1313,7 @@ def _nix_attr_to_neo(nix_obj):
                 if not len(values):
                     if prop.definition == EMPTYANNOTATION:
                         values = list()
-                    elif prop.data_type == nix.DataType.String:
+                    elif prop.data_type == nixio.DataType.String:
                         values = ""
                 elif len(values) == 1:
                     values = values[0]