Merge pull request #539 from AllenInstitute/release-1.0.5

Release 1.0.5

CHANGELOG.md

@@ -6,7 +6,10 @@ All notable changes to this project will be documented in this file.
 ### Added
 
 ### Changed
-- adjusted get_stimulus_epoch to require a complete stimulus (both onset and offset) to define the stimulus epoch
+
+## [1.0.5] = 2021-12-13
+Bug fixes: 
+- Converts nwb_version attribute to string if it is in utf-8 encoded bytes.
 
 ## [1.0.4] = 2021-07-29
 Changed:

ipfx/dataset/create.py

@@ -11,7 +11,7 @@
 from ipfx.stimulus import StimulusOntology
 from ipfx.dataset.hbg_nwb_data import HBGNWBData
 from ipfx.dataset.mies_nwb_data import MIESNWBData
-from ipfx import py2to3
+from ipfx.string_utils import to_str
 from ipfx.dataset.labnotebook import LabNotebookReaderIgorNwb
 
 
@@ -59,20 +59,20 @@ def get_nwb_version(nwb_file: str) -> Dict[str, Any]:
     with h5py.File(nwb_file, 'r') as f:
         if "nwb_version" in f:         # In version 0 and 1 this is a dataset
             nwb_version = get_scalar_value(f["nwb_version"][()])
-            nwb_version_str = py2to3.to_str(nwb_version)
+            nwb_version_str = to_str(nwb_version)
             if nwb_version is not None and re.match("^NWB-", nwb_version_str):
                 return {
                     "major": int(nwb_version_str[4]), 
                     "full": nwb_version_str
                 }
 
         elif "nwb_version" in f.attrs:   # in version 2 this is an attribute
-            nwb_version = f.attrs["nwb_version"]
-            if nwb_version is not None and (
-                    re.match("^2", nwb_version) or
-                    re.match("^NWB-2", nwb_version)
+            nwb_version_str = to_str(f.attrs["nwb_version"])
+            if nwb_version_str is not None and (
+                    re.match("^2", nwb_version_str) or
+                    re.match("^NWB-2", nwb_version_str)
             ):
-                return {"major": 2, "full": nwb_version}
+                return {"major": 2, "full": nwb_version_str}
 
     return {"major": None, "full": None}
 

ipfx/dataset/labnotebook.py

@@ -1,6 +1,6 @@
 import h5py
 import math
-from ipfx.py2to3 import to_str
+from ipfx.string_utils import to_str
 
 class LabNotebookReader(object):
     """

ipfx/lims_queries.py

@@ -5,7 +5,7 @@
 from allensdk.core.authentication import credential_injector
 from allensdk.core.auth_config import LIMS_DB_CREDENTIAL_MAP
 
-from ipfx.py2to3 import to_str
+from ipfx.string_utils import to_str
 
 
 TIMEOUT = os.environ.get(

ipfx/string_utils.py

@@ -0,0 +1,20 @@
+from typing import Union
+
+def to_str(s: Union[str, bytes]
+)-> str:
+    """Convert bytes to string if not string
+
+
+    Parameters
+    ----------
+        s (Union[str,bytes]): variable to convert
+
+    Returns
+    -------
+        str
+    """
+    if isinstance(s, bytes):
+        return s.decode('utf-8')
+    else:
+        return s
+

ipfx/version.txt

@@ -1 +1 @@
-1.0.4
+1.0.5

requirements_docs.txt

@@ -1,4 +1,5 @@
 sphinx
 sphinx-gallery
 m2r
-numpydoc>=0.6.0,<1.0.0
+numpydoc>=0.6.0,<1.0.0
+mistune<2

tests/test_string_utils.py

@@ -0,0 +1,22 @@
+from ipfx.string_utils import to_str
+import pytest
+
+
+
+
+@pytest.mark.parametrize(
+    "input, expected",
+    [
+        # Case 0: supplied string
+        (
+            "a_string", "a_string"
+        ),
+        # Case 1: supplied bytes
+        (
+            b"a_string", "a_string"
+        ),
+    ]
+)
+def test_to_string(input, expected):
+    obtained = to_str(input)
+    assert obtained == expected