Support only latest PyNWB

CHANGELOG.md

@@ -9,6 +9,8 @@
 ### Improvements
 * Removed the `robust_ros3_read` utility helper. [#506](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/506)
 * Simplified the `nwbinspector.testing` configuration framework. [#509](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/509)
+* Cleaned old references to non-recent PyNWB and HDMF versions. Current policy is that latest NWB Inspector releases should only support compatibility with latest PyNWB and HDMF. [#510](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/510)
+
 
 
 # v0.5.2

requirements.txt

@@ -1,4 +1,4 @@
-pynwb
+pynwb>=2.8  # NWB Inspector should always be used with most recent minor versions of PyNWB
 hdmf-zarr
 fsspec
 s3fs

src/nwbinspector/_dandi_inspection.py

@@ -241,9 +241,8 @@ def inspect_url(
         h5py.File(name=byte_stream) as file,
         pynwb.NWBHDF5IO(file=file) as io,
     ):
-        if not skip_validate:
+        if skip_validate is False:
             validation_errors = pynwb.validate(io=io)
-
             for validation_error in validation_errors:
                 yield InspectorMessage(
                     message=validation_error.reason,

src/nwbinspector/_nwb_inspection.py

@@ -10,7 +10,6 @@
 
 import pynwb
 from natsort import natsorted
-from packaging.version import Version
 from tqdm import tqdm
 
 from . import available_checks, configure_checks
@@ -20,7 +19,6 @@
     OptionalListOfStrings,
     PathType,
     calculate_number_of_cpu,
-    get_package_version,
 )
 
 
@@ -73,8 +71,8 @@ def inspect_all(
         all available CPUs minus x.
         Set to 1 (also the default) to disable.
     skip_validate : bool, optional
-        Skip the PyNWB validation step. This may be desired for older NWBFiles (< schema version v2.10).
-        The default is False, which is also recommended.
+        Skip the PyNWB validation step.
+        The default is False, which is recommended.
     progress_bar : bool, optional
         Display a progress bar while scanning NWBFiles.
         Defaults to True.
@@ -232,8 +230,8 @@ def inspect_nwbfile(
     nwbfile_path : FilePathType
         Path to the NWB file on disk or on S3.
     skip_validate : bool
-        Skip the PyNWB validation step. This may be desired for older NWBFiles (< schema version v2.10).
-        The default is False, which is also recommended.
+        Skip the PyNWB validation step.
+        The default is False, which is recommended.
     checks : list, optional
         List of checks to run.
     config : dict
@@ -269,7 +267,7 @@ def inspect_nwbfile(
     filterwarnings(action="ignore", message="No cached namespaces found in .*")
     filterwarnings(action="ignore", message="Ignoring cached namespace .*")
 
-    if not skip_validate and get_package_version("pynwb") >= Version("2.2.0"):
+    if not skip_validate:
         validation_error_list, _ = pynwb.validate(paths=[nwbfile_path])
         for validation_namespace_errors in validation_error_list:
             for validation_error in validation_namespace_errors:
@@ -282,17 +280,6 @@ def inspect_nwbfile(
                 )
 
     with pynwb.NWBHDF5IO(path=nwbfile_path, mode="r", load_namespaces=True) as io:
-        if not skip_validate and get_package_version("pynwb") < Version("2.2.0"):
-            validation_errors = pynwb.validate(io=io)
-            for validation_error in validation_errors:
-                yield InspectorMessage(
-                    message=validation_error.reason,
-                    importance=Importance.PYNWB_VALIDATION,
-                    check_function_name=validation_error.name,
-                    location=validation_error.location,
-                    file_path=nwbfile_path,
-                )
-
         try:
             in_memory_nwbfile = io.read()
 
@@ -321,7 +308,7 @@ def _intercept_in_vitro_protein(nwbfile_object: pynwb.NWBFile, checks: Optional[
     If the special 'protein' subject_id is specified, return a truncated list of checks to run.
 
     This is a temporary method for allowing upload of certain in vitro data to DANDI and
-    is expected to replaced in future versions.
+    is expected to be replaced in future versions.
     """
     subject_related_check_names = [
         "check_subject_exists",

src/nwbinspector/checks/_images.py

@@ -1,38 +1,36 @@
 """Checks specific to the Images neurodata type."""
 
-from packaging.version import Version
+from pynwb.base import Images
 from pynwb.image import IndexSeries
 
 from .._registration import Importance, InspectorMessage, register_check
-from ..utils import get_package_version
-
-# The Images neurodata type was unavailable prior to PyNWB v.2.1.0
-if get_package_version(name="pynwb") >= Version("2.1.0"):
-    from pynwb.base import Images
-
-    @register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=Images)
-    def check_order_of_images_unique(images: Images):
-        """Check that all the values in the order_of_images field of an Images object are unique."""
-        if images.order_of_images is None:
-            return
-        if not len(set(images.order_of_images)) == len(images.order_of_images):
-            return InspectorMessage(message="order_of_images should have unique values.")
-
-    @register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=Images)
-    def check_order_of_images_len(images: Images):
-        """Check that all the values in the order_of_images field of an Images object are unique."""
-        if images.order_of_images is None:
-            return
-        if not len(images.order_of_images) == len(images.images):
-            return InspectorMessage(
-                message=f"Length of order_of_images ({len(images.order_of_images)}) does not match the number of "
-                f"images ({len(images.images)})."
-            )
-
-    @register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=IndexSeries)
-    def check_index_series_points_to_image(index_series: IndexSeries):
-        if index_series.indexed_timeseries is not None:
-            return InspectorMessage(
-                message="Pointing an IndexSeries to a TimeSeries will be deprecated. Please point to an Images "
-                "container instead."
-            )
+
+
+@register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=Images)
+def check_order_of_images_unique(images: Images):
+    """Check that all the values in the order_of_images field of an Images object are unique."""
+    if images.order_of_images is None:
+        return
+    if not len(set(images.order_of_images)) == len(images.order_of_images):
+        return InspectorMessage(message="order_of_images should have unique values.")
+
+
+@register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=Images)
+def check_order_of_images_len(images: Images):
+    """Check that all the values in the order_of_images field of an Images object are unique."""
+    if images.order_of_images is None:
+        return
+    if not len(images.order_of_images) == len(images.images):
+        return InspectorMessage(
+            message=f"Length of order_of_images ({len(images.order_of_images)}) does not match the number of "
+            f"images ({len(images.images)})."
+        )
+
+
+@register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=IndexSeries)
+def check_index_series_points_to_image(index_series: IndexSeries):
+    if index_series.indexed_timeseries is not None:
+        return InspectorMessage(
+            message="Pointing an IndexSeries to a TimeSeries will be deprecated. Please point to an Images "
+            "container instead."
+        )

tests/unit_tests/test_icephys.py

@@ -1,24 +1,16 @@
-import pytest
-from packaging.version import Version
 from pynwb.device import Device
 from pynwb.icephys import IntracellularElectrode
 
 from nwbinspector import Importance, InspectorMessage
 from nwbinspector.checks import check_intracellular_electrode_cell_id_exists
-from nwbinspector.utils import get_package_version
 
-PYNWB_VERSION_LOWER_2_1_0 = get_package_version(name="pynwb") < Version("2.1.0")
-PYNWB_VERSION_LOWER_SKIP_REASON = "This test requires PyNWB>=2.1.0"
 
-
-@pytest.mark.skipif(PYNWB_VERSION_LOWER_2_1_0, reason=PYNWB_VERSION_LOWER_SKIP_REASON)
 def test_pass_check_intracellular_electrode_cell_id_exists():
     device = Device(name="device")
     ielec = IntracellularElectrode(name="ielec", cell_id="123", device=device, description="an intracellular electrode")
     assert check_intracellular_electrode_cell_id_exists(ielec) is None
 
 
-@pytest.mark.skipif(PYNWB_VERSION_LOWER_2_1_0, reason=PYNWB_VERSION_LOWER_SKIP_REASON)
 def test_fail_check_intracellular_electrode_cell_id_exists():
     device = Device(name="device")
     ielec = IntracellularElectrode(name="ielec", device=device, description="an intracellular electrode")
@@ -30,10 +22,3 @@ def test_fail_check_intracellular_electrode_cell_id_exists():
         object_name="ielec",
         location="/",
     )
-
-
-@pytest.mark.skipif(not PYNWB_VERSION_LOWER_2_1_0, reason="This test requires PyNWB<2.1.0")
-def test_skip_check_for_lower_versions():
-    device = Device(name="device")
-    ielec = IntracellularElectrode(name="ielec", device=device, description="an intracellular electrode")
-    assert check_intracellular_electrode_cell_id_exists(ielec) is None

tests/unit_tests/test_images.py

@@ -1,7 +1,6 @@
 import numpy as np
-import pytest
-from packaging.version import Version
 from pynwb import TimeSeries
+from pynwb.base import ImageReferences, Images
 from pynwb.image import GrayscaleImage, IndexSeries
 
 from nwbinspector import Importance, InspectorMessage
@@ -10,15 +9,8 @@
     check_order_of_images_len,
     check_order_of_images_unique,
 )
-from nwbinspector.utils import get_package_version
 
-HAVE_IMAGES = get_package_version(name="pynwb") >= Version("2.1.0")
-skip_reason = "You must have PyNWB>=v2.1.0 to run these tests!"
-if HAVE_IMAGES:
-    from pynwb.base import ImageReferences, Images
 
-
-@pytest.mark.skipif(not HAVE_IMAGES, reason=skip_reason)
 def test_check_order_of_images_unique():
     imgs = [GrayscaleImage(name=f"image{i}", data=np.random.randn(10, 10)) for i in range(5)]
     img_refs = ImageReferences(name="order_of_images", data=imgs + [imgs[0]])
@@ -34,7 +26,6 @@ def test_check_order_of_images_unique():
     )
 
 
-@pytest.mark.skipif(not HAVE_IMAGES, reason=skip_reason)
 def test_pass_check_order_of_images_unique():
     imgs = [GrayscaleImage(name=f"image{i}", data=np.random.randn(10, 10)) for i in range(5)]
     img_refs = ImageReferences(name="order_of_images", data=imgs)
@@ -43,7 +34,6 @@ def test_pass_check_order_of_images_unique():
     assert check_order_of_images_unique(images) is None
 
 
-@pytest.mark.skipif(not HAVE_IMAGES, reason=skip_reason)
 def test_check_order_of_images_len():
     imgs = [GrayscaleImage(name=f"image{i}", data=np.random.randn(10, 10)) for i in range(5)]
     img_refs = ImageReferences(name="order_of_images", data=imgs + [imgs[0]])
@@ -59,7 +49,6 @@ def test_check_order_of_images_len():
     )
 
 
-@pytest.mark.skipif(not HAVE_IMAGES, reason=skip_reason)
 def test_pass_check_order_of_images_len():
     imgs = [GrayscaleImage(name=f"image{i}", data=np.random.randn(10, 10)) for i in range(5)]
     img_refs = ImageReferences(name="order_of_images", data=imgs)
@@ -68,7 +57,6 @@ def test_pass_check_order_of_images_len():
     assert check_order_of_images_len(images) is None
 
 
-@pytest.mark.skipif(not HAVE_IMAGES, reason=skip_reason)
 def test_pass_check_index_series_points_to_image():
     gs_img = GrayscaleImage(
         name="random grayscale",
@@ -95,7 +83,6 @@ def test_pass_check_index_series_points_to_image():
     assert check_index_series_points_to_image(idx_series) is None
 
 
-@pytest.mark.skipif(not HAVE_IMAGES, reason=skip_reason)
 def test_fail_check_index_series_points_to_image():
     time_series = TimeSeries(
         name="TimeSeries",