Remove numpy and h5py restrictions (#536)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Steph Prince <[email protected]>

CHANGELOG.md

@@ -1,5 +1,8 @@
 # Upcoming
 
+### Improvements
+* Added support for Numpy 2 and h5py 3.12, and pinned PyNWB to <3.0 temporarily. [#536](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/536)
+
 ### Fixes
 * Fixed issue where the description check failed if the description was a list. [#535](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/535)
 

pyproject.toml

@@ -32,7 +32,7 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "pynwb>=2.8",   # NWB Inspector should always be used with most recent minor versions of PyNWB
+    "pynwb>=2.8,<3",   # NWB Inspector should always be used with most recent minor versions of PyNWB
     "hdmf-zarr",
     "fsspec",
     "s3fs",
@@ -45,8 +45,6 @@ dependencies = [
     "click",
     "tqdm",
     "isodate",
-    "numpy>=1.22.0,<2.0.0", # TODO: add compatibility for 2.0 - HDMF Zarr and others also still have some troubles
-    "h5py<3.12.0", # TODO: remove pin when https://github.com/h5py/h5py/issues/2505 is fixed and released
 ]
 
 [project.optional-dependencies]

src/nwbinspector/checks/_tables.py

@@ -155,7 +155,7 @@ def check_column_binary_capability(
                 ["hit", "miss"],
             ]
             if any([set(parsed_unique_values) == set(pair) for pair in pairs_to_check]):  # type: ignore
-                saved_bytes = (unique_values.dtype.itemsize - 1) * np.product(
+                saved_bytes = (unique_values.dtype.itemsize - 1) * np.prod(
                     get_data_shape(data=column.data, strict_no_data_load=True)
                 )
                 if unique_values.dtype == "float":

tests/unit_tests/test_tables.py

@@ -4,6 +4,7 @@
 
 import numpy as np
 from hdmf.common import DynamicTable, DynamicTableRegion
+from numpy.lib import NumpyVersion
 from pynwb.file import Device, ElectrodeGroup, ElectrodeTable, TimeIntervals, Units
 
 from nwbinspector import Importance, InspectorMessage
@@ -187,7 +188,8 @@ def test_binary_int_fail(self):
         self.table.add_column(name="test_col", description="")
         for x in [1, 0, 1, 0, 1]:
             self.table.add_row(test_col=x)
-        if platform.system() == "Windows":
+        # the default numpy int in Windows with NumPy < 2 is int32. otherwise it is int64.
+        if platform.system() == "Windows" and NumpyVersion(np.__version__) < "2.0.0":
             platform_saved_bytes = "15.00B"
         else:
             platform_saved_bytes = "35.00B"