Prepare for release of PyNWB 2.8.2 (#1960)

* update changelog

* update dependencies

* update requirements-doc.txt

* revert opt requirements update

* update numpy requirement

* update environment

* add family driver file validation, ignore dandi file validation

* revert warning filtering in validation

* Update CHANGELOG.md

* Update environment-ros3.yml

CHANGELOG.md

@@ -1,6 +1,6 @@
 # PyNWB Changelog
 
-## PyNWB 2.8.2 (Upcoming)
+## PyNWB 2.8.2 (September 9, 2024)
 
 ### Enhancements and minor changes
 - Added support for numpy 2.0. @mavaylon1 [#1956](https://github.com/NeurodataWithoutBorders/pynwb/pull/1956)

environment-ros3.yml

@@ -6,9 +6,9 @@ channels:
 dependencies:
   - python==3.12
   - h5py==3.11.0
-  - hdmf==3.14.1
-  - matplotlib==3.8.0
-  - numpy==1.26.4
+  - hdmf==3.14.3
+  - matplotlib==3.8.4
+  - numpy==2.1.1
   - pandas==2.2.2
   - python-dateutil==2.9.0
   - setuptools

test.py

@@ -3,6 +3,7 @@
 import re
 import argparse
 import glob
+import h5py
 import inspect
 import logging
 import os.path
@@ -152,6 +153,9 @@ def validate_nwbs():
     logging.info('running validation tests on NWB files')
     examples_nwbs = glob.glob('*.nwb')
 
+    # exclude files downloaded from dandi, validation of those files is handled by dandisets-health-status checks
+    examples_nwbs = [x for x in examples_nwbs if not x.startswith('sub-')]
+
     import pynwb
     from pynwb.validate import get_cached_namespaces_to_validate
 
@@ -162,15 +166,34 @@ def validate_nwbs():
             ws = list()
             with warnings.catch_warnings(record=True) as tmp:
                 logging.info("Validating with pynwb.validate method.")
-                with pynwb.NWBHDF5IO(nwb, mode='r') as io:
-                    errors = pynwb.validate(io)
-                    TOTAL += 1
+                is_family_nwb_file = False
+                try:
+                    with pynwb.NWBHDF5IO(nwb, mode='r') as io:
+                        errors = pynwb.validate(io)
+                except OSError as e:
+                    # if the file was created with the family driver, need to use the family driver to open it
+                    if 'family driver should be used' in str(e):
+                        is_family_nwb_file = True
+                        match = re.search(r'(\d+)', nwb)
+                        filename_pattern = nwb[:match.start()] + '%d' + nwb[match.end():]  # infer the filename pattern
+                        memb_size = 1024**2  # note: the memb_size must be the same as the one used to create the file
+                        with h5py.File(filename_pattern, mode='r', driver='family', memb_size=memb_size) as f:
+                            with pynwb.NWBHDF5IO(file=f, manager=None, mode='r') as io:
+                                errors = pynwb.validate(io)
+                    else:
+                        raise e
+
+                TOTAL += 1
+
+                if errors:
+                    FAILURES += 1
+                    ERRORS += 1
+                    for err in errors:
+                        print("Error: %s" % err)
 
-                    if errors:
-                        FAILURES += 1
-                        ERRORS += 1
-                        for err in errors:
-                            print("Error: %s" % err)
+                # if file was created with family driver, skip pynwb.validate CLI because not yet supported
+                if is_family_nwb_file:
+                    continue
 
                 namespaces, _, _ = get_cached_namespaces_to_validate(nwb)