Merge branch 'dev' into timeseries_timestamps_data_length_mismatch_ra…

…ise_error
NeurodataWithoutBorders · Feb 18, 2025 · 49237f3 · 49237f3
2 parents f68d334 + e43a602
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,7 +16,8 @@
 ### Documentation and tutorial enhancements
 - Updated `SpikeEventSeries`, `DecompositionSeries`, and `FilteredEphys` examples. @stephprince [#2012](https://github.com/NeurodataWithoutBorders/pynwb/pull/2012)
 - Replaced deprecated `scipy.misc.face` dataset in the images tutorial with another example. @stephprince [#2016](https://github.com/NeurodataWithoutBorders/pynwb/pull/2016)
-
+- Removed Allen Brain Observatory example which was unnecessary and difficult to maintain. @rly [#2026](https://github.com/NeurodataWithoutBorders/pynwb/pull/2026)
+
 ## PyNWB 2.8.3 (November 19, 2024)
 
 ### Enhancements and minor changes

diff --git a/docs/gallery/domain/brain_observatory.py b/docs/gallery/domain/brain_observatory.py
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -84,7 +84,6 @@ class CustomSphinxGallerySectionSortKey(ExampleTitleSortKey):
             "icephys.py",
             "plot_behavior.py",
             "images.py",
-            "brain_observatory.py"
         ],
         'advanced_io': []
     }

diff --git a/requirements-doc.txt b/requirements-doc.txt
@@ -4,8 +4,6 @@ sphinx>=4  # improved support for docutils>=0.17
 sphinx_rtd_theme>=1  # <1 does not work with docutils>=0.17
 matplotlib
 sphinx-gallery
-# allensdk>=2.13.2  # allensdk reinstalls pynwb and hdmf. TODO set up a separate workflow to test allensdk
-# MarkupSafe==2.0.1  # resolve incompatibility between jinja2 and markupsafe: https://github.com/AllenInstitute/AllenSDK/issues/2308
 Pillow
 sphinx-copybutton
 dataframe_image   # used to render large dataframe as image in the sphinx gallery to improve html display

diff --git a/test.py b/test.py
@@ -86,10 +86,6 @@ def _import_from_file(script):
     os.path.join('advanced_io', 'streaming.py'),
 ]
 
-allensdk_examples = [
-    os.path.join('domain', 'brain_observatory.py'),  # TODO create separate workflow for this
-]
-
 
 def run_example_tests():
     """Run the Sphinx gallery example files, excluding ROS3-dependent ones, to check for errors."""
@@ -99,7 +95,7 @@ def run_example_tests():
         for f in files:
             if f.endswith(".py"):
                 name_with_parent_dir = os.path.join(os.path.basename(root), f)
-                if name_with_parent_dir in ros3_examples or name_with_parent_dir in allensdk_examples:
+                if name_with_parent_dir in ros3_examples:
                     logging.info("Skipping %s" % name_with_parent_dir)
                     continue
                 examples_scripts.append(os.path.join(root, f))
@@ -277,7 +273,6 @@ def clean_up_tests():
         "basic_sparse_iterwrite_*.npy",
         "basics_tutorial.nwb",
         "behavioral_tutorial.nwb",
-        "brain_observatory.nwb",
         "cache_spec_example.nwb",
         "ecephys_tutorial.nwb",
         "ecog.extensions.yaml",