Support numpy 1.24.x, make tests pass with latest dependencies

.github/workflows/github-actions-ci.yml

@@ -26,7 +26,7 @@ jobs:
     name: Lint
     runs-on: "ubuntu-latest"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: flake8 linting
         run: |
           pip install flake8
@@ -43,15 +43,16 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ["macos-latest", "windows-latest", "ubuntu-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        # macos-15-intel for x86_64, macos-latest for ARM64
+        os: ["macos-15-intel", "macos-latest", "windows-latest", "ubuntu-latest"]
+        python-version: ["3.10", "3.11"]
       fail-fast: false
     defaults:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -71,9 +72,9 @@ jobs:
     runs-on: ["self-hosted"]
     strategy:
       matrix:
-        image: ["allensdk_local_py38:latest"]
+        image: ["allensdk_local_py310:latest"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: run test in docker
         run: |
           docker run \

.github/workflows/nightly.yml

@@ -10,10 +10,10 @@ jobs:
     runs-on: ["self-hosted"]
     strategy:
       matrix:
-        image: ["allensdk_local_py38:latest"]
+        image: ["allensdk_local_py310:latest"]
         branch: ["master", "rc/**"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           ref: ${{ matrix.branch }}
       - name: run test in docker

.github/workflows/notebook_runner.yml

@@ -9,11 +9,11 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.8"]
+        python-version: ["3.10"]
       fail-fast: false
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v4
         with:

allensdk/brain_observatory/behavior/data_objects/running_speed/running_acquisition.py

@@ -129,7 +129,7 @@ def from_nwb(
         cls,
         nwbfile: NWBFile
     ) -> "RunningAcquisition":
-        running_module = nwbfile.modules['running']
+        running_module = nwbfile.processing['running']
         dx_interface = running_module.get_data_interface('dx')
 
         dx = dx_interface.data

allensdk/brain_observatory/behavior/data_objects/running_speed/running_speed.py

@@ -188,7 +188,7 @@ def from_nwb(
         nwbfile: NWBFile,
         filtered=True
     ) -> "RunningSpeed":
-        running_module = nwbfile.modules['running']
+        running_module = nwbfile.processing['running']
         interface_name = 'speed' if filtered else 'speed_unfiltered'
         running_interface = running_module.get_data_interface(interface_name)
 

allensdk/brain_observatory/behavior/data_objects/stimuli/templates.py

@@ -1,4 +1,5 @@
 import os
+import warnings
 import numpy as np
 from pathlib import Path
 from typing import Optional, List, Dict
@@ -184,17 +185,44 @@ def to_nwb(self, nwbfile: NWBFile,
 
             nwbfile.add_stimulus_template(visual_stimulus_image_series)
 
+        # DEPRECATED (11/2025): _add_image_index_to_nwb is no longer called.
+        # The IndexSeries using indexed_timeseries is deprecated in pynwb 2.x
+        # and would require significant refactoring to use indexed_images instead.
+        # Since this NWB writing code will not be used for new data generation,
+        # we skip this step rather than refactor. The stimulus template data
+        # is still written above; only the IndexSeries linking is skipped.
+        # See: https://pynwb.readthedocs.io/en/stable/pynwb.image.html#pynwb.image.IndexSeries
         if 'image_index' in stimulus_presentations.value \
                 and self._image_template_key is not None:
-            nwbfile = self._add_image_index_to_nwb(
-                nwbfile=nwbfile, presentations=stimulus_presentations)
+            warnings.warn(
+                "As of 11/2025, Templates.to_nwb() no longer adds the image "
+                "index (IndexSeries) to the NWB file. The IndexSeries "
+                "indexed_timeseries field is deprecated in pynwb 2.x. "
+                "The stimulus template data is still written.",
+                UserWarning,
+                stacklevel=2
+            )
 
         return nwbfile
 
     def _add_image_index_to_nwb(
             self, nwbfile: NWBFile, presentations: Presentations):
         """Adds the image index and start_time for all stimulus templates
-        to NWB"""
+        to NWB
+
+        .. deprecated:: 2.16.3
+            This method is deprecated as of 11/2025. The IndexSeries
+            indexed_timeseries field is deprecated in pynwb 2.x. This method
+            is no longer called from to_nwb() and will be removed in a future
+            release.
+        """
+        warnings.warn(
+            "_add_image_index_to_nwb is deprecated and will be removed in a "
+            "future release. The IndexSeries indexed_timeseries field is "
+            "deprecated in pynwb 2.x.",
+            DeprecationWarning,
+            stacklevel=2
+        )
         stimulus_templates = self.value[self._image_template_key]
         presentations = presentations.value
 
@@ -208,7 +236,7 @@ def _add_image_index_to_nwb(
         image_index = IndexSeries(
             name=nwb_template.name,
             data=stimulus_index['image_index'].values,
-            unit='None',
+            unit='N/A',
             indexed_timeseries=nwb_template,
             timestamps=stimulus_index['start_time'].values)
         nwbfile.add_stimulus(image_index)

allensdk/brain_observatory/ecephys/ecephys_project_api/http_engine.py

@@ -93,10 +93,10 @@ def write_bytes(path: str, stream: Iterable[bytes]):
 class AsyncHttpEngine(HttpEngine):
 
     def __init__(
-        self, 
-        scheme: str, 
-        host: str, 
-        session: Optional[aiohttp.ClientSession] = None, 
+        self,
+        scheme: str,
+        host: str,
+        session: Optional[aiohttp.ClientSession] = None,
         **kwargs
     ):
         """ Simple tool for making asynchronous streaming http requests.
@@ -105,11 +105,11 @@ def __init__(
         ----------
         scheme :
             e.g "http" or "https"
-        host : 
+        host :
             will be used as the base for request urls
-        session : 
-            If provided, this preconstructed session will be used rather than 
-            a new one. Keep in mind that AsyncHttpEngine closes its session 
+        session :
+            If provided, this preconstructed session will be used rather than
+            a new one. Keep in mind that AsyncHttpEngine closes its session
             when it is garbage collected!
         **kwargs :
             Will be passed to parent.
@@ -119,14 +119,25 @@ def __init__(
         super(AsyncHttpEngine, self).__init__(scheme, host, **kwargs)
 
         if session:
-            self.session = session
+            self._session = session
+            self._owns_session = False
             warnings.warn(
                 "Recieved preconstructed session, ignoring timeout parameter."
             )
         else:
-            self.session = aiohttp.ClientSession(
+            # Defer session creation until actually needed in an async context
+            # (aiohttp 3.9+ requires ClientSession to be created within an event loop)
+            self._session = None
+            self._owns_session = True
+
+    @property
+    def session(self) -> aiohttp.ClientSession:
+        """Lazily create the aiohttp session when first accessed."""
+        if self._session is None:
+            self._session = aiohttp.ClientSession(
                 timeout=aiohttp.client.ClientTimeout(self.timeout)
             )
+        return self._session
 
     async def _stream_coroutine(
         self, 
@@ -169,10 +180,10 @@ def stream(
         return functools.partial(self._stream_coroutine, route)
 
     def __del__(self):
-        if hasattr(self, "session"):
+        if hasattr(self, "_session") and self._session is not None:
             nest_asyncio.apply()
             loop = asyncio.get_event_loop()
-            loop.run_until_complete(self.session.close())
+            loop.run_until_complete(self._session.close())
 
     @staticmethod
     def write_bytes(

allensdk/brain_observatory/gaze_mapping/_gaze_mapper.py

@@ -289,7 +289,9 @@ def pupil_position_on_monitor_in_degrees(self,
 
         mag = np.linalg.norm(self.monitor.position)
         meridian = np.degrees(np.arctan(x / mag))
-        elevation = np.degrees(np.arctan(y / np.linalg.norm([x, mag], axis=0)))
+        # Use np.vstack to create a homogeneous 2D array (numpy 1.24+ compatibility)
+        elevation = np.degrees(np.arctan(y / np.linalg.norm(
+            np.vstack([x, np.full_like(x, mag, dtype=float)]), axis=0)))
 
         angles = np.vstack([meridian, elevation]).T
 

allensdk/brain_observatory/nwb/nwb_api.py

@@ -59,9 +59,9 @@ def get_running_speed(self, lowpass=True) -> RunningSpeed:
         """
 
         interface_name = 'speed' if lowpass else 'speed_unfiltered'
-        values = self.nwbfile.modules['running'].get_data_interface(
+        values = self.nwbfile.processing['running'].get_data_interface(
             interface_name).data[:]
-        timestamps = self.nwbfile.modules['running'].get_data_interface(
+        timestamps = self.nwbfile.processing['running'].get_data_interface(
             interface_name).timestamps[:]
 
         return RunningSpeed(
@@ -87,7 +87,7 @@ def get_image(self, name, module, image_api=None) -> sitk.Image:
         if image_api is None:
             image_api = ImageApi
 
-        nwb_img = self.nwbfile.modules[module].get_data_interface(
+        nwb_img = self.nwbfile.processing[module].get_data_interface(
             'images')[name]
         data = nwb_img.data
         resolution = nwb_img.resolution  # px/cm

allensdk/mouse_connectivity/grid/utilities/image_utilities.py

@@ -1,27 +1,23 @@
-from __future__ import division
 import logging
 import os
 import sys
 
-from six import iteritems
 import numpy as np
 import SimpleITK as sitk
 from skimage.draw import polygon
 
 from allensdk.config.manifest import Manifest
 
 
-if sys.version_info[0] > 2:
-    failed_import = (ImportError, ModuleNotFoundError)
-else:
-    failed_import = (ImportError,)
+# Exception types to catch when importing optional JPEG2000 libraries
+failed_import = (ImportError, ModuleNotFoundError)
 
 
 # use np_sitk_convert or sitk_np_convert to access
 # TODO: check if this already exists. If not: add more dtypes
 # it does not
 NUMPY_SITK_TYPE_LOOKUP = {np.dtype(np.float32): sitk.sitkFloat32}
-SITK_NUMPY_TYPE_LOOKUP = {v: k for k, v in iteritems(NUMPY_SITK_TYPE_LOOKUP)}
+SITK_NUMPY_TYPE_LOOKUP = {v: k for k, v in NUMPY_SITK_TYPE_LOOKUP.items()}
 
 
 # ITK/Numpy
@@ -273,19 +269,55 @@ def __read_intensity_image_with_glymur(path):
     return glymur.Jp2k(path)[:]
 
 
-try:
+def _get_jpeg_readers():
+    """Get the appropriate JPEG2000 readers based on available libraries.
+
+    Returns a tuple of (read_segmentation_image, read_intensity_image) functions.
+    Raises ImportError if neither jpeg_twok nor glymur is available.
+    """
     # we use a proprietary library called kakadu internally
     # (jpeg_twok is a python interface around that library)
     # kakadu offers really good performance as well as support for
     # advanced jp2 features
     # however, since it is proprietary, we can't share it
     # alongside the allensdk,
     # so we default to glymur (a python openjpeg) for external users.
-    sys.path.append('/shared/bioapps/itk/itk_shared/jp2/build')
-    import jpeg_twok
-    read_segmentation_image = __read_segmentation_image_with_kakadu
-    read_intensity_image = __read_intensity_image_with_kakadu
-except failed_import:
-    import glymur
-    read_segmentation_image = __read_segmentation_image_with_glymur
-    read_intensity_image = __read_intensity_image_with_glymur
+    try:
+        sys.path.append('/shared/bioapps/itk/itk_shared/jp2/build')
+        import jpeg_twok
+        return (__read_segmentation_image_with_kakadu,
+                __read_intensity_image_with_kakadu)
+    except failed_import:
+        pass
+
+    try:
+        import glymur
+        return (__read_segmentation_image_with_glymur,
+                __read_intensity_image_with_glymur)
+    except failed_import:
+        pass
+
+    raise ImportError(
+        "Neither jpeg_twok nor glymur is available. "
+        "Please install glymur (pip install glymur) and ensure openjpeg "
+        "is installed on your system."
+    )
+
+
+try:
+    read_segmentation_image, read_intensity_image = _get_jpeg_readers()
+except ImportError:
+    # Define placeholder functions that raise on use rather than on import
+    def read_segmentation_image(path):
+        raise ImportError(
+            "Neither jpeg_twok nor glymur is available. "
+            "Please install glymur (pip install glymur) and ensure openjpeg "
+            "is installed on your system."
+        )
+
+    def read_intensity_image(path, reduce_level=None, channel=None):
+        raise ImportError(
+            "Neither jpeg_twok nor glymur is available. "
+            "Please install glymur (pip install glymur) and ensure openjpeg "
+            "is installed on your system."
+        )