Merge branch 'rc/2.9.0'

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

@@ -22,12 +22,28 @@ env:
   MTRAIN_PASSWORD: password
 
 jobs:
-  osx:
+  lint:
+    name: Lint
+    runs-on: "ubuntu-latest"
+    steps:
+      - uses: actions/checkout@v2
+      - name: flake8 linting
+        run: |
+          pip install flake8
+          export PATH="/home/runner/.local/bin:${PATH}"
+          git fetch origin master
+          # `|| true` to force exit code 0 even if no files found
+          CHANGED_PYFILES=$(git diff --name-only --diff-filter AM origin/master | grep .py || true)
+          echo "List of changed files:"
+          echo ${CHANGED_PYFILES}
+          flake8 ${CHANGED_PYFILES} --count
+
+  allensdk:
     name: ${{ matrix.python-version }}, ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ["macos-latest", "windows-latest"]
+        os: ["macos-latest", "windows-latest", "ubuntu-latest"]
         python-version: ["3.6", "3.7"]
     defaults:
       run:

CHANGELOG.md

@@ -1,7 +1,11 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
-## [2.8.0] = TBD
+## [2.9.0] = 2021-03-08
+- Updates to Session metadata; refactors implementation to use class rather than dict internally
+- Fixes a bug that was preventing Allen Institute Windows users from accessing gratings images
+
+## [2.8.0] = 2021-02-25
 - Created lookup table to get monitor_delay for cases where calculation from data fails
 - If sync timestamp file has more timestamps than eye tracking moving has frame, trim excess timestamps (up to 15)
 - Session API returns both warped and unwarped stimulus images, and both are written to NWB

README.md

@@ -2,7 +2,6 @@
 
 [![Join the chat at https://gitter.im/AllenInstitute/AllenSDK](https://badges.gitter.im/AllenInstitute/AllenSDK.svg)](https://gitter.im/AllenInstitute/AllenSDK?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 [![Documentation Status](https://readthedocs.org/projects/allensdk/badge/?version=latest)](https://allensdk.readthedocs.io/en/latest/?badge=latest)
-[![AllenInstitute](https://circleci.com/gh/AllenInstitute/AllenSDK.svg?style=svg)](https://app.circleci.com/pipelines/github/AllenInstitute/AllenSDK)
 [![Actions Status](https://github.com/AllenInstitute/AllenSDK/workflows/ci/github-actions/badge.svg)](https://github.com/AllenInstitute/AllenSDK/actions)
 
 

allensdk/__init__.py

@@ -35,7 +35,7 @@
 #
 import logging
 
-__version__ = '2.8.0'
+__version__ = '2.9.0'
 
 
 try:

allensdk/brain_observatory/behavior/behavior_ophys_session.py

@@ -168,6 +168,13 @@ def ophys_experiment_id(self) -> int:
         """
         return self._ophys_experiment_id
 
+    @property
+    def ophys_session_id(self) -> int:
+        """Unique identifier for this ophys session.
+        :rtype: int
+        """
+        return self._ophys_session_id
+
     @property
     def max_projection(self) -> Image:
         """2D max projection image.
@@ -309,11 +316,14 @@ def eye_tracking(self) -> pd.DataFrame:
           gaze location), with (0, 0) being the upper-left corner of the
           eye-tracking image.
         - The 'likely_blink' column is True for any row (frame) where the pupil
-          fit failed OR eye fit failed OR an outlier fit was identified on the pupil or eye fit.
-        - The pupil_area, cr_area, eye_area columns are set to NaN wherever 'likely_blink' == True.
-        - The pupil_area_raw, cr_area_raw, eye_area_raw columns contains all pupil fit values (including where 'likely_blink' == True).
+          fit failed OR eye fit failed OR an outlier fit was identified on the
+          pupil or eye fit.
+        - The pupil_area, cr_area, eye_area columns are set to NaN wherever
+          'likely_blink' == True.
+        - The pupil_area_raw, cr_area_raw, eye_area_raw columns contains all
+          pupil fit values (including where 'likely_blink' == True).
         - All ellipse fits are derived from tracking points that were output by
-          a DeepLabCut model that was trained on hand-annotated data frome a
+          a DeepLabCut model that was trained on hand-annotated data from a
           subset of imaging sessions on optical physiology rigs.
         - Raw DeepLabCut tracking points are not publicly available.
 

allensdk/brain_observatory/behavior/behavior_session.py

@@ -4,12 +4,13 @@
 import numpy as np
 import inspect
 
-from allensdk.brain_observatory.behavior.stimulus_processing import \
-    StimulusTemplate
+from allensdk.brain_observatory.behavior.metadata.behavior_metadata import \
+    BehaviorMetadata
 from allensdk.core.lazy_property import LazyPropertyMixin
 from allensdk.brain_observatory.behavior.session_apis.data_io import (
     BehaviorLimsApi, BehaviorNwbApi)
-from allensdk.brain_observatory.behavior.session_apis.abcs import BehaviorBase
+from allensdk.brain_observatory.behavior.session_apis.abcs.\
+    session_base.behavior_base import BehaviorBase
 from allensdk.brain_observatory.behavior.trials_processing import (
     calculate_reward_rate)
 from allensdk.brain_observatory.behavior.dprime import (
@@ -385,7 +386,13 @@ def metadata(self) -> Dict[str, Any]:
         """Return metadata about the session.
         :rtype: dict
         """
-        return self._metadata
+        if isinstance(self._metadata, BehaviorMetadata):
+            metadata = self._metadata.to_dict()
+        else:
+            # NWB API returns as dict
+            metadata = self._metadata
+
+        return metadata
 
     @metadata.setter
     def metadata(self, value):