Merge branch 'rc/2.16.1'

Author: morriscb

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

@@ -77,7 +77,7 @@ jobs:
       - name: run test in docker
         run: |
           docker run \
-              --env-file /home/github_worker/env.list \
+              --env-file ~/env.list \
               --mount type=bind,source=$PWD,target=/home/ghworker,bind-propagation=rshared \
               --mount type=bind,source=/data/informatics/module_test_data/,target=/data/informatics/module_test_data/,bind-propagation=rshared,ro \
               --mount type=bind,source=/allen/,target=/allen/,bind-propagation=rshared,ro \

.github/workflows/nightly.yml

@@ -19,7 +19,7 @@ jobs:
       - name: run test in docker
         run: |
           docker run \
-              --env-file /home/github_worker/env_nightly.list \
+              --env-file ~/env_nightly.list \
               --mount type=bind,source=$PWD,target=/home/ghworker,bind-propagation=rshared \
               --mount type=bind,source=/data/informatics/module_test_data/,target=/data/informatics/module_test_data/,bind-propagation=rshared,ro \
               --mount type=bind,source=/allen/,target=/allen/,bind-propagation=rshared,ro \

.readthedocs.yml

@@ -7,12 +7,15 @@ version: 2
 sphinx:
   builder: html
 
+build:
+  os: ubuntu-22.04
+  tools:
+      python: "3.8"
+
 python:
-   version: 3.8
    install:
       - requirements: doc_requirements.txt
 
 formats:
   - epub
-  - pdf
-
+  - pdf

CHANGELOG.md

@@ -1,6 +1,12 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
+## [2.16.1] = 2023-11-13
+- See release notes on Github
+- Update testing
+- Update readthedocs configuration
+- Fix bug in trials change time loading.
+
 ## [2.16.0] = 2023-11-09
 - Python 3.10 and 3.11 support
 - Support for VBO update release.

allensdk/__init__.py

@@ -35,7 +35,7 @@
 #
 import logging
 
-__version__ = '2.16.0'
+__version__ = '2.16.1'
 
 
 try:

allensdk/brain_observatory/behavior/data_objects/trials/trials.py

@@ -275,7 +275,10 @@ def index(self) -> pd.Index:
 
     @property
     def change_time(self) -> pd.Series:
-        return self.data["change_time"]
+        if "change_time" in self.data:
+            return self.data["change_time"]
+        elif "change_time_no_display_delay" in self.data:
+            return self.data["change_time_no_display_delay"]
 
     @property
     def lick_times(self) -> pd.Series:

doc_requirements.txt

@@ -1,37 +1,37 @@
-pep8==1.7.0,<2.0.0
-flake8>=1.5.0,<4.0.0
-pylint>=1.5.4,<3.0.0
-numpydoc>=0.6.0,<1.0.0
-jupyter>=1.0.0,<2.0.0
+pep8
+flake8
+pylint
+numpydoc
+jupyter
 # from here on, this file should contain a subset of the packages specified in requirements.txt
 # some packages are excluded because they can't be installed on readthedocs
 # these ought to be mocked out in doc_template/conf.py so that docs are generated for allensdk modules that import 
 # those packages
 # known examples: tables
-psycopg2-binary>=2.7,<3.0.0
-h5py>=2.8,<3.0.0
-matplotlib>=1.4.3,<4.0.0
-numpy>=1.15.4,<1.19.0
-pandas>=0.25.1,<=0.25.3
-jinja2>=2.7.3,<2.12.0
-scipy>=0.15.1,<2.0.0
-six>=1.9.0,<2.0.0
-pynrrd>=0.2.1,<1.0.0
-future >= 0.14.3,<1.0.0
-requests<3.0.0
-requests-toolbelt<1.0.0
-simplejson>=3.10.0,<4.0.0
-scikit-image>=0.14.0,<0.17.0
-scikit-build<1.0.0
-statsmodels==0.9.0
-simpleitk>=2.0.2,<3.0.0
-argschema>=3.0.1,<4.0.0
-glymur==0.8.19
-xarray<0.16.0
-hdmf==1.0.2
-pynwb==1.0.2
-seaborn<1.0.0
-aiohttp==3.7.4
-nest_asyncio==1.2.0
-docutils<0.18
-markupsafe==2.0.1
+psycopg2-binary
+h5py
+matplotlib
+numpy<1.24
+pandas==1.5.3
+jinja2
+scipy<1.11
+six
+pynrrd
+future
+requests
+requests-toolbelt
+simplejson
+scikit-image
+scikit-build
+statsmodels
+simpleitk
+argschema
+glymur
+xarray<2023.2.0
+hdmf!=3.5.*,!=3.6.*,!=3.7.*,!=3.8.*
+pynwb
+seaborn
+aiohttp
+nest_asyncio
+docutils
+markupsafe