Merge pull request #1848 from AllenInstitute/rc/2.7.0

rc/2.7.0

Author: djkapner

.circleci/config.yml

@@ -1,24 +1,27 @@
+env-vars: &env-vars
+  TEST_NWB_FILES: skip
+  TEST_OBSERVATORY_EXPERIMENT_PLOTS_DATA: skip
+  TEST_API_ENDPOINT: http://api.brain-map.org
+  TEST_COMPLETE: false
+  TEST_BAMBOO: false
+  LIMS_DBNAME: db
+  LIMS_PORT: 1234
+  LIMS_PASSWORD: password
+  LIMS_HOST: host
+  LIMS_USER: user
+  MTRAIN_DBNAME: db
+  MTRAIN_USER: user
+  MTRAIN_HOST: host
+  MTRAIN_PORT: 1234
+  MTRAIN_PASSWORD: password
+
 jobs:
   linux-py36: &linux-template
     executor:
       name: python/default
       tag: "3.6.12"
     environment:
-      TEST_NWB_FILES: skip
-      TEST_OBSERVATORY_EXPERIMENT_PLOTS_DATA: skip
-      TEST_API_ENDPOINT: http://api.brain-map.org
-      TEST_COMPLETE: false
-      TEST_BAMBOO: false
-      LIMS_DBNAME: db
-      LIMS_PORT: 1234
-      LIMS_PASSWORD: password
-      LIMS_HOST: host
-      LIMS_USER: user
-      MTRAIN_DBNAME: db
-      MTRAIN_USER: user
-      MTRAIN_HOST: host
-      MTRAIN_PORT: 1234
-      MTRAIN_PASSWORD: password
+      <<: *env-vars
     steps:
       - checkout
       - run: sudo apt-get update
@@ -41,11 +44,71 @@ jobs:
       name: python/default
       tag: "3.7.7"
 
+  osx-py36:
+    parameters:
+      pyversion:
+        default: "3.6.12"
+        type: string
+    macos:
+      xcode: 11.3.0
+    environment:
+      <<: *env-vars
+    steps:
+      - checkout
+      - run:
+          command: |
+            brew install wget
+          name: Install Wget
+      - run:
+          command: |
+            wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh
+            bash miniconda.sh -b -p $HOME/miniconda
+            export PATH="$HOME/miniconda/bin:$PATH"
+            hash -r
+            conda config --set always_yes yes --set changeps1 no
+            conda update -q conda
+            conda create -q -n test-environment python=<<parameters.pyversion>> pip
+            source activate test-environment
+          name: Create conda test environment
+      - run:
+          command: |
+            export PATH="$HOME/miniconda/bin:$PATH"
+            source activate test-environment
+            pip install codecov
+            pip install -r test_requirements.txt
+            pip install .
+          name: Install Allensdk
+      - run:
+          command: |
+            export PATH="$HOME/miniconda/bin:$PATH"
+            source activate test-environment
+            python -m pytest -n 4 --cov allensdk --cov-report xml
+          name: Test
+    
+  lint:
+    executor: python/default
+    steps:
+      - checkout
+      - run:
+          command: |
+            pip install flake8
+            # `|| true` to force exit code 0 even if no files found
+            CHANGED_PYFILES=$(git diff --name-only --diff-filter AM origin/master | grep .py || true)
+            echo "List of changed files:"
+            echo ${CHANGED_PYFILES}
+            echo ${CHANGED_PYFILES} | xargs -r flake8 --count
+          name: Lint
+
 orbs:
   python: circleci/[email protected]
 version: 2.1
 workflows:
   main:
     jobs:
+      # disable lint build, for merge to default branch
+      # turn back on when rc/2.8.0 is started
+      # - lint
       - linux-py36
       - linux-py37
+      # disabled osx build. covered by github-actions
+      # - osx-py36

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

@@ -0,0 +1,46 @@
+name: ci/github-actions
+on: [pull_request]
+env:
+  TEST_NWB_FILES: skip
+  TEST_OBSERVATORY_EXPERIMENT_PLOTS_DATA: skip
+  TEST_API_ENDPOINT: http://api.brain-map.org
+  TEST_COMPLETE: false
+  TEST_BAMBOO: false
+  LIMS_DBNAME: db
+  LIMS_PORT: 1234
+  LIMS_PASSWORD: password
+  LIMS_HOST: host
+  LIMS_USER: user
+  MTRAIN_DBNAME: db
+  MTRAIN_USER: user
+  MTRAIN_HOST: host
+  MTRAIN_PORT: 1234
+  MTRAIN_PASSWORD: password
+
+jobs:
+  osx:
+    name: ${{ matrix.python-version }}, ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ["macos-latest", "windows-latest"]
+        python-version: ["3.6", "3.7"]
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          activate-environment: test-env
+      - name: Install
+        run: |
+          conda activate test-env
+          pip install codecov
+          pip install -r test_requirements.txt
+          pip install .
+      - name: Test
+        run: |
+          py.test --cov=allensdk -n 4

.travis.yml

@@ -1,6 +1,19 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
+## [2.7.0] = TBD
+- Refactored behavior and ophys session and data APIs to remove a circular inheritance issue
+- Fixed segmentation mask and roi_mask misregistration in 'BehaviorOphysSession'
+- Replaces BehaviorOphysSession.get_roi_masks() method with roi_masks property
+- Fixes bug which prevented the SDK from loading stimuli dataframes for static gratings
+- Return event detection data through session API
+- Read/write event detection data from/to NWB
+- Time stamps for events in trial_log are set to the exact sync timestamp of the corresponding frame.
+- For behavior-only sessions, sync-like timestamp of the first frame is set to zero.
+- stimulus_templates in Session API returns new object with key of image name
+- Refactored BehaviorOphysSession to inherit methods and properties from BehaviorSession
+- Fixed a test for checking that Behavior and BehaviorOphysSessions contain the same data regardless of which API (LIMS/JSON/NWB) is used. Also fixed resulting failure cases.
+
 ## [2.6.0] = 2021-02-05
 - Adds ability to write and read behavior only NWB files
 - Adds eye tracking ellipse fits and metadata as new NWB data stream

CHANGELOG.md

@@ -2,6 +2,8 @@
 
 [![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)
 
 
 This repository contains code for processing and analyzing data
@@ -11,4 +13,4 @@ Please visit http://alleninstitute.github.io/AllenSDK for more information.
 
 We welcome contributions! See the [contribution guide](CONTRIBUTING.md) here. See here for [the list of authors](doc_template/authors.rst).
 
-If you have more general questions or comments about the AllenSDK please post them to the [Allen Brain Map Community Forum](https://community.brain-map.org).
+If you have more general questions or comments about the AllenSDK please post them to the [Allen Brain Map Community Forum](https://community.brain-map.org).

README.md

@@ -38,7 +38,7 @@
 
 
 
-__version__ = '2.6.0'
+__version__ = '2.7.0'
 
 
 try: