Drop py36 support, update CI, reqs, tests for rc/2.0.0 (#1377)

.circleci/config.yml

@@ -38,13 +38,6 @@ references:
         username: hdmf
         password: $DOCKERHUB_PASSWORD
 
-  py36: &py36
-    docker:
-    - image: circleci/python:3.6.13-buster
-      auth:
-        username: hdmf
-        password: $DOCKERHUB_PASSWORD
-
   conda-image: &conda-image
     docker:
     - image: continuumio/miniconda3:4.9.2
@@ -161,14 +154,6 @@ jobs:
       - run:
           <<: *run-style-check
 
-  python36:
-    <<: *py36
-    environment:
-      - TEST_TOX_ENV: "py36"
-      - BUILD_TOX_ENV: "build-py36"
-      - TEST_WHEELINSTALL_ENV: "wheelinstall"
-    <<: *ci-steps
-
   python37:
     <<: *py37
     environment:
@@ -183,7 +168,6 @@ jobs:
       - TEST_TOX_ENV: "py38"
       - BUILD_TOX_ENV: "build-py38"
       - TEST_WHEELINSTALL_ENV: "wheelinstall"
-      - UPLOAD_WHEELS: "true"
     <<: *ci-steps
 
   python39:
@@ -192,41 +176,33 @@ jobs:
       - TEST_TOX_ENV: "py39"
       - BUILD_TOX_ENV: "build-py39"
       - TEST_WHEELINSTALL_ENV: "wheelinstall"
+      - UPLOAD_WHEELS: "true"  # upload distributions from only this job to pypi
     <<: *ci-steps
 
-  python38-upgrade-dev:
-    <<: *py38
+  python39-upgrade-dev:
+    <<: *py39
     environment:
-      - TEST_TOX_ENV: "py38-upgrade-dev"
-      - BUILD_TOX_ENV: "build-py38-upgrade-dev"
+      - TEST_TOX_ENV: "py39-upgrade-dev"
+      - BUILD_TOX_ENV: "build-py39-upgrade-dev"
       - TEST_WHEELINSTALL_ENV: "wheelinstall"
     <<: *ci-steps
 
-  python38-upgrade-dev-pre:
-    <<: *py38
+  python39-upgrade-dev-pre:
+    <<: *py39
     environment:
-      - TEST_TOX_ENV: "py38-upgrade-dev-pre"
-      - BUILD_TOX_ENV: "build-py38-upgrade-dev-pre"
+      - TEST_TOX_ENV: "py39-upgrade-dev-pre"
+      - BUILD_TOX_ENV: "build-py39-upgrade-dev-pre"
       - TEST_WHEELINSTALL_ENV: "wheelinstall"
     <<: *ci-steps
 
-  python36-min-req:
-    <<: *py36
+  python37-min-req:
+    <<: *py37
     environment:
-      - TEST_TOX_ENV: "py36-min-req"
-      - BUILD_TOX_ENV: "build-py36-min-req"
+      - TEST_TOX_ENV: "py37-min-req"
+      - BUILD_TOX_ENV: "build-py37-min-req"
       - TEST_WHEELINSTALL_ENV: "wheelinstall"
     <<: *ci-steps
 
-  miniconda36:
-    <<: *conda-image
-    environment:
-      - CONDA_PYTHON_VER: "3.6.*=*_cpython"  # avoid using pypy compiler
-      - TEST_TOX_ENV: "py36"
-      - BUILD_TOX_ENV: "build-py36"
-      - TEST_WHEELINSTALL_ENV: "wheelinstall"
-    <<: *conda-steps
-
   miniconda37:
     <<: *conda-image
     environment:
@@ -254,12 +230,6 @@ jobs:
       - TEST_WHEELINSTALL_ENV: "wheelinstall"
     <<: *conda-steps
 
-  gallery36:
-    <<: *py36
-    environment:
-      - TEST_TOX_ENV: "gallery-py36"
-    <<: *gallery-steps
-
   gallery37:
     <<: *py37
     environment:
@@ -278,26 +248,26 @@ jobs:
       - TEST_TOX_ENV: "gallery-py39"
     <<: *gallery-steps
 
-  gallery38-upgrade-dev:
-    <<: *py38
+  gallery39-upgrade-dev:
+    <<: *py39
     environment:
-      - TEST_TOX_ENV: "gallery-py38-upgrade-dev"
+      - TEST_TOX_ENV: "gallery-py39-upgrade-dev"
     <<: *gallery-steps
 
-  gallery38-upgrade-dev-pre:
-    <<: *py38
+  gallery39-upgrade-dev-pre:
+    <<: *py39
     environment:
-      - TEST_TOX_ENV: "gallery-py38-upgrade-dev-pre"
+      - TEST_TOX_ENV: "gallery-py39-upgrade-dev-pre"
     <<: *gallery-steps
 
-  gallery36-min-req:
-    <<: *py36
+  gallery37-min-req:
+    <<: *py37
     environment:
-      - TEST_TOX_ENV: "gallery-py36-min-req"
+      - TEST_TOX_ENV: "gallery-py37-min-req"
     <<: *gallery-steps
 
   test-validation:
-    <<: *py38
+    <<: *py39
     steps:
       - checkout
       - run: git submodule sync
@@ -309,13 +279,13 @@ jobs:
           command: |
             . ../venv/bin/activate
             pip install tox
-            tox -e validation-py38
+            tox -e validation-py39
           # Install is expected to be quick. Increase timeout in case there are some network issues.
           # While pip installing tox does not output by default. Circle thinks task is dead after 10 min.
           no_output_timeout: 30m
 
   deploy-dev:
-    <<: *py38
+    <<: *py39
     steps:
       - checkout
       - attach_workspace:
@@ -336,7 +306,7 @@ jobs:
                 --exit-success-if-missing-token
 
   deploy-release:
-    <<: *py38
+    <<: *py39
     steps:
       - attach_workspace:
           at: ./
@@ -366,27 +336,27 @@ workflows:
     jobs:
       - flake8:
           <<: *no_filters
-      - python38:
+      - python37-min-req:
           <<: *no_filters
-      - python36-min-req:
+      - python39:
           <<: *no_filters
-      - miniconda36:
+      - miniconda37:
           <<: *no_filters
-      - miniconda38:
+      - miniconda39:
           <<: *no_filters
-      - gallery38:
+      - gallery37-min-req:
           <<: *no_filters
-      - gallery36-min-req:
+      - gallery38:  # TODO replace with gallery39 after allensdk support py39
           <<: *no_filters
       - deploy-dev:
           requires:
             - flake8
-            - python38
-            - python36-min-req
-            - miniconda36
-            - miniconda38
-            - gallery38
-            - gallery36-min-req
+            - python37-min-req
+            - python39
+            - miniconda37
+            - miniconda39
+            - gallery37-min-req
+            - gallery38  # gallery39
           filters:
             tags:
               ignore:
@@ -400,12 +370,12 @@ workflows:
       - deploy-release:
           requires:
             - flake8
-            - python38
-            - python36-min-req
-            - miniconda36
-            - miniconda38
-            - gallery38
-            - gallery36-min-req
+            - python37-min-req
+            - python39
+            - miniconda37
+            - miniconda39
+            - gallery37-min-req
+            - gallery38  # gallery39
           filters:
             tags:
               only: /^[0-9]+(\.[0-9]+)*(\.post[0-9]+)?$/
@@ -424,41 +394,33 @@ workflows:
     jobs:
       - flake8:
           <<: *no_filters
-      - python36:
-          <<: *no_filters
       - python37:
           <<: *no_filters
+      - python37-min-req:
+          <<: *no_filters
       - python38:
           <<: *no_filters
       - python39:
           <<: *no_filters
-      - python38-upgrade-dev:
-          <<: *no_filters
-      - python36-min-req:
+      - python39-upgrade-dev:
           <<: *no_filters
-      - miniconda36:
+      - python39-upgrade-dev-pre:
           <<: *no_filters
       - miniconda37:
           <<: *no_filters
       - miniconda38:
           <<: *no_filters
       - miniconda39:
           <<: *no_filters
-      - gallery36:
-          <<: *no_filters
       - gallery37:
           <<: *no_filters
+      - gallery37-min-req:
+          <<: *no_filters
       - gallery38:
           <<: *no_filters
       - gallery39:
           <<: *no_filters
-      - gallery38-upgrade-dev:
-          <<: *no_filters
-      - gallery36-min-req:
-          <<: *no_filters
-      - python38-upgrade-dev-pre:
-          <<: *no_filters
-      - gallery38-upgrade-dev-pre:
+      - gallery39-upgrade-dev:
           <<: *no_filters
-      - test-validation:
+      - gallery39-upgrade-dev-pre:
           <<: *no_filters

.github/ISSUE_TEMPLATE/bug_report.md

@@ -20,7 +20,7 @@ assignees: ''
 <!--Please describe your environment according to the following bullet points.-->
 
     Python Executable: Conda or Python
-    Python Version: Python 3.6, 3.7, or 3.8
+    Python Version: Python 3.7, 3.8, or 3.9
     Operating System: Windows, macOS or Linux
     HDMF Version:
     PyNWB Version:

.github/workflows/workflow.yml

@@ -15,7 +15,7 @@ jobs:
         os: [ubuntu-latest, macos-latest, windows-latest]
     env:
       OS: ${{ matrix.os }}
-      PYTHON: '3.8'
+      PYTHON: '3.9'
     steps:
     - name: Cancel Workflow Action
       uses: styfle/[email protected]
@@ -27,7 +27,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

CHANGELOG.md

@@ -6,10 +6,12 @@
 -
 -
 -
--
+- Drop Python 3.6 support, add Python 3.9 support. @rly (#1377)
+- Update requirements to allow compatibility with HDMF 3 and h5py 3. @rly (#1377)
 
 ### Minor new features:
 - Add RRID for citing PyNWB to the docs. @oruebel (#1372)
+- Update CI and tests to handle deprecations in libraries. @rly (#1377)
 
 ### Bug fixes:
 - Enforce electrode ID uniqueness during insertion into table. @CodyCBakerPhD (#1344)