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Fix miniconda 3.7 CI error #1427

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Mar 9, 2022
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34 changes: 21 additions & 13 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -14,33 +14,34 @@ references:
initialize-venv: &initialize-venv
name: Initialize Virtual Environment
command: |
pip install --upgrade pip
python -m virtualenv ../venv || python -m venv ../venv
. ../venv/bin/activate

py39: &py39
docker:
- image: circleci/python:3.9.2-buster
- image: circleci/python:3.9
auth:
username: hdmf
password: $DOCKERHUB_PASSWORD

py38: &py38
docker:
- image: circleci/python:3.8.8-buster
- image: circleci/python:3.8
auth:
username: hdmf
password: $DOCKERHUB_PASSWORD

py37: &py37
docker:
- image: circleci/python:3.7.10-buster
- image: circleci/python:3.7
auth:
username: hdmf
password: $DOCKERHUB_PASSWORD

conda-image: &conda-image
docker:
- image: continuumio/miniconda3:4.9.2
- image: continuumio/miniconda3:latest
auth:
username: hdmf
password: $DOCKERHUB_PASSWORD
Expand Down Expand Up @@ -95,10 +96,17 @@ references:
- run:
name: Configure conda
command: |
pip install --upgrade pip
conda update -n base -c defaults conda
conda config --set always_yes yes --set changeps1 no
conda config --add channels conda-forge
conda install python=$CONDA_PYTHON_VER
conda install virtualenv
# work around incompatibilities between virtualenv & importlib-metadata
if [[ "${TEST_TOX_ENV}" == *"py37"* ]]; then
conda install "importlib-metadata=1.7"
else
conda install importlib-metadata
fi
conda install tox
- run:
name: Run the tests
Expand Down Expand Up @@ -146,7 +154,7 @@ references:

jobs:
flake8:
<<: *py38
<<: *py39
steps:
- checkout
- run:
Expand Down Expand Up @@ -176,7 +184,6 @@ 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

python39-upgrade-dev:
Expand All @@ -185,6 +192,7 @@ jobs:
- TEST_TOX_ENV: "py39-upgrade-dev"
- BUILD_TOX_ENV: "build-py39-upgrade-dev"
- TEST_WHEELINSTALL_ENV: "wheelinstall"
- UPLOAD_WHEELS: "true" # upload distributions from only this job to pypi
<<: *ci-steps

python39-upgrade-dev-pre:
Expand Down Expand Up @@ -366,27 +374,27 @@ workflows:
<<: *no_filters
- python37-min-req:
<<: *no_filters
- python39:
- python39-upgrade-dev:
<<: *no_filters
- miniconda37:
<<: *no_filters
- miniconda39:
<<: *no_filters
- gallery37-min-req:
<<: *no_filters
- gallery38: # TODO replace with gallery39 after allensdk support py39
- gallery38: # TODO replace with gallery39 after allensdk support py39
<<: *no_filters
- miniconda39-ros3:
<<: *no_filters
- deploy-dev:
requires:
- flake8
- python37-min-req
- python39
- python39-upgrade-dev # distributions from this job uploaded to PyPI
- miniconda37
- miniconda39
- gallery37-min-req
- gallery38 # gallery39
- gallery38 # TODO gallery39
- miniconda39-ros3
filters:
tags:
Expand All @@ -402,11 +410,11 @@ workflows:
requires:
- flake8
- python37-min-req
- python39
- python39-upgrade-dev # distributions from this job uploaded to PyPI
- miniconda37
- miniconda39
- gallery37-min-req
- gallery38 # gallery39
- gallery38 # TODO gallery39
- miniconda39-ros3
filters:
tags:
Expand Down
1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
- Add `environment-ros3.yml` to `MANIFEST.in` for inclusion in source distributions. @rly (#1398)
- Fix bad error check in ``IntracellularRecordingsTable.add_recording`` when adding ``IZeroClampSeries``. @oruebel (#1410)
- Skip ros3 tests if internet access or the ros3 driver are not available. @oruebel (#1414)
- Fix CI issues. @rly (#1427)

### Documentation and tutorial enhancements:
- Enhanced ordering of sphinx gallery tutorials to use alphabetic ordering based on tutorial headings. @oruebel (#1399)
Expand Down
28 changes: 14 additions & 14 deletions azure-pipelines-nightly.yml
Original file line number Diff line number Diff line change
Expand Up @@ -16,84 +16,84 @@ jobs:
strategy:
matrix:
macOS-py3.9:
imageName: 'macos-10.15'
imageName: 'macOS-latest'
pythonVersion: '3.9'
testToxEnv: 'py39'
buildToxEnv: 'build-py39'
testWheelInstallEnv: 'wheelinstall'

macOS-py3.9-upgrade-dev-pre:
imageName: 'macos-10.15'
imageName: 'macOS-latest'
pythonVersion: '3.9'
testToxEnv: 'py39-upgrade-dev-pre'
buildToxEnv: 'build-py39-upgrade-dev-pre'
testWheelInstallEnv: 'wheelinstall'

macOS-py3.9-upgrade-dev:
imageName: 'macos-10.15'
imageName: 'macOS-latest'
pythonVersion: '3.9'
testToxEnv: 'py39-upgrade-dev'
buildToxEnv: 'build-py39-upgrade-dev'
testWheelInstallEnv: 'wheelinstall'

macOS-py3.8:
imageName: 'macos-10.15'
imageName: 'macOS-latest'
pythonVersion: '3.8'
testToxEnv: 'py38'
buildToxEnv: 'build-py38'
testWheelInstallEnv: 'wheelinstall'

macOS-py3.7:
imageName: 'macos-10.15'
imageName: 'macOS-latest'
pythonVersion: '3.7'
testToxEnv: 'py37'
buildToxEnv: 'build-py37'
testWheelInstallEnv: 'wheelinstall'

macOS-py3.7-min-req:
imageName: 'macos-10.15'
imageName: 'macOS-latest'
pythonVersion: '3.7'
testToxEnv: 'py37-min-req'
buildToxEnv: 'build-py37-min-req'
testWheelInstallEnv: 'wheelinstall'

Windows-py3.9:
imageName: 'vs2017-win2016'
imageName: 'windows-latest'
pythonVersion: '3.9'
testToxEnv: 'py39'
buildToxEnv: 'build-py39'
testWheelInstallEnv: 'wheelinstall'

Windows-py3.9-upgrade-dev-pre:
imageName: 'vs2017-win2016'
imageName: 'windows-latest'
pythonVersion: '3.9'
testToxEnv: 'py39-upgrade-dev-pre'
buildToxEnv: 'build-py39-upgrade-dev-pre'
testWheelInstallEnv: 'wheelinstall'

Windows-py3.9-upgrade-dev:
imageName: 'vs2017-win2016'
imageName: 'windows-latest'
pythonVersion: '3.9'
testToxEnv: 'py39-upgrade-dev'
buildToxEnv: 'build-py39-upgrade-dev'
testWheelInstallEnv: 'wheelinstall'

Windows-py3.8:
imageName: 'vs2017-win2016'
imageName: 'windows-latest'
pythonVersion: '3.8'
testToxEnv: 'py38'
buildToxEnv: 'build-py38'
testWheelInstallEnv: 'wheelinstall'

Windows-py3.7:
imageName: 'vs2017-win2016'
imageName: 'windows-latest'
pythonVersion: '3.7'
testToxEnv: 'py37'
buildToxEnv: 'build-py37'
testWheelInstallEnv: 'wheelinstall'

Windows-py3.7-min-req:
imageName: 'vs2017-win2016'
imageName: 'windows-latest'
pythonVersion: '3.7'
testToxEnv: 'py37-min-req'
buildToxEnv: 'build-py37-min-req'
Expand Down Expand Up @@ -135,7 +135,7 @@ jobs:
displayName: "Test PyNWB with Conda and ROS3 on Windows"

pool:
vmImage: 'vs2017-win2016'
vmImage: 'windows-latest'

steps:

Expand Down Expand Up @@ -169,7 +169,7 @@ jobs:
displayName: "Test PyNWB with Conda and ROS3 on macOS"

pool:
vmImage: 'macos-10.15'
vmImage: 'macos-latest'

steps:

Expand Down
8 changes: 4 additions & 4 deletions azure-pipelines.yml
Original file line number Diff line number Diff line change
Expand Up @@ -9,28 +9,28 @@ jobs:
strategy:
matrix:
macOS-py3.9:
imageName: 'macos-10.15'
imageName: 'macOS-latest'
pythonVersion: '3.9'
testToxEnv: 'py39'
buildToxEnv: 'build-py39'
testWheelInstallEnv: 'wheelinstall'

macOS-py3.7-min-req:
imageName: 'macos-10.15'
imageName: 'macOS-latest'
pythonVersion: '3.7'
testToxEnv: 'py37-min-req'
buildToxEnv: 'build-py37-min-req'
testWheelInstallEnv: 'wheelinstall'

Windows-py3.9:
imageName: 'vs2017-win2016'
imageName: 'windows-latest'
pythonVersion: '3.9'
testToxEnv: 'py39'
buildToxEnv: 'build-py39'
testWheelInstallEnv: 'wheelinstall'

Windows-py3.7-min-req:
imageName: 'vs2017-win2016'
imageName: 'windows-latest'
pythonVersion: '3.7'
testToxEnv: 'py37-min-req'
buildToxEnv: 'build-py37-min-req'
Expand Down
1 change: 1 addition & 0 deletions requirements-doc.txt
Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,5 @@ matplotlib
sphinx_rtd_theme
sphinx-gallery
allensdk>=2.11.0 # python 3.8 is not supported in allensdk<2.11
MarkupSafe==2.0.1 # resolve incompatibility between jinja2 and markupsafe: https://github.com/AllenInstitute/AllenSDK/issues/2308
Pillow