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Refactored logic when pulling annotations #3507

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Refactored logic when pulling annotations

Refactored logic when pulling annotations #3507

Workflow file for this run

.github/workflows/test.yml at 35d1e4d
# Built from:
# https://docs.github.com/en/actions/guides/building-and-testing-python
# https://github.com/Sage-Bionetworks/challengeutils/blob/master/.github/workflows/pythonapp.yml
# https://github.com/snok/install-poetry#workflows-and-tips
name: Test schematic
on:
push:
branches: ['main']
pull_request:
branches: ['*']
workflow_dispatch: # Allow manually triggering the workflow
concurrency:
# cancel the current running workflow from the same branch, PR when a new workflow is triggered
# when the trigger is not a PR but a push, it will use the commit sha to generate the concurrency group
# {{ github.workflow }}: the workflow name is used to generate the concurrency group. This allows you to have more than one workflows
# {{ github.ref_type }}: the type of Git ref object created in the repository. Can be either branch or tag
# {{ github.event.pull_request.number}}: get PR number
# {{ github.sha }}: full commit sha
# credit: https://github.com/Sage-Bionetworks-Workflows/sagetasks/blob/main/.github/workflows/ci.yml
group: >-
${{ github.workflow }}-${{ github.ref_type }}-
${{ github.event.pull_request.number || github.sha }}
cancel-in-progress: true
jobs:
test:
runs-on: ubuntu-latest
env:
POETRY_VERSION: 1.2.0
strategy:
fail-fast: false
matrix:
python-version: ["3.9", "3.10"]
steps:
#----------------------------------------------
# check-out repo and set-up python
#----------------------------------------------
- name: Check out repository
uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
#----------------------------------------------
# install & configure poetry
#----------------------------------------------
- name: Install Poetry
run: |
curl -sSL https://install.python-poetry.org \
| python3 - --version ${{ env.POETRY_VERSION }};
poetry config virtualenvs.create true;
poetry config virtualenvs.in-project true;
#----------------------------------------------
# load cached venv if cache exists
#----------------------------------------------
- name: Load cached venv
id: cached-poetry-dependencies
uses: actions/cache@v2
with:
path: .venv
key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
#----------------------------------------------
# install dependencies if cache does not exist
#----------------------------------------------
- name: Install dependencies
if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
run: poetry install --no-interaction --no-root --all-extras
#----------------------------------------------
# install your root project, if required
#----------------------------------------------
- name: Install library
run: poetry install --no-interaction
#----------------------------------------------
# perform linting
#----------------------------------------------
# Disabled until we agree to turn it on
# - name: Lint with flake8
# run: |
# # stop the build if there are Python syntax errors or undefined names
# flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
# flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
#----------------------------------------------
# check formatting
#----------------------------------------------
- name: Code formatting with black
run: |
# ran only on certain files for now
# add here when checked
poetry run black schematic/configuration/*.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py --check
#----------------------------------------------
# type checking/enforcement
#----------------------------------------------
- name: Type checking with mypy
run: |
# ran only on certain files for now
# add here when checked
# poetry run mypy --install-types --non-interactive
# add here when enforced
poetry run mypy --disallow-untyped-defs --install-types --non-interactive schematic/configuration/*.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py
#----------------------------------------------
# linting
#----------------------------------------------
- name: Lint with pylint
run: |
# ran only on certain files for now
# add here when checked
poetry run pylint schematic/configuration/*.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py
#----------------------------------------------
# run test suite
#----------------------------------------------
- name: Run regular tests and rule combination tests
env:
SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }}
if: ${{ contains(github.event.head_commit.message, 'runcombos') }}
run: >
source .venv/bin/activate;
pytest --cov-report=term --cov-report=html:htmlcov --cov=schematic/
-m "not (google_credentials_needed or schematic_api or table_operations)"
- name: Run tests
env:
SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }}
SERVICE_ACCOUNT_CREDS: ${{ secrets.SERVICE_ACCOUNT_CREDS }}
if: ${{ false == contains(github.event.head_commit.message, 'runcombos') }}
run: >
source .venv/bin/activate;
pytest --cov-report=term --cov-report=html:htmlcov --cov=schematic/
-m "not (google_credentials_needed or rule_combos or schematic_api or table_operations)"
- name: Upload pytest test results
uses: actions/upload-artifact@v2
with:
name: pytest-results-${{ matrix.python-version }}
path: htmlcov
# Use always() to always run this step to publish test results when there are test failures
if: ${{ always() }}