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add all path variations of CWLProv operations (relates to https://git… #4506

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add all path variations of CWLProv operations (relates to https://git…

add all path variations of CWLProv operations (relates to https://git… #4506

Workflow file for this run

.github/workflows/tests.yml at 34fe955
# run test suites
name: Tests
on:
- pull_request
- push
- release
- workflow_dispatch
# cancel the current workflow if another commit was pushed on the same PR or reference
# uses the GitHub workflow name to avoid collision with other workflows running on the same PR/reference
concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
jobs:
# see: https://github.com/fkirc/skip-duplicate-actions
skip_duplicate:
continue-on-error: true
runs-on: ubuntu-latest
outputs:
should_skip: ${{ steps.skip_duplicate.outputs.should_skip && ! contains(github.ref, 'refs/tags') && ! contains(github.ref, 'refs/heads/master') }}
steps:
- uses: fkirc/skip-duplicate-actions@master
with:
concurrent_skipping: "same_content_newer"
skip_after_successful_duplicate: "true"
do_not_skip: '["workflow_dispatch", "schedule", "release"]'
# see: https://github.com/actions/setup-python
tests:
needs: skip_duplicate
if: ${{ needs.skip_duplicate.outputs.should_skip != 'true' }}
runs-on: ${{ matrix.os }}
continue-on-error: ${{ matrix.allow-failure }}
env:
# override make command to install directly in active python
CONDA_CMD: ""
DOCKER_TEST_EXEC_ARGS: "-T"
services:
# Label used to access the service container
mongodb:
image: mongo:5.0 # DockerHub
ports:
- "27017:27017"
strategy:
matrix:
os: [ubuntu-latest]
python-version: ["3.8", "3.9", "3.10", "3.11"]
allow-failure: [false]
test-case: [test-unit-only, test-func-only]
include:
# experimental python
- os: ubuntu-latest
python-version: "3.12"
allow-failure: true
test-case: test-unit-only
- os: ubuntu-latest
python-version: "3.12"
allow-failure: true
test-case: test-func-only
# linter tests
- os: ubuntu-latest
python-version: "3.10"
allow-failure: false
test-case: check-all
# documentation build
- os: ubuntu-latest
python-version: "3.10"
allow-failure: false
test-case: docs
# coverage test
- os: ubuntu-latest
python-version: "3.10"
allow-failure: false
test-case: test-coverage-only
# smoke test of Docker image
- os: ubuntu-latest
python-version: "3.10" # doesn't matter which one (in docker), but match default of repo
allow-failure: false
test-case: test-docker
# EMS end-2-end Workflow tests
- os: ubuntu-latest
python-version: "3.10"
allow-failure: true
test-case: test-workflow-only
steps:
- uses: actions/checkout@v2
with:
fetch-depth: "0"
- name: Setup Python
# skip python setup if running with docker
if: ${{ matrix.test-case != 'test-docker' }}
uses: actions/setup-python@v5
with:
python-version: "${{ matrix.python-version }}"
cache: 'pip'
- name: Parse Python Version
id: python-semver
run: |
echo "::set-output name=major:$(echo ${{ matrix.python-version }} | cut -d '.' -f 1)"
echo "::set-output name=minor:$(echo ${{ matrix.python-version }} | cut -d '.' -f 2)"
- uses: actions/cache@v3
name: Check Proj Lib Pre-Built in Cache
id: cache-proj
with:
# note: '22' is v8, '21' is v7
path: /tmp/proj-8.2.1/install
key: ${{ runner.os }}-python${{ matrix.python-version }}-proj
- name: Install Dependencies
# skip python setup if running with docker
if: ${{ matrix.test-case != 'test-docker' }}
# install package and dependencies directly,
# skip sys/conda setup to use active python
run: make install-sys install-pkg install-pip install-raw install-dev install-dev-npm
- name: Display Packages
# skip python setup if running with docker
if: ${{ matrix.test-case != 'test-docker' }}
run: |
pip freeze
npm list
make version
#- name: Setup Environment Variables
# uses: c-py/action-dotenv-to-setenv@v2
# with:
# env-file: ./ci/weaver.env
- name: Display Environment Variables
run: |
hash -r
env | sort
- name: Run Tests
run: make stop ${{ matrix.test-case }}
# disable due to confusing and unhelpful messages created by codecov
# (see )https://github.com/codecov/feedback/issues/304#issuecomment-2492675117)
# - name: Upload test results to Codecov
# if: ${{ !cancelled() && success() && matrix.test-case == 'test-coverage-only' }}
# uses: codecov/test-results-action@v1
# with:
# files: reports/coverage-junit.xml,!./cache
# flags: ${{ matrix.python-version }}
# token: ${{ secrets.CODECOV_TOKEN }}
- name: Upload coverage report
uses: codecov/codecov-action@v2
if: ${{ success() && matrix.test-case == 'test-coverage-only' }}
with:
token: ${{ secrets.CODECOV_TOKEN }}
files: ./reports/coverage.xml
fail_ci_if_error: true
verbose: true
deploy-docker:
needs: tests
if: ${{ success() && (contains(github.ref, 'refs/tags') || github.ref == 'refs/heads/master') }}
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
with:
fetch-depth: "0"
- name: Get Tag Version
id: version
shell: bash
run: |
if [[ "${GITHUB_REF}" == "refs/heads/master" ]]; then
echo "::set-output name=TAG_VERSION::latest"
else
echo "::set-output name=TAG_VERSION::${GITHUB_REF##*/}"
fi
- name: Build Docker
run: |
make DOCKER_REPO=pavics/weaver APP_VERSION=${{ steps.version.outputs.TAG_VERSION }} docker-info docker-build
- name: Login to DockerHub
uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
- name: Push to DockerHub
run: |
make DOCKER_REPO=pavics/weaver APP_VERSION=${{ steps.version.outputs.TAG_VERSION }} docker-push