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https://github.com/galaxyproject/galaxy.git
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mvdbeek
3a2e936401
Should help with nodeenv failing in CI tests, e.g. ``` Installing node into /home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage with nodeenv. * Install prebuilt node (18.12.1) .Incomplete read while readingfrom https://nodejs.org/download/release/v18.12.1/node-v18.12.1-linux-x64.tar.gz . Traceback (most recent call last): File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/bin/nodeenv", line 10, in <module> sys.exit(main()) File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 1104, in main create_environment(env_dir, args) File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 980, in create_environment install_node(env_dir, src_dir, args) File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 739, in install_node install_node_wrapped(env_dir, src_dir, args) File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 762, in install_node_wrapped download_node_src(node_url, src_dir, args) File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 602, in download_node_src with ctx as archive: File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/contextlib.py", line 112, in __enter__ return next(self.gen) File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 573, in tarfile_open tf = tarfile.open(*args, **kwargs) File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/tarfile.py", line 1573, in open saved_pos = fileobj.tell() AttributeError: 'bytes' object has no attribute 'tell' ``` from https://github.com/galaxyproject/galaxy/actions/runs/4883207488/jobs/8714237674?pr=16036
75 lines
2.5 KiB
YAML
75 lines
2.5 KiB
YAML
name: CWL conformance
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on:
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push:
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paths-ignore:
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- 'client/**'
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- 'doc/**'
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pull_request:
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paths-ignore:
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- 'client/**'
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- 'doc/**'
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env:
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GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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test:
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name: Test
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if: ${{ false }}
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runs-on: ubuntu-latest
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continue-on-error: ${{ startsWith(matrix.marker, 'red') }}
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strategy:
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fail-fast: false
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matrix:
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python-version: ['3.7']
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marker: ['green', 'red and required', 'red and not required']
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conformance-version: ['cwl_conformance_v1_0'] #, 'cwl_conformance_v1_1', 'cwl_conformance_v1_2']
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services:
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postgres:
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image: postgres:13
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env:
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POSTGRES_USER: postgres
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POSTGRES_PASSWORD: postgres
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POSTGRES_DB: postgres
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ports:
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- 5432:5432
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steps:
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- uses: actions/checkout@v3
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with:
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path: 'galaxy root'
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- uses: actions/setup-node@v3
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with:
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node-version: '18.12.1'
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cache: 'yarn'
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cache-dependency-path: 'galaxy root/client/yarn.lock'
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Get full Python version
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id: full-python-version
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shell: bash
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run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
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- name: Cache pip dir
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uses: actions/cache@v3
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with:
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path: ~/.cache/pip
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key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
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- name: Cache galaxy venv
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uses: actions/cache@v3
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with:
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path: 'galaxy root/.venv'
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key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}
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- name: Run tests
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run: ./run_tests.sh --coverage --skip_flakey_fails -cwl lib/galaxy_test/api/cwl -- -m "${{ matrix.marker }} and ${{ matrix.conformance-version }}"
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working-directory: 'galaxy root'
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- uses: codecov/codecov-action@v3
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with:
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flags: cwl-conformance
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working-directory: 'galaxy root'
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- uses: actions/upload-artifact@v3
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if: failure()
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with:
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name: CWL conformance test results (${{ matrix.python-version }}, ${{ matrix.marker }}, ${{ matrix.conformance-version }})
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path: 'galaxy root/run_cwl_tests.html'
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