mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-28 02:58:18 +08:00
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
77 lines
2.7 KiB
YAML
77 lines
2.7 KiB
YAML
name: Converter tests
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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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schedule:
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# Run at midnight UTC every Tuesday
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- cron: '0 0 * * 2'
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env:
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GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
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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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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.7']
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steps:
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- if: github.event_name == 'schedule'
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run: |
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echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
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echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
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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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- name: Clone galaxyproject/galaxy-test-data
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uses: actions/checkout@v3
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with:
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repository: galaxyproject/galaxy-test-data
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path: galaxy-test-data
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache venv dir
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uses: actions/cache@v3
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id: pip-cache
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with:
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path: ~/.cache/pip
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key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
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- name: Move test data
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run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/'
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- name: Install planemo
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run: pip install planemo
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- name: Determine converters to check
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run: |
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ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -v -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip > tool_list.txt
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echo "Skipping checks for the following converters:"
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ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip
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echo "Checking only the following converters:"
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cat tool_list.txt
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- name: Lint converters
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run: |
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mapfile -t TOOL_ARRAY < tool_list.txt
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planemo lint --skip citations,stdio,help --report_level warn "${TOOL_ARRAY[@]}"
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- name: Run tests
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run: |
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mapfile -t TOOL_ARRAY < tool_list.txt
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planemo test --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' "${TOOL_ARRAY[@]}"
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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: Converter test results (${{ matrix.python-version }})
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path: tool_test_output.html
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