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Use promises for URLs in IGV to have fresh signing each time they used #8071

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Use promises for URLs in IGV to have fresh signing each time they used

Use promises for URLs in IGV to have fresh signing each time they used #8071

Workflow file for this run

.github/workflows/py-ci.yml at fad10e9
on:
push:
branches:
- master
tags:
- "*"
pull_request:
merge_group:
jobs:
linter:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.7'
- name: Install dependencies
run: |
python -m pip install --upgrade pip setuptools
python -m pip install 'pylint==2.10.2' 'pycodestyle>=2.6.1'
- name: Run pylint
run: |
pylint $(find -name '*.py' -not -path './venv/*')
- name: Run pycodestyle
run: |
pycodestyle $(find -name '*.py' -not -path './venv/*')
isort:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.7'
- name: Install dependencies
run: |
python -m pip install --upgrade pip setuptools
python -m pip install isort
- name: Run isort
run: |
isort --check --diff .
test-gendocs:
runs-on: ubuntu-latest
env:
QUILT_DISABLE_USAGE_METRICS: true
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
# on newer versions it crashes with
# TypeError: <classmethod(<function Package.install at 0x105219f30>)> is not a callable object
python-version: '3.9'
- name: install deps
run: |
python -m pip install --upgrade pip setuptools
python -m pip install api/python nbconvert git+https://github.com/quiltdata/pydoc-markdown.git@quilt
- name: generate docs
run: cd gendocs && python build.py
- name: show invisible changes via cat
run: git diff | cat -A
- name: check there are no changes
run: git diff --exit-code
test-testdocs:
runs-on: ubuntu-latest
env:
QUILT_DISABLE_USAGE_METRICS: true
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.10'
- name: install poetry
run: python -m pip install poetry
- name: install deps
run: cd testdocs && poetry install
- name: test codeblocks
run: cd testdocs && poetry run pytest --codeblocks ../docs
test-client:
strategy:
matrix:
os: [ubuntu-latest, windows-latest]
python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
runs-on: ${{ matrix.os }}
env:
QUILT_DISABLE_USAGE_METRICS: true
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip setuptools
python -m pip install -e api/python[tests]
- name: Run Pytest
run: |
pytest --cov=api/python api/python
- uses: codecov/codecov-action@v4
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
OS: ${{ matrix.os }}
PYTHON_VERSION: ${{ matrix.python-version }}
with:
flags: api-python
name: ${{ github.job }}
env_vars: OS,PYTHON_VERSION
pypi-release-tag-check:
needs: test-client
runs-on: ubuntu-latest
outputs:
check: ${{ steps.check.outputs.check }}
if: github.ref_type == 'tag'
steps:
- name: check git tag
id: check
run: |
if [[ ${{ github.ref_name }} =~ ^[0-9]+(\.[0-9]+)*([abrc]+[0-9]+)?$ ]]; then
echo ::set-output name=check::true
fi
pypi-release:
needs: pypi-release-tag-check
if: github.ref_type == 'tag' && needs.pypi-release-tag-check.outputs.check == 'true'
runs-on: ubuntu-latest
defaults:
run:
working-directory: api/python
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.7'
- name: verify git tag vs. version
env:
CIRCLE_TAG: ${{ github.ref_name }}
run: python setup.py verify
- name: Install dependencies
run: |
python -m pip install --upgrade pip setuptools
python -m pip install build==0.8.0 twine==4.0.0
- name: build
run: python -m build
- name: upload to PyPI
env:
TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
run: twine upload dist/*
test-lambda:
strategy:
fail-fast: false
matrix:
path:
- access_counts
- indexer
- molecule
- pkgevents
- pkgpush
- pkgselect
- preview
- s3hash
- s3select
- shared
- status_reports
- tabular_preview
- thumbnail
- transcode
runs-on: ubuntu-latest
env:
QUILT_DISABLE_USAGE_METRICS: true
PYTHONPATH: deps
JUPYTER_PATH: deps/share/jupyter # Jupyter is not smart enough to handle custom Python paths
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version-file: lambdas/${{ matrix.path }}/.python-version
- name: Install dependencies
run: |
# Due to behavior change in pip>=23.1 installing tifffile==0.15.1
# from thumbnail lambda fails whithout installed wheel.
# See https://github.com/pypa/pip/issues/8559.
python -m pip install wheel
if [ ${{ matrix.path }} == "shared" ]
python -m pip install -e lambdas/shared[tests]
then
python -m pip install -e lambdas/shared
python -m pip install -e lambdas/${{ matrix.path }}
fi
python -m pip install -r lambdas/${{ matrix.path }}/test-requirements.txt
# Try to simulate the lambda .zip file:
# - Use --no-deps to ensure that second-order dependencies are included in the requirements file
# - Remove "tests" directories
# - Run "strip" on shared libraries
python -m pip install -t deps --no-deps -r lambdas/${{ matrix.path }}/requirements.txt
find deps -name tests -type d -exec rm -r \{} \+
find deps \( -name '*.so.*' -o -name '*.so' \) -type f -exec strip \{} \+
- name: Pytest
run: |
pytest --cov=lambdas lambdas/${{ matrix.path }}
- uses: codecov/codecov-action@v4
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
LAMBDA: ${{ matrix.path }}
with:
flags: lambda
name: ${{ github.job }}
env_vars: LAMBDA