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updated to make ci pass #6

updated to make ci pass

updated to make ci pass #6

Workflow file for this run

name: run_tox
on:
workflow_dispatch:
push:
paths-ignore:
- README.md
- .gitignore
pull_request:
# schedule:
# - cron: "0 8 * * *"
concurrency:
group: runtests-${{ github.ref }}
cancel-in-progress: true
jobs:
test:
name: test with ${{ matrix.py }} on ${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
py:
# - "3.12"
# - "3.11"
- "3.10"
# - "3.9"
- "3.8"
# - "3.7" # end-of-life reached
os:
- ubuntu-latest
# - macos-latest
# - windows-latest
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
token: ${{ secrets.PAT }} # the special secrets.GITHUB_TOKEN only allows access to the current repository, so we added a personal access token with scope "repo" as a secret to this repo
submodules: true
- name: Setup python for test ${{ matrix.py }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.py }}
- name: Install minimap2
run: curl -L https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-2.26_x64-linux.tar.bz2 | tar -jxvf -
- name: Fix pyproject for tox
run: |
sed -i'.backup' "s@{root:uri}@file://$(pwd)@g" pyproject.toml
# does not work
# replace {root:uri} by "file:." in pyproject.toml since tox does not understand it
# sed -i 's/{root:uri}/file:./g' pyproject.toml
# remove line that contains {root:uri}
# sed -i '/{root:uri}/d' pyproject.toml
- name: Install tox
run: python -m pip install tox-gh>=1.2
- name: Setup test suite
run: tox -vv --notest
- name: Run test suite
run: PATH="$(pwd)/minimap2-2.26_x64-linux:$PATH" tox --skip-pkg-install
# run: PATH="$(pwd)/minimap2-2.26_x64-linux:$PATH" tox --skip-pkg-install -- tests/usecase_helpers/test_run_simulator_with_readfish.py
- name: archive if failure
if: ${{ failure() }}
uses: actions/upload-artifact@v3
with:
name: ${{ matrix.os }}-${{ matrix.py }}-${{ github.sha }}
retention-days: 1
path: /tmp/pytest-of-runner/
# path: /tmp/pytest-of-runner/pytest-0/test_simulator_with_readfish0/data/run_dir/simulator_run/reads