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update sourmash and snakemake dependencies #163

update sourmash and snakemake dependencies

update sourmash and snakemake dependencies #163

Workflow file for this run

name: Test
on: [push, pull_request]
jobs:
test:
runs-on: ubuntu-latest
strategy:
matrix:
python: [3.9]
name: Python ${{ matrix.python }}
# We want to run on external PRs, but not on our own internal PRs as they'll be run by the push to the branch.
if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python }}
uses: actions/setup-python@v1
with:
python-version: ${{ matrix.python }}
- run: pip install -U pip setuptools
- name: Setup conda
uses: s-weigand/setup-conda@v1
with:
activate-conda: true
- run: conda env update -n base -f environment.yml
- name: Install coverage dependencies
run: pip install pytest-cov pytest-dependency
- name: Build
run: python setup.py build_ext --inplace
- name: Install charcoal
run: pip install -e .
- run: pytest tests
# - run: pytest tests --cov=.
# - name: Upload coverage to Codecov
# uses: codecov/codecov-action@v1