diff --git a/.github/workflows/github_tests.yml b/.github/workflows/github_tests.yml index c6cfc76..2fddbc1 100644 --- a/.github/workflows/github_tests.yml +++ b/.github/workflows/github_tests.yml @@ -44,6 +44,9 @@ jobs: # path-to-lcov: "coverage.lcov" tests-functional: runs-on: ubuntu-latest + defaults: + run: + shell: bash -l {0} steps: - name: Checkout Repo @@ -63,11 +66,13 @@ jobs: - name: Simulate reads run: | marbel --n-species 3 --n-orthogroups 10 --n-samples 2 4 --library-size 5000 --outdir run_spec10_orth200_samp5-10/ - - name: Create conda env for tests - run: | - conda create -n marbel-tests scikit-bio - name: Execute functional tests + uses: conda-incubator/setup-miniconda@v3 + with: + activate-environment: anaconda-client-env + environment-file: tests/env_functional.yml + auto-activate-base: true run: | - conda activate marbel-tests || true + conda info echo $CONDA_PREFIX python tests/tests_functional.py run_spec10_orth200_samp5-10/