From 634790d39859181dd426236e6bde6df14c4ef276 Mon Sep 17 00:00:00 2001 From: graefea Date: Mon, 6 Jan 2025 16:33:51 +0300 Subject: [PATCH] edit workflow --- .github/workflows/python_ci.yml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml index 94ea2014..3530b924 100644 --- a/.github/workflows/python_ci.yml +++ b/.github/workflows/python_ci.yml @@ -17,8 +17,8 @@ jobs: - name: Checkout code uses: actions/checkout@v3 with: - submodules: true # This ensures submodules are checked out - name: Checkout code - + submodules: true + - name: Set up Python uses: actions/setup-python@v4 with: @@ -29,10 +29,14 @@ jobs: python3 -m pip install --upgrade pip python3 -m pip install --editable .[test,docs] python3 -m pip install --editable ./submodules/phenopacket_mapper # Install the submodule package - + + - name: Configure BioPortal API Key for Oaklib + run: | + mkdir -p ~/.config/ontology-access-kit + echo "${{ secrets.BIOPORTAL_API_TOKEN }}" > ~/.config/ontology-access-kit/bioportal-apikey.txt + - name: Run tests with pytest + env: + BIOPORTAL_API_TOKEN: ${{ secrets.BIOPORTAL_API_TOKEN }} run: | pytest - -env: - BIOPORTAL_API_TOKEN: ${{ secrets.BIOPORTAL_API_TOKEN }} \ No newline at end of file