diff --git a/.github/workflows/pipeline_run.yml b/.github/workflows/pipeline_run.yml index 787dd1fd..d6fdbb1a 100644 --- a/.github/workflows/pipeline_run.yml +++ b/.github/workflows/pipeline_run.yml @@ -10,15 +10,15 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: '3.10' - name: Create Environment and run pipeline shell: bash run: | - wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" - bash Miniforge3.sh -b -p "${HOME}/conda" - source "${HOME}/conda/etc/profile.d/conda.sh" - conda init --all - source "${HOME}/.bash_profile" - conda env create -f environment-prod.yml - conda activate boreholes-prod + python -m pip install --upgrade pip + python -m venv env + source env/bin/activate + pip install -e . echo "Running pipeline" boreholes-extract-layers -l -i example/example_borehole_profile.pdf -o example/ -p example/predictions.json \ No newline at end of file diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 9e0f06cf..395abb60 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -10,16 +10,16 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: '3.10' - name: Create Environment and run tests shell: bash run: | - wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" - bash Miniforge3.sh -b -p "${HOME}/conda" - source "${HOME}/conda/etc/profile.d/conda.sh" - conda init --all - source "${HOME}/.bash_profile" - conda env create -f environment-dev.yml - conda activate boreholes-dev + python -m pip install --upgrade pip + python -m venv env + source env/bin/activate + pip install -e .[test] pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=stratigraphy tests/ | tee pytest-coverage.txt - name: Pytest coverage comment # For more information see: https://github.com/MishaKav/pytest-coverage-comment/ uses: MishaKav/pytest-coverage-comment@main