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Fix CI using package installation.
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redur committed May 31, 2024
1 parent 900ee43 commit edb6832
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Showing 2 changed files with 14 additions and 14 deletions.
14 changes: 7 additions & 7 deletions .github/workflows/pipeline_run.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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 "${HOME}/.bash_profile"
conda env create -f environment-prod.yml
conda activate boreholes-prod
python -m pip install --upgrade pip
python -m venv env
source env/bin/activate
pip install -e .
echo "Running pipeline"
boreholes-extract-layers -l -i example/example_borehole_profile.pdf -o example/ -p example/predictions.json
14 changes: 7 additions & 7 deletions .github/workflows/pytest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,16 +10,16 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.10'
- name: Create Environment and run tests
shell: bash
run: |
wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(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
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