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Dev #19

Workflow file for this run

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
name: CI testing
on:
pull_request:
branches: [ "master", "dev" ]
permissions:
contents: read
jobs:
build:
runs-on: ubuntu-latest
defaults:
run:
shell: bash -el {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
python-version: 3.8
mamba-version: "*"
channels: conda-forge,bioconda,defaults
channel-priority: true
- name: install dependancies
run: |
wget https://raw.githubusercontent.com/jodyphelan/TBProfiler/dev/conda/linux-latest.txt
conda create --name test --file linux-latest.txt
- name: Install dependencies
run: |
conda activate test
pip install --force-reinstall git+https://github.com/jodyphelan/pathogen-profiler.git@dev
pip install --force-reinstall .
- name: Run tests
run: |
cd tests
mamba install pytest -y
pytest -x .