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Final fix for yesterdays changes #265

Final fix for yesterdays changes

Final fix for yesterdays changes #265

Workflow file for this run

# This is a basic workflow to help you get started with Actions
name: Testing
# Controls when the workflow will run
on:
# Triggers the workflow on push or pull request events but only for the main branch
push:
branches:
- main
- dev
- dev_1.0
pull_request:
branches:
- main
- dev
- dev_1.0
workflow_dispatch: # make is manually start-able
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
# This workflow contains a single job called "test"
test:
runs-on: 'ubuntu-latest'
steps:
- uses: actions/checkout@v3
- name: Setup Mamba
uses: conda-incubator/setup-miniconda@v2
with:
python-version: '3.10'
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: MPP
use-mamba: true
- name: Install environment
shell: bash -l {0}
run: |
mamba install -c conda-forge -c bioconda -y numpy pandas networkx matplotlib pytest setuptools pyscipopt"<4.0.0" foldseek mmseqs2 cd-hit mash tmalign diamond cvxpy pytest-cov rdkit">=2022.09.1" pytest-cases scikit-learn">=1.2,<1.6" pyyaml h5py
pip install grakel
- name: Run tests
shell: bash -l {0}
run: |
cd tests
pytest -m "not todo and not issue" --cov=../datasail/ --cov-report=xml
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v3
with:
token: ${{ secrets.CODECOV_TOKEN }}
fail_ci_if_error: false
files: coverage.xml