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Add a fallback to the fully symbolic attractor detection if the NFVS search fails #558

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Add a fallback to the fully symbolic attractor detection if the NFVS search fails

Add a fallback to the fully symbolic attractor detection if the NFVS search fails #558

Workflow file for this run

.github/workflows/test.yml at d0b156e
name: test
on:
push:
pull_request:
jobs:
# First, check if the types/formatting is correct.
types-and-linting:
runs-on: ubuntu-latest
strategy:
fail-fast: false
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: 3.11
architecture: x64
- name: Install Python dependencies
run: |
python -m pip install --upgrade pip
python -m pip install flake8 black mypy
python -m pip install -r requirements.txt
- name: Lint with Black
uses: rickstaa/action-black@v1
with:
black_args: ". --check --diff"
- name: Check types
run: |
mypy biobalm
- name: Lint with flake8
run: |
# stop the build if there are Python syntax errors or undefined names
flake8 biobalm --count --select=E9,F63,F7,F82 --show-source --statistics
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 biobalm --ignore=E203,W503,C901 --select=C,E,F,W,B,B950 --max-line-length=127 --statistics --count --max-complexity=10
doctests:
runs-on: ubuntu-latest
timeout-minutes: 5
needs: [types-and-linting]
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Install clingo
run: sudo apt-get -y install gringo
- name: Install Python
uses: actions/setup-python@v5
with:
python-version: 3.11
architecture: x64
- name: Fetch and install native Pint
run: |
wget https://github.com/pauleve/pint/releases/download//2019-05-24/pint_2019-05-24_amd64.deb
sudo apt install ./pint_2019-05-24_amd64.deb
- name: Install repo dependencies
run: pip install -r requirements.txt
- name: Run doctests
run: python -m doctest biobalm/*.py
# Then do a "small" test run with code coverage.
coverage:
runs-on: ubuntu-latest
timeout-minutes: 20
needs: [types-and-linting, doctests]
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Install clingo
run: sudo apt-get -y install gringo
- name: Install Python
uses: actions/setup-python@v5
with:
python-version: 3.11
architecture: x64
- name: Fetch and install native Pint
run: |
wget https://github.com/pauleve/pint/releases/download//2019-05-24/pint_2019-05-24_amd64.deb
sudo apt install ./pint_2019-05-24_amd64.deb
- name: Install repo dependencies
run: pip install -r requirements.txt
- name: Install pytest
run: pip install pytest pytest-cov
- name: Run pytest with coverage
run: python3 -m pytest --networksize 20 --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=biobalm tests/ | tee pytest-coverage.txt
- name: Pytest coverage comment
uses: MishaKav/pytest-coverage-comment@main
with:
pytest-coverage-path: ./pytest-coverage.txt
junitxml-path: ./pytest.xml
# Then do a full test for correctness using larger networks.
tests:
runs-on: ubuntu-latest
timeout-minutes: 20
needs: [types-and-linting, doctests, coverage]
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Install clingo
run: sudo apt-get -y install gringo
- name: Install Python
uses: actions/setup-python@v5
with:
python-version: 3.11
architecture: x64
- name: Fetch and install native Pint
run: |
wget https://github.com/pauleve/pint/releases/download//2019-05-24/pint_2019-05-24_amd64.deb
sudo apt install ./pint_2019-05-24_amd64.deb
- name: Install repo dependencies
run: pip install -r requirements.txt
- name: Install pytest
run: pip install pytest
- name: Run pytest (without coverage)
run: python3 -m pytest --networksize 30 tests/