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Automatically infer regulatory graph for instantiated Boolean network… #121

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Automatically infer regulatory graph for instantiated Boolean network…

Automatically infer regulatory graph for instantiated Boolean network… #121

Workflow file for this run

.github/workflows/test.yml at 4d4f6b4
# This runs on every commit that is not on a dev-* branch. It should be reasonably fast,
# as it links to Z3 dynamically.
# Specifically, we check that:
# - Rust formatting is correct.
# - Rust project has no errors.
# - Rust project has no `clippy` issues.
# - Python tests have no `mypy` issues.
# - Everything compiles and tests pass on linux/macOS/windows with dynamically linked Z3.
# * On macOS, we also measure code coverage of the Python tests (on linux this seems broken now).
name: test
on:
push:
branches-ignore:
- 'dev-*'
pull_request:
branches:
- '*'
env:
# A fixed version used for testing, so that the builds don't
# spontaneously break after a few years.
# Make sure to update this from time to time.
RUST_VERSION: "1.79.0"
# This is the version currently used by `z3-sys`.
# If this ever changes, you might also need to increase
# the minimum macOS version below.
Z3_VERSION: "4.8.12"
MACOS_TARGET: "11.0"
PYTHON_VERSION: "3.12"
jobs:
# Checks syntax formatting (does not need z3).
fmt:
name: rustfmt
runs-on: ubuntu-latest
env:
RUSTFLAGS: "-D warnings"
steps:
- uses: actions/checkout@v4
- uses: dtolnay/rust-toolchain@stable
with:
toolchain: ${{ env.RUST_VERSION }}
components: rustfmt
- run: cargo fmt --all -- --check
# Run basic code validity check.
check:
needs: fmt
name: check
runs-on: ubuntu-latest
env:
RUSTFLAGS: "-D warnings"
steps:
- uses: actions/checkout@v4
- name: Setup Z3.
id: z3
uses: daemontus/[email protected]
with:
version: ${{ env.Z3_VERSION }}
add_to_library_path: true
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- uses: dtolnay/rust-toolchain@stable
with:
toolchain: ${{ env.RUST_VERSION }}
- run: cargo check
# Checks code style.
clippy:
needs: check
name: clippy
runs-on: ubuntu-latest
env:
RUSTFLAGS: "-D warnings"
steps:
- uses: actions/checkout@v4
- name: Setup Z3.
id: z3
uses: daemontus/[email protected]
with:
version: ${{ env.Z3_VERSION }}
add_to_library_path: true
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- uses: dtolnay/rust-toolchain@stable
with:
toolchain: ${{ env.RUST_VERSION }}
components: clippy
# Should use shared z3 for faster runtime.
- run: cargo clippy
mypy:
needs: check
name: mypy
runs-on: ubuntu-latest
steps:
- name: Checkout.
uses: actions/checkout@v4
- name: Setup Z3.
id: z3
uses: daemontus/[email protected]
with:
version: ${{ env.Z3_VERSION }}
add_to_library_path: true
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- name: Setup Python.
uses: actions/setup-python@v5
with:
python-version: ${{ env.PYTHON_VERSION }}
architecture: x64
- uses: dtolnay/rust-toolchain@stable
with:
toolchain: ${{ env.RUST_VERSION }}
- name: Install and run mypy.
run: |
python3 -m venv venv
source ./venv/bin/activate
./venv/bin/pip3 install -r dev-requirements.txt
maturin develop
mypy ./tests --check-untyped-defs
tests-linux:
# This also tests that compilation with dynamic Z3 linking is not broken.
needs: check
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
# Linux builds run with all supported versions of python. Other
# operating systems just run the latest recommended version.
python: ["3.9", "3.10", "3.11", "3.12"]
steps:
- name: Checkout.
uses: actions/checkout@v4
- name: Setup Z3.
id: z3
uses: daemontus/[email protected]
with:
version: ${{ env.Z3_VERSION }}
add_to_library_path: true
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- name: Setup Python.
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python }}
architecture: x64
- uses: dtolnay/rust-toolchain@stable
with:
toolchain: ${{ env.RUST_VERSION }}
- name: Run tests.
run: |
python3 -m venv venv
source ./venv/bin/activate
./venv/bin/pip3 install -r dev-requirements.txt
maturin develop
pytest ./tests
tests-windows:
# This also tests that compilation with dynamic Z3 linking is not broken.
needs: check
runs-on: windows-latest
steps:
- name: Checkout.
uses: actions/checkout@v4
- name: Setup Z3.
id: z3
uses: daemontus/[email protected]
with:
version: ${{ env.Z3_VERSION }}
add_to_library_path: true
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- name: Setup Python.
uses: actions/setup-python@v5
with:
python-version: ${{ env.PYTHON_VERSION }}
architecture: x64
- uses: dtolnay/rust-toolchain@stable
with:
toolchain: ${{ env.RUST_VERSION }}
- name: Run tests.
run: |
python3 -m venv venv
.\venv\Scripts\activate
pip3 install -r dev-requirements.txt
maturin develop
pytest .\tests
tests-macos-and-coverage:
needs: check
# For reasons unbeknownst to mankind, llvm-cov segfaults on ubuntu runners
# when combined with pytest. The solution for now is to use macOS.
runs-on: macos-12
env:
# These are the env variables set by llvm-cov, but modified such that they actually work in GH actions.
# In particular, we changed the paths from absolute to relative.
RUSTFLAGS: '-C instrument-coverage --cfg=coverage --cfg=trybuild_no_target'
LLVM_PROFILE_FILE: './target/biodivine-aeon-py-%p-%4m.profraw'
CARGO_LLVM_COV: 1
CARGO_LLVM_COV_SHOW_ENV: 1
CARGO_LLVM_COV_TARGET_DIR: './target'
steps:
# Here, we don't need to bother with the `manylinux` container,
# since we are only testing, not building multiplatform `wheel` files.
- name: Checkout.
uses: actions/checkout@v4
- name: Setup Z3.
id: z3
uses: daemontus/[email protected]
with:
version: ${{ env.Z3_VERSION }}
add_to_library_path: true
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- name: Setup Python.
uses: actions/setup-python@v5
with:
python-version: ${{ env.PYTHON_VERSION }}
architecture: x64
- uses: dtolnay/rust-toolchain@stable
with:
toolchain: ${{ env.RUST_VERSION }}
- name: Setup Rust/Python environment.
run: |
rustup component add llvm-tools-preview
cargo install cargo-llvm-cov
python3 -m venv venv
./venv/bin/pip3 install -r dev-requirements.txt
- name: Run tests with coverage.
run: |
source ./venv/bin/activate
cargo llvm-cov clean --workspace
cargo test
maturin develop
pytest ./tests --cov=biodivine_aeon --cov-report xml
cargo llvm-cov report --lcov --output-path coverage.lcov
- uses: codecov/codecov-action@v4
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
files: coverage.lcov,coverage.xml