conftest.py

import pytest

# Command line options for pytest must be added from conftest.py from where
# `pytest` is called.
def pytest_addoption(parser):
    parser.addoption(
        "--internet-tests",
        action="store_true",
        default=False,
        help="Run tests that retrieve stuff from the internet. This increases test time.",
    )


def pytest_collection_modifyitems(config, items):
    run_internet = config.getoption("--internet-tests")
    skip_internet = pytest.mark.skip(reason="need --internet-tests option to run")
    for item in items:
        # All tests marked with `pytest.mark.internet` get skipped unless
        # `--run-internet` passed
        if not run_internet and ("internet" in item.keywords):
            item.add_marker(skip_internet)


# These fixtures provide a per test new copy of pbmc3k with some preprocessing run on it,
# without having to hit the disk or recompute normalization.
# The private fixture creates the object while the public one returns a deep copy.
@pytest.fixture(scope="session")
def _pbmc3k_normalized():
    import scanpy as sc

    pbmc = sc.datasets.pbmc3k()
    pbmc.X = pbmc.X.astype("float64")  # For better accuracy
    sc.pp.filter_genes(pbmc, min_counts=1)
    sc.pp.log1p(pbmc)
    sc.pp.normalize_total(pbmc)
    sc.pp.highly_variable_genes(pbmc)
    return pbmc


@pytest.fixture
def pbmc3k_normalized(_pbmc3k_normalized):
    return _pbmc3k_normalized.copy()