Revision 1be0a68711f6967925f89523667cad9907e4946f authored by Pau Badia i Mompel on 21 March 2022, 16:08:29 UTC, committed by GitHub on 21 March 2022, 16:08:29 UTC
The packages dorothea-py and progeny-py are now deprecated, instead one should use decoupler (https://github.com/saezlab/decoupler-py). It contains both prior knowledge resources plus many more since it integrates the meta-resource OmniPath, and it also contains many footprint enrichment methods instead of a fixed one.
1 parent a8bd4cf
conftest.py
import pytest
# In case pytest-nunit is not installed, defines a dummy fixture
try:
import pytest_nunit
except ModuleNotFoundError:
@pytest.fixture
def add_nunit_attachment(request):
def noop(file, description):
pass
return noop
# 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()
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