Speed up tests (#601)

* Start 0.8.0 Signed-off-by: zethson <[email protected]> * Speed up tests and fix some warnings Signed-off-by: zethson <[email protected]> * Fix augur test Signed-off-by: zethson <[email protected]> * Further speed up tests and introduce new profile Signed-off-by: zethson <[email protected]> * Proper strategy syntax Signed-off-by: zethson <[email protected]> * Readd fast profile Signed-off-by: zethson <[email protected]> * Readd fast profile Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]>
scverse · May 21, 2024 · 72e0864 · 72e0864
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commit 72e0864
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Showing 6 changed files with 24 additions and 7 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -23,10 +23,16 @@ jobs:
  include:
  - os: ubuntu-latest
  python: "3.10"
+ run_mode: "slow"
  - os: ubuntu-latest
  python: "3.11"
+ run_mode: "slow"
  - os: ubuntu-latest
  python: "3.11"
+ run_mode: "fast"
+ - os: ubuntu-latest
+ python: "3.11"
+ run_mode: slow
  pip-flags: "--pre"
 
  env:
@@ -52,7 +58,12 @@ jobs:
  MPLBACKEND: agg
  PLATFORM: ${{ matrix.os }}
  DISPLAY: :42
- run: coverage run -m pytest -v --color=yes --runslow
+ run: |
+ pytest_args="-m pytest -v --color=yes"
+ if [ "${{ matrix.run_mode }}" = "slow" ]; then
+ pytest_args="$pytest_args --runslow"
+ fi
+ coverage run $pytest_args
 
  - name: Show coverage report
  run: coverage report -m

diff --git a/tests/metadata/test_cell_line.py b/tests/metadata/test_cell_line.py
@@ -62,6 +62,7 @@ def test_protein_expression_annotation(adata):
  )
 
 
+@pytest.mark.slow
 def test_bulk_rna_expression_annotation(adata):
  pt_metadata.annotate(adata)
  pt_metadata.annotate_bulk_rna(adata, query_id="DepMap_ID", cell_line_source="broad")

diff --git a/tests/tools/_coda/test_sccoda.py b/tests/tools/_coda/test_sccoda.py
@@ -96,6 +96,7 @@ def test_credible_effects(adata):
  assert sccoda.credible_effects(mdata)["condition[T.Salmonella]"]["Enterocyte"]
 
 
+@pytest.mark.slow
 def test_make_arviz(adata):
  adata_salm = adata[adata.obs["condition"].isin(["Control", "Salmonella"])]
  mdata = sccoda.load(

diff --git a/tests/tools/_distances/test_distance_tests.py b/tests/tools/_distances/test_distance_tests.py
@@ -1,7 +1,7 @@
 import pertpy as pt
+import pytest
 import scanpy as sc
 from pandas import DataFrame
-from pytest import fixture, mark
 
 distances = [
  "edistance",
@@ -27,16 +27,19 @@
 count_distances = ["nb_ll"]
 
 
-@fixture
+@pytest.fixture
 def adata():
  adata = pt.dt.distance_example()
  adata = sc.pp.subsample(adata, 0.1, copy=True)
 
  return adata
 
 
-@mark.parametrize("distance", distances)
+@pytest.mark.parametrize("distance", distances)
 def test_distancetest(adata, distance):
+ if distance == "wasserstein":
+ pytest.mark.apply(pytest.mark.slow)
+
  etest = pt.tl.DistanceTest(distance, n_perms=10, obsm_key="X_pca", alpha=0.05, correction="holm-sidak")
  tab = etest(adata, groupby="perturbation", contrast="control")
 

diff --git a/tests/tools/test_augur.py b/tests/tools/test_augur.py
@@ -168,6 +168,7 @@ def test_differential_prioritization():
  """Test differential prioritization run."""
  # Requires the full dataset or it fails because of a lack of statistical power
  adata = pt.dt.sc_sim_augur()
+ adata = sc.pp.subsample(adata, n_obs=500, copy=True, random_state=10)
  ag = pt.tl.Augur("random_forest_classifier", Params(random_state=42))
  ag.load(adata)
 

diff --git a/tests/tools/test_mixscape.py b/tests/tools/test_mixscape.py
@@ -4,19 +4,19 @@
 import numpy as np
 import pandas as pd
 import pertpy as pt
-from _pytest.fixtures import fixture
+import pytest
 from scipy import sparse
 
 CWD = Path(__file__).parent.resolve()
 
 # Random generate data settings
-num_cells_per_group = 100
+num_cells_per_group = 10
 num_not_de = 10
 num_de = 10
 accuracy_threshold = 0.8
 
 
-@fixture
+@pytest.fixture
 def adata():
  rng = np.random.default_rng(seed=1)
  # generate not differentially expressed genes