From b08162fde042f880ebb4d2856165647a3e63f347 Mon Sep 17 00:00:00 2001 From: Arya Massarat <23412689+aryarm@users.noreply.github.com> Date: Tue, 26 Nov 2024 22:34:34 +0000 Subject: [PATCH] fix failing example tests with --out-thresh --- noxfile.py | 2 +- tests/test_examples.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/noxfile.py b/noxfile.py index 4955926..f127938 100644 --- a/noxfile.py +++ b/noxfile.py @@ -46,7 +46,7 @@ def install_handle_python_numpy(session): handle incompatibilities with python and numpy versions see https://github.com/cjolowicz/nox-poetry/issues/1116 """ - if session._session.python in ["3.11", "3.12"]: + if session._session.python in ["3.11", "3.12", "3.13"]: session._session.install(".") else: session.install(".") diff --git a/tests/test_examples.py b/tests/test_examples.py index 1604532..5f25730 100644 --- a/tests/test_examples.py +++ b/tests/test_examples.py @@ -716,7 +716,7 @@ def test_1000G_simulated_maf(capfd): out_vars = ("rs1046282", "rs36046716") for maf in (0.05, 0.30, 0.31, 0.38): - cmd = f"run --maf {maf} -o {out_hp_file} {gt_file} {pt_file}" + cmd = f"run --out-thresh 1 --maf {maf} -o {out_hp_file} {gt_file} {pt_file}" runner = CliRunner() result = runner.invoke(main, cmd.split(" "), catch_exceptions=False) captured = capfd.readouterr() @@ -758,7 +758,7 @@ def test_1000G_real(capfd, caplog): caplog.set_level(logging.INFO) for maf in (0.05, 0.14, 0.22, 0.23, 0.35): - cmd = f"run --maf {maf} -o {out_hp_file} {gt_file} {pt_file}" + cmd = f"run --out-thresh 1 --maf {maf} -o {out_hp_file} {gt_file} {pt_file}" runner = CliRunner() result = runner.invoke(main, cmd.split(" "), catch_exceptions=False) captured = capfd.readouterr()