fix failing example tests with --out-thresh

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(".")

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()