Pass arguments to pytest; Plot tests skippable

Added ability to pass command line arguments to pytest.
In addition, I marked tests which do plotting as 'plottest'.
This combination allows the following invocation:

    python -m lifelines.tests -m "not plottest"

Which will skip plotting tests. Any arguments that pytests
accepts can be passed now.

Signed-off-by: Jonas Kalderstam <[email protected]>

lifelines/tests/__main__.py

@@ -4,4 +4,4 @@
 
 if __name__ == '__main__':
     # Exit with correct code
-    sys.exit(pytest.main("--pyargs lifelines.tests"))
+    sys.exit(pytest.main(["--pyargs", "lifelines.tests"] + sys.argv[1:]))

lifelines/tests/test_estimation.py

@@ -192,6 +192,7 @@ def test_kmf_left_censorship_stats(self):
         assert kmf.cumulative_density_[kmf._label].ix[0] == 0.0
         assert kmf.cumulative_density_[kmf._label].ix[12] == 1.0
 
+    @pytest.mark.plottest
     @pytest.mark.skipif("DISPLAY" not in os.environ, reason="requires display")
     def test_kmf_left_censorship_plots(self):
         kmf = KaplanMeierFitter()
@@ -662,6 +663,7 @@ def test_large_dimensions_for_recursion_error(self):
         aaf = AalenAdditiveFitter()
         aaf.fit(X)
 
+    @pytest.mark.plottest
     @pytest.mark.skipif("DISPLAY" not in os.environ, reason="requires display")
     def test_aaf_panel_dataset(self):
         panel_dataset = load_panel_test()
@@ -688,6 +690,7 @@ def test_aalen_additive_median_predictions_split_data(self):
         T_pred = aaf.predict_median(X[list(range(6))])
         assert abs((T_pred.values > T).mean() - 0.5) < 0.05
 
+    @pytest.mark.plottest
     @pytest.mark.skipif("DISPLAY" not in os.environ, reason="requires display")
     def test_aalen_additive_fit_no_censor(self):
         # this is a visual test of the fitting the cumulative
@@ -713,6 +716,7 @@ def test_aalen_additive_fit_no_censor(self):
         plt.show()
         return
 
+    @pytest.mark.plottest
     @pytest.mark.skipif("DISPLAY" not in os.environ, reason="requires display")
     def test_aalen_additive_fit_with_censor(self):
         # this is a visual test of the fitting the cumulative

lifelines/tests/test_plotting.py

@@ -9,6 +9,7 @@
 from ..plotting import plot_lifetimes
 
 
+@pytest.mark.plottest
 @pytest.mark.skipif("DISPLAY" not in os.environ, reason="requires display")
 class TestPlotting():