MAINT: Add decorator for tests that use matplotlib

Add decorator for tests requirign matplotlib
Automatically skip if mpl is missing
Add option to skip from the command line

statsmodels/conftest.py

@@ -1,5 +1,13 @@
 import pytest
 
+try:
+ import matplotlib
+
+ matplotlib.use('agg')
+ HAVE_MATPLOTLIB = True
+except ImportError:
+ HAVE_MATPLOTLIB = False
+
 
 def pytest_addoption(parser):
  parser.addoption("--skip-slow", action="store_true",
@@ -8,6 +16,8 @@ def pytest_addoption(parser):
  help="run only slow tests")
  parser.addoption("--skip-examples", action="store_true",
  help="skip tests of examples")
+ parser.addoption("--skip-matplotlib", action="store_true",
+ help="skip tests that depend on matplotlib")
 
 
 def pytest_runtest_setup(item):
@@ -20,6 +30,12 @@ def pytest_runtest_setup(item):
  if 'example' in item.keywords and item.config.getoption("--skip-examples"):
  pytest.skip("skipping due to --skip-examples")
 
+ if 'requires_matplotlib' in item.keywords and item.config.getoption("--skip-matplotlib"):
+ pytest.skip("skipping due to --skip-matplotlib")
+
+ if 'requires_matplotlib' in item.keywords and not HAVE_MATPLOTLIB:
+ pytest.skip("skipping since matplotlib is not intalled")
+
 
 def pytest_configure(config):
  try:

statsmodels/duration/tests/test_survfunc.py

@@ -13,9 +13,8 @@
 
 try:
  import matplotlib.pyplot as plt
- have_matplotlib = True
 except ImportError:
- have_matplotlib = False
+ pass
 
 
 def close_or_save(pdf, fig):
@@ -189,7 +188,7 @@ def test_survdiff():
  assert_allclose(stat, 13.35259, atol=1e-4, rtol=1e-4)
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='requires matplotlib')
+@pytest.mark.requires_matplotlib
 def test_plot_km(close_figures):
 
  if pdf_output:

statsmodels/genmod/tests/test_gee.py

@@ -29,10 +29,9 @@
 import warnings
 
 try:
- import matplotlib.pyplot as plt # makes plt available for test functions
- have_matplotlib = True
-except:
- have_matplotlib = False
+ import matplotlib.pyplot as plt
+except ImportError:
+ pass
 
 pdf_output = False
 
@@ -156,7 +155,7 @@ def test_margins_multinomial(self):
  assert_allclose(marg.margeff, np.r_[-0.41197961], rtol=1e-5)
  assert_allclose(marg.margeff_se, np.r_[0.1379962], rtol=1e-6)
 
- @pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+ @pytest.mark.requires_matplotlib
  def test_nominal_plot(self, close_figures):
  np.random.seed(34234)
  endog = np.r_[0, 0, 0, 0, 1, 1, 1, 1]
@@ -802,7 +801,7 @@ def test_nominal_independence(self):
  model1 = NominalGEE(y, x, groups, cov_struct=nmi)
  model1.fit()
 
- @pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+ @pytest.mark.requires_matplotlib
  def test_ordinal_plot(self, close_figures):
  family = Binomial()
 
@@ -1555,7 +1554,7 @@ def test_wrapper(self):
  check_wrapper(rslt2)
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_plots(close_figures):
 
  np.random.seed(378)

statsmodels/genmod/tests/test_glm.py

@@ -29,10 +29,9 @@
 DECIMAL_0 = 0
 
 try:
- import matplotlib.pyplot as plt #makes plt available for test functions
- have_matplotlib = True
+ import matplotlib.pyplot as plt
 except:
- have_matplotlib = False
+ pass
 
 pdf_output = False
 
@@ -42,14 +41,16 @@
 else:
  pdf = None
 
+
 def close_or_save(pdf, fig):
  if pdf_output:
  pdf.savefig(fig)
 
+
 def teardown_module():
- if have_matplotlib:
- if pdf_output:
- pdf.close()
+ if pdf_output:
+ pdf.close()
+
 
 class CheckModelResultsMixin(object):
  '''
@@ -900,7 +901,7 @@ def test_formula_missing_exposure():
  exposure=exposure, family=family)
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_plots(close_figures):
 
  np.random.seed(378)

statsmodels/graphics/tests/test_agreement.py

@@ -7,12 +7,11 @@
 
 try:
  import matplotlib.pyplot as plt
- have_matplotlib = True
-except:
- have_matplotlib = False
+except ImportError:
+ pass
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_mean_diff_plot(close_figures):
 
  # Seed the random number generator.
@@ -40,10 +39,10 @@ def test_mean_diff_plot(close_figures):
  mean_diff_plot(m1, m2, sd_limit=0)
 
  # Test asethetic controls.
- mean_diff_plot(m1, m2, scatter_kwds={'color':'green', 's':10})
+ mean_diff_plot(m1, m2, scatter_kwds={'color': 'green', 's': 10})
 
- mean_diff_plot(m1, m2, mean_line_kwds={'color':'green', 'lw':5})
+ mean_diff_plot(m1, m2, mean_line_kwds={'color': 'green', 'lw': 5})
 
- mean_diff_plot(m1, m2, limit_lines_kwds={'color':'green',
- 'lw':5,
- 'ls':'dotted'})
+ mean_diff_plot(m1, m2, limit_lines_kwds={'color': 'green',
+ 'lw': 5,
+ 'ls': 'dotted'})

statsmodels/graphics/tests/test_boxplots.py

@@ -4,15 +4,13 @@
 from statsmodels.graphics.boxplots import violinplot, beanplot
 from statsmodels.datasets import anes96
 
-
 try:
  import matplotlib.pyplot as plt
- have_matplotlib = True
-except:
- have_matplotlib = False
+except ImportError:
+ pass
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_violinplot_beanplot(close_figures):
  # Test violinplot and beanplot with the same dataset.
  data = anes96.load_pandas()

statsmodels/graphics/tests/test_correlation.py

@@ -4,15 +4,13 @@
 from statsmodels.graphics.correlation import plot_corr, plot_corr_grid
 from statsmodels.datasets import randhie
 
-
 try:
  import matplotlib.pyplot as plt
- have_matplotlib = True
-except:
- have_matplotlib = False
+except ImportError:
+ pass
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_plot_corr(close_figures):
  hie_data = randhie.load_pandas()
  corr_matrix = np.corrcoef(hie_data.data.values.T)
@@ -24,7 +22,7 @@ def test_plot_corr(close_figures):
  plot_corr(corr_matrix, normcolor=True, title='', cmap='jet')
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_plot_corr_grid(close_figures):
  hie_data = randhie.load_pandas()
  corr_matrix = np.corrcoef(hie_data.data.values.T)

statsmodels/graphics/tests/test_dotplot.py

@@ -10,16 +10,16 @@
 try:
  import matplotlib.pyplot as plt
  import matplotlib
- have_matplotlib = True
 except ImportError:
- have_matplotlib = False
+ pass
 
 
 def close_or_save(pdf, fig):
  if pdf_output:
  pdf.savefig(fig)
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+
+@pytest.mark.requires_matplotlib
 def test_all(close_figures):
 
  if pdf_output:

statsmodels/graphics/tests/test_factorplots.py

@@ -8,32 +8,30 @@
 try:
  import matplotlib.pyplot as plt
  import matplotlib
- have_matplotlib = True
 except ImportError:
- have_matplotlib = False
+ pass
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
 class TestInteractionPlot(object):
 
  @classmethod
  def setup_class(cls):
- if not have_matplotlib:
- pytest.skip('matplotlib not available')
  np.random.seed(12345)
  cls.weight = np.random.randint(1,4,size=60)
  cls.duration = np.random.randint(1,3,size=60)
  cls.days = np.log(np.random.randint(1,30, size=60))
 
-
+ @pytest.mark.requires_matplotlib
  def test_plot_both(self, close_figures):
  fig = interaction_plot(self.weight, self.duration, self.days,
  colors=['red','blue'], markers=['D','^'], ms=10)
 
+ @pytest.mark.requires_matplotlib
  def test_plot_rainbow(self, close_figures):
  fig = interaction_plot(self.weight, self.duration, self.days,
  markers=['D','^'], ms=10)
 
+ @pytest.mark.requires_matplotlib
  def test_plot_pandas(self, close_figures):
  weight = Series(self.weight, name='Weight')
  duration = Series(self.duration, name='Duration')
@@ -46,6 +44,7 @@ def test_plot_pandas(self, close_figures):
  assert_equal(ax.get_ylabel(), 'mean of Days')
  assert_equal(ax.get_xlabel(), 'Weight')
 
+ @pytest.mark.requires_matplotlib
  def test_plot_string_data(self, close_figures):
  weight = Series(self.weight, name='Weight').astype('str')
  duration = Series(self.duration, name='Duration')
@@ -58,15 +57,18 @@ def test_plot_string_data(self, close_figures):
  assert_equal(ax.get_ylabel(), 'mean of Days')
  assert_equal(ax.get_xlabel(), 'Weight')
 
+ @pytest.mark.requires_matplotlib
  def test_formatting(self, close_figures):
  fig = interaction_plot(self.weight, self.duration, self.days, colors=['r','g'], linestyles=['--','-.'])
  assert_equal(isinstance(fig, plt.Figure), True)
 
+ @pytest.mark.requires_matplotlib
  def test_formatting_errors(self, close_figures):
  assert_raises(ValueError, interaction_plot, self.weight, self.duration, self.days, markers=['D'])
  assert_raises(ValueError, interaction_plot, self.weight, self.duration, self.days, colors=['b','r','g'])
  assert_raises(ValueError, interaction_plot, self.weight, self.duration, self.days, linestyles=['--','-.',':'])
 
+ @pytest.mark.requires_matplotlib
  def test_plottype(self, close_figures):
  fig = interaction_plot(self.weight, self.duration, self.days, plottype='line')
  assert_equal(isinstance(fig, plt.Figure), True)

statsmodels/graphics/tests/test_functional.py

@@ -8,20 +8,18 @@
 from statsmodels.graphics.functional import \
  hdrboxplot, banddepth, fboxplot, rainbowplot
 
-
 try:
  import matplotlib.pyplot as plt
- have_matplotlib = True
 except ImportError:
- have_matplotlib = False
+ pass
 
 
 data = elnino.load(as_pandas=False)
 labels = data.raw_data[:, 0].astype(int)
 data = data.raw_data[:, 1:]
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_hdr_basic(close_figures):
  _, hdr = hdrboxplot(data, labels=labels, seed=12345)
 
@@ -59,7 +57,7 @@ def test_hdr_basic(close_figures):
  assert_equal(labels[hdr.outliers_idx], outliers)
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_hdr_basic_brute(close_figures):
  _, hdr = hdrboxplot(data, labels=labels, use_brute=True)
 
@@ -71,7 +69,7 @@ def test_hdr_basic_brute(close_figures):
  assert_almost_equal(hdr.median, median_t, decimal=2)
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_hdr_plot(close_figures):
  fig = plt.figure()
  ax = fig.add_subplot(111)
@@ -85,7 +83,7 @@ def test_hdr_plot(close_figures):
  ax.set_xlim([-0.2, 11.2])
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_hdr_alpha(close_figures):
  _, hdr = hdrboxplot(data, alpha=[0.7], seed=12345)
  extra_quant_t = np.vstack([[25.1, 26.5, 27.0, 26.4, 25.4, 24.1,
@@ -95,7 +93,7 @@ def test_hdr_alpha(close_figures):
  assert_almost_equal(hdr.extra_quantiles, extra_quant_t, decimal=0)
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_hdr_multiple_alpha(close_figures):
  _, hdr = hdrboxplot(data, alpha=[0.4, 0.92], seed=12345)
  extra_quant_t = [[25.712, 27.052, 27.711, 27.200,
@@ -114,7 +112,7 @@ def test_hdr_multiple_alpha(close_figures):
  decimal=0)
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_hdr_threshold(close_figures):
  _, hdr = hdrboxplot(data, alpha=[0.8], threshold=0.93, seed=12345)
  labels_pos = np.all(np.in1d(data, hdr.outliers).reshape(data.shape),
@@ -123,15 +121,15 @@ def test_hdr_threshold(close_figures):
  assert_equal([1968, 1982, 1983, 1997, 1998], outliers)
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_hdr_bw(close_figures):
  _, hdr = hdrboxplot(data, bw='cv_ml', seed=12345)
  median_t = [24.25, 25.64, 25.99, 25.04, 23.71, 22.38,
  21.31, 20.44, 20.24, 20.51, 21.19, 22.38]
  assert_almost_equal(hdr.median, median_t, decimal=2)
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_hdr_ncomp(close_figures):
  _, hdr = hdrboxplot(data, ncomp=3, seed=12345)
  median_t = [24.33, 25.71, 26.04, 25.08, 23.74, 22.40,
@@ -174,7 +172,7 @@ def test_banddepth_MBD():
  assert_almost_equal(depth, expected_depth, decimal=4)
 
 
-@pytest.mark.skipif(not have_matplotlib, reason='matplotlib not available')
+@pytest.mark.requires_matplotlib
 def test_fboxplot_rainbowplot(close_figures):
  # Test fboxplot and rainbowplot together, is much faster.
  def harmfunc(t):