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Fix to non-deterministic behaviour by removing long-range side effects (
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#248)

* Trying to stream CI

* Added plt.figure to all fixtures

* try `plt.figure()` specifically in the problematic `test_AreaPlot`

* fix flake8

* create pytest fixture for opening new figure after closing all others

* attempt explicitly closing box plot figures

* remove new figure fixture since it did not do the trick

* explicitly close figures after `.groupby` for good measure

* trigger actions

* Removing groupby code to see if this fixes

* lint correction

* Speculatively removed fixtures

* Lint correction

* Trying to make things more object oriented

* belt and braces for boxplot

* Attempt to eradicate all side effects

* Upgraded to parallel tests again

* provide new figure and axes explicitly for `test_AreaPlot`

Co-authored-by: Lukas Hergt <[email protected]>
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@williamjameshandley @lukashergt
williamjameshandley and lukashergt authored Jan 17, 2023
1 parent 9f57446 commit f349603
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Showing 5 changed files with 48 additions and 119 deletions.
4 changes: 2 additions & 2 deletions .github/workflows/CI.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ jobs:
run: python -m pip install -r requirements_extras.txt

- name: Test with pytest
run: python -m pytest --cov=anesthetic tests
run: python -m pytest --cov=anesthetic -n auto tests

- name: Upload coverage to Codecov
uses: codecov/codecov-action@v1
Expand Down Expand Up @@ -93,7 +93,7 @@ jobs:
- name: Test with pytest
shell: bash -l {0}
run: python -m pytest --cov=anesthetic tests
run: python -m pytest --cov=anesthetic -n auto tests

- name: Upload coverage to Codecov
uses: codecov/codecov-action@v1
52 changes: 9 additions & 43 deletions tests/test_plot.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -112,7 +112,6 @@ def test_make_1d_axes():
# Check unexpected kwargs
with pytest.raises((AttributeError, TypeError)):
make_1d_axes(paramnames, spam='ham')
plt.close("all")


def test_make_2d_axes_inputs_outputs():
Expand Down Expand Up @@ -145,7 +144,6 @@ def test_make_2d_axes_inputs_outputs():
assert fig is not fig0
fig, axes = make_2d_axes(paramnames_x, fig=fig0)
assert fig is fig0
plt.close("all")

# Check gridspec argument
grid = gs.GridSpec(2, 2, width_ratios=[3, 1], height_ratios=[3, 1])
Expand Down Expand Up @@ -203,7 +201,6 @@ def calc_n(axes):
assert ns['upper'] == upper * nx*(nx-1)//2
assert ns['lower'] == lower * nx*(nx-1)//2
assert ns['diagonal'] == diagonal * nx
plt.close("all")

params = [paramnames_x, paramnames_y]
all_params = paramnames_x + paramnames_y
Expand All @@ -224,7 +221,6 @@ def calc_n(axes):
assert ns['upper'] == upper * nu
assert ns['lower'] == lower * nl
assert ns['diagonal'] == diagonal * nd
plt.close("all")


@pytest.mark.parametrize('upper', [False, True])
Expand All @@ -249,7 +245,6 @@ def test_make_2d_axes_ticks(upper, ticks):
assert np.array_equal(xticks, ax.get_xticks())
else:
assert not np.array_equal(xticks, ax.get_xticks())
plt.close("all")
with pytest.raises(ValueError):
make_2d_axes(paramnames, upper=upper, ticks='spam')

Expand Down Expand Up @@ -288,7 +283,6 @@ def test_2d_axes_axlines(axesparams, params, upper):
kwargs = dict(c='k', ls='--', lw=0.5)
fig, axes = make_2d_axes(axesparams, upper=upper)
axes.axlines(params, **kwargs)
plt.close("all")


@pytest.mark.parametrize('axesparams', [['A', 'B', 'C', 'D'],
Expand All @@ -302,7 +296,6 @@ def test_2d_axes_axspans(axesparams, params, upper):
kwargs = dict(c='k', alpha=0.5)
fig, axes = make_2d_axes(axesparams, upper=upper)
axes.axspans(params, **kwargs)
plt.close("all")


@pytest.mark.parametrize('axesparams', [['A', 'B', 'C', 'D'],
Expand All @@ -316,7 +309,6 @@ def test_2d_axes_scatter(axesparams, params, upper):
kwargs = dict(c='k', marker='*')
fig, axes = make_2d_axes(axesparams, upper=upper)
axes.scatter(params, **kwargs)
plt.close("all")


@pytest.mark.parametrize('plot_1d', [kde_plot_1d, fastkde_plot_1d])
Expand Down Expand Up @@ -356,13 +348,11 @@ def test_kde_plot_1d(plot_1d):
line, fill = plot_1d(ax, data, fc=True, color='k', ec=None)
assert len(fill[0].get_edgecolor()) == 0
assert (to_rgba(line[0].get_color()) == to_rgba('k'))
plt.close("all")

# Check levels
with pytest.raises(ValueError):
ax = plt.gca()
fig, ax = plt.subplots()
plot_1d(ax, data, fc=True, levels=[0.68, 0.95])
plt.close("all")

# Check xlim, Gaussian (i.e. limits reduced to relevant data range)
fig, ax = plt.subplots()
Expand All @@ -371,15 +361,13 @@ def test_kde_plot_1d(plot_1d):
xmin, xmax = ax.get_xlim()
assert xmin > 0.4
assert xmax < 0.6
plt.close("all")
# Check xlim, Uniform (i.e. data and limits span entire prior boundary)
fig, ax = plt.subplots()
data = np.random.uniform(size=1000)
plot_1d(ax, data, q=0)
xmin, xmax = ax.get_xlim()
assert xmin <= 0
assert xmax >= 1
plt.close("all")

except ImportError:
if 'fastkde' not in sys.modules:
Expand All @@ -396,30 +384,25 @@ def test_fastkde_min_max():
_, ax = plt.subplots()
line, = fastkde_plot_1d(ax, data_x, xmin=xmin)
assert (line.get_xdata() >= xmin).all()
plt.close("all")

_, ax = plt.subplots()
line, = fastkde_plot_1d(ax, data_x, xmax=xmax)
assert (line.get_xdata() <= xmax).all()
plt.close("all")

_, ax = plt.subplots()
line, = fastkde_plot_1d(ax, data_x, xmin=xmin, xmax=xmax)
assert (line.get_xdata() >= xmin).all()
assert (line.get_xdata() <= xmax).all()
plt.close("all")

_, ax = plt.subplots()
fastkde_contour_plot_2d(ax, data_x, data_y, xmin=xmin, ymin=ymin)
assert ax.get_xlim()[0] >= xmin
assert ax.get_ylim()[0] >= ymin
plt.close()

_, ax = plt.subplots()
fastkde_contour_plot_2d(ax, data_x, data_y, xmax=xmax, ymax=ymax)
assert ax.get_xlim()[1] <= xmax
assert ax.get_ylim()[1] <= ymax
plt.close()

_, ax = plt.subplots()
fastkde_contour_plot_2d(ax, data_x, data_y,
Expand All @@ -428,7 +411,6 @@ def test_fastkde_min_max():
assert ax.get_xlim()[1] <= xmax
assert ax.get_ylim()[0] >= ymin
assert ax.get_ylim()[1] <= ymax
plt.close()

except ImportError:
if 'fastkde' not in sys.modules:
Expand Down Expand Up @@ -475,7 +457,6 @@ def test_hist_plot_1d():
polygon, = hist_plot_1d(ax, data, histtype='step', cmap=plt.cm.viridis,
color='r')
assert polygon.get_ec() == ColorConverter.to_rgba('r')
plt.close("all")


@pytest.mark.parametrize('bins', ['knuth', 'freedman', 'blocks'])
Expand All @@ -488,7 +469,6 @@ def test_astropyhist_plot_1d(bins):
assert np.all([isinstance(b, Patch) for b in bars])
assert max([b.get_height() for b in bars]) == 1.
assert np.all(np.array([b.get_height() for b in bars]) <= 1.)
plt.close("all")
except ImportError:
if 'astropy' not in sys.modules:
pass
Expand Down Expand Up @@ -553,8 +533,6 @@ def test_1d_density_kwarg(plot_1d, s):
gauss_norm = 1 / np.sqrt(2 * np.pi * s**2)
assert kde_height == pytest.approx(gauss_norm, rel=0.1)

plt.close("all")

except ImportError:
if 'fastkde' not in sys.modules:
pass
Expand All @@ -564,7 +542,7 @@ def test_1d_density_kwarg(plot_1d, s):
fastkde_contour_plot_2d])
def test_contour_plot_2d(contour_plot_2d):
try:
ax = plt.gca()
fig, ax = plt.subplots()
np.random.seed(1)
data_x = np.random.randn(1000)
data_y = np.random.randn(1000)
Expand All @@ -574,17 +552,16 @@ def test_contour_plot_2d(contour_plot_2d):

# Check levels
with pytest.raises(ValueError):
ax = plt.gca()
fig, ax = plt.subplots()
contour_plot_2d(ax, data_x, data_y, levels=[0.68, 0.95])

# Check q
ax = plt.gca()
fig, ax = plt.subplots()
contour_plot_2d(ax, data_x, data_y, q=0)
plt.close()

# Check unfilled
cmap = basic_cmap('C2')
ax = plt.gca()
fig, ax = plt.subplots()
cf1, ct1 = contour_plot_2d(ax, data_x, data_y, facecolor='C2')
cf2, ct2 = contour_plot_2d(ax, data_x, data_y, fc='None', cmap=cmap)
# filled `contourf` and unfilled `contour` colors are the same:
Expand All @@ -595,8 +572,7 @@ def test_contour_plot_2d(contour_plot_2d):
cf, ct = contour_plot_2d(ax, data_x, data_y, ec='C0', cmap=plt.cm.Reds)
assert cf.get_cmap() == plt.cm.Reds
assert ct.colors == 'C0'
plt.close("all")
ax = plt.gca()
fig, ax = plt.subplots()
cf, ct = contour_plot_2d(ax, data_x, data_y, fc=None)
assert cf is None
assert ct.colors is None
Expand All @@ -612,7 +588,6 @@ def test_contour_plot_2d(contour_plot_2d):
assert cf is None
assert ct.colors is None
assert ct.get_cmap() == plt.cm.Reds
plt.close("all")

# Check limits, Gaussian (i.e. limits reduced to relevant data range)
fig, ax = plt.subplots()
Expand All @@ -625,7 +600,6 @@ def test_contour_plot_2d(contour_plot_2d):
assert xmax < 0.6
assert ymin > 0.4
assert ymax < 0.6
plt.close("all")
# Check limits, Uniform (i.e. data & limits span entire prior boundary)
fig, ax = plt.subplots()
data_x = np.random.uniform(size=1000)
Expand All @@ -643,7 +617,6 @@ def test_contour_plot_2d(contour_plot_2d):
assert xmax == pytest.approx(1, abs=0.01)
assert ymin == pytest.approx(0, abs=0.01)
assert ymax == pytest.approx(1, abs=0.01)
plt.close("all")

except ImportError:
if 'fastkde' not in sys.modules:
Expand All @@ -656,14 +629,12 @@ def test_kde_plot_nplot():
data = np.random.randn(1000)
line, = kde_plot_1d(ax, data, ncompress=1000, nplot_1d=200)
assert line.get_xdata().size == 200
plt.close("all")

fig, ax = plt.subplots()
np.random.seed(0)
data_x = np.random.randn(1000)
data_y = np.random.randn(1000)
kde_contour_plot_2d(ax, data_x, data_y, ncompress=1000, nplot_2d=900)
plt.close("all")


@pytest.mark.parametrize('contour_plot_2d', [kde_contour_plot_2d,
Expand All @@ -679,9 +650,8 @@ def test_contour_plot_2d_levels(contour_plot_2d, levels):
y = np.random.randn(1000)
cmap = plt.cm.viridis

ax1 = plt.subplot(211)
fig, (ax1, ax2) = plt.subplots(2)
contour_plot_2d(ax1, x, y, levels=levels, cmap=cmap)
ax2 = plt.subplot(212)
contour_plot_2d(ax2, x, y, levels=levels, cmap=cmap, fc=None)

# assert that color between filled and unfilled contours matches
Expand All @@ -694,8 +664,6 @@ def test_contour_plot_2d_levels(contour_plot_2d, levels):
color2 = ax2.collections[len(levels)-1].get_edgecolor()
assert_array_equal(color1, color2)

plt.close("all")

except ImportError:
if 'fastkde' not in sys.modules:
pass
Expand All @@ -709,7 +677,7 @@ def test_scatter_plot_2d():
lines, = scatter_plot_2d(ax, data_x, data_y)
assert isinstance(lines, Line2D)

ax = plt.gca()
fig, ax = plt.subplots()
points, = scatter_plot_2d(ax, data_x, data_y, color='C0', lw=1)
assert (points.get_color() == 'C0')
points, = scatter_plot_2d(ax, data_x, data_y, cmap=plt.cm.viridis)
Expand All @@ -718,12 +686,10 @@ def test_scatter_plot_2d():
assert (points.get_color() == 'C0')
assert (points.get_markerfacecolor() == 'C1')
assert (points.get_markeredgecolor() == 'C2')
plt.close()

# Check that q is ignored
ax = plt.gca()
fig, ax = plt.subplots()
scatter_plot_2d(ax, data_x, data_y, q=0)
plt.close()


@pytest.mark.parametrize('sigmas', [(1, '1sigma', 0.682689492137086),
Expand Down
6 changes: 0 additions & 6 deletions tests/test_reader.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@
import numpy as np
from numpy.testing import assert_array_equal, assert_array_almost_equal
from pandas.testing import assert_frame_equal
import matplotlib.pyplot as plt
from anesthetic import MCMCSamples, NestedSamples
from anesthetic import read_chains
from anesthetic.read.polychord import read_polychord
Expand Down Expand Up @@ -44,7 +43,6 @@ def test_read_getdist():
assert_array_equal(mcmc.get_labels(), labels)
mcmc.plot_2d(['x0', 'x1', 'x2', 'x3'])
mcmc.plot_1d(['x0', 'x1', 'x2', 'x3'])
plt.close("all")

os.rename('./tests/example_data/gd.paramnames',
'./tests/example_data/gd.paramnames_')
Expand Down Expand Up @@ -81,7 +79,6 @@ def test_read_cobayamcmc():

mcmc.plot_2d(['x0', 'x1'])
mcmc.plot_1d(['x0', 'x1'])
plt.close("all")

# single chain file
mcmc = read_cobaya('./tests/example_data/cb_single_chain')
Expand Down Expand Up @@ -144,7 +141,6 @@ def test_read_montepython():
assert isinstance(mcmc, MCMCSamples)
mcmc.plot_2d(['x0', 'x1', 'x2', 'x3'])
mcmc.plot_1d(['x0', 'x1', 'x2', 'x3'])
plt.close("all")


def test_read_multinest():
Expand Down Expand Up @@ -174,7 +170,6 @@ def test_read_multinest():
assert isinstance(ns, NestedSamples)
ns.plot_2d(['x0', 'x1', 'x2', 'x3'])
ns.plot_1d(['x0', 'x1', 'x2', 'x3'])
plt.close("all")


def test_read_polychord():
Expand All @@ -199,7 +194,6 @@ def test_read_polychord():

ns.plot_2d(['x0', 'x1', 'x2', 'x3'])
ns.plot_1d(['x0', 'x1', 'x2', 'x3'])
plt.close("all")

os.rename('./tests/example_data/pc_phys_live-birth.txt',
'./tests/example_data/pc_phys_live-birth.txt_')
Expand Down
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1 comment on commit f349603

@AdamOrmondroyd
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Removing all the plt.close("all") from the tests leads to a warning that too many figures are open. I see this as an opportunity to group the tests into classes, as I think inheriting from pandas's TestPlotBase would take care of this.

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