Pytest with 89% coverage #19
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POT now build with a certain number of tests. I will merge this PR today unless somebody objects. |
| before_script: # configure a headless display to test plot generation | ||
| - "export DISPLAY=:99.0" | ||
| - "sh -e /etc/init.d/xvfb start" | ||
| - sleep 3 # give xvfb some time to start |
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do you use only matplotlib? if so just use the Agg backend
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I tried to use the Agg backedn here
https://github.com/rflamary/POT/blob/pytest/test/test_plot.py
but travis still failed with DISPLAY error
https://travis-ci.org/rflamary/POT/builds/256924206
maybe the test_plot.py is not good but I don't see the problem
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that's weird. You seem to have done it right. Are you sure matplotlib is not imported anywhere before?
you should also nest the imports to matplotlib in the or source tree. So matplotlib is not imported when you do import ot
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| pytest : FORCE | ||
| python -m py.test -v test/ | ||
| python -m py.test -v test/ --cov=ot |
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you should have a native pytest command:
pytest -v test/ --cov=ot
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Under Debian/Ubuntu logilab-common install a useless executable named pytest. It's a well known bug but takes time to be corrected. This line ensure that the proper py.test is executed.
test/test_bregman.py
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| reg = 1e-3 | ||
| bary_wass = ot.bregman.barycenter(A, M, reg, weights) | ||
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| assert np.allclose(1, np.sum(bary_wass)) |
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you have an assert_allclose function in numpy
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@rflamary please wait. I'll do a proper review in the next 2 days. |
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ok you win
sklearn is not as careful
https://github.com/scikit-learn/scikit-learn/blob/master/build_tools/travis/test_script.sh#L25
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test/test_bregman.py
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| def test_sinkhorn_empty(): | ||
| # test sinkhorn | ||
| n = 100 | ||
| np.random.seed(0) |
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use a random state
rng = np.random.RandomState(42)
x = rng.randn(n, 2)
etc.
ie don't change the global seed.
test/test_bregman.py
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| G, log = ot.sinkhorn([], [], M, 1, stopThr=1e-10, verbose=True, log=True) | ||
| # check constratints | ||
| assert np.allclose(u, G.sum(1), atol=1e-05) # cf convergence sinkhorn | ||
| assert np.allclose(u, G.sum(0), atol=1e-05) # cf convergence sinkhorn |
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use np.testing.assert_allclose
it makes errors clearer than just an assert
test/test_bregman.py
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| # Gaussian distributions | ||
| a1 = ot.datasets.get_1D_gauss(n, m=30, s=10) # m= mean, s= std | ||
| a2 = ot.datasets.get_1D_gauss(n, m=40, s=10) |
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as I was saying it should be named in the future
make_1d_gauss
test/test_bregman.py
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| def test_unmix(): | ||
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| n = 50 # nb bins |
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n -> n_bins
as n can mean n_samples etc.
if you call it n_bins no need to write nb bins :)
test/test_da.py
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| import ot | ||
| import numpy as np |
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import numpy before ot
as ot depends on numpy
it's for convention
test/test_da.py
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| # import pytest | ||
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| def test_OTDA(): |
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test_OTDA -> test_otda
no caps in function names
test/test_da.py
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| n = 150 # nb bins | ||
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| xs, ys = ot.datasets.get_data_classif('3gauss', n) | ||
| xt, yt = ot.datasets.get_data_classif('3gauss2', n) |
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get_data_classif -> make_classification
would be sklearn consistent.
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OK we should open an issue and handle that in a separate PR I think, this one is mainly for testing
test/test_dr.py
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| import pytest | ||
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| try: # test if cudamat installed | ||
| import ot.dr |
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test for what you really need to test ie if cudamat is available
try:
import cudamat
has_cudamat = False
except ...:
has_cudamat = True
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OK @agramfort I took care of most your reviews. What remains and will be opened as Issues :
If the travis build work I will merge the PR since I introduced no features in the toolbox only tests. |
| def test_otda(): | ||
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| n_samples = 150 # nb samples | ||
| np.random.seed(0) |
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RandomState
the get_data_classif function should take the rng in param and use it instead of np.random.randn
see the check_random_state function in sklearn
| def test_conditional_gradient(): | ||
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| n_bins = 100 # nb bins | ||
| np.random.seed(0) |
test/test_utils.py
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| l2 = ot.utils.parmap(f, a) | ||
| l2 = list(ot.utils.parmap(f, a)) | ||
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| assert np.allclose(l1, l2) |
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use np.testing.assert_allclose
test/test_utils.py
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| # dist shoul return squared euclidean | ||
| assert np.allclose(D, D2) | ||
| assert np.allclose(D, D3) |
test/test_utils.py
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| M = ot.utils.dist0(n, method='lin_square') | ||
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| # dist0 default to linear sampling with quadratic loss | ||
| assert np.allclose(M[0, -1], (n - 1) * (n - 1)) |
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ok no more nitpicks after these |
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OK great thank you again, I won't handle the rng stuff in this PR I will add it to the Issue about the make_datasets function. |
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k
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+1 for merge |
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OK let's merge this PR, We now have a 89% coverage of the code when all libraries are installed (cudamat, pymanopt, autograd). Also the Makefile include the test target that checks for PEP8 violations and and run the tests. I have created Issue #20 for the dataset function names and random state problems. |
Will merge soon since currently POT do not build.