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dputhier / pygtftk

A python package and a set of shell commands to handle GTF files
GNU General Public License v3.0
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FAIL: Doctest: pygtftk.stats.intersect.modl.dict_learning.squish_matrix #138

Closed dputhier closed 3 years ago

dputhier commented 3 years ago

Hi @qferre , I'm currently in branch release/1.2.0. There is an issue with make nose. Could you try on your side:

make nose

...

./stats/intersect/modl/dict_learning.py
./Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/model_selection/_split.py:297: FutureWarning: Setting a random_state has no effect since shuffle is False. This will raise an error in 0.24. You should leave random_state to its default (None), or set shuffle=True.
  FutureWarning
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/decomposition/_dict_learning.py:414: RuntimeWarning: invalid value encountered in true_divide
  dictionary[:, k] /= atom_norm
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0004
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0002
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0001
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.00030000000000000003
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/decomposition/_dict_learning.py:414: RuntimeWarning: invalid value encountered in true_divide
  dictionary[:, k] /= atom_norm
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.00030000000000000003
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0004
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0001
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0002
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0005
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0006000000000000001
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/decomposition/_dict_learning.py:414: RuntimeWarning: invalid value encountered in true_divide
  dictionary[:, k] /= atom_norm
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.00030000000000000003
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0002
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0001
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0004
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0005
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0006000000000000001
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 0.0, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/decomposition/_dict_learning.py:414: RuntimeWarning: invalid value encountered in true_divide
  dictionary[:, k] /= atom_norm
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0004
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.00030000000000000003
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0002
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0001
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0005
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0
  tol, rng, random, positive)
/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/scikit_learn-0.23.2-py3.7-macosx-10.9-x86_64.egg/sklearn/linear_model/_coordinate_descent.py:527: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: nan, tolerance: 0.0006000000000000001
  tol, rng, random, positive)
.F
======================================================================
FAIL: Doctest: pygtftk.stats.intersect.modl.dict_learning.squish_matrix
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/doctest.py", line 2204, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for pygtftk.stats.intersect.modl.dict_learning.squish_matrix
  File "/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/pygtftk-1.2.0-py3.7-macosx-10.9-x86_64.egg/pygtftk/stats/intersect/modl/dict_learning.py", line 83, in squish_matrix

----------------------------------------------------------------------
File "/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/pygtftk-1.2.0-py3.7-macosx-10.9-x86_64.egg/pygtftk/stats/intersect/modl/dict_learning.py", line 94, in pygtftk.stats.intersect.modl.dict_learning.squish_matrix
Failed example:
    np.testing.assert_equal(X_squished, np.array([[0,0,1,1]]*1 + [[1,1,0,0]]*32)) # Note that the rows have been sorted by abundance
Exception raised:
    Traceback (most recent call last):
      File "/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/doctest.py", line 1337, in __run
        compileflags, 1), test.globs)
      File "<doctest pygtftk.stats.intersect.modl.dict_learning.squish_matrix[3]>", line 1, in <module>
        np.testing.assert_equal(X_squished, np.array([[0,0,1,1]]*1 + [[1,1,0,0]]*32)) # Note that the rows have been sorted by abundance
      File "/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/numpy/testing/_private/utils.py", line 342, in assert_equal
        return assert_array_equal(actual, desired, err_msg, verbose)
      File "/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/numpy/testing/_private/utils.py", line 931, in assert_array_equal
        verbose=verbose, header='Arrays are not equal')
      File "/Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/numpy/testing/_private/utils.py", line 759, in assert_array_compare
        raise AssertionError(msg)
    AssertionError:
    Arrays are not equal

    (shapes (5, 4), (33, 4) mismatch)
     x: array([[0, 0, 1, 1],
           [1, 1, 0, 0],
           [1, 1, 0, 0],...
     y: array([[0, 0, 1, 1],
           [1, 1, 0, 0],
           [1, 1, 0, 0],...

----------------------------------------------------------------------
Ran 3 tests in 3.404s

FAILED (failures=1)
=================
./stats/intersect/modl/tree.py
.
qferre commented 3 years ago

My bad, there was a typo in the unitary test. Fixed in 5bb1edb in develop.

qferre commented 3 years ago

Should I switch to release/1.2.0 or do we keep merging from develop ?

dputhier commented 3 years ago

You should switch now to release/1.2.0 (and merge develop if you did some modification recently).

Le mer. 9 sept. 2020 à 11:35, Quentin Ferré notifications@github.com a écrit :

Should I switch to release/1.2.0 or do we keep merging from develop ?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/dputhier/pygtftk/issues/138#issuecomment-689448091, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAN7CHUG2TY5PETDUQVUXPTSE5D47ANCNFSM4RBPFCWA .

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Denis Puthier laboratoire INSERM TAGC/INSERM U 1090 Parc Scientifique de Luminy case 928 163, avenue de Luminy 13288 MARSEILLE cedex 09 FRANCE Mail: denis.puthier@univ-amu.fr Tel: (National) 04 91 82 87 31 / (International) 33 4 91 82 87 31 Fax: (National) 04 91 82 87 01 / (International) 33 4 91 82 87 01

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qferre commented 3 years ago

It is done. I only had to merge the 5bb1edb commit. I am now working on release/1.2.0