[MRG] Remove shogun dependency (scikit-learn-contrib#216)

* Remove shogun dependency

* Finalize removing of shogun LMNN

* Remove LMNN useless base class

Author: wdevazelhes

README.rst

@@ -41,13 +41,6 @@ package installed).
 
 See the `sphinx documentation`_ for full documentation about installation, API, usage, and examples.
 
-**Notes**
-
-If a recent version of the Shogun Python modular (``modshogun``) library
-is available, the LMNN implementation will use the fast C++ version from
-there. The two implementations differ slightly, and the C++ version is
-more complete.
-
 
 .. _sphinx documentation: http://metric-learn.github.io/metric-learn/
 

bench/benchmarks/iris.py

@@ -13,16 +13,9 @@
     'NCA': metric_learn.NCA(max_iter=700, n_components=2),
     'RCA_Supervised': metric_learn.RCA_Supervised(dim=2, num_chunks=30,
                                                   chunk_size=2),
-    'SDML_Supervised': metric_learn.SDML_Supervised(num_constraints=1500),
+    'SDML_Supervised': metric_learn.SDML_Supervised(num_constraints=1500)
 }
 
-try:
-  from metric_learn.lmnn import python_LMNN
-  if python_LMNN is not metric_learn.LMNN:
-    CLASSES['python_LMNN'] = python_LMNN(k=5, learn_rate=1e-6, verbose=False)
-except ImportError:
-  pass
-
 
 class IrisDataset(object):
   params = [sorted(CLASSES)]

doc/getting_started.rst

@@ -23,14 +23,6 @@ Alternately, download the source repository and run:
   (install from commit `a0ed406 <https://github.com/skggm/skggm/commit/a0ed406586c4364ea3297a658f415e13b5cbdaf8>`_).
 -  For running the examples only: matplotlib
 
-**Notes**
-
-If a recent version of the Shogun Python modular (``modshogun``) library
-is available, the LMNN implementation will use the fast C++ version from
-there. The two implementations differ slightly, and the C++ version is
-more complete.
-
-
 Quick start
 ===========
 

doc/supervised.rst

@@ -87,11 +87,6 @@ indicates :math:`\mathbf{x}_{i}, \mathbf{x}_{j}` belong to different class,
     lmnn = LMNN(k=5, learn_rate=1e-6)
     lmnn.fit(X, Y, verbose=False)
 
-If a recent version of the Shogun Python modular (``modshogun``) library
-is available, the LMNN implementation will use the fast C++ version from
-there. Otherwise, the included pure-Python version will be used.
-The two implementations differ slightly, and the C++ version is more complete.
-
 .. topic:: References:
 
     .. [1] `Distance Metric Learning for Large Margin Nearest Neighbor

metric_learn/lmnn.py

@@ -25,8 +25,7 @@
 from .base_metric import MahalanobisMixin
 
 
-# commonality between LMNN implementations
-class _base_LMNN(MahalanobisMixin, TransformerMixin):
+class LMNN(MahalanobisMixin, TransformerMixin):
   def __init__(self, init=None, k=3, min_iter=50, max_iter=1000,
                learn_rate=1e-7, regularization=0.5, convergence_tol=0.001,
                use_pca=True, verbose=False, preprocessor=None,
@@ -114,11 +113,7 @@ def __init__(self, init=None, k=3, min_iter=50, max_iter=1000,
     self.n_components = n_components
     self.num_dims = num_dims
     self.random_state = random_state
-    super(_base_LMNN, self).__init__(preprocessor)
-
-
-# slower Python version
-class python_LMNN(_base_LMNN):
+    super(LMNN, self).__init__(preprocessor)
 
   def fit(self, X, y):
     if self.num_dims != 'deprecated':
@@ -344,40 +339,3 @@ def _sum_outer_products(data, a_inds, b_inds, weights=None):
   if weights is not None:
     return np.dot(Xab.T, Xab * weights[:,None])
   return np.dot(Xab.T, Xab)
-
-
-try:
-  # use the fast C++ version, if available
-  from modshogun import LMNN as shogun_LMNN
-  from modshogun import RealFeatures, MulticlassLabels
-
-  class LMNN(_base_LMNN):
-    """Large Margin Nearest Neighbor (LMNN)
-
-    Attributes
-    ----------
-    n_iter_ : `int`
-        The number of iterations the solver has run.
-
-    transformer_ : `numpy.ndarray`, shape=(n_components, n_features)
-        The learned linear transformation ``L``.
-    """
-
-    def fit(self, X, y):
-      X, y = self._prepare_inputs(X, y, dtype=float,
-                                  ensure_min_samples=2)
-      labels = MulticlassLabels(y)
-      self._lmnn = shogun_LMNN(RealFeatures(X.T), labels, self.k)
-      self._lmnn.set_maxiter(self.max_iter)
-      self._lmnn.set_obj_threshold(self.convergence_tol)
-      self._lmnn.set_regularization(self.regularization)
-      self._lmnn.set_stepsize(self.learn_rate)
-      if self.use_pca:
-        self._lmnn.train()
-      else:
-        self._lmnn.train(np.eye(X.shape[1]))
-      self.transformer_ = self._lmnn.get_linear_transform(X)
-      return self
-
-except ImportError:
-  LMNN = python_LMNN

test/metric_learn_test.py

@@ -23,7 +23,7 @@
                           RCA_Supervised, MMC_Supervised, SDML, ITML, LSML)
 # Import this specially for testing.
 from metric_learn.constraints import wrap_pairs
-from metric_learn.lmnn import python_LMNN, _sum_outer_products
+from metric_learn.lmnn import _sum_outer_products
 
 
 def class_separation(X, labels):
@@ -213,14 +213,12 @@ def test_bounds_parameters_invalid(bounds):
 
 class TestLMNN(MetricTestCase):
   def test_iris(self):
-    # Test both impls, if available.
-    for LMNN_cls in set((LMNN, python_LMNN)):
-      lmnn = LMNN_cls(k=5, learn_rate=1e-6, verbose=False)
-      lmnn.fit(self.iris_points, self.iris_labels)
+    lmnn = LMNN(k=5, learn_rate=1e-6, verbose=False)
+    lmnn.fit(self.iris_points, self.iris_labels)
 
-      csep = class_separation(lmnn.transform(self.iris_points),
-                              self.iris_labels)
-      self.assertLess(csep, 0.25)
+    csep = class_separation(lmnn.transform(self.iris_points),
+                            self.iris_labels)
+    self.assertLess(csep, 0.25)
 
   def test_loss_grad_lbfgs(self):
     """Test gradient of loss function
@@ -336,7 +334,7 @@ def test_convergence_simple_example(capsys):
   # LMNN should converge on this simple example, which it did not with
   # this issue: https://github.com/metric-learn/metric-learn/issues/88
   X, y = make_classification(random_state=0)
-  lmnn = python_LMNN(verbose=True)
+  lmnn = LMNN(verbose=True)
   lmnn.fit(X, y)
   out, _ = capsys.readouterr()
   assert "LMNN converged with objective" in out
@@ -346,7 +344,7 @@ def test_no_twice_same_objective(capsys):
   # test that the objective function never has twice the same value
   # see https://github.com/metric-learn/metric-learn/issues/88
   X, y = make_classification(random_state=0)
-  lmnn = python_LMNN(verbose=True)
+  lmnn = LMNN(verbose=True)
   lmnn.fit(X, y)
   out, _ = capsys.readouterr()
   lines = re.split("\n+", out)

test/test_base_metric.py

@@ -19,13 +19,14 @@ def test_covariance(self):
                      remove_spaces("Covariance(preprocessor=None)"))
 
   def test_lmnn(self):
-    self.assertRegexpMatches(
-      str(metric_learn.LMNN()),
-        r"(python_)?LMNN\(convergence_tol=0.001, init=None, k=3, "
-        r"learn_rate=1e-07,\s+"
-        r"max_iter=1000, min_iter=50, n_components=None, "
-        r"num_dims='deprecated',\s+preprocessor=None, random_state=None, "
-        r"regularization=0.5,\s+use_pca=True, verbose=False\)")
+    self.assertEqual(
+        remove_spaces(str(metric_learn.LMNN())),
+        remove_spaces(
+          "LMNN(convergence_tol=0.001, init=None, k=3, "
+          "learn_rate=1e-07, "
+          "max_iter=1000, min_iter=50, n_components=None, "
+          "num_dims='deprecated', preprocessor=None, random_state=None, "
+          "regularization=0.5, use_pca=True, verbose=False)"))
 
   def test_nca(self):
     self.assertEqual(remove_spaces(str(metric_learn.NCA())),