Merge pull request #47 from egbn17/master

FIX: scitkits error + testing

.travis.yml

@@ -6,36 +6,89 @@
 # I would prefer to test against what is in neurodebian
 language: python
 python:
-  - "2.7"
   - "3.5"
   - "3.5-dev"  # 3.5 development branch
   - "3.6"
   - "3.6-dev"  # 3.6 development branch
   - "3.7-dev"  # 3.7 development branch
 env:
-  - VNUMPY=1.8.2
-  - VNUMPY=1.12.1
-  - VNUMPY=1.16.1
+  - VNUMPY=1.8.2  VSCI=0.21.2
+  - VNUMPY=1.8.2  VSCI=0.20.0
+  - VNUMPY=1.8.2  VSCI=0.18
+  - VNUMPY=1.12.1  VSCI=0.21.2
+  - VNUMPY=1.12.1  VSCI=0.20.0
+  - VNUMPY=1.12.1  VSCI=0.18
+  - VNUMPY=1.16.1  VSCI=0.21.2
+  - VNUMPY=1.16.1  VSCI=0.20.0
+  - VNUMPY=1.16.1  VSCI=0.18
+
 cache:
   - apt
 matrix:
-# old numpy + new python has problems setting up
+  include:
+  - python: "2.7"
+    env: VNUMPY=1.7.1  VSCI=0.14
+  - python: "2.7"
+    env: VNUMPY=1.8.2  VSCI=0.19.2
+  - python: "2.7"
+    env: VNUMPY=1.16.1  VSCI=0.14
+  - python: "2.7"
+    env: VNUMPY=1.16.1  VSCI=0.19.2
+
+# old packagese + new python has problems setting up
   exclude:
     - python: "3.7-dev"
-      env: VNUMPY=1.8.2
+      env: VNUMPY=1.8.2  VSCI=0.21.2
+    - python: "3.7-dev"
+      env: VNUMPY=1.8.2  VSCI=0.20.0
+    - python: "3.7-dev"
+      env: VNUMPY=1.8.2  VSCI=0.18
+    - python: "3.7-dev"
+      env: VNUMPY=1.12.1  VSCI=0.21.2
     - python: "3.7-dev"
-      env: VNUMPY=1.12.1
+      env: VNUMPY=1.12.1  VSCI=0.20.0
+    - python: "3.7-dev"
+      env: VNUMPY=1.12.1  VSCI=0.18
+    - python: "3.7-dev"
+      env: VNUMPY=1.16.1  VSCI=0.18
+    - python: "3.6-dev"
+      env: VNUMPY=1.8.2  VSCI=0.21.2
+    - python: "3.6-dev"
+      env: VNUMPY=1.8.2  VSCI=0.20.0
     - python: "3.6-dev"
-      env: VNUMPY=1.8.2
+      env: VNUMPY=1.8.2  VSCI=0.18
+    - python: "3.6-dev"
+      env: VNUMPY=1.12.1  VSCI=0.18
+    - python: "3.6-dev"
+      env: VNUMPY=1.16.1  VSCI=0.18
+    - python: "3.6"
+      env: VNUMPY=1.8.2  VSCI=0.21.2
+    - python: "3.6"
+      env: VNUMPY=1.8.2  VSCI=0.20.0
     - python: "3.6"
-      env: VNUMPY=1.8.2
+      env: VNUMPY=1.8.2  VSCI=0.18
+    - python: "3.6"
+      env: VNUMPY=1.12.1  VSCI=0.18
+    - python: "3.6"
+      env: VNUMPY=1.16.1  VSCI=0.18
+    - python: "3.5-dev"
+      env: VNUMPY=1.8.2  VSCI=0.21.2
+    - python: "3.5-dev"
+      env: VNUMPY=1.8.2  VSCI=0.20.0
+    - python: "3.5"
+      env: VNUMPY=1.8.2  VSCI=0.21.2
+    - python: "3.5"
+      env: VNUMPY=1.8.2  VSCI=0.20.0
+
+
 
 before_install:
     # The ultimate one-liner setup for NeuroDebian repository
    - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
-   - travis_retry sudo apt-get install python-joblib python-sklearn
+   - travis_retry sudo apt-get install python-joblib
 install:
-    - pip install -v numpy==$VNUMPY
+    - pip install scipy
+    - pip install -v numpy==$VNUMPY scikit-learn==$VSCI
     - pip install -v pytest==4.0.0 pytest-cov>=2.5.0 coveralls future
 script:
     - pytest --cov-report= --cov-config=.coveragerc --cov=mdp --seed=725021957 mdp

mdp/test/test_nodes_generic.py

@@ -192,6 +192,12 @@ def test_dtype_consistency(klass, init_args, inp_arg_gen,
     supported_types = klass(*args).get_supported_dtypes()
     for dtype in supported_types:
         inp = inp_arg_gen()
+        # The code was written before the following was included in
+        # scikit-learn. If more new nodes show up, that require the
+        # following fix, switch to a more generic solution.
+        # See: https://github.com/mdp-toolkit/mdp-toolkit/pull/47
+        if klass.__name__ == "ComplementNBScikitsLearnNode":
+            inp = numx.absolute(inp)
         args = call_init_args(init_args)
         node = klass(dtype=dtype, *args)
         _train_if_necessary(inp, node, sup_arg_gen)
@@ -210,6 +216,12 @@ def test_outputdim_consistency(klass, init_args, inp_arg_gen,
                                sup_arg_gen, execute_arg_gen):
     args = call_init_args(init_args)
     inp = inp_arg_gen()
+    # The code was written before the following was included in
+    # scikit-learn. If more new nodes show up, that require the
+    # following fix, switch to a more generic solution.
+    # See: https://github.com/mdp-toolkit/mdp-toolkit/pull/47
+    if klass.__name__ == "ComplementNBScikitsLearnNode":
+        inp = numx.absolute(inp)
     # support generators
     if isinstance(inp, Iter):
         for x in inp:
@@ -250,16 +262,16 @@ def _test(node):
             # raises an appropriate error
             # case 1: both in the constructor
             pytest.raises(InconsistentDimException,
-                           'klass(input_dim=inp.shape[1], output_dim=output_dim, *args)')
+                          'klass(input_dim=inp.shape[1], output_dim=output_dim, *args)')
             # case 2: first input_dim, then output_dim
             node = klass(input_dim=inp.shape[1], *args)
             pytest.raises(InconsistentDimException,
-                           'node.output_dim = output_dim')
+                          'node.output_dim = output_dim')
             # case 3: first output_dim, then input_dim
             node = klass(output_dim=output_dim, *args)
             node.output_dim = output_dim
             pytest.raises(InconsistentDimException,
-                           'node.input_dim = inp.shape[1]')
+                          'node.input_dim = inp.shape[1]')
 
         # check that output_dim is set to whatever the output dim is
         node = klass(*args)
@@ -278,6 +290,12 @@ def test_dimdtypeset(klass, init_args, inp_arg_gen,
                      sup_arg_gen, execute_arg_gen):
     init_args = call_init_args(init_args)
     inp = inp_arg_gen()
+    # The code was written before the following was included in
+    # scikit-learn. If more new nodes show up, that require the
+    # following fix, switch to a more generic solution.
+    # See: https://github.com/mdp-toolkit/mdp-toolkit/pull/47
+    if klass.__name__ == "ComplementNBScikitsLearnNode":
+        inp = numx.absolute(inp)
     node = klass(*init_args)
     _train_if_necessary(inp, node, sup_arg_gen)
     _stop_training_or_execute(node, inp)

testall.py

@@ -7,9 +7,9 @@
 # $ python testall.py /home/tiziano/python/x86_64/lib/pythonVERSION/site-packages
 
 PARMS = {
-         '3.4': ('numpy', None, 'joblib', 'scikits'),
-         '3.5': ('numpy', None, 'joblib', 'scikits'),
-         '2.7': ('scipy', None, 'parallel_python', 'libsvm', 'joblib', 'scikits'),
+         '3.4': ('numpy', None, 'joblib', 'scikit-learn'),
+         '3.5': ('numpy', None, 'joblib', 'scikit-learn'),
+         '2.7': ('scipy', None, 'parallel_python', 'libsvm', 'joblib', 'scikit-learn'),
          }
 
 import os