add skorch compat

devtools/conda-recipe/meta.yaml

@@ -33,6 +33,8 @@ test:
     - nose
     - nose-timer
     - gpy
+    - skorch
+    - pytorch
     - msmbuilder
     - msmb_data
     - mdtraj

devtools/travis-ci/build_docs.sh

@@ -8,18 +8,17 @@ conda create --yes -n docenv python=$CONDA_PY
 source activate docenv
 conda install -yq --use-local osprey
 
-
 # Install doc requirements
 conda install --yes --file docs/requirements.txt
 
-
 # We don't use conda for these:
 # sphinx_rtd_theme's latest releases are not available
 # neither is msmb_theme
 # neither is sphinx > 1.3.1 (fix #1892 autodoc problem)
 pip install -I sphinx==1.3.5
 pip install -I sphinx_rtd_theme==0.1.9 msmb_theme==1.2.0
 
+
 # Make docs
 cd docs && make html && cd -
 

osprey/data/torch_skeleton_config.yaml

@@ -0,0 +1,38 @@
+estimator:
+        eval: Pipeline([
+                ('scale', RobustScaler()),
+                ('classifier', NeuralNetClassifier(nn.Sequential(nn.Linear(64, 32),
+                                                                 nn.ReLU(),
+                                                                 nn.Linear(32, 10),
+                                                                 nn.Softmax(dim=1)),
+                                                   max_epochs=10)), 
+              ])
+        eval_scope: ['sklearn', 'torch']
+
+scoring: accuracy
+
+strategy:
+  name: gp
+  params:
+    seeds: 5
+
+search_space:
+  classifier__lr:
+      min: 1e-3
+      max: 1e-1
+      num: 10
+      type: jump
+      var_type: float
+      warp: log
+
+cv: 5
+
+dataset_loader:
+  name: sklearn_dataset
+  params:
+    method: load_digits
+
+trials:
+    uri: sqlite:///osprey-trials.db
+
+random_seed: 42

osprey/eval_scopes.py

@@ -7,7 +7,7 @@
 
 from sklearn.base import BaseEstimator
 
-__all__ = ['msmbuilder', 'import_all_estimators']
+__all__ = ['msmbuilder', 'torch', 'import_all_estimators']
 
 
 def msmbuilder():
@@ -21,6 +21,20 @@ def msmbuilder():
     return scope
 
 
+def torch():
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore", category=DeprecationWarning)
+        import torch
+        from torch import nn
+        import skorch
+        from sklearn.pipeline import Pipeline
+
+    scope = import_all_estimators(skorch)
+    scope.update({'nn': nn})
+    scope['Pipeline'] = Pipeline
+    return scope
+
+
 def import_all_estimators(pkg):
     def estimator_in_module(mod):
         for name, obj in inspect.getmembers(mod):

osprey/execute_skeleton.py

@@ -8,7 +8,8 @@
              'random_example': 'random_example.yaml',
              'bayes_example': 'sklearn_skeleton_config.yaml',
              'grid_example': 'grid_example.yaml',
-             'msmb_feat_select': 'msmb_feat_select_skeleton_config.yaml'}
+             'msmb_feat_select': 'msmb_feat_select_skeleton_config.yaml',
+             'torch': 'torch_skeleton_config.yaml'}
 
 
 def execute(args, parser):

osprey/tests/test_cli_worker_and_dump.py

@@ -17,6 +17,13 @@
 except:
     HAVE_MSMBUILDER = False
 
+try:
+    __import__('skorch')
+    HAVE_SKORCH = True
+except:
+    HAVE_SKORCH = False
+
+
 OSPREY_BIN = find_executable('osprey')
 
 
@@ -151,6 +158,30 @@ def test_gp_example():
         shutil.rmtree(dirname)
 
 
+@skipif(not HAVE_SKORCH, 'this test requires Skorch')
+def test_torch_example():
+    assert OSPREY_BIN is not None
+    cwd = os.path.abspath(os.curdir)
+    dirname = tempfile.mkdtemp()
+
+    try:
+        os.chdir(dirname)
+        subprocess.check_call([OSPREY_BIN, 'skeleton', '-t', 'torch',
+                              '-f', 'config.yaml'])
+        subprocess.check_call([OSPREY_BIN, 'worker', 'config.yaml', '-n', '1'])
+        assert os.path.exists('osprey-trials.db')
+
+        subprocess.check_call([OSPREY_BIN, 'current_best', 'config.yaml'])
+
+        yield _test_dump_1
+
+        yield _test_plot_1
+
+    finally:
+        os.chdir(cwd)
+        shutil.rmtree(dirname)
+
+
 def test_grid_example():
     assert OSPREY_BIN is not None
     cwd = os.path.abspath(os.curdir)