Merge branch 'develop' into setup_caching

Author: janvanrijn

.gitignore

@@ -73,6 +73,3 @@ target/
 # IDE
 .idea
 *.swp
-
-# Other
-*.pkl

.travis.yml

@@ -15,10 +15,12 @@ env:
   - TEST_DIR=/tmp/test_dir/
   - MODULE=openml
   matrix:
-  - DISTRIB="conda" PYTHON_VERSION="2.7" NUMPY_VERSION="1.11" SCIPY_VERSION="0.17.0" CYTHON_VERSION="0.21" SKLEARN_VERSION="0.18.1"
-  - DISTRIB="conda" PYTHON_VERSION="3.4" NUMPY_VERSION="1.11" SCIPY_VERSION="0.17.0" CYTHON_VERSION="0.23.4" SKLEARN_VERSION="0.18.1"
-  - DISTRIB="conda" PYTHON_VERSION="3.5" NUMPY_VERSION="1.11" SCIPY_VERSION="0.17.0" CYTHON_VERSION="0.23.4" SKLEARN_VERSION="0.18.1"
-  - DISTRIB="conda" PYTHON_VERSION="3.6" COVERAGE="true" NUMPY_VERSION="1.12.1" SCIPY_VERSION="0.19.0" CYTHON_VERSION="0.25.2" SKLEARN_VERSION="0.18.1"
+  - DISTRIB="conda" PYTHON_VERSION="2.7" SKLEARN_VERSION="0.18.2"
+  - DISTRIB="conda" PYTHON_VERSION="3.4" SKLEARN_VERSION="0.18.2"
+  - DISTRIB="conda" PYTHON_VERSION="3.5" SKLEARN_VERSION="0.18.2"
+  - DISTRIB="conda" PYTHON_VERSION="3.6" COVERAGE="true" SKLEARN_VERSION="0.18.2"
+  - DISTRIB="conda" PYTHON_VERSION="3.6" EXAMPLES="true" SKLEARN_VERSION="0.18.2"
+  - DISTRIB="conda" PYTHON_VERSION="3.6" DOCTEST="true" SKLEARN_VERSION="0.18.2"
 
 install: source ci_scripts/install.sh
 script: bash ci_scripts/test.sh

LICENSE

@@ -0,0 +1,30 @@
+BSD 3-Clause License
+
+Copyright (c) 2014-2017, Matthias Feurer, Jan van Rijn, Andreas Müller, 
+Joaquin Vanschoren and others.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

ci_scripts/install.sh

@@ -24,12 +24,18 @@ popd
 
 # Configure the conda environment and put it in the path using the
 # provided versions
-conda create -n testenv --yes python=$PYTHON_VERSION pip nose \
-   numpy=$NUMPY_VERSION scipy=$SCIPY_VERSION cython=$CYTHON_VERSION  \
-   scikit-learn=$SKLEARN_VERSION pandas
+conda create -n testenv --yes python=$PYTHON_VERSION pip
 source activate testenv
+pip install nose numpy scipy cython scikit-learn==$SKLEARN_VERSION \
+    oslo.concurrency
 
-pip install matplotlib jupyter notebook nbconvert nbformat jupyter_client ipython ipykernel
+if [[ "$EXAMPLES" == "true" ]]; then
+    pip install matplotlib jupyter notebook nbconvert nbformat jupyter_client \
+        ipython ipykernel pandas seaborn
+fi
+if [[ "$DOCTEST" == "true" ]]; then
+    pip install pandas sphinx_bootstrap_theme
+fi
 if [[ "$COVERAGE" == "true" ]]; then
     pip install codecov
 fi

ci_scripts/test.sh

@@ -6,11 +6,16 @@ mkdir -p $TEST_DIR
 
 cwd=`pwd`
 test_dir=$cwd/tests
+doctest_dir=$cwd/doc
 
 cd $TEST_DIR
 
-if [[ "$COVERAGE" == "true" ]]; then
-    nosetests -sv --with-coverage --cover-package=$MODULE $test_dir
+if [[ "$EXAMPLES" == "true" ]]; then
+    nosetests -sv $test_dir/test_examples/
+elif [[ "$DOCTEST" == "true" ]]; then
+    python -m doctest $doctest_dir/usage.rst
+elif [[ "$COVERAGE" == "true" ]]; then
+    nosetests --processes=4 --process-timeout=600 -sv --ignore-files="test_OpenMLDemo\.py" --with-coverage --cover-package=$MODULE $test_dir
 else
-    nosetests -sv $test_dir
+    nosetests --processes=4 --process-timeout=600 -sv --ignore-files="test_OpenMLDemo\.py" $test_dir
 fi

doc/api.rst

@@ -18,6 +18,7 @@ Top-level Classes
    OpenMLTask
    OpenMLSplit
    OpenMLFlow
+   OpenMLEvaluation
 
 
 :mod:`openml.datasets`: Dataset Functions
@@ -33,6 +34,30 @@ Top-level Classes
     get_datasets
     list_datasets
 
+:mod:`openml.evaluations`: Evaluation Functions
+-----------------------------------------------
+.. currentmodule:: openml.evaluations
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
+    list_evaluations
+
+:mod:`openml.flows`: Flow Functions
+-----------------------------------
+.. currentmodule:: openml.flows
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
+    flow_exists
+    flow_to_sklearn
+    get_flow
+    list_flows
+    sklearn_to_flow
+
 :mod:`openml.runs`: Run Functions
 ----------------------------------
 .. currentmodule:: openml.runs
@@ -41,14 +66,37 @@ Top-level Classes
    :toctree: generated/
    :template: function.rst
 
-   run_task
-   get_run
-   list_runs
-   list_runs_by_flow
-   list_runs_by_tag
-   list_runs_by_task
-   list_runs_by_uploader
-   list_runs_by_filters
+    get_run
+    get_runs
+    get_run_trace
+    initialize_model_from_run
+    initialize_model_from_trace
+    list_runs
+    run_model_on_task
+    run_flow_on_task
+
+:mod:`openml.setups`: Setup Functions
+-------------------------------------
+.. currentmodule:: openml.setups
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
+    get_setup
+    initialize_model
+    list_setups
+    setup_exists
+
+:mod:`openml.study`: Study Functions
+------------------------------------
+.. currentmodule:: openml.study
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
+    get_study
 
 :mod:`openml.tasks`: Task Functions
 -----------------------------------
@@ -59,13 +107,8 @@ Top-level Classes
    :template: function.rst
 
     get_task
+    get_tasks
     list_tasks
 
-:mod:`openml.flows`: Flow Functions
------------------------------------
-.. currentmodule:: openml.flow
 
-.. autosummary::
-   :toctree: generated/
-   :template: function.rst
 

doc/conf.py

@@ -63,8 +63,8 @@
 
 # General information about the project.
 project = u'OpenML'
-copyright = u'2014-2016, Matthias Feurer, Andreas Müller, Farzan Majdani, ' \
-            u'Joaquin Vanschoren and Pieter Gijsbers'
+copyright = u'2014-2017, Matthias Feurer, Andreas Müller, Farzan Majdani, ' \
+            u'Joaquin Vanschoren, Jan van Rijn and Pieter Gijsbers'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the