EHN Refactoring to use pandas and simplify the API (#17)

* EHN huge refactoring

* Add cyhon

* Update metrics

* MAIN add pandas

* EHN windows

* coverage

* compatibility windows

* several update

* update

* add test extraction

* DOC update sections

* DOC update examples in docstring

.coveragerc

@@ -6,6 +6,9 @@ source = skcycling
 include = */skcycling/*
 omit =
 omit =
+     */skcycling/__check_build/*
+     */skcycling/extraction/setup.py
+     */skcycling/setup.py
      */setup.py
 
 [report]

.gitignore

@@ -244,4 +244,6 @@ install_manifest.txt
 
 .ipynb_checkpoints
 
-coverage/
+coverage/
+
+cythonize.dat

appveyor.yml

@@ -24,7 +24,7 @@ install:
   # Add Library/bin directory to fix issue
   # https://github.com/conda/conda/issues/1753
   - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PYTHON%\\Library\\bin;%PATH%"
-  - conda install pip numpy scipy six joblib pytest pytest-cov -y -q
+  - conda install pip numpy scipy pandas cython scikit-learn six joblib pytest pytest-cov -y -q
   - pip install fitparse
   - pip install .
 

build_tools/travis/install.sh

@@ -47,12 +47,11 @@ if [[ "$DISTRIB" == "conda" ]]; then
     # provided versions
     conda create -n testenv --yes python=$PYTHON_VERSION pip
     source activate testenv
-    conda install --yes numpy scipy six joblib
+    conda install --yes numpy scipy pandas six joblib scikit-learn cython
     pip install fitparse
 
     conda install --yes nose pytest pytest-cov
-    # Install nose-timer via pip
-    pip install nose-timer codecov
+    pip install codecov
 
 elif [[ "$DISTRIB" == "ubuntu" ]]; then
     # At the time of writing numpy 1.9.1 is included in the travis
@@ -62,8 +61,8 @@ elif [[ "$DISTRIB" == "ubuntu" ]]; then
     # Create a new virtualenv using system site packages for python, numpy
     virtualenv --system-site-packages testvenv
     source testvenv/bin/activate
-    pip install --upgrade joblib six fitparse nose nose-timer pytest pytest-cov \
-        codecov
+    pip install --upgrade pandas joblib scikit-learn six fitparse \
+        pytest pytest-cov codecov cython
 
 fi
 

doc/_templates/class.rst

@@ -0,0 +1,16 @@
+:mod:`{{module}}`.{{objname}}
+{{ underline }}==============
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+
+   {% block methods %}
+   .. automethod:: __init__
+   {% endblock %}
+
+.. include:: {{module}}.{{objname}}.examples
+
+.. raw:: html
+
+    <div style='clear:both'></div>

doc/_templates/function.rst

@@ -0,0 +1,12 @@
+:mod:`{{module}}`.{{objname}}
+{{ underline }}====================
+
+.. currentmodule:: {{ module }}
+
+.. autofunction:: {{ objname }}
+
+.. include:: {{module}}.{{objname}}.examples
+
+.. raw:: html
+
+    <div style='clear:both'></div>

doc/_templates/numpydoc_docstring.py

@@ -0,0 +1,16 @@
+{{index}}
+{{summary}}
+{{extended_summary}}
+{{parameters}}
+{{returns}}
+{{yields}}
+{{other_parameters}}
+{{attributes}}
+{{raises}}
+{{warns}}
+{{warnings}}
+{{see_also}}
+{{notes}}
+{{references}}
+{{examples}}
+{{methods}}

doc/api.rst

@@ -1,6 +1,6 @@
-##################################
-`scikit-cycling` API documentation
-##################################
+####################
+`scikit-cycling` API
+####################
 
 This is the full API documentation of `scikit-cycling`
 
@@ -9,121 +9,113 @@ This is the full API documentation of `scikit-cycling`
 Data-management
 ===============
 
-.. automodule:: skcycling.data_management
-    :no-members:
-    :no-inherited-members:
-
 .. currentmodule:: skcycling
 
 .. autosummary::
    :toctree: generated/
 
-   data_management.Rider
+   Rider
 
-.. _datasets_ref:
+.. _extraction_ref:
 
-Datasets
-========
+Extraction
+==========
 
-.. automodule:: skcycling.datasets
+.. automodule:: skcycling.extraction
     :no-members:
     :no-inherited-members:
 
 .. currentmodule:: skcycling
 
 .. autosummary::
    :toctree: generated/
+   :template: function.rst
 
-   datasets.load_toy
+   extraction.activity_power_profile
 
-.. _power_profile_ref:
+.. _metrics_ref:
 
-Power profile
-=============
+Extraction
+==========
 
-.. automodule:: skcycling.power_profile
+.. automodule:: skcycling.metrics
     :no-members:
     :no-inherited-members:
 
 .. currentmodule:: skcycling
 
+Single cycling activity
+-----------------------
+
 .. autosummary::
    :toctree: generated/
+   :template: function.rst
 
-   power_profile.RidePowerProfile
-   power_profile.RecordPowerProfile
-
-.. _restoration_ref:
-
-Restoration
-===========
-
-.. automodule:: skcycling.restoration
-    :no-members:
-    :no-inherited-members:
+   metrics.normalized_power_score
+   metrics.intensity_factor_ftp_score
+   metrics.intensity_factor_mpa_score
+   metrics.training_stress_ftp_score
+   metrics.training_stress_mpa_score
+   metrics.training_stress_mpa_grappe_score
+   metrics.training_stress_ftp_grappe_score
 
-.. currentmodule:: skcycling
+Power-profile
+-------------
 
 .. autosummary::
    :toctree: generated/
+   :template: function.rst
 
-   restoration.moving_average
-   restoration.outliers_rejection
+   metrics.aerobic_meta_model
 
-.. _utilities_ref:
+.. _utils_ref:
 
 Utilities
 =========
 
-.. _io_utilities_ref:
-
-IO utilities
-------------
-
-.. automodule:: skcycling.utils.io_fit
+.. automodule:: skcycling.utils
     :no-members:
     :no-inherited-members:
 
 .. currentmodule:: skcycling
 
 .. autosummary::
    :toctree: generated/
+   :template: function.rst
 
-   utils.load_power_from_fit
+   utils.validate_filenames
 
-.. _fit_utilities_ref:
+.. _io_ref:
 
-Fit utilities
--------------
+IO interaction
+==============
 
-.. automodule:: skcycling.utils.fit
+.. automodule:: skcycling.io
     :no-members:
     :no-inherited-members:
 
 .. currentmodule:: skcycling
 
 .. autosummary::
    :toctree: generated/
+   :template: function.rst
 
-   utils.res_std_dev
-   utils.r_squared
-   utils.log_linear_fitting
-   utils.linear_model
-   utils.log_linear_model
+   io.bikeread
 
-.. _checker_utilities_ref:
+.. _datasets_ref:
 
-Checker utilities
------------------
+Datasets
+========
 
-.. automodule:: skcycling.utils.checker
+.. automodule:: skcycling.datasets
     :no-members:
     :no-inherited-members:
 
 .. currentmodule:: skcycling
 
 .. autosummary::
    :toctree: generated/
+   :template: function.rst
 
-   utils.check_tuple_date
-   utils.check_filename_fit
+   datasets.load_fit
+   datasets.load_rider

doc/index.rst

@@ -18,10 +18,17 @@ Contents:
 .. toctree::
    :maxdepth: 2
    :hidden:
-   :caption: API Documentation
+   :caption: Documentation
 
    api
 
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+   :caption: Tutorial - Examples
+
+   auto_examples/index
+
 .. toctree::
    :maxdepth: 1
    :hidden:
@@ -42,20 +49,18 @@ The exact API of all functions and classes, as given in the
 doctring. The API documents expected types and allowed features for
 all functions, and all parameters available for the algorithms.
 
+`Examples <auto_examples/index.html>`_
+--------------------------------------
+
+A set of examples illustrating the use of the different algorithms. It
+complements the `User Guide <user_guide.html>`_.
+
 `What's new <whats_new.html>`_
 ------------------------------
 
 Log of the scikit-cycling history.
 
-`About imbalanced-learn <about.html>`_
+`About scikit-cycling <about.html>`_
 --------------------------------------
 
 Just to know about history of scikit-cycling.
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

doc/install.rst

@@ -4,13 +4,12 @@ Getting Started
 Install
 -------
 
-The install of ``scikit-cycling`` is almost straightforward. You need to clone it from GitHub_::
+The install of ``scikit-cycling`` is almost straightforward. You need to clone
+it from GitHub_::
 
-  $ git clone --recursive https://github.com/glemaitre/scikit-cycling.git
-  $ cd third-party/python-fitparse
-  $ python setup.py install
-  $ cd ../../
-  $ python setup.py install
+  $ git clone https://github.com/glemaitre/scikit-cycling.git
+  $ cd scikit-cycling
+  $ pip install .
 
 Test and coverage
 -----------------
@@ -26,6 +25,8 @@ You wish to test the coverage of your version::
 Contribute
 ----------
 
-You can contribute to this code through Pull Request on GitHub_. Please, make sure that your code is coming with unit tests to ensure full coverage and continuous integration in the API.
+You can contribute to this code through Pull Request on GitHub_. Please, make
+sure that your code is coming with unit tests to ensure full coverage and
+continuous integration in the API.
 
 .. _GitHub: https://github.com/glemaitre/scikit-cycling

examples/plot_power_profile.py

@@ -0,0 +1,35 @@
+"""
+======================================
+Workflow to exploit cycling power data
+======================================
+
+This example illustrates the typical workflow to use to investigate cycling
+power data.
+
+"""
+
+# Authors: Guillaume Lemaitre <g.lemaitre58@gmail.com>
+#          Cedric Lemaitre
+# License: BSD 3 clause
+
+import matplotlib.pyplot as plt
+
+from skcycling import Rider
+# from skcycling.datasets import load_fit
+from skcycling.datasets import load_rider
+
+print(__doc__)
+
+# rider = Rider(n_jobs=-1)
+# rider.add_activities(load_fit())
+rider = Rider.from_csv(load_rider())
+
+rider.power_profile_.plot()
+plt.xlabel('Time')
+plt.ylabel('Power (W)')
+
+rider.record_power_profile().plot(alpha=0.5, style='--', legend=True)
+plt.xlabel('Time')
+plt.ylabel('Power (W)')
+
+plt.show()

requirements.txt

@@ -1,5 +1,8 @@
 scipy
 numpy
+pandas
 joblib
+scikit-learn
 fitparse
 six
+cython