Merge branch 'release/0.4'

.gitignore

@@ -105,3 +105,8 @@ ENV/
 
 #IDE metadata
 .idea/
+
+pip-wheel-metadata/
+
+# macOS DS_Store
+.DS_Store

.travis.yml

@@ -16,7 +16,8 @@ matrix:
     - name: "Python 3.7.3 on Windows"
       os: windows           # Windows 10.0.17134 N/A Build 17134
       language: shell       # 'language: python' is an error on Travis CI Windows
-      before_install: choco install python
+      before_install:
+        - choco install python3 --version=3.7.3
       env: PATH=/c/Python37:/c/Python37/Scripts:$PATH
     - name: "Coverage and pep 8 tests on Python 3.7.1 on Xenial Linux"
       python: 3.7           # this works for Linux but is ignored on macOS or Windows

README.rst

@@ -4,7 +4,7 @@
 scikit-fda: Functional Data Analysis in Python
 ===================================================
 
-|python|_ |build-status| |docs| |Codecov|_ |PyPIBadge|_ |license|_
+|python|_ |build-status| |docs| |Codecov|_ |PyPIBadge|_ |license|_ |doi|
 
 Functional Data Analysis, or FDA, is the field of Statistics that analyses
 data that depend on a continuous parameter.
@@ -44,37 +44,35 @@ Installation from source
 It is possible to install the latest version of the package, available in the
 develop branch,  by cloning this repository and doing a manual installation.
 
-.. code::
+.. code:: bash
 
     git clone https://github.com/GAA-UAM/scikit-fda.git
-    cd scikit-fda/
-    pip install -r requirements.txt    # Install dependencies
-    python setup.py install
+    pip install ./scikit-fda
 
 Make sure that your default Python version is currently supported, or change
 the python and pip commands by specifying a version, such as ``python3.6``:
 
-.. code::
+.. code:: bash
 
     git clone https://github.com/GAA-UAM/scikit-fda.git
-    cd scikit-fda/
-    python3.6 -m pip install -r requirements.txt    # Install dependencies
-    python3.6 setup.py install
+    python3.6 -m pip install ./scikit-fda
 
 Requirements
 ------------
 *scikit-fda* depends on the following packages:
 
-* `setuptools <https://github.com/pypa/setuptools>`_ - Python Packaging
 * `cython <https://github.com/cython/cython>`_ - Python to C compiler
-* `numpy <https://github.com/numpy/numpy>`_ - The fundamental package for scientific computing with Python
-* `pandas <https://github.com/pandas-dev/pandas>`_ - Powerful Python data analysis toolkit
-* `scipy <https://github.com/scipy/scipy>`_ - Scientific computation in Python
-* `scikit-learn <https://github.com/scikit-learn/scikit-learn>`_ - Machine learning in Python
+* `findiff <https://github.com/maroba/findiff>`_ - Finite differences
 * `matplotlib <https://github.com/matplotlib/matplotlib>`_ - Plotting with Python
 * `mpldatacursor <https://github.com/joferkington/mpldatacursor/>`_ - Interactive data cursors for matplotlib
+* `multimethod <https://github.com/coady/multimethod>`_ - Multiple dispatch
+* `numpy <https://github.com/numpy/numpy>`_ - The fundamental package for scientific computing with Python
+* `pandas <https://github.com/pandas-dev/pandas>`_ - Powerful Python data analysis toolkit
 * `rdata <https://github.com/vnmabus/rdata>`_ - Reader of R datasets in .rda format in Python
 * `scikit-datasets <https://github.com/daviddiazvico/scikit-datasets>`_ - Scikit-learn compatible datasets
+* `scikit-learn <https://github.com/scikit-learn/scikit-learn>`_ - Machine learning in Python
+* `scipy <https://github.com/scipy/scipy>`_ - Scientific computation in Python
+* `setuptools <https://github.com/pypa/setuptools>`_ - Python Packaging
 
 The dependencies are automatically installed.
 
@@ -88,11 +86,11 @@ The people involved at some point in the development of the package can be
 found in the `contributors
 file <https://github.com/GAA-UAM/scikit-fda/blob/develop/THANKS.txt>`_.
 
-Citation
-========
-If you find this project useful, please cite:
+.. Citation
+   ========
+   If you find this project useful, please cite:
 
-.. todo:: Include citation to scikit-fda paper.
+   .. todo:: Include citation to scikit-fda paper.
 
 License
 =======
@@ -109,7 +107,7 @@ license_ can be found along with the code.
 .. |build-status| image:: https://travis-ci.org/GAA-UAM/scikit-fda.svg?branch=develop
     :alt: build status
     :scale: 100%
-    :target: https://travis-ci.org/GAA-UAM/scikit-fda
+    :target: https://travis-ci.com/GAA-UAM/scikit-fda
 
 .. |docs| image:: https://readthedocs.org/projects/fda/badge/?version=latest
     :alt: Documentation Status
@@ -124,3 +122,6 @@ license_ can be found along with the code.
 
 .. |license| image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg
 .. _license: https://github.com/GAA-UAM/scikit-fda/blob/master/LICENSE.txt
+
+.. |doi| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3468127.svg
+    :target: https://doi.org/10.5281/zenodo.3468127

VERSION

@@ -1 +1 @@
-0.3
+0.4

conftest.py

@@ -7,6 +7,6 @@
 except TypeError:
     pass
 
-collect_ignore = ['setup.py']
+collect_ignore = ['setup.py', 'docs/conf.py']
 
 pytest.register_assert_rewrite("skfda")

docs/Makefile

@@ -60,6 +60,7 @@ clean:
 	rm -rf modules/misc/autosummary
 	rm -rf modules/ml/autosummary
 	rm -rf modules/ml/clustering/autosummary
+	rm -rf modules/inference/autosummary
 	rm -rf backreferences
 
 .PHONY: html

docs/_templates/autosummary/base.rst

@@ -1,4 +1,4 @@
-{{ fullname | escape | underline}}
+{{ objname | escape | underline}}
 
 .. currentmodule:: {{ module }}
 

docs/_templates/autosummary/class.rst

@@ -1,12 +1,10 @@
-{{ fullname | escape | underline}}
+{{ objname | escape | underline}}
 
 .. currentmodule:: {{ module }}
 
 .. autoclass:: {{ objname }}
 
    {% block methods %}
-   .. automethod:: __init__
-
    {% if methods %}
    .. rubric:: Methods
 
@@ -15,6 +13,8 @@
       ~{{ name }}.{{ item }}
    {%- endfor %}
    {% endif %}
+
+   .. automethod:: __init__
    {% endblock %}
 
    {% block attributes %}

docs/apilist.rst

@@ -13,3 +13,4 @@ API Reference
    modules/datasets
    modules/misc
    modules/ml
+   modules/inference

docs/conf.py

@@ -17,9 +17,6 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
-# import sys
-# sys.path.insert(0, '/home/miguel/Desktop/fda/fda')
 
 import os
 import sys
@@ -55,7 +52,8 @@
               'sphinx_rtd_theme',
               'sphinx_gallery.gen_gallery',
               'sphinx.ext.intersphinx',
-              'sphinx.ext.doctest']
+              'sphinx.ext.doctest',
+              'jupyter_sphinx']
 
 autodoc_default_flags = ['members', 'inherited-members']
 
@@ -79,7 +77,8 @@
 
 # General information about the project.
 project = 'scikit-fda'
-copyright = '2017, Author'
+copyright = ('2019, Grupo de Aprendizaje Automático - ' +
+             'Universidad Autónoma de Madrid')
 author = 'Author'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
@@ -238,3 +237,47 @@
 }
 
 autosummary_generate = True
+
+
+# Napoleon fix for attributes
+# Taken from
+# https://michaelgoerz.net/notes/extending-sphinx-napoleon-docstring-sections.html
+
+# -- Extensions to the  Napoleon GoogleDocstring class ---------------------
+from sphinx.ext.napoleon.docstring import GoogleDocstring
+
+# first, we define new methods for any new sections and add them to the class
+
+
+def parse_keys_section(self, section):
+    return self._format_fields('Keys', self._consume_fields())
+
+
+GoogleDocstring._parse_keys_section = parse_keys_section
+
+
+def parse_attributes_section(self, section):
+    return self._format_fields('Attributes', self._consume_fields())
+
+
+GoogleDocstring._parse_attributes_section = parse_attributes_section
+
+
+def parse_class_attributes_section(self, section):
+    return self._format_fields('Class Attributes', self._consume_fields())
+
+
+GoogleDocstring._parse_class_attributes_section = parse_class_attributes_section
+
+# we now patch the parse method to guarantee that the the above methods are
+# assigned to the _section dict
+
+
+def patched_parse(self):
+    self._sections['keys'] = self._parse_keys_section
+    self._sections['class attributes'] = self._parse_class_attributes_section
+    self._unpatched_parse()
+
+
+GoogleDocstring._unpatched_parse = GoogleDocstring._parse
+GoogleDocstring._parse = patched_parse

docs/index.rst

@@ -5,18 +5,78 @@
 Welcome to scikit-fda's documentation!
 ======================================
 
+This package offers classes, methods and functions to give support to
+Functional Data Analysis in Python. Includes a wide range of utils to work with
+functional data, and its representation, exploratory analysis, or
+preprocessing, among other tasks such as inference, classification, regression
+or clustering of functional data.
+
+In the `project page <https://github.com/GAA-UAM/scikit-fda>`_ hosted by
+Github you can find more information related to the development of the package.
+
+
 .. toctree::
-   :includehidden:
-   :maxdepth: 4
+   :maxdepth: 2
    :caption: Contents:
    :titlesonly:
 
    apilist
+
+
+.. toctree::
+   :maxdepth: 1
+   :titlesonly:
+
    auto_examples/index
 
-Indices and tables
-==================
+An exhaustive list of all the contents of the package can be found in the
+:ref:`genindex`.
+
+Installation
+------------
+
+Currently, scikit-fda is available in Python 3.6 and 3.7, regardless of the
+platform. The stable version can be installed via
+`PyPI <https://pypi.org/project/scikit-fda/>`_:
+
+.. code-block:: bash
+
+   pip install scikit-fda
+
+
+It is possible to install the latest version of the package, available in
+the develop branch, by cloning this repository and doing a manual installation.
+
+.. code-block:: bash
+
+   git clone https://github.com/GAA-UAM/scikit-fda.git
+   pip install ./scikit-fda
+
+
+In this type of installation make sure that your default Python version is
+currently supported, or change the python and pip commands by specifying a
+version, such as python3.6.
+
+
+Contributions
+-------------
+
+All contributions are welcome. You can help this project grow in multiple ways,
+from creating an issue, reporting an improvement or a bug, to doing a
+repository fork and creating a pull request to the development branch.
+The people involved at some point in the development of the package can be
+found in the `contributors file
+<https://github.com/GAA-UAM/scikit-fda/blob/develop/THANKS.txt>`_.
+
+.. Citation
+   --------
+   If you find this project useful, please cite:
+
+   .. todo:: Include citation to scikit-fda paper.
+
+License
+-------
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+The package is licensed under the BSD 3-Clause License. A copy of the
+`license <https://github.com/GAA-UAM/scikit-fda/blob/develop/LICENSE.txt>`_
+can be found along with the code or in the project page.

docs/make.bat

@@ -5,7 +5,7 @@ REM Command file for Sphinx documentation
 pushd %~dp0
 
 if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=python -msphinx
+	set SPHINXBUILD=sphinx-build
 )
 set BUILDDIR=_build
 set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
@@ -54,7 +54,7 @@ if "%1" == "clean" (
 
 REM Check if sphinx-build is available
 %SPHINXBUILD% 1>NUL 2>NUL
-if errorlevel 1 (
+if errorlevel 9009 (
 	echo.
 	echo.The Sphinx module was not found. Make sure you have Sphinx installed,
 	echo.then set the SPHINXBUILD environment variable to point to the full

docs/modules/datasets.rst

@@ -17,6 +17,8 @@ The following functions are used to retrieve specific functional datasets:
    skfda.datasets.fetch_medflies
    skfda.datasets.fetch_weather
    skfda.datasets.fetch_aemet
+   skfda.datasets.fetch_octane
+   skfda.datasets.fetch_gait
 
 Those functions return a dictionary with at least a "data" field containing the
 instance data, and a "target" field containing the class labels or regression values,

docs/modules/exploratory.rst

@@ -10,4 +10,4 @@ and visualize functional data.
 
    exploratory/visualization
    exploratory/depth
-   exploratory/outliers
+   exploratory/outliers