Refactoring of visualization and depth functions.

Merge branch 'release/0.3'

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,33 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Code to reproduce the behavior:
+
+```python
+import skfda
+...
+
+```
+
+**Expected behavior**
+A clear and concise description of what you expected to happen, results or figures.
+
+
+**Version information**
+ - OS: [e.g. Linux, MacOs, Windows]
+ - Python version: [e.g. 3.6, 3.7]
+ - scikit-fda version: [e.g. develop, 0.23]
+ - Version of other packages involved [e.g. numpy, scipy, matplotlib, ... ]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.travis.yml

@@ -6,6 +6,9 @@ matrix:
     - name: "Python 3.7.1 on Xenial Linux"
       python: 3.7           # this works for Linux but is ignored on macOS or Windows
       dist: xenial          # required for Python >= 3.7
+      env:
+        - COVERAGE=true    # coverage test are only run in python 3.7
+        - PEP8=true        # pep8 checks are only run in python 3.7
     - name: "Python 3.7.2 on macOS"
       os: osx
       osx_image: xcode10.2  # Python 3.7.2 running on macOS 10.14.3
@@ -15,8 +18,33 @@ matrix:
       language: shell       # 'language: python' is an error on Travis CI Windows
       before_install: choco install python
       env: PATH=/c/Python37:/c/Python37/Scripts:$PATH
-install: pip3 install --upgrade pip cython numpy || pip3 install --upgrade --user pip cython numpy # all three OSes agree about 'pip3'
+    - 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
+      dist: xenial          # required for Python >= 3.7
+      env:
+        - PEP8COVERAGE=true    # coverage test are only 
+install:
+  - pip3 install --upgrade pip cython numpy || pip3 install --upgrade --user pip cython numpy # all three OSes agree about 'pip3'
+  - |
+      if [[ $PEP8COVERAGE == true ]]; then
+        pip3 install flake8 || pip3 install --user flake8
+        pip3 install codecov pytest-cov || pip3 install --user codecov pytest-cov
+      fi
 
 # 'python' points to Python 2.7 on macOS but points to Python 3.7 on Linux and Windows
 # 'python3' is a 'command not found' error on Windows but 'py' works on Windows only
-script: python3 setup.py test || python setup.py test
+script:
+    - |
+      if [[ $PEP8COVERAGE == true ]]; then
+        flake8 --exit-zero skfda;
+        coverage run --source=skfda/ setup.py test;
+      else
+        python3 setup.py test || python setup.py test;
+      fi
+
+
+after_success:
+    - |
+      if [[ $PEP8COVERAGE == true ]]; then
+        codecov
+      fi

MANIFEST.in

@@ -1,7 +1,6 @@
 include README.rst
 include MANIFEST.in
-include LICENSE
 include VERSION
 include pyproject.toml
 include *.txt
-recursive-include deps *
+recursive-include deps *

README.rst

@@ -1,48 +1,112 @@
-scikit-fda
-==========
-
-|build-status| |docs|
+.. image:: https://raw.githubusercontent.com/GAA-UAM/scikit-fda/develop/docs/logos/title_logo/title_logo.png
+	:alt: scikit-fda: Functional Data Analysis in Python
 
 scikit-fda: Functional Data Analysis in Python
+===================================================
+
+|python|_ |build-status| |docs| |Codecov|_ |PyPIBadge|_ |license|_
+
+Functional Data Analysis, or FDA, is the field of Statistics that analyses
+data that depend on a continuous parameter.
 
-Functional Data Analysis is the field of Statistics that analyses data that
-come in the shape of functions. To know more about fda have a look at fda_ or read [RS05]_.
+This package offers classes, methods and functions to give support to FDA
+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.
+See documentation for further information on the features included in the
+package.
+
+Documentation
+=============
 
-This package offers classes, methods and functions to give support to fda
-in Python. The idea is to give a wide range of utils to work with functional data
-in Python. This utils include discrete points and basis representation of functional
-data and allows to calculate basic statistics such as mean, variance or covariance,
-smooth the functional data, calculate norms, distances, perform linear regression and
-much more.
+The documentation is available at
+`fda.readthedocs.io/en/stable/ <https://fda.readthedocs.io/en/stable/>`_, which
+includes detailed information of the different modules, classes and methods of
+the package, along with several examples showing different funcionalities.
 
-For more information read the documentation.
+The documentation of the latest version, corresponding with the develop
+version of the package, can be found at
+`fda.readthedocs.io/en/latest/ <https://fda.readthedocs.io/en/latest/>`_.
 
 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_:
+
+.. code::
+
+    pip install scikit-fda
+
+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.
 
-Under construction. 
+.. code::
 
-.. todo:: installation
+    git clone https://github.com/GAA-UAM/scikit-fda.git
+    cd scikit-fda/
+    pip install -r requirements.txt    # Install dependencies
+    python setup.py install
+
+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::
+
+    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
 
 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
+* `matplotlib <https://github.com/matplotlib/matplotlib>`_ - Plotting with Python
+* `mpldatacursor <https://github.com/joferkington/mpldatacursor/>`_ - Interactive data cursors for matplotlib
+* `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
+
+The dependencies are automatically installed.
+
+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.
 
-fda is available in Python 3.5 or above, in all operating systems.
+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>`_.
 
-.. todo:: test for other python versions
+Citation
+========
+If you find this project useful, please cite:
 
-Documentation
-=============
-The documentation can be found in https://fda.readthedocs.io/en/latest/
+.. todo:: Include citation to scikit-fda paper.
+
+License
+=======
 
-References
-==========
+The package is licensed under the BSD 3-Clause License. A copy of the
+license_ can be found along with the code.
 
-.. [RS05] Ramsay, J., Silverman, B. W. (2005). *Functional Data Analysis*. Springer.
+.. _examples: https://fda.readthedocs.io/en/latest/auto_examples/index.html
+.. _PyPI: https://pypi.org/project/scikit-fda/
 
-.. _fda: http://www.functionaldata.org/
+.. |python| image:: https://img.shields.io/pypi/pyversions/scikit-fda.svg
+.. _python: https://badge.fury.io/py/scikit-fda
 
-.. |build-status| image:: https://travis-ci.org/GAA-UAM/scikit-fda.svg
+.. |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
@@ -51,3 +115,12 @@ References
     :alt: Documentation Status
     :scale: 100%
     :target: http://fda.readthedocs.io/en/latest/?badge=latest
+
+.. |Codecov| image:: https://codecov.io/gh/GAA-UAM/scikit-fda/branch/develop/graph/badge.svg
+.. _Codecov: https://codecov.io/github/GAA-UAM/scikit-fda?branch=develop
+
+.. |PyPIBadge| image:: https://badge.fury.io/py/scikit-fda.svg
+.. _PyPIBadge: https://badge.fury.io/py/scikit-fda
+
+.. |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

THANKS.txt

@@ -4,4 +4,5 @@ Miguel Carbajo Berrocal for the basis and discrete representations of functional
 Carlos Ramos Carreño for the design, reviews and supervision, and for contributing the datasets module.
 Pablo Marcos Manchón for the registration functions, including integration with fdasrsf.
 Amanda Hernando Bernabé for visualization and clustering functions.
-Pablo Pérez Manso for regression and related utilities.
+Pablo Pérez Manso for regression and related utilities.
+Sergio Ruiz Lozano for the design of the logo.

VERSION

@@ -1 +1 @@
-0.2.3
+0.3

conftest.py

@@ -1,8 +1,12 @@
-#https://github.com/scikit-learn/scikit-learn/issues/8959
+import pytest
+
+# https://github.com/scikit-learn/scikit-learn/issues/8959
 import numpy as np
 try:
     np.set_printoptions(sign=' ')
 except TypeError:
     pass
 
 collect_ignore = ['setup.py']
+
+pytest.register_assert_rewrite("skfda")

docs/.gitignore

@@ -1,2 +1,3 @@
 /auto_examples/
 /backreferences/
+**/autosummary/

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 backreferences
 
 .PHONY: html
 html:

docs/_templates/autosummary/base.rst

@@ -0,0 +1,7 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. auto{{ objtype }}:: {{ objname }}
+
+.. include:: {{package}}/backreferences/{{fullname}}.examples

docs/_templates/autosummary/class.rst

@@ -0,0 +1,31 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+
+   {% block methods %}
+   .. automethod:: __init__
+
+   {% if methods %}
+   .. rubric:: Methods
+
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Attributes
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+.. include:: {{package}}/backreferences/{{fullname}}.examples

docs/apilist.rst

@@ -2,8 +2,10 @@ API Reference
 =============
 
 .. toctree::
+   :includehidden:
    :maxdepth: 4
    :caption: Modules:
+   :titlesonly:
 
    modules/representation
    modules/preprocessing