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The package is for developing algorithm in prediction.

Project description

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deepdata_alpha
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The package is for developing algorithm in prediction.

Project Setup
*************

Here we provide some details about the project setup. Most of the choices are explained in the `guide <https://guide.esciencecenter.nl>`_. Links to the relevant sections are included below.
Feel free to remove this text when the development of the software package takes off.

For a quick reference on software development, we refer to `the software guide checklist <https://guide.esciencecenter.nl/best_practices/checklist.html>`_.

Version control
---------------

Once your Python package is created, put it under
`version control <https://guide.esciencecenter.nl/best_practices/version_control.html>`_!
We recommend using `git <http://git-scm.com/>`_ and `github <https://github.com/>`_.

.. code-block:: console

cd deepdata_alpha
git init
git add -A
git commit

To put your code on github, follow `this tutorial <https://help.github.com/articles/adding-an-existing-project-to-github-using-the-command-line/>`_.

Python versions
---------------

This repository is set up with Python versions:
* 3.4
* 3.5
* 3.6

Add or remove Python versions based on project requirements. `The guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html>`_ contains more information about Python versions and writing Python 2 and 3 compatible code.

Package management and dependencies
-----------------------------------

You can use either `pip` or `conda` for installing dependencies and package management. This repository does not force you to use one or the other, as project requirements differ. For advice on what to use, please check `the relevant section of the guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html#dependencies-and-package-management>`_.

* Dependencies should be added to `setup.py` in the `install_requires` list.

Packaging/One command install
-----------------------------

You can distribute your code using pipy or conda. Again, the project template does not enforce the use of either one. `The guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html#building-and-packaging-code>`_ can help you decide which tool to use for packaging.

Testing and code coverage
-------------------------

* Tests should be put in the ``tests`` folder.
* The ``tests`` folder contains:

- Example tests that you should replace with your own meaningful tests (file: ``test_deepdata_alpha``)
- A test that checks whether your code conforms to the Python style guide (PEP 8) (file: ``test_lint.py``)

* The testing framework used is `PyTest <https://pytest.org>`_

- `PyTest introduction <http://pythontesting.net/framework/pytest/pytest-introduction/>`_

* Tests can be run with ``python setup.py test``

- This is configured in ``setup.py`` and ``setup.cfg``

* Use `Travis CI <https://travis-ci.com/>`_ to automatically run tests and to test using multiple Python versions

- Configuration can be found in ``.travis.yml``
- `Getting started with Travis CI <https://docs.travis-ci.com/user/getting-started/>`_

* TODO: add something about code quality/coverage tool?
* `Relevant section in the guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html#testing>`_

Documentation
-------------

* Documentation should be put in the ``docs`` folder. The contents have been generated using ``sphinx-quickstart`` (Sphinx version 1.6.5).
* We recommend writing the documentation using Restructured Text (reST) and Google style docstrings.

- `Restructured Text (reST) and Sphinx CheatSheet <http://openalea.gforge.inria.fr/doc/openalea/doc/_build/html/source/sphinx/rest_syntax.html>`_
- `Google style docstring examples <http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html>`_.

* The documentation is set up with the Read the Docs Sphinx Theme.

- Check out the `configuration options <https://sphinx-rtd-theme.readthedocs.io/en/latest/>`_.

* To generate html documentation run ``python setup.py build_sphinx``

- This is configured in ``setup.cfg``
- Alternatively, run ``make html`` in the ``docs`` folder.

* The ``docs/_templates`` directory contains an (empty) ``.gitignore`` file, to be able to add it to the repository. This file can be safely removed (or you can just leave it there).
* To put the documentation on `Read the Docs <https://readthedocs.org>`_, log in to your Read the Docs account, and import the repository (under 'My Projects').

- Include the link to the documentation in this README_.

* `Relevant section in the guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html#writingdocumentation>`_

Coding style conventions and code quality
-----------------------------------------

* Check your code style with ``prospector``
* You may need run ``pip install .[dev]`` first, to install the required dependencies
* You can use ``yapf`` to fix the readability of your code style and ``isort`` to format and group your imports
* `Relevant section in the guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html#coding-style-conventions>`_

Package version number
----------------------

* We recommend using `semantic versioning <https://guide.esciencecenter.nl/best_practices/releases.html#semantic-versioning>`_.
* For convenience, the package version is stored in a single place: ``deepdata_alpha/__version__.py``. For updating the version number, you only have to change this file.
* Don't forget to update the version number before `making a release <https://guide.esciencecenter.nl/best_practices/releases.html>`_!

CHANGELOG.rst
-------------

* Document changes to your software package
* `Relevant section in the guide <https://guide.esciencecenter.nl/software/releases.html#changelogmd>`_

CITATION.cff
------------

* To allow others to cite your software, add a ``CITATION.cff`` file
* It only makes sense to do this once there is something to cite (e.g., a software release with a DOI).
* Follow the `making software citable <https://guide.esciencecenter.nl/citable_software/making_software_citable.html>`_ section in the guide.

CODE_OF_CONDUCT.rst
-------------------

* Information about how to behave professionally
* `Relevant section in the guide <https://guide.esciencecenter.nl/software/documentation.html#code-of-conduct>`_

CONTRIBUTING.rst
----------------

* Information about how to contribute to this software package
* `Relevant section in the guide <https://guide.esciencecenter.nl/software/documentation.html#contribution-guidelines>`_

MANIFEST.in
-----------

* List non-Python files that should be included in a source distribution
* `Relevant section in the guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html#building-and-packaging-code>`_

NOTICE
------

* List of attributions of this project and Apache-license dependencies
* `Relevant section in the guide <https://guide.esciencecenter.nl/best_practices/licensing.html#notice>`_

Installation
------------

To install deepdata_alpha, do:

.. code-block:: console

git clone https://github.com/John/deepdata_alpha.git
cd deepdata_alpha
pip install .


Run tests (including coverage) with:

.. code-block:: console

python setup.py test


Documentation
*************

.. _README:

Include a link to your project's full documentation here.

Contributing
************

If you want to contribute to the development of deepdata_alpha,
have a look at the `contribution guidelines <CONTRIBUTING.rst>`_.

License
*******

Copyright (c) 2018, John J. H. Lin


Credits
*******

This package was created with `Cookiecutter <https://github.com/audreyr/cookiecutter>`_ and the `NLeSC/python-template <https://github.com/NLeSC/python-template>`_.

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