Added rst contributing file

CONTRIBUTING.rst

+Contributing to this project
+============================
+
+Please take a moment to review this document in order to make the
+contribution process easy and effective for everyone involved.
+
+Following these guidelines helps to communicate that you respect the
+time of the developers managing and developing this open source project.
+In return, they should reciprocate that respect in addressing your issue
+or assessing patches and features.
+
+Using the issue tracker
+-----------------------
+
+The issue tracker is the preferred channel for `bug reports <#bugs>`__,
+`features requests <#features>`__ and `submitting pull
+requests <#pull-requests>`__, but please respect the following
+restrictions:
+
+-  Please **do not** use the issue tracker for personal support requests
+   (use `ARIA mailing
+   list <http://groups.yahoo.com/group/aria-discuss>`__ or
+   `chatlab <https://chatlab.pasteur.fr/bis-aria/channels/ariaec>`__).
+
+-  Please **do not** derail or troll issues. Keep the discussion on
+   topic and respect the opinions of others.
+
+ ## Bug reports
+
+A bug is a *demonstrable problem* that is caused by the code in the
+repository. Good bug reports are extremely helpful - thank you!
+
+Guidelines for bug reports:
+
+1. **Use the `Gitlab issue
+   search <https://gitlab.pasteur.fr/bis-aria/Ariaec/issues#filtered-search-issues>`__**
+   — check if the issue has already been reported.
+
+2. **Check if the issue has been fixed** — try to reproduce it using the
+   latest ``master`` or development branch in the repository.
+
+3. **Isolate the problem** — create a `reduced test
+   case <http://css-tricks.com/reduced-test-cases/>`__ and a live
+   example.
+
+A good bug report shouldn't leave others needing to chase you up for
+more information. Please try to be as detailed as possible in your
+report. What is your environment? What steps will reproduce the issue?
+What browser(s) and OS experience the problem? What would you expect to
+be the outcome? All these details will help people to fix any potential
+bugs.
+
+Example:
+
+    Short and descriptive example bug report title
+
+    A summary of the issue and the browser/OS environment in which it
+    occurs. If suitable, include the steps required to reproduce the
+    bug.
+
+    1. This is the first step
+    2. This is the second step
+    3. Further steps, etc.
+
+    ``<url>`` - a link to the reduced test case
+
+    Any other information you want to share that is relevant to the
+    issue being reported. This might include the lines of code that you
+    have identified as causing the bug, and potential solutions (and
+    your opinions on their merits).
+
+
+Feature requests
+----------------
+
+Feature requests are welcome. But take a moment to find out whether your
+idea fits with the scope and aims of the project. It's up to *you* to
+make a strong case to convince the project's developers of the merits of
+this feature. Please provide as much detail and context as possible.
+
+
+Pull requests
+-------------
+
+Good pull requests - patches, improvements, new features - are a
+fantastic help. They should remain focused in scope and avoid containing
+unrelated commits.
+
+**Please ask first** before embarking on any significant pull request
+(e.g. implementing features, refactoring code, porting to a different
+language), otherwise you risk spending a lot of time working on
+something that the project's developers might not want to merge into the
+project.
+
+Please adhere to the coding conventions used throughout a project
+(indentation, accurate comments, etc.) and any other requirements (such
+as test coverage).
+
+Follow this process if you'd like your work considered for inclusion in
+the project:
+
+1. `Fork <https://docs.gitlab.com/ce/gitlab-basics/fork-project.html>`__
+   the project, clone your fork, and configure the remotes:
+
+   ``bash    # Clone your fork of the repo into the current directory    git clone https://gitlab.pasteur.fr/bis-aria/Ariaec.git    # Navigate to the newly cloned directory    cd Ariaec    # Assign the original repo to a remote called "upstream"    git remote add upstream https://gitlab.pasteur.fr/bis-aria/Ariaec.git``
+
+2. If you cloned a while ago, get the latest changes from upstream:
+
+   ``bash    git checkout <dev-branch>    git pull upstream <dev-branch>``
+
+3. Create a new topic branch (off the main project development branch)
+   to contain your feature, change, or fix:
+
+   ``bash    git checkout -b <topic-branch-name>``
+
+4. Commit your changes in logical chunks. Please adhere to these `git
+   commit message
+   guidelines <http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html>`__
+   or your code is unlikely be merged into the main project. Use Git's
+   `interactive
+   rebase <https://help.github.com/articles/interactive-rebase>`__
+   feature to tidy up your commits before making them public.
+
+5. Locally merge (or rebase) the upstream development branch into your
+   topic branch:
+
+   ``bash    git pull [--rebase] upstream <dev-branch>``
+
+6. Push your topic branch up to your fork:
+
+   ``bash    git push origin <topic-branch-name>``
+
+7. `Open a Merge
+   Request <https://about.gitlab.com/2014/09/29/gitlab-flow/#mergepull-requests-with-gitlab-flow>`__
+   with a clear title and description.
+
+**IMPORTANT**: By submitting a patch, you agree to allow the project
+owner to license your work under the same license as that used by the
+project.

README.rst

@@ -40,21 +40,21 @@ your python installation or virtual environment.
 Then the easiest solution is to call the ``pip`` command below :
 
 
-.. code-block:: shell
+.. code-block:: console
 
-   pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec
+   $ pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec
 
 
 Another possibility is to download the ZIP_ or TAR_ version from Gitlab_,
 extract the files and run ``pip install .`` inside the new directory
 
 For more information about installation and usage, please refer to the
-`ARIAEC documentation<http://bis-aria.pages.pasteur.fr/ariaec>`_.
+`ARIAEC documentation <http://bis-aria.pages.pasteur.fr/ariaec>`_.
 
 Contributing
 ------------
 
-Please read `guidelines for contributing <CONTRIBUTING.md>`_ for any
+Please read `guidelines for contributing <https://gitlab.pasteur.fr/bis-aria/ariaec/blob/master/CONTRIBUTING.md>`_ for any
 suggestions or bug report.
 
 

docs/conf.py

@@ -98,6 +98,7 @@ extensions = [
     'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
+    'numpydoc',
     # 'sphinx.ext.nbsphinx'
 ]
 
@@ -108,7 +109,11 @@ templates_path = ['_templates']
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ['.rst', '.md']
+
+source_parsers = {
+   '.md': 'recommonmark.parser.CommonMarkParser',
+}
 
 # The master toctree document.
 master_doc = 'index'
@@ -167,7 +172,8 @@ html_theme_options = {
     'logo_only': True
 }
 
-html_logo = "_static/logo.jpg"
+# html_logo = "_static/logo.jpg"
+html_logo = "_static/ariaec_white_ed.png"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

docs/contents.rst

@@ -4,8 +4,9 @@
 
    changelog
    installation
-   usage
    configuration
+   usage
+   contributing
 
 .. toctree::
    :maxdepth: 2

docs/contributing.rst

+Contributing to this project
+============================
+
+Please take a moment to review this document in order to make the contribution
+process easy and effective for everyone involved.
+
+Following these guidelines helps to communicate that you respect the time of
+the developers managing and developing this open source project. In return,
+they should reciprocate that respect in addressing your issue or assessing
+patches and features.
+
+
+Using the issue tracker
+-----------------------
+
+The issue tracker is the preferred channel for `bug reports (#bugs)`,
+[features requests](#features) and [submitting pull
+requests](#pull-requests), but please respect the following restrictions:
+
+* Please **do not** use the issue tracker for personal support requests (use 
+[ARIA mailing list](http://groups.yahoo.com/group/aria-discuss) or 
+[chatlab](https://chatlab.pasteur.fr/bis-aria/channels/ariaec)).
+
+* Please **do not** derail or troll issues. Keep the discussion on topic and
+  respect the opinions of others.
+
+
+<a name="bugs"></a>
+## Bug reports
+
+A bug is a _demonstrable problem_ that is caused by the code in the repository.
+Good bug reports are extremely helpful - thank you!
+
+Guidelines for bug reports:
+
+1. **Use the [Gitlab issue search](https://gitlab.pasteur.fr/bis-aria/Ariaec/issues#filtered-search-issues)** &mdash; check if the issue has already been
+   reported.
+
+2. **Check if the issue has been fixed** &mdash; try to reproduce it using the
+   latest `master` or development branch in the repository.
+
+3. **Isolate the problem** &mdash; create a [reduced test
+   case](http://css-tricks.com/reduced-test-cases/) and a live example.
+
+A good bug report shouldn't leave others needing to chase you up for more
+information. Please try to be as detailed as possible in your report. What is
+your environment? What steps will reproduce the issue? What browser(s) and OS
+experience the problem? What would you expect to be the outcome? All these
+details will help people to fix any potential bugs.
+
+Example:
+
+> Short and descriptive example bug report title
+>
+> A summary of the issue and the browser/OS environment in which it occurs. If
+> suitable, include the steps required to reproduce the bug.
+>
+> 1. This is the first step
+> 2. This is the second step
+> 3. Further steps, etc.
+>
+> `<url>` - a link to the reduced test case
+>
+> Any other information you want to share that is relevant to the issue being
+> reported. This might include the lines of code that you have identified as
+> causing the bug, and potential solutions (and your opinions on their
+> merits).
+
+
+<a name="features"></a>
+## Feature requests
+
+Feature requests are welcome. But take a moment to find out whether your idea
+fits with the scope and aims of the project. It's up to *you* to make a strong
+case to convince the project's developers of the merits of this feature. Please
+provide as much detail and context as possible.
+
+
+<a name="pull-requests"></a>
+## Pull requests
+
+Good pull requests - patches, improvements, new features - are a fantastic
+help. They should remain focused in scope and avoid containing unrelated
+commits.
+
+**Please ask first** before embarking on any significant pull request (e.g.
+implementing features, refactoring code, porting to a different language),
+otherwise you risk spending a lot of time working on something that the
+project's developers might not want to merge into the project.
+
+Please adhere to the coding conventions used throughout a project (indentation,
+accurate comments, etc.) and any other requirements (such as test coverage).
+
+Follow this process if you'd like your work considered for inclusion in the
+project:
+
+1. [Fork](https://docs.gitlab.com/ce/gitlab-basics/fork-project.html) the project, clone your fork,
+   and configure the remotes:
+
+       ```bash
+       # Clone your fork of the repo into the current directory
+       git clone https://gitlab.pasteur.fr/bis-aria/Ariaec.git
+       # Navigate to the newly cloned directory
+       cd Ariaec
+       # Assign the original repo to a remote called "upstream"
+       git remote add upstream https://gitlab.pasteur.fr/bis-aria/Ariaec.git
+       ```
+
+2. If you cloned a while ago, get the latest changes from upstream:
+
+       ```bash
+       git checkout <dev-branch>
+       git pull upstream <dev-branch>
+       ```
+
+3. Create a new topic branch (off the main project development branch) to
+   contain your feature, change, or fix:
+
+       ```bash
+       git checkout -b <topic-branch-name>
+       ```
+
+4. Commit your changes in logical chunks. Please adhere to these [git commit
+   message guidelines](http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html)
+   or your code is unlikely be merged into the main project. Use Git's
+   [interactive rebase](https://help.github.com/articles/interactive-rebase)
+   feature to tidy up your commits before making them public.
+
+5. Locally merge (or rebase) the upstream development branch into your topic branch:
+
+       ```bash
+       git pull [--rebase] upstream <dev-branch>
+       ```
+
+6. Push your topic branch up to your fork:
+
+       ```bash
+       git push origin <topic-branch-name>
+       ```
+
+7. [Open a Merge Request](https://about.gitlab.com/2014/09/29/gitlab-flow/#mergepull-requests-with-gitlab-flow)
+    with a clear title and description.
+
+
+**IMPORTANT**: By submitting a patch, you agree to allow the project owner to
+license your work under the same license as that used by the project.

setup.py

@@ -237,6 +237,8 @@ def setup_package():
             'hdbscan',
             'conkit',
             'nbsphinx',
+            'recommonmark',
+            'numpydoc',
             # 'scikit-bio'          Doesn't works with python 2.7. Only 3.4 +
         ],
         entry_points={