Commit 0b807b0b authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
Browse files

Added rst contributing file

parent d00926ab
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.
......@@ -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.
......
......@@ -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,
......
......@@ -4,8 +4,9 @@
changelog
installation
usage
configuration
usage
contributing
.. toctree::
:maxdepth: 2
......
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.
......@@ -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={
......
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