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.. sidebar:: General Information

    .. contents:: :local:

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.. _contributing:

How to contribute?

This webpage is actually a repository of files that document application development efforts during the pilot projects
and Extended Software Development Workshops (ESDWs) of E-CAM. How you contribute will depend on whether you are an
attendee at and ESDW or working on a pilot project.

In  both cases you will simply be adding a simple text file that uses ReST_ and we have prepared some examples to help
you get started:

* :ref:`example`
* :ref:`pilot`

You will find these examples within the repository of this documentation under the directory *modules*. You should make
a copy of the appropriate directory (renaming it).

Contribution Guidelines
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GitLab account

If you do not have a (free) GitLab account yet on the E-CAM GitLab service, you'll need to get one via .

Fork the repository

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First, you'll need to fork the repository on GitLab you want to work with. Go to , and click the grey 'Fork' button under the repository name.
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SSH public key @ GitLab

You also need to register an SSH public key, so you can easily clone, push to and pull from your repository. This can be done via if you're logged in on GitLab.

In the following it is assumed that an SSH public key has been registered, the possibility of using the HTTP protocol to access GitLab is not covered (but is possible).

Clone your fork of the repository

Clone your fork of the repository to your favorite workstation.

.. code-block:: bash

    git clone ssh://<Your GitLab username>/Classical-MD-Modules.git

Pull the master branch from the main repository:

.. code-block:: bash

    cd Classical-MD-Modules
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    git remote add upstream
    git pull upstream master
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Keep your master branch up-to-date

Make sure you update it every time you create a feature branch (see below):

.. code-block:: bash

    git checkout master
    git pull upstream master
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Pick a branch name for your work that makes sense, so you can track things easily and make sense if you end up having several branches in flight at once (each PR is a new branch).





Create a feature branch for your work (after updating your master), and check it out

.. code-block:: bash

    git checkout master
    git branch BRANCH_NAME
    git checkout BRANCH_NAME

Make sure to always base your features branches on master!

After creating the branch, implement your contributions: new modules, enhancements or updates to existing modules, bug fixes, structure changes, whatever you like. Make sure you commit your work, and try to do it in bite-size chunks, so the commit log remains clear.

For example:

.. code-block:: bash

    git add modules/gromacs_gpu/readme.rst
    git commit -m "add details on GPU support within GROMACS"

If you are working on several things at the same time, try and keep things isolated in separate branches, to keep it manageable (both for you, and for reviewing your contributions).

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Contributing module documentation

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Your contribution to this repository will include a module documentation file. There are already several examples of these in the repository, but we provide a template for a generic module as a guide:
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.. toctree::
    :maxdepth: 1


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Checking your contribution locally

You can locally build the documentation to check that the changes you make look as you expect them. To do this you will need the Sphinx python package to be installed (see this `link <>`_ for information on how to install this tool on your operating system).

.. code-block:: bash

    make html # in root directory of repository
    firefox _build/html/index.html # Use your browser to view the end result

If you do not have Latex installed on your system you are likely to get related errors. Other (non-latex) errors are likely to come from your additions. 

Contributing back your input

When you've finished the implementation of a particular contribution, here's how to get it into the main repository.

Push your branch to *your* copy of the repository on GitLab

.. code-block:: bash

    git push origin <BRANCH_NAME>

Issue a *Merge Request* for your branch into the main repository. To do this go to and select the *New Merge Request* button.

Make sure the branch you just pushed is selected (not master!) issue a merge request for your branch to the master branch of the main repository.

Updating your contribution

It is common for there to be updates required to contributions, you do **not** need to open a new Merge Request to do this. 

To update your contribution you update the appropriate files on your contribution branch. Firstly you need to ensure that you are up to date with the remote repository on GitLab. Make sure you are in the directory of the cloned repository and then check which branch you want to check out:

.. code-block:: bash

    git branch # List all available local branches, to include remote branches add the -r flag
    git checkout <BRANCH_NAME> # Check out the branch we want to update 
    git pull origin <BRANCH_NAME> # Make sure we have any updates we made to our own branch
    git pull upstream master # Also pull in any changes to the main repository
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Now that everything is in sync, you can edit your update your files, when you are finished you commit your changes and push the changes back to GitLab

.. code-block:: bash

    git add modules/gromacs_gpu/readme.rst
    git commit -m "update documention on how to trigger the GPU support"
    git push origin <BRANCH_NAME>

The Merge  Request will now be automatically updated with the changed files.
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.. _ReST: