This webpage is actually a repository of files that (typically) document application development efforts during the pilot projects and Extended Software Development Workshops (ESDWs) of E-CAM. This documentation is completely open however and we welcome both internal and external contributions. If you would like to contribute to this effort then please follow the steps below to allow us to include your contribution.
In any case you will simply be adding a simple text file that uses ReST and we have prepared an example to help you get started:
You will find the example within the repository of this documentation under the directory example_module. You should make a copy of this directory (renaming it) and place it in the appropriate scientific area directory.
If you do not have a (free) GitLab account yet on the E-CAM GitLab service, you’ll need to get one via https://gitlab.e-cam2020.eu/.
You should also register an SSH public key with GitLab (if you have not already done so), so you can easily clone, push to and pull from your repositories. This can be done via https://gitlab.e-cam2020.eu/profile/keys (once you’re logged in on GitLab).
In the following it is assumed that an SSH public key has been registered with GitLab (see note above), the possibility of using the HTTPS protocol to access GitLab is not covered (but is possible).
Firstly, you’ll need to fork the repository on GitLab you want to work with. Go to https://gitlab.e-cam2020.eu/e-cam/E-CAM-Library , and click the grey ‘Fork’ button either beside or under the repository name (or just click this fork link).
Clone your fork of the repository to your favorite workstation.
git clone ssh://firstname.lastname@example.org:10022/<Your GitLab username>/E-CAM-Library.git
Pull the master branch from the main repository:
cd E-CAM-Library git remote add upstream https://email@example.com/e-cam/E-CAM-Library.git git pull upstream master
Make sure you update it every time you create a feature branch (see below):
git checkout master git pull upstream master
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
git checkout master git branch BRANCH_NAME git checkout BRANCH_NAME
Make sure to always base your features branches on master!
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).
Your contribution to this repository will primarily be a module documentation file (this repository is not for source code, the documentation file will link to source code which is usually somewhere else). There are already several examples of these in the repository, but we provide a template for a generic module as a guide:
After creating the branch, implement your contributions: new modules, enhancements or updates to existing modules, bug fixes, structure changes, whatever you like.
Make sure to put your work in the appropriate directory. There are 4 scientific
areas in E-CAM and your module is likely most relevant in one of those. Each of these directories has a
subdirectory, create a new directory within it to contain all files relevant to your specific module. In the example
below, this directory has been called
Make sure you commit your work, and try to do it in bite-size chunks, so the commit log remains clear, for example:
git add Classical-MD-Modules/modules/gromacs_gpu/readme.rst git commit -m "add details on improved GPU support within GROMACS"
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 installation link for information on how to install this tool on your operating system).
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.
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
git push origin <BRANCH_NAME>
Issue a Merge Request for your branch into the main repository. To do this go to https://gitlab.e-cam2020.eu/Your_GitLab_Username/E-CAM-Library/merge_requests 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.
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:
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
Now that everything is in sync, you can edit and update your files, when you are finished you commit your changes and push the changes back to GitLab:
git add modules/gromacs_gpu/readme.rst git commit -m "update documentation on how to trigger the GPU support" git push origin <BRANCH_NAME>
The Merge Request will now be automatically updated with the changed files.