"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line LAMMPS GitHub tutorial :h3 [written by Stefan Paquay] :line This document briefly describes how to use GitHub to merge changes you make into LAMMPS, using GitHub. It assumes that you are familiar with git. You may want to have a look at the "Git book"_http://git-scm.com/book/ to reacquaint yourself. :line [Making an account] First of all, you need a GitHub account. This is fairly simple, just go to "GitHub"_https://github.com and create an account by clicking the "Sign up for GitHub" button. Once your account is created, you can sign in by clicking the button in the top left and filling in your username or e-mail address and password. :line [Forking the repository] To get changes into LAMMPS, you need to first fork the repository. At the time of writing, master is the preferred branch. Go to "LAMMPS on GitHub"_https://github.com/lammps/lammps and make sure branch is set to "master", see the figure below. :c,image(JPG/tutorial_branch.png) If it is not, use the button to change it to master. Once it is, use the fork button to create a fork. :c,image(JPG/tutorial_fork.png) This will create your own fork of the LAMMPS repository. You can make changes in this fork and later file {pull requests} to allow the upstream repository to merge changes from your own fork into the one we just forked from. At the same time, you can set things up, so you can include changes from upstream into your repository. :line [Adding changes to your own fork] Additions to the upstream version of LAMMPS are handled using {feature branches}. For every new feature, a so-called feature branch is created, which contains only those modification relevant to one specific feature. For example, adding a single fix would consist of creating a branch with only the fix header and source file and nothing else. It is explained in more detail here: "feature branch workflow"_https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow. [Feature branches] First of all, create a clone of your version on github on your local machine via HTTPS $ git clone https://github.com//lammps.git :pre or, if you have SSH keys setup, using your SSH key: $ git clone git@github.com:/lammps.git :pre You can find the proper url by clicking the "Clone or download"-button: :c,image(JPG/tutorial_https_block.png) The above command copies ("clones") the git repository to your local machine to a directory with the name you chose. If none is given, it will default to "lammps". Typical names are "mylammps" or something similar. You can use this local clone to make changes and test them without interfering with the repository on Github. To pull changes from upstream into this copy, you can go to the directory and use git pull: $ cd mylammps $ git checkout master $ git pull https://github.com/lammps/lammps :pre You can also add this url as a remote: $ git remote add lammps_upstream https://www.github.com/lammps/lammps :pre At this point, you typically make a feature branch from the updated master branch for the feature you want to work on. This tutorial contains the workflow that updated this tutorial, and hence we will call the branch "github-tutorial-update": $ git checkout -b github-tutorial-update master :pre Now that we have changed branches, we can make our changes to our local repository. Just remember that if you want to start working on another, unrelated feature, you should switch branches! [After changes are made] After everything is done, add the files to the branch and commit them: $ git add doc/src/tutorial_github.txt $ git add doc/src/JPG/tutorial_*.png :pre IMPORTANT NOTE: Do not use `git commit -a`. The -a flag will automatically include _all_ modified or new files and that is rarely the behavior you want. It can easily lead to accidentally adding unrelated and unwanted changes into the repository. Instead it is preferable to explicitly use `git add`, `git rm`, `git mv` for adding, removing, renaming files, respectively, and then `git commit` to finalize the commit. If you find doing this on the command line too tedious, consider using a GUI, for example the one included in git distributions written in Tk, i.e. use `git gui` (on some Linux distributions it may be required to install an additional package to use it). After adding all files, the change set can be committed with some useful message that explains the change. $ git commit -m 'Finally updated the github tutorial' :pre After the commit, the changes can be pushed to the same branch on GitHub: $ git push :pre Git will ask you for your user name and password on GitHub if you have not configured anything. If your local branch is not present on Github yet, it will ask you to add it by running $ git push --set-upstream origin github-tutorial-update :pre If you correctly type your user name and password, the feature branch should be added to your fork on GitHub. If you want to make really sure you push to the right repository (which is good practice), you can provide it explicitly: $ git push origin :pre or using an explicit URL: $ git push git@github.com:Pakketeretet2/lammps.git :pre [Filing a pull request] Up to this point in the tutorial, all changes were to {your} clones of LAMMPS. Eventually, however, you want this feature to be included again upstream. To do this, you will want to file a pull request by clicking on the "New pull request" button: :c,image(JPG/tutorial_new_pull_request.png) Make sure that the current branch is set to the correct one, which, in this case, is "github-tutorial-update". If done correctly, the only changes you will see are those that were made on this branch. This will open up a new window that lists changes made to the repository. If you are just adding new files, there is not much to do, but I suppose merge conflicts are to be resolved here if there are changes in existing files. If all changes can automatically be merged, green text at the top will say so and you can click the "Create pull request" button, see image. :c,image(JPG/tutorial_create_new_pull_request1.png) Before creating the pull request, make sure the short title is accurate and add a comment with details about your pull request. I guess here you write what your modifications do and why they should be incorporated upstream. Note the checkbox that says "Allow edits from maintainers". This is checked by default checkbox (although in my version of Firefox, only the checkmark is visible): :c,image(JPG/tutorial_edits_maintainers.png) If it is checked, maintainers can immediately add their own edits to the pull request. This helps the inclusion of your branch significantly, as simple/trivial changes can be made by the maintainers directly. The alternative would be that they make changes on their own version of the branch and file a reverse pull request to you. Just leave this box checked unless you have a very good reason not to. Now just write some nice comments and click on "Create pull request". :c,image(JPG/tutorial_create_new_pull_request2.png) :line [After filing a pull request] NOTE: When you submit a pull request (or ask for a pull request), you will receive an invitation to become a LAMMPS project collaborator. This will simplify certain administrative tasks and will probably speed up the merging of your feature. You will notice that after filing the pull request, some checks are performed automatically: :c,image(JPG/tutorial_automated_checks.png) If all is fine, you will see this: :c,image(JPG/tutorial_automated_checks_passed.png) A few further interesting things (can) happen to pull requests before they are included. [Additional changes] First of all, any additional changes you push into your branch in your repository will automatically become part of the pull request: :c,image(JPG/tutorial_additional_changes.png) This means you can add changes that should be part of the feature after filing the pull request, which is useful in case you have forgotten them, or if a developer has ruled that something needs to change before the feature can be accepted upstream. After each push, the automated checks are run again. [Assignees] There is an assignee label for pull requests. If the request has not been reviewed by any developer yet, it is not assigned to anyone. After revision, a developer can choose to assign it to either a) you, b) a LAMMPS developer (including him/herself) or c) Steve Plimpton (sjplimp). Case a) happens if changes are required on your part :ulb,l Case b) means that at the moment, it is being tested and reviewed by a LAMMPS developer. After review, the developer can choose to implement changes or suggest them to you. :l Case c) means that the pull request has been assigned to the lead developer Steve Plimpton, and means it is considered ready for merging. :ule,l In this case, Axel assigned the tutorial to Steve: :c,image(JPG/tutorial_steve_assignee.png) [Edits from LAMMPS maintainers] If you allowed edits from maintainers (the default), any LAMMPS maintainer can add changes to your pull request. In this case, both Axel and Richard made changes to the tutorial: :c,image(JPG/tutorial_changes_others.png) :line [After a merge] When everything is fine, the feature branch is merged into the master branch. :c,image(JPG/tutorial_merged.png) Now one question remains: What to do with the feature branch that got merged into upstream? It is in principle safe to delete them from your own fork. This helps keep it a bit more tidy. Note that you first have to switch to another branch! $ git checkout master $ git pull master $ git branch -d github-tutorial-update :pre If you do not pull first, it is not really a problem but git will warn you at the next statement that you are deleting a local branch that was not yet fully merged into HEAD. This is because git does not yet know your branch just got merged into lammps-icms upstream. If you first delete and then pull, everything should still be fine. Finally, if you delete the branch locally, you might want to push this to your remote(s) as well: $ git push origin :github-tutorial-update :pre [Recent changes in the workflow] Some changes to the workflow are not captured in this tutorial. For example, in addition to the master branch, to which all new features should be submitted, there is now also an "unstable" and a "stable" branch. Furthermore, the naming of the patches now follow the pattern "patch_" so simplify comparisons between releases. Finally, all patches and submissions are subject to automatic testing and code checks to make sure they at the very least compile.