# LAMMPS GitHub tutorial

**written by Stefan Paquay**

------------------------------------------------------------------------

This document describes the process of how to use GitHub to integrate
changes or additions you have made to LAMMPS into the official LAMMPS
distribution. It uses the process of updating this very tutorial as an
example to describe the individual steps and options. You need to be
familiar with git and you may want to have a look at the [git
book](https://git-scm.com/book/)\_ to familiarize yourself with some of
the more advanced git features used below.

As of fall 2016, submitting contributions to LAMMPS via pull requests on
GitHub is the preferred option for integrating contributed features or
improvements to LAMMPS, as it significantly reduces the amount of work
required by the LAMMPS developers. Consequently, creating a pull request
will increase your chances to have your contribution included and will
reduce the time until the integration is complete. For more information
on the requirements to have your code included into LAMMPS please see
[this page](Modify_contribute).

------------------------------------------------------------------------

**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.

------------------------------------------------------------------------

**Forking the repository**

To get changes into LAMMPS, you need to first fork the
[lammps/lammps]{.title-ref} repository on GitHub. At the time of
writing, *develop* is the preferred target branch. Thus go to [LAMMPS on
GitHub](https://github.com/lammps/lammps)\_ and make sure branch is set
to \"develop\", as shown in the figure below.

![image](JPG/tutorial_branch.png){.align-center}

If it is not, use the button to change it to *develop*. Once it is, use
the fork button to create a fork.

![image](JPG/tutorial_fork.png){.align-center}

This will create a fork (which is essentially a copy, but uses less
resources) of the LAMMPS repository under your own GitHub account. 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 (or others that were forked from the same
repository). At the same time, you can set things up, so you can include
changes from upstream into your repository and thus keep it in sync with
the ongoing LAMMPS development.

------------------------------------------------------------------------

**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:

``` bash
git clone https://github.com/<your user name>/lammps.git <some name>
```

or, if you have set up your GitHub account for using SSH keys, via SSH:

``` bash
git clone git@github.com:<your user name>/lammps.git
```

You can find the proper URL by clicking the \"Clone or
download\"-button:

![image](JPG/tutorial_https_block.png){.align-center}

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:

``` bash
cd mylammps
git checkout develop
git pull https://github.com/lammps/lammps develop
```

You can also add this URL as a remote:

``` bash
git remote add upstream https://www.github.com/lammps/lammps
```

From then on you can update your upstream branches with:

``` bash
git fetch upstream
```

and then refer to the upstream repository branches with
[upstream/develop]{.title-ref} or [upstream/release]{.title-ref} and so
on.

At this point, you typically make a feature branch from the updated
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\":

``` bash
git fetch upstream
git checkout -b github-tutorial-update upstream/develop
```

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!

:::: note
::: title
Note
:::

Committing changes to the *develop*, *release*, or *stable* branches is
strongly discouraged. While it may be convenient initially, it will
create more work in the long run. Various texts and tutorials on using
git effectively discuss the motivation for using feature branches
instead.
::::

**After changes are made**

After everything is done, add the files to the branch and commit them:

``` bash
git add doc/src/Howto_github.txt
git add doc/src/JPG/tutorial*.png
```

:::: warning
::: title
Warning
:::

Do not use *git commit -a* (or *git add -A*). The -a flag (or -A flag)
will automatically include **all** modified **and** 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 individual files, respectively, and then *git commit*
to finalize the commit. Carefully check all pending changes with *git
status* before committing them. 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.

``` bash
git commit -m 'Finally updated the GitHub tutorial'
```

After the commit, the changes can be pushed to the same branch on
GitHub:

``` bash
git push
```

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

``` bash
git push --set-upstream origin github-tutorial-update
```

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:

``` bash
git push origin
```

or using an explicit URL:

``` bash
git push git@github.com:Pakketeretet2/lammps.git
```

------------------------------------------------------------------------

**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 into
the official LAMMPS version. To do this, you will want to file a pull
request by clicking on the \"New pull request\" button:

![image](JPG/tutorial_new_pull_request.png){.align-center}

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.

![image](JPG/tutorial_create_new_pull_request1.png){.align-center}

Before creating the pull request, make sure the short title is accurate
and add a comment with details about your pull request. 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):

![image](JPG/tutorial_edits_maintainers.png){.align-center}

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 added directly to your pull request branch
by the LAMMPS maintainers. 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\".

![image](JPG/tutorial_create_new_pull_request2.png){.align-center}

------------------------------------------------------------------------

**After filing a pull request**

:::: note
::: title
Note
:::

When you submit a pull request (or ask for a pull request) for the first
time, you will receive an invitation to become a LAMMPS project
collaborator. Please accept this invite as being a collaborator will
simplify certain administrative tasks and will probably speed up the
merging of your feature, too.
::::

You will notice that after filing the pull request, some checks are
performed automatically:

![image](JPG/tutorial_automated_checks.png){.align-center}

If all is fine, you will see this:

![image](JPG/tutorial_automated_checks_passed.png){.align-center}

If any of the checks are failing, your pull request will not be
processed, as your changes may break compilation for certain
configurations or may not merge cleanly. It is your responsibility to
remove the reason(s) for the failed test(s). If you need help with this,
please contact the LAMMPS developers by adding a comment explaining your
problems with resolving the failed tests.

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:

![image](JPG/tutorial_additional_changes.png){.align-center}

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 requested that something needs to be changed
before the feature can be accepted into the official LAMMPS version.
After each push, the automated checks are run again.

**Labels**

LAMMPS developers may add labels to your pull request to assign it to
categories (mostly for bookkeeping purposes), but a few of them are
important: *needs_work*, *work_in_progress*, *run_tests*,
*test_for_regression*, and *ready_for_merge*. The first two indicate,
that your pull request is not considered to be complete. With
\"needs_work\" the burden is on exclusively on you; while
\"work_in_progress\" can also mean, that a LAMMPS developer may want to
add changes. Please watch the comments to the pull requests. The two
\"test\" labels are used to trigger extended tests before the code is
merged. This is sometimes done by LAMMPS developers, if they suspect
that there may be some subtle side effects from your changes. It is not
done by default, because those tests are very time-consuming. The
*ready_for_merge* label is usually attached when the LAMMPS developer
assigned to the pull request considers this request complete and to
trigger a final full test evaluation.

**Reviews**

As of Fall 2021, a pull request needs to pass all automatic tests and at
least 1 approving review from a LAMMPS developer with write access to
the repository before it is eligible for merging. In case your changes
touch code that certain developers are associated with, they are
auto-requested by the GitHub software. Those associations are set in the
file
[.github/CODEOWNERS](https://github.com/lammps/lammps/blob/develop/.github/CODEOWNERS)\_
Thus if you want to be automatically notified to review when anybody
changes files or packages, that **you** have contributed to LAMMPS, you
can add suitable patterns to that file, or a LAMMPS developer may add
you.

Otherwise, you can also manually request reviews from specific
developers, or LAMMPS developers - in their assessment of your pull
request - may determine who else should be reviewing your contribution
and add that person. Through reviews, LAMMPS developers also may request
specific changes from you. If those are not addressed, your pull
requests cannot be merged.

**Assignees**

There is an assignee property 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) Axel Kohlmeyer
(akohlmey).

-   Case a) happens if changes are required on your part
-   Case b) means that at the moment, it is being tested and reviewed by
    a LAMMPS developer with the expectation that some changes would be
    required. After the review, the developer can choose to implement
    changes directly or suggest them to you.
-   Case c) means that the pull request has been assigned to the
    developer overseeing the merging of pull requests into the *develop*
    branch.

In this case, Axel assigned the tutorial to Steve:

![image](JPG/tutorial_steve_assignee.png){.align-center}

**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:

![image](JPG/tutorial_changes_others.png){.align-center}

**Reverse pull requests**

Sometimes, however, you might not feel comfortable having other people
push changes into your own branch, or maybe the maintainers are not sure
their idea was the right one. In such a case, they can make changes,
reassign you as the assignee, and file a \"reverse pull request\", i.e.
file a pull request in **your** forked GitHub repository to include
changes in the branch, that you have submitted as a pull request
yourself. In that case, you can choose to merge their changes back into
your branch, possibly make additional changes or corrections and proceed
from there. It looks something like this:

![image](JPG/tutorial_reverse_pull_request.png){.align-center}

For some reason, the highlighted button did not work in my case, but I
can go to my own repository and merge the pull request from there:

![image](JPG/tutorial_reverse_pull_request2.png){.align-center}

Be sure to check the changes to see if you agree with them by clicking
on the tab button:

![image](JPG/tutorial_reverse_pull_request3.png){.align-center}

In this case, most of it is changes in the markup and a short rewrite of
Axel\'s explanation of the \"git gui\" and \"git add\" commands.

![image](JPG/tutorial_reverse_pull_request4.png){.align-center}

Because the changes are OK with us, we are going to merge by clicking on
\"Merge pull request\". After a merge it looks like this:

![image](JPG/tutorial_reverse_pull_request5.png){.align-center}

Now, since in the meantime our local text for the tutorial also changed,
we need to pull Axel\'s change back into our branch, and merge them:

``` bash
git add Howto_github.txt
git add JPG/tutorial_reverse_pull_request*.png
git commit -m "Updated text and images on reverse pull requests"
git pull
```

In this case, the merge was painless because git could auto-merge:

![image](JPG/tutorial_reverse_pull_request6.png){.align-center}

With Axel\'s changes merged in and some final text updates, our feature
branch is now perfect as far as we are concerned, so we are going to
commit and push again:

``` bash
git add Howto_github.txt
git add JPG/tutorial_reverse_pull_request6.png
git commit -m "Merged Axel's suggestions and updated text"
git push git@github.com:Pakketeretet2/lammps
```

This merge also shows up on the lammps GitHub page:

![image](JPG/tutorial_reverse_pull_request7.png){.align-center}

------------------------------------------------------------------------

**After a merge**

When everything is fine, the feature branch is merged into the *develop*
branch:

![image](JPG/tutorial_merged.png){.align-center}

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!

``` bash
git checkout develop
git pull https://github.com/lammps/lammps develop
git branch -d github-tutorial-update
```

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 upstream. If you first delete
and then pull, everything should still be fine. You can display all
branches that are fully merged by:

Finally, if you delete the branch locally, you might want to push this
to your remote(s) as well:

``` bash
git push origin :github-tutorial-update
```

**Recent changes in the workflow**

Some recent changes to the workflow are not captured in this tutorial.
For example, in addition to the *develop* branch, to which all new
features should be submitted, there is also a *release*, a *stable*, and
a *maintenance* branch; the *release* branch is updated from the
*develop* as part of a feature release, and *stable* (together with
*release*) are updated from *develop* when a stable release is made. In
between stable releases, selected bug fixes and infrastructure updates
are back-ported from the *develop* branch to the *maintenance* branch
and occasionally merged to *stable* as an update release.

Furthermore, the naming of the release tags now follow the pattern
\"[patch]()\<Day\>\<Month\>\<Year\>\" to simplify comparisons between
releases. For stable releases additional
\"[stable]()\<Day\>\<Month\>\<Year\>\" tags are applied and update
releases are tagged with
\"[stable]()\<Day\>\<Month\>\<Year\>\_update\<Number\>\", Finally, all
releases and submissions are subject to automatic testing and code
checks to make sure they compile with a variety of compilers and popular
operating systems. Some unit and regression testing is applied as well.

A detailed discussion of the LAMMPS developer GitHub workflow can be
found in the file
[doc/github-development-workflow.md](https://github.com/lammps/lammps/blob/develop/doc/github-development-workflow.md)\_