What is Git LFS?

If you have a Mac, you can install the git-lfs application outside the container using Homebrew: brew install git-lfs. If you have a Windows or a Linux machine or if.

Git is a distributed version control system, meaning the entire history of the repository is transferred to the client during the cloning process. For projects containing large files, particularly large files that are modified regularly, this initial clone can take a huge amount of time, as every version of every file has to be downloaded by the client. Git LFS (Large File Storage) is a Git extension developed by Atlassian, GitHub, and a few other open source contributors, that reduces the impact of large files in your repository by downloading the relevant versions of them lazily. Specifically, large files are downloaded during the checkout process rather than during cloning or fetching.

Git LFS does this by replacing large files in your repository with tiny pointer files. During normal usage, you'll never see these pointer files as they are handled automatically by Git LFS:

1. When you add a file to your repository, Git LFS replaces its contents with a pointer, and stores the file contents in a local Git LFS cache.

2. When you push new commits to the server, any Git LFS files referenced by the newly pushed commits are transferred from your local Git LFS cache to the remote Git LFS store tied to your Git repository.

3. When you checkout a commit that contains Git LFS pointers, they are replaced with files from your local Git LFS cache, or downloaded from the remote Git LFS store.

Git LFS is seamless: in your working copy you'll only see your actual file content. This means you can use Git LFS without changing your existing Git workflow; you simply git checkout, edit, git add, and git commit as normal. git clone and git pull operations will be significantly faster as you only download the versions of large files referenced by commits that you actually check out, rather than every version of the file that ever existed.

To use Git LFS, you will need a Git LFS aware host such as Bitbucket Cloud or Bitbucket Server. Repository users will need to have the Git LFS command-line client installed, or a Git LFS aware GUI client such as Sourcetree. Fun fact: Steve Streeting, the Atlassian developer who invented Sourcetree, is also a major contributor to the Git LFS project, so Sourcetree and Git LFS work together rather well.

What is Git LFS?

Installing Git LFS

1. There are three easy ways to install Git LFS:

   a. Install it using your favorite package manager. git-lfs packages are available for Homebrew, MacPorts, dnf, and packagecloud; or

   b. Download and install Git LFS from the project website; or

   c. Install Sourcetree, a free Git GUI client that comes bundled with Git LFS.

2. Once git-lfs is on your path, run git lfs install to initialize Git LFS (you can skip this step if you installed Sourcetree):

   You'll only need to run git lfs install once. Once initialized for your system, Git LFS will bootstrap itself automatically when you clone a repository containing Git LFS content.

Creating a new Git LFS repository

To create a new Git LFS aware repository, you'll need to run git lfs install after you create the repository:

This installs a special pre-pushGit hook in your repository that will transfer Git LFS files to the server when you git push.

Git LFS is automatically enabled for all Bitbucket Cloud repositories. For Bitbucket Server, you'll need to enable Git LFS in your repository settings:

Once Git LFS is initialized for your repository, you can specify which files to track using git lfs track.

Cloning an existing Git LFS repository

Once Git LFS is installed, you can clone a Git LFS repository as normal using git clone. At the end of the cloning process Git will check out the default branch (usually master), and any Git LFS files needed to complete the checkout process will be automatically downloaded for you. For example:

There are four PNGs in this repository being tracked by Git LFS. When running git clone, Git LFS files are downloaded one at a time as pointer files are checked out of your repository.

Speeding up clones

If you're cloning a repository with a large number of LFS files, the explicit git lfs clone command offers far better performance:

Rather than downloading Git LFS files one at a time, the git lfs clone command waits until the checkout is complete, and then downloads any required Git LFS files as a batch. This takes advantage of parallelized downloads, and dramatically reduces the number of HTTP requests and processes spawned (which is especially important for improving performance on Windows).

Pulling and checking out

Just like cloning, you can pull from a Git LFS repository using a normal git pull. Any needed Git LFS files will be downloaded as part of the automatic checkout process once the pull completes:

No explicit commands are needed to retrieve Git LFS content. However, if the checkout fails for an unexpected reason, you can download any missing Git LFS content for the current commit with git lfs pull:

Speeding up pulls

Like git lfs clone, git lfs pull downloads your Git LFS files as a batch. If you know a large number of files have changed since the last time you pulled, you may wish to disable the automatic Git LFS download during checkout, and then batch download your Git LFS content with an explicit git lfs pull. This can be done by overriding your Git config with the -c option when you invoke git pull:

Since that's rather a lot of typing, you may wish to create a simple Git alias to perform a batched Git and Git LFS pull for you:

This will greatly improve performance when a large number of Git LFS files need to be downloaded (again, especially on Windows).

Tracking files with Git LFS

When you add a new type of large file to your repository, you'll need to tell Git LFS to track it by specifying a pattern using the git lfs track command:

Note that the quotes around '*.ogg' are important. Omitting them will cause the wildcard to be expanded by your shell, and individual entries will be created for each .ogg file in your current directory:

The patterns supported by Git LFS are the same as those supported by .gitignore, for example:

These patterns are relative to the directory in which you ran the git lfs track command. To keep things simple, it is best to run git lfs track from the root of your repository. Note that Git LFS does not support negative patterns like .gitignore does.

After running git lfs track, you'll notice a new file named .gitattributes in the directory you ran the command from. .gitattributes is a Git mechanism for binding special behaviors to certain file patterns. Git LFS automatically creates or updates .gitattributes files to bind tracked file patterns to the Git LFS filter. However, you will need to commit any changes to the .gitattributes file to your repository yourself:

For ease of maintenance, it is simplest to keep all Git LFS patterns in a single .gitattributes file by always running git lfs track from the root of your repository. However, you can display a list of all patterns that are currently tracked by Git LFS (and the .gitattributes files they are defined in) by invoking git lfs track with no arguments:

You can stop tracking a particular pattern with Git LFS by simply removing the appropriate line from your .gitattributes file, or by running the git lfs untrack command:

After running git lfs untrack you will again have to commit the changes to .gitattributes yourself.

Committing and pushing

You can commit and push as normal to a repository that contains Git LFS content. If you have committed changes to files tracked by Git LFS, you will see some additional output from git push as the Git LFS content is transferred to the server:

If transferring the LFS files fails for some reason, the push will be aborted and you can safely try again. Like Git, Git LFS storage is content addressable: content is stored against a key which is a SHA-256 hash of the content itself. This means it is always safe to re-attempt transferring Git LFS files to the server; you can't accidentally overwrite a Git LFS file's contents with the wrong version.

Moving a Git LFS repository between hosts

To migrate a Git LFS repository from one hosting provider to another, you can use a combination of git lfs fetch and git lfs push with the --all option specified.

For example, to move all Git and Git LFS repository from a remote named github to a remote named bitbucket 😉 :

Fetching extra Git LFS history

Git LFS typically only downloads the files needed for commits that you actually checkout locally. However, you can force Git LFS to download extra content for other recently modified branches using git lfs fetch --recent:

This is useful for batch downloading new Git LFS content while you're out at lunch, or if you're planning on reviewing work from your teammates and will not be able to download content later on due to limited internet connectivity. For example, you may wish to run git lfs fetch --recent before jumping on a plane!

Git LFS considers any branch or tag containing a commit newer than seven days as recent. You can configure the number of days considered as recent by setting the lfs.fetchrecentrefsdays property:

By default, git lfs fetch --recent will only download Git LFS content for the commit at the tip of a recent branch or tag.

However you can configure Git LFS to download content for earlier commits on recent branches and tags by configuring the lfs.fetchrecentcommitsdays property:

Use this setting with care: if you have fast moving branches, this can result in a huge amount of data being downloaded. However it can be useful if you need to review interstitial changes on a branch, cherry picking commits across branches, or rewrite history.

As discussed in Moving a Git LFS repository between hosts, you can also elect to fetch all Git LFS content for your repository with git lfs fetch --all:

Deleting local Git LFS files

You can delete files from your local Git LFS cache with the git lfs prune command:

This will delete any local Git LFS files that are considered old. An old file is any file not referenced by:

• the currently checked out commit
• a commit that has not yet been pushed (to origin, or whatever lfs.pruneremotetocheck is set to)
• a recent commit

By default, a recent commit is any commit created in the last ten days. This is calculated by adding:

• the value of the lfs.fetchrecentrefsdays property discussed in Fetching extra Git LFS history (which defaults to seven); to
• the value of the lfs.pruneoffsetdays property (which defaults to three)

You can configure the prune offset to retain Git LFS content for a longer period:

Unlike Git's built-in garbage collection, Git LFS content is not pruned automatically, so running git lfs prune on a regular basis is a good idea to keep your local repository size down.

You can test out what effect a prune operation will have with git lfs prune --dry-run:

And exactly which Git LFS objects will be pruned with git lfs prune --verbose --dry-run:

The long hexadecimal strings output by --verbose mode are SHA-256 hashes (also known as Object IDs, or OIDs) of the Git LFS objects to be pruned. You can use the techniques described in Finding paths or commits that reference a Git LFS object to find our more about the objects that will be pruned.

As an additional safety check, you can use the --verify-remote option to check whether the remote Git LFS store has a copy of your Git LFS objects before they are pruned:

This makes the pruning process significantly slower, but gives you peace of mind knowing that any pruned objects are recoverable from the server. You can enable the --verify-remote option permanently for your system by configuring the lfs.pruneverifyremotealways property globally:

Or you can enable remote verification for just the context repository by omitting the --global option from the command above.

Deleting remote Git LFS files from the server

The Git LFS command-line client doesn't support pruning files from the server, so how you delete them depends on your hosting provider.

In Bitbucket Cloud, you can view and delete Git LFS files via Repository Settings > Git LFS:

Note that each Git LFS file is indexed by its SHA-256 OID; the paths that reference each file are not visible via the UI. This is because there could be many different paths at many different commits that may refer to a given object, so looking them up would be a very slow process.

To determine what a given Git LFS file actually contains, you have three options:

• look at the file preview image and file type in the left hand column of the Bitbucket Git LFS UI
• download the file using the link in the right hand column of the Bitbucket Git LFS UI -search for commits referencing the Git LFS object's SHA-256 OID, as discussed in the next section

Finding paths or commits that reference a Git LFS object

If you have a Git LFS SHA-256 OID, you can determine which commits reference it with git log --all -p -S <OID>:

This git log incantation generates a patch (-p) from commits on any branch (--all) that add or remove a line (-S) containing the specified string (a Git LFS SHA-256 OID).

The patch shows you the commit and the path to the LFS object, as well as who added it, and when it was committed. You can simply checkout the commit, and Git LFS will download the file if needed and place it in your working copy.

If you suspect that a particular Git LFS object is in your current HEAD, or on a particular branch, you can use git grep to find the file path that references it:

You can replace HEAD or power-ups with any ref, commit, or tree that contains the Git LFS object.

Including/excluding Git LFS files

In some situations you may want to only download a subset of the available Git LFS content for a particular commit. For example, when configuring a CI build to run unit tests, you may only need your source code, so may want to exclude heavyweight files that aren't necessary to build your code.

You can exclude a pattern or subdirectory using git lfs fetch -X (or --exclude):

Alternatively, you may want to only include a particular pattern or subdirectory. For example, an audio engineer could fetch just ogg and wav files with git lfs fetch -I (or --include):

If you combine includes and excludes, only files that match an include pattern and do not match an exclude pattern will be fetched. For example, you can fetch everything in your Assets directory exceptgifs with:

Excludes and includes support the same patterns as git lfs track and .gitignore. You can make these patterns permanent for a particular repository by setting the lfs.fetchinclude and lfs.fetchexclude config properties:

These settings can also be applied to every repository on your system by appending the --global option.

Locking Git LFS files

Unfortunately, there is no easy way of resolving binary merge conflicts. With Git LFS file locking, you can lock files by extension or by file name and prevent binary files from being overwritten during a merge.

In order to take advantage of LFS' file locking feature, you first need to tell Git which type of files are lockable. In the example below, the `--lockable` flag is appended to the `git lfs track` command which both stores PSD files in LFS and marks them as lockable.

Then add the following to your .gitattributes file:

When preparing to make changes to an LFS file, you'll use the lock command in order to register the file as locked on your Git server.

Once you no longer need the file lock, you can remove it using Git LFS' unlock command.

Git LFS file locks can be overridden, similar to git push, using a --force flag. Do not use the --force flag unless you’re absolutely sure you know what you’re doing.

How Git LFS works

If you're interested in learning more about clean and smudge filters, pre-push hooks, and the other interesting computer science behind Git LFS, check out this presentation from Atlassian on Git LFS at LinuxCon 2016:

This page describes how to use Git LFS for DM development.

DM uses Git LFS to manage test datasets within our normal Git workflow.Git LFS is developed by GitHub, though DM uses its own backend storage infrastructure (see SQR-001: The Git LFS Architecture for background).

All DM repositories should use Git LFS to store binary data, such as FITS files, for CI.Examples of LFS-backed repositories are lsst/afw, lsst/hsc_ci, lsst/testdata_decam and lsst/testdata_cfht.

On this page

Installing Git LFS¶

Download and install the git-lfs client by visiting the Git LFS homepage.Many package managers, like Homebrew on the Mac, also provide git-lfs (brewinstallgit-lfs for example).

We recommend using the latest Git LFS client.The minimum usable client version for LSST is git-lfs is 2.3.4.

Git LFS requires Git version 1.8.2 or later to be installed.

Before you can use Git LFS with LSST data you’ll need to configure by following the next section.

Configuring Git LFS¶

Basic configuration¶

After you’ve installed Git LFS, run:

This is the regular Git LFS configuration step that adds a filter'lfs' section to ~/.gitconfig.Additional configurations for LSST are next.

Configuration for LSST¶

LSST uses its own Git LFS servers.This section describes how to configure Git LFS to pull from LSST’s servers.If you are running an older client, version 1.2 or earlier, follow the note at the end of this section.

First, add these lines into your ~/.gitconfig file:

Then add these lines into your ~/.git-credentials files (create one, if necessary):

Trying cloning a small data repository to test your configuration:

That’s it.

Note

Configuration for Git LFS v1.2 and earlier*

The legacy Git LFS client (versions earlier than 1.3) has two configuration differences compared to the modern configuration described above.

First, add these lines into your ~/.gitconfig file:

Then add these lines into your ~/.git-credentials file (create one, if necessary):

Authenticating for push access¶

If you want to push to a LSST Git LFS-backed repository you’ll need to configure and cache your credentials.

First, set up a credential helper to manage your GitHub credentials (Git LFS won’t use your SSH keys).We describe how to set up a credential helper for your system in the Git set up guide.

Then the next time you run a Git command that requires authentication, Git will ask you to authenticate with LSST’s Git LFS server: For mac os x high sierra download ulysses 12.1 without virus.

At the prompts, enter your GitHub username and password.

Once your credentials are cached, you won’t need to repeat this process on your system (unless you opted for the cache-based credential helper).

Note

Working with GitHub Two Factor Authentication

If you have GitHub’s two-factor authentication enabled, use a personal access token instead of a password.You can set up a personal token at https://github.com/settings/tokens with public_repo and read:org permissions.

Using Git LFS-enabled repositories¶

Git LFS operates transparently to the user.Just use the repo as you normally would any other Git repo.All of the regular Git commands just work, whether you are working with LFS-managed files or not.

There are two caveats for working with LFS: HTTPS is always used, and Git LFS must be told to track new binary file types.

First, DM’s LFS implementation mandates the HTTPS transport protocol.Developers used to working with ssh-agent for passwordless GitHub interaction should use a Git credential helper, and follow the directions above for configuring their credentials.

Note this does not preclude using git+git or git+ssh for working with a Git remote itself; it is only the LFS traffic that always uses HTTPS.

Second, in an LFS-backed repository, you need to specify what files are stored by LFS rather than regular Git storage.You can run

to see what file types are being tracked by LFS in your repository.We describe how to track additional file types below.

Tracking new file types¶

Only file types that are specifically tracked are stored in Git LFS rather than the standard Git storage.

To see what file types are already being tracked in a repository:

To track a new file type (FITS files, for example):

Git LFS stores information about tracked types in the .gitattributes file.This file is part of the repo and tracked by Git itself.

You can gitadd, commit and do any other Git operations against these Git LFS-managed files.

To see what files are being managed by Git LFS, run:

Creating a new Git LFS-enabled repository¶

Configuring a new Git repository to store files with DM’s Git LFS is easy.First, initialize the current directory as a repository:

Make a file called .lfsconfigwithin the repository, and write these lines into it:

Note that older versions of Git LFS used .gitconfig rather than .lfsconfig.As of Git LFS version 1.1 .gitconfig has been deprecated, but support will not be dropped until LFS version 2.

Next, track some files types.For example, to have FITS and *.gz files tracked by Git LFS,

Add and commit the .lfsconfig and .gitattributes files to your repository.

You can then push the repo up to github with

We also recommend that you include a link to this documentation page in your README to help those who aren’t familiar with DM’s Git LFS.

In the repository’s README, we recommend that you include this section: