Setting up LaminR¶

This guide provides more detailed instructions for how to set up {laminr}.

Installing {laminr}¶

The {laminr} package can be installed from CRAN:

install.packages("laminr")

Additional packages¶

Some functionality in {laminr} requires additional packages. To install all suggested dependencies use:

install.packages("laminr", dependencies = TRUE)

If you choose not to install all additional packages you will be prompted to do so as needed.

Installing the development version¶

The current development version of {laminr} can be installed from GitHub using:

if (!requireNamespace("laminr", quietly = TRUE)) {
  install.packages("remotes")
}
remotes::install_github("laminlabs/laminr")

This version may have bug fixes and new features but could also be unstable so is not recommended for most users.

Installing Python lamindb¶

Using {laminr} requires the Python lamindb package to be available. For most users, lamindb and other packages should be installed automatically as they are required. This is done using the {reticulate} package requirement system.

If you encounter problems importing lamindb or connecting to a LaminDB instance this is often caused by failing to find a valid Python environment. You can check which environment is being used with reticulate::py_config().

Forcing the automatic environment¶

If {reticulate} has detected another environment and you want to force it use the automatically created one, run Sys.setenv("RETICULATE_USE_MANAGED_VENV" = "yes") before loading {laminr} or any other package that uses {reticulate}.

Using another environment¶

In some cases you may prefer to use another Python environment. This may be because you use another R package which requires a Python module or you are already managing your own Python environment including lamindb.

Specifying another Python environment to use should be done before loading {laminr} (or {reticulate}) using one of these methods:

Loading another R package that sets the Python environment
Using reticulate::use_virtualenv(), reticulate::use_condaenv() or reticulate::use_python()
Setting the RETICULATE_PYTHON or RETICULATE_PYTHON_ENV environment variables

Details of the current Python environment can be viewed using reticulate::py_config(). For more information about setting the active Python environment see vignette("versions", package = "reticulate") (also available here).

Creating a lamindb environment¶

In previous version of {laminr} we recommended using the install_lamindb() function to create an environment with the correct dependencies. This function has now been deprecated and we recommend using the automatic requirement system instead.

Logging in to LaminDB¶

If you have not used LaminDB before you will need to login to access public instances. To do this you will need a user API key which you can get by logging in to LaminHub and going to your user settings.

You can then login with:

laminr::lamin_login(api_key = "your_api_key")

Switching users¶

If you have already given an API key for a user you can log in as them by giving the user name:

laminr::lamin_login(user = "user_handle")

Setting a default instance¶

Using import_module("lamindb") will connect to the current default LaminDB instance. The default instance can be set using:

laminr::lamin_connect("<owner>/<name>")

Note that this must be called before attempting to connect to a default instance and cannot be changed once the default instance is connected without first calling lamin_disconnect().