AnnData-Environment.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/basilisk.R
\docType{data}
\name{AnnData-Environment}
\alias{AnnData-Environment}
\alias{.AnnDataVersions}
\alias{AnnDataDependencies}
\alias{zellkonverterAnnDataEnv}
\title{AnnData environment}
\format{
For \code{.AnnDataVersions} a character vector containing allowed \strong{anndata}
version strings.
}
\usage{
.AnnDataVersions

AnnDataDependencies(version = .AnnDataVersions)

zellkonverterAnnDataEnv(version = .AnnDataVersions)
}
\arguments{
\item{version}{A string giving the version of the \strong{anndata} Python library
to use. Allowed values are available in \code{.AnnDataVersions}. By default the
latest version is used.}
}
\value{
For \code{AnnDataDependencies} a character vector containing the pinned versions
of all Python packages to be used by \code{zellkonverterAnnDataEnv()}.

For \code{zellkonverterAnnDataEnv} a \code{\link[basilisk:BasiliskEnvironment-class]{basilisk::BasiliskEnvironment()}} containing
\strong{zellkonverter}'s AnnData Python environment.
}
\description{
The Python environment used by \strong{zellkonverter} for interfacing with the
\strong{anndata} Python library (and H5AD files) is described by the dependencies
in returned by \code{AnnDataDependencies()}. The \code{zellkonverterAnnDataEnv()}
functions returns the \code{\link[basilisk:BasiliskEnvironment-class]{basilisk::BasiliskEnvironment()}} containing these
dependencies used by \strong{zellkonverter}. Allowed versions of \strong{anndata} are
available in \code{.AnnDataVersions}.
}
\details{
\subsection{Using Python environments}{

When a \strong{zellkonverter} is first run a conda environment containing all of
the necessary dependencies for that version with be instantiated. This will
not be performed on any subsequent run or if any other \strong{zellkonverter}
function has been run prior with the same environment version.

By default the \strong{zellkonverter} conda environment will become the shared R
Python environment if one does not already exist. When one does exist (for
example when a \strong{zellkonverter} function has already been run using a
a different environment version) then a separate environment will be used.
See \code{\link[basilisk:basiliskOptions]{basilisk::setBasiliskShared()}} for more information on this behaviour.
Note the when the environment is not shared progress messages are lost.
}

\subsection{Development}{

The \code{AnnDataDependencies()} function is exposed for use by other package
developers who want an easy way to define the dependencies required for
creating a Python environment to work with AnnData objects, most typically
within a \strong{basilisk} context. For example, we can simply combine this
vector with additional dependencies to create a \strong{basilisk} environment with
Python package versions that are consistent with those in \strong{zellkonverter}.

If you want to run code in the exact environment used by \strong{zellkonverter}
this can be done using \code{zellkonverterAnnDataEnv()} in combination with
\code{\link[basilisk:basiliskStart]{basilisk::basiliskStart()}} and/or \code{\link[basilisk:basiliskStart]{basilisk::basiliskRun()}}. Please refer to
the \strong{basilisk} documentation for more information on using these
environments.
}
}
\examples{
.AnnDataVersions

AnnDataDependencies()
AnnDataDependencies(version = "0.7.6")

cl <- basilisk::basiliskStart(zellkonverterAnnDataEnv())
anndata <- reticulate::import("anndata")
basilisk::basiliskStop(cl)
}
\author{
Luke Zappia

Aaron Lun
}
\keyword{datasets}