The Python environment used by zellkonverter for interfacing with the
anndata Python library (and H5AD files) is described by the dependencies
in .AnnDataDependencies. The zellkonverterAnnDataEnv variable is the
basilisk::BasiliskEnvironment() used by zellkonverter.
.AnnDataDependencies
zellkonverterAnnDataEnvA character vector containing the pinned versions of all Python packages in
zellkonverterAnnDataEnv.
A basilisk::BasiliskEnvironment() containing zellkonverter's AnnData
Python environment.
The .AnnDataDependencies variable 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 basilisk context. For example, we can simply combine this
vector with additional dependencies to create a basilisk environment with
Python package versions that are consistent with those in zellkonverter.
If you want to run code in the exact environment used by zellkonverter
this can be done using zellkonverterAnnDataEnv in combination with
basilisk::basiliskStart() and/or basilisk::basiliskRun(). Please refer to
the basilisk documentation for more information on using these
environments.
.AnnDataDependencies
#> [1] "anndata==0.7.6" "h5py==3.2.1" "hdf5==1.10.6" "natsort==7.1.1"
#> [5] "numpy==1.20.2" "packaging==20.9" "pandas==1.2.4" "scipy==1.6.3"
#> [9] "sqlite==3.35.5"
cl <- basilisk::basiliskStart(zellkonverterAnnDataEnv)
anndata <- reticulate::import("anndata")
basilisk::basiliskStop(cl)