[Python] Run external program inside a conda environment in R

I am trying to run stitchr in R. For programs that run in Python, I use reticulate. I create a conda environment named r-reticulate, where I want to install stitchr and run it.

I try the following:

if (!('r-reticulate' %in% reticulate::conda_list()[,1])){
reticulate::conda_create(envname = 'r-reticulate', packages = 'python=3.10')
}
reticulate::use_condaenv('r-reticulate')
reticulate:y_install("stitchr", pip = TRUE)

system("stitchr -h") # this does not work


But obviously enough, the system() call does not work, with the message error in running command.

What would be the right way to do this?

I had success in the past with anndata, for example. But this is an R package wrapper, so I can just do:

reticulate::use_condaenv('r-reticulate')
reticulate:y_install("anndata", pip = TRUE)

data_h5ad <- anndata::read_h5ad("file.h5ad")


How can I approach the stitchr case?

EDIT:

So I retrieved stitchr.py location during the package installation: /usr/local/Caskroom/miniconda/base/envs/r-reticulate/lib/python3.10/site-packages/Stitchr/stitchr.py

I tried all the following but nothing works (see error messages):

pyloc="/usr/local/Caskroom/miniconda/base/envs/r-reticulate/lib/python3.10/site-packages/Stitchr/stitchr.py"
reticulate::source_python(pyloc)

Error in py_run_file_impl(file, local, convert) : ImportError: attempted relative import with no known parent package Run reticulate:y_last_error() for details.
​

reticulate:y_run_file(pyloc)

Error in py_run_file_impl(file, local, convert) : ImportError: attempted relative import with no known parent package Run reticulate:y_last_error() for details.
​

reticulate:y_run_string(paste(pyloc, "-h"))

Error in py_run_string_impl(code, local, convert) : File "", line 1 /usr/local/Caskroom/miniconda/base/envs/r-reticulate/lib/python3.10/site-packages/Stitchr/stitchr.py -h SyntaxError: invalid syntax Run reticulate:y_last_error() for details.
​

I am absolutely clueless on how to proceed here.

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