reticulate repl_python() failed on import while python interpreter succeeded

[fafesche]

Hi,
I used reticulate to install python 3.12:latest and configure a virtual environment. In that environment, I have installed spyder whose startup script is just a python script.

the main command to launch spyder is the following: from spyder.app.start import main

I tested two scenarios:
1] Use reticulate::repl_python(): copy this command and get:
_Python 3.12.7 (/home/fafesche/.myEnv/12_IAE-M1/bin/python)
Reticulate 1.39.0 REPL -- A Python interpreter in R.
Enter 'exit' or 'quit' to exit the REPL and return to R.

from spyder.app.start import main
Traceback (most recent call last):
File "", line 1, in
File "/home/fafesche/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
return _run_hook(name, _hook)
^^^^^^^^^^^^^^^^^^^^^^
File "/home/fafesche/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 96, in _run_hook
module = hook()
^^^^^^
File "/home/fafesche/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 120, in _hook
return find_and_load(name, import)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fafesche/.myEnv/12_IAE-M1/lib/python3.12/site-packages/spyder/app/start.py", line 22, in
import logging
File "/home/fafesche/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
return _run_hook(name, _hook)
^^^^^^^^^^^^^^^^^^^^^^
File "/home/fafesche/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 96, in _run_hook
module = hook()
^^^^^^
File "/home/fafesche/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 120, in hook
return find_and_load(name, import)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'logging'

2] Use python - from the environment - using source activate (under linux):
same command no error.

This failed under linux (mint) and under Windows (v10). I get the same error in both cases.

I also tried to launch the spyder script using reticulate::py_run_file() got the same error.

My py_config() is the following:
> py_config()
python: /home/fafesche/.myEnv/12_IAE-M1/bin/python
libpython: /home/fafesche/.pyenv/versions/3.12.7/lib/libpython3.12.so
pythonhome: /home/fafesche/.myEnv/12_IAE-M1:/home/fafesche/.myEnv/12_IAE-M1
version: 3.12.7 (main, Oct 21 2024, 16:36:21) [Clang 14.0.6 ]
numpy: /home/fafesche/.myEnv/12_IAE-M1/lib/python3.12/site-packages/numpy
numpy_version: 2.1.2

To configure my virtual env, I have used the environment variable WORK_HOME as documented to put the virtual environment into another directory than the default one.

The encountered error means that it is not possible to run spyder from the repl_python() of reticulate which could be cool when working with students :)

Thanks in advance,
Fabien

[t-kalinowski]

Hi, could you provide instructions I can follow to reproduce the error locally?

[fafesche]

Hi,
a minimal script which mimics what I did - perhaps incorrectly - is the following:

Sys.setenv(WORKON_HOME = "C:/IAEpython")
library(reticulate)
pver <- "3.12"
reticulate::install_python(version=pver)
myEnv.name <- "myEnv"
reticulate::virtualenv_create(myEnv.name, python = pver)
reticulate::use_virtualenv(myEnv.name)

fn.pkg_install <- function(name = "", my.env = "") {
  if (requireNamespace("reticulate", quietly = TRUE)) {
    if (!reticulate::py_module_available(name)) {
      reticulate::py_install(name, my.env)
      return(TRUE)
    }
  }
  return(FALSE)
}
pkgs <- c("pandas", "spyder")
res <- sapply(pkgs, fn.pkg_install, my.env = myEnv.name)
reticulate::repl_python()
# Enter from spyder.app.start import main
# -> ModuleNotFoundError: No module named 'logging' after a long trace

If I activate the python env using command-line then launch python - the one of the environment which is btw the only python installed in the system - i get no error from this import and thus spyder is perfectly working in that environment.
Thanks in advance,
Fabien