conda subprocess

Run a subprocess in a different conda environment.

Installation

conda_subprocess is available on PyPI and conda-forge:

pip install conda_subprocess

or

conda install -c conda-forge conda_subprocess

The @conda decorator additionally requires executorlib, which can be installed via the executorlib extra:

pip install conda_subprocess[executorlib]

A working conda (or mamba) installation is required at runtime - conda_subprocess locates it via the CONDA_EXE environment variable, which is set automatically inside an activated conda environment.

Example

Create a new conda environment - in this example a conda environment for Python 3.12:

conda create -n py312 python=3.12 

Subprocess Interface

conda_subprocess mirrors the subprocess module (call(), check_call(), check_output(), run(), Popen()) and adds two keyword arguments to all of them to select the target environment:

• prefix_name - the name of the target conda environment, e.g. "py312"
• prefix_path - the absolute path of the target conda environment, e.g. "/home/user/mambaforge/envs/py312"

If neither is given, the currently active conda environment is used, just like with a plain subprocess call.

Open a python shell in your base environment where conda_subprocess is installed and execute python --version in the py312 environment:

from conda_subprocess import check_output
check_output("python --version", prefix_name="py312")
>>> b'Python 3.12.1\n'

Alternatively, the environment can be specified with the absolute path:

from conda_subprocess import check_output
check_output("python --version", prefix_path="/Users/janssen/mambaforge/envs/py312")
>>> b'Python 3.12.1\n'

As expected the process for the arguments for the subprocess call can also be defined as list:

from conda_subprocess import check_output
check_output(["python", "--version"], prefix_path="/Users/janssen/mambaforge/envs/py312")
>>> b'Python 3.12.1\n'

In addition to the check_output() function also the check_call() function is implemented:

from conda_subprocess import check_call
check_call("python --version", prefix_name="py312")
>>> Python 3.12.1
>>> 0

As well as the call() function:

from conda_subprocess import call
call("python --version", prefix_name="py312")
>>> Python 3.12.1
>>> 0

And the run() function:

from conda_subprocess import run
run("python --version", prefix_name="py312")
>>> Python 3.12.1
>>> CompletedProcess(args=['/bin/bash', '/var/folders/9p/rztyv06d0xv4h26cyv8nrw3m0000gq/T/tmpm8b8i0r3'], returncode=0)

As the CompletedProcess arguments illustrate conda_subprocess is internally writing the commands to a temporary file for execution, to guarantee the conda environment is correctly activated.

For interactive communication conda_subprocess implements the Popen interface:

from subprocess import PIPE
from conda_subprocess import Popen
process = Popen(["python", "--version"], stdout=PIPE, prefix_name="py312")
process.communicate()
>>> (b'Python 3.12.1\n', None)

Decorator

In analogy to the subprocess interface the conda_subprocess also introduces the @conda decorator to execute python functions in a separate conda environment:

from conda_subprocess.decorator import conda

@conda(prefix_name="py312")
def add_function(parameter_1, parameter_2):
    return parameter_1 + parameter_2

add_function(parameter_1=1, parameter_2=2)
>>> 3

Remarks

• The shell parameter and the env parameter are not supported in Popen() and all derived methods.
• The pipesize parameter and the process_group parameter were removed for compatibility with python 3.9.

Documentation

• conda_subprocess
  • Installation
  • Example
  • Remarks
• demo
  • Setup
  • Subprocess interface
  • The conda decorator
  • Remarks
  • Cleanup
• Interface