[BUG] conda activation crashes standalone execution

[francois-rozet]

Issue description

In the standalone backend on Unix systems, the os.system(command) used here

awflow/awflow/backends/standalone/executor.py

Lines 53 to 60 in 1fcf255

	if node.tasks > 1:
	for task_index in range(node.tasks):
	task_command = command + ' ' + str(task_index)
	return_code = os.system(task_command)
	if return_code != 0:
	break
	else:
	return_code = os.system(command)

actually calls /bin/sh. For some OS, like Ubuntu, sh links to dash which does not support the scripting features required by conda activations. This results in runtime errors like

sh: 5: /home/username/miniconda3/envs/envname/etc/conda/activate.d/activate-binutils_linux-64.sh: Syntax error: "(" unexpected

Proposed solution

A solution would be to change the shell with which the commands are called. This is possible thanks to the subprocess package. A good default would be bash as almost all Unix systems use it.

    if node.tasks > 1:
        for task_index in range(node.tasks):
            task_command = command + ' ' + str(task_index)
            return_code = subprocess.call(task_command, shell=True, executable='/bin/bash')
    else:
        return_code = subprocess.call(command, shell=True, executable='/bin/bash')

One could also add a way to change this default. Additionally, wouldn't it be better to launch the tasks as background jobs for the standalone backend (simply add & at the end of the command) ?

[JoeriHermans]

Fixed in next version with breaking API changes. https://github.com/JoeriHermans/awflow/tree/dawgz