Setting env in CommandFunction overrides PATH env var

[niansong1996]

According to the examples here, the field env can be used to pass in env variables:

By default, the function hides stdout and returns it at the end:

import submitit
function = submitit.helpers.CommandFunction(["which", "python"])  # commands must be provided as a list!
print(function())  # This returns your python path (which you be inside your virtualenv)
# for me: /private/home/jrapin/.conda/envs/dfconda/bin/python
Some useful parameters of the CommandFunction class:

cwd: to choose from which directory the command is run.
env: to provide specific environment variables.
verbose: set to False if you do not want any logging.
As an experimental feature, you can also provide arguments when calling the instance:

However, it seems that adding this field would lead to the execution failure due to the job unable to find the executable.

After some digging, I found that because we directly pass in env for the subprocess.Popen as in here:

with subprocess.Popen(
            full_command,
            stdout=subprocess.PIPE,
            stderr=subprocess.PIPE,
            shell=False,
            cwd=self.cwd,
            env=self.env,
        ) as process:

But according to the docs of Python, this could easily lead to such error as env will override all the env variables, including PATH:

Resolving the path of executable (or the first item of args) is platform dependent. For POSIX, see [os.execvpe()]
(https://docs.python.org/3/library/os.html#os.execvpe), and note that when resolving or searching for the executable path, cwd 
overrides the current working directory and env can override the PATH environment variable.

So I would suggest instead of simply doing evn=self.env, we should dump all the current env vars and only override the ones that presented in env. Or at least adding a warning in the examples to note that this could lead to overridden of other env vars like PATH.