I use a bash script to call several python scripts. I installed the bash plugin for PyCharm. I can run the script, but I don't see stdout during runtime, even though I see it after everything finished. How can I make that visible during runtime?
Without all of the required information, my guess would be that this is due to Python buffering its output, which is its default behavior. You can easily disable this by passing python the -u flag or by setting the PYTHONUNBUFFERED environment variable.
This is described in this SO answer.
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Question
My default Python is 2.7, but I have a script that requires Python 3.4. I am trying to create a function in R that will:
Switch to Python 3.4
Run this script
Switch back to Python 2.7
Import results into R
To switch between Python versions, I use my cluster's "dotkit" system, like this:
use Python-2.7
use Python-3.4
"use" is a bash function that is imported in my .bashrc file. It sets all of my path variables (PATH, LIBRARY_PATH, LD_LIBRARY_PATH, CPATH, C_INCLUDE_PATH, etc). The problem is that when I try to call this function in R, I get the following error:
system('use Python-3.4')
sh: use: command not found
It seems like this is a problem with my PATH. I am using the correct shell:
system('echo $SHELL')
/bin/bash
My $PATH variable also looks good. However, when I create a script that essentially does the same thing:
load_py34.sh:
#!/bin/bash
source ~/.bashrc
use Python-3.4
and call this script through R, then it actually runs, but for some reason, it doesn't change my python version within R. (I have verified that this script works from the command line.)
> R
> system('python --version')
Python 2.7.1
> system('sh load_py34.sh')
Prepending: R-3.4 (ok)
> system('python --version')
Python 2.7.1
So I'm a little confused, but if anyone can help, I would really appreciate it.
Suggested fixes
When I combine them into a single command, I still have the same problem:
> system("sh load_py34.sh; python --version")
Prepending: Python-3.4 (already loaded)
Python 2.7.1
When I try calling bash directly, I still have a problem with the PATH:
> system("bash -c 'use Python-3.4; python --version'")
bash: use: command not found
Python 2.7.1
.bashrc is only loaded for interactive bash sessions.
"use" is a bash function that is imported in my .bashrc file. It sets
all of my path variables.
If set via export, the environment of the calling process will not be altered.
export [-fn] [name[=word]] ... The supplied names are marked for automatic export to the environment of subsequently executed commands. (https://man7.org/linux/man-pages/man1/bash.1.html)
Child processes do not normally have access to the parent process' environment. (This poses a problem because system() creates a sub-process.)
The source and . built-ins execute the commands in the current shell environment, hence why your script works.
Other commands (executables, non-shell-builtins) are executed by the fork-and-exec mechanism, whereby the executing shell process forks, creating a child process with an identical environment and state. This new child process is the process in which the command is executed. Changes to the environment of that process are not replicated to the parent's environment.
This means that you will not be able to rely on system('...') to modify the environment of the R process, or that of processes spawned by subsequent system() invocations.
In a single invocation to system(), you can construct a command-line that changes the environment of the spawned shell like so:
bash -c 'source ~/.bashrc; use Python-3.4; python --version'
Mind you, ~/.bashrc is not really the best place to put this functionality (might be subjective).
When you call system() it uses /bin/sh, not /bin/bash. sh doesn't read your .bashrc file when it starts up, so it does not know any of the functions you've defined there.
To use the function from your .bashrc, you must get bash to run it instead:
system("bash -c 'use Python-3.4; python --version'")
Edit: placement of closing single quote.
I have a tcsh shell script that sets up all the necessary environment including PYTHONPATH, which then run an executable at the end of it. I also have a python script that gets sent to the shell script as an input. So the following works perfectly fine when it is ran from Terminal:
path to shell script path to python script
Now, the problem occurs when I want to do the same thing from a subprocess. The python script fails to be ran since it cannot find many of the modules that's already supposed to be set via the shell script. And clearly, the PYTHONPATH ends up having many missing paths compared to the parent environment the subprocess was ran from or the shell script itself! It seems like the subprocess does not respect the environment the shell script sets up.
I've tried all sorts of things already but none help!
cmd = [shell_script_path, py_script_path]
process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=os.environ.copy())
It makes no difference if env is not given either!
Any idea how to fix this?!
Knowing the subprocess inherits all the parent process environment and they are supposed to be ran under same environment, making the shell script to not setup any environment, fixed it.
This solves the environment being retained, but now the problem is, the process just hangs! (it does not happen when it is ran directly from shell)
I have the virutalenv created and installed. I have also installed jsnapy tool inside my virutal env.
This is the script that we are using:
Filename : venv.py
import os
os.system('/bin/bash --rcfile ~/TestAutomation/End2EndAutomation/bin/activate')
os.system('End2EndAutomation/bin/jsnapy')
ubuntu#server:~/TestAutomation$ python venv.py
(End2EndAutomation) ubuntu#sdno-server:~/TestAutomation$ ^C
We need to know, is how we can get into virutalenv, run a command and deactivate it using python script?
[EDIT1]
i used the code given in the comment. its just entering virutal env. When i issue exit, its running jsnapy command.
ubuntu#server:~/TestAutomation$ python venv.py
(End2EndAutomation) ubuntu#server:~/TestAutomation$ exit
exit
usage:
This tool enables you to capture and audit runtime environment of
networked devices running the Junos operating system (Junos OS)
Tool to capture snapshots and compare them
It supports four subcommands:
--snap, --check, --snapcheck, --diff
1. Take snapshot:
jsnapy --snap pre_snapfile -f main_configfil
Each call to os.system() will create a new bash instance and terminate the previous one. To run all the commands in one bash instance you could put all your commands inside a single bash script and call that from os.system()
run.sh
source ~/TestAutomation/End2EndAutomation/bin/activate
End2EndAutomation/bin/jsnapy
deactivate
Python
os.system('source run.sh')
Alternatively, you could write a multiline bash command, as long as it's all in one os.system() call.
Two successive calls to os.system() will create two independent processes, one after the other. The second will run when the first finishes. Any effects of commands executed in the first process will have been forgotten and flushed when the second runs.
You want to run the activation and the command which needs to be run in the virtualenv in the same process, i.e. the same single shell instance.
To do that, you can use bash -c '...' to run a sequence of commands. See below.
However, a better solution is to simply activate the virtual environment from within Python itself.
p = os.path.expanduser('~/TestAutomation/End2EndAutomation/bin/activate_this.py')
execfile(p, dict(__file__=p))
subprocess.check_call(['./End2EndAutomation/bin/jsnapy'])
For completeness, here is the Bash solution, with comments.
import subprocess
subprocess.check_call(['bash', '-c', """
. ~/TestAutomation/End2EndAutomation/bin/activate
./End2EndAutomation/bin/jsnapy"""])
The preference for subprocess over os.system is recommended even in the os.system documentation.
There is no need to explicitly deactivate; when the bash command finishes, that will implicitly also deactivate the virtual environment.
The --rcfile trick is a nice idea, but it doesn't work when the shell you are calling isn't interactive.
subprocess.run('export FOO=BAR', shell=True)
This simply doesn't work, and I have no idea why.
All I am trying to do I set an environment variable from my python (3.5.1) script, and when I run the above line, nothing happens. No errors are raised, and when I check the environment variable myself, it has not been set.
Other shell commands with subprocess.run() do work, such as ls and pwd, but not export.
.run() was added in Python 3.5 (in case you didn't recognise it), but I have also tried the above line with .call() and .Popen(), with no change in results.
I am aware that I can set environment variables in python with os.environ['FOO'] = "BAR", but I will be using shell commands a lot in my project, and I expect that I will need to string multiple commands together, which will make using export easier than os.environ.
My project will run on Linux, which is what my machine is running on.
It works fine; however, the variable setting only exists in the subprocess. You cannot affect the environment of the local process from a child.
os.environ is the correct solution, as it changes the environment of the local process, and those changes will be inherited by any process started with subprocess.run.
You can also use the env argument to run:
subprocess.run(["cmdname", "arg1", "arg number 2"], env=dict(FOO='BAR', **os.environ))
This runs the command in a modified environment that includes FOO=BAR without modifying the current environment.
In my build (I'm using Linux) I need to call a Python script and set some env variables. I need these variables to be set even after I exit the script. I am able to set it using os.environ within the script but whenever I exit the script and try to see if the env variable is set from the terminal (echo $myenv) - I get nothing.
I am new to Python and did quite a bit googling to figure this out. However, I am not quite sure if it's possible. I tried using the subprocess:
subprocess.call('setenv myenv 4s3', shell=True)
Also tried using os.system:
os.system("setenv myenv 4s3")
So far, I didn't succeed.
You cannot set environment variables from a child process and have them be visible in the parent process. Every process gets its own copy of the environment, and changes do not propagate upwards.
What you could do is have the Python script print the settings it wants to change and have the outside shell execute the appropriate commands.
Maybe if you find some equivalent function like c vfork for Python.
When you vfork, both processes share memory space so, you might overwrite environment variables in parent process from child process.
Warning: vfork has many security issues, and therefore not recommended. Just use it if you are desperate.