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-1

I am using Pycharm for Python development. Code is running in Pycharm venv from where I want to call a bash script which activates and deactivates conda environments (this one: https://github.com/lykaust15/DeepSimulator).

So I need to deactivate the Pycharm venv when calling the script via subprocess.call(), as far as I understand. Otherwise I get errors. How do I do this?

My call is:

 result = subprocess.call([deppsim_path, "-i", fasta, "-c", "4",
 "-C", "1", "-n", "100",
 "-H", os.path.dirname(deppsim_path),
 "-o", tmp_path], shell=False)

EDIT:

Some of the errors:

/home/user/path/bin/venv/bin/python /home/user/path/bin/sim_seq.py
Pre-process input genome...
/home/user/path/bin/DeepSimulator/deep_simulator.sh: Zeile 207: deactivate: Datei oder Verzeichnis nicht gefunden
Pre-process input genome done!
Executing the preprocessing step...
Traceback (most recent call last):
 File "/home/user/path/bin/DeepSimulator/util/genome_sampling.py", line 5, in <module>
 import scipy.stats as st
ImportError: No module named scipy.stats

python pycharm subprocess virtualenv

share|improve this question

edited Mar 24 at 17:42

Michael

asked Mar 24 at 17:08

MichaelMichael

313320

add a comment | 

-1

I am using Pycharm for Python development. Code is running in Pycharm venv from where I want to call a bash script which activates and deactivates conda environments (this one: https://github.com/lykaust15/DeepSimulator).

So I need to deactivate the Pycharm venv when calling the script via subprocess.call(), as far as I understand. Otherwise I get errors. How do I do this?

My call is:

 result = subprocess.call([deppsim_path, "-i", fasta, "-c", "4",
 "-C", "1", "-n", "100",
 "-H", os.path.dirname(deppsim_path),
 "-o", tmp_path], shell=False)

EDIT:

Some of the errors:

/home/user/path/bin/venv/bin/python /home/user/path/bin/sim_seq.py
Pre-process input genome...
/home/user/path/bin/DeepSimulator/deep_simulator.sh: Zeile 207: deactivate: Datei oder Verzeichnis nicht gefunden
Pre-process input genome done!
Executing the preprocessing step...
Traceback (most recent call last):
 File "/home/user/path/bin/DeepSimulator/util/genome_sampling.py", line 5, in <module>
 import scipy.stats as st
ImportError: No module named scipy.stats

python pycharm subprocess virtualenv

share|improve this question

edited Mar 24 at 17:42

Michael

asked Mar 24 at 17:08

MichaelMichael

313320

add a comment | 

I am using Pycharm for Python development. Code is running in Pycharm venv from where I want to call a bash script which activates and deactivates conda environments (this one: https://github.com/lykaust15/DeepSimulator).

So I need to deactivate the Pycharm venv when calling the script via subprocess.call(), as far as I understand. Otherwise I get errors. How do I do this?

My call is:

 result = subprocess.call([deppsim_path, "-i", fasta, "-c", "4",
 "-C", "1", "-n", "100",
 "-H", os.path.dirname(deppsim_path),
 "-o", tmp_path], shell=False)

EDIT:

Some of the errors:

/home/user/path/bin/venv/bin/python /home/user/path/bin/sim_seq.py
Pre-process input genome...
/home/user/path/bin/DeepSimulator/deep_simulator.sh: Zeile 207: deactivate: Datei oder Verzeichnis nicht gefunden
Pre-process input genome done!
Executing the preprocessing step...
Traceback (most recent call last):
 File "/home/user/path/bin/DeepSimulator/util/genome_sampling.py", line 5, in <module>
 import scipy.stats as st
ImportError: No module named scipy.stats

python pycharm subprocess virtualenv

share|improve this question

edited Mar 24 at 17:42

Michael

asked Mar 24 at 17:08

MichaelMichael

313320

 result = subprocess.call([deppsim_path, "-i", fasta, "-c", "4",
 "-C", "1", "-n", "100",
 "-H", os.path.dirname(deppsim_path),
 "-o", tmp_path], shell=False)

/home/user/path/bin/venv/bin/python /home/user/path/bin/sim_seq.py
Pre-process input genome...
/home/user/path/bin/DeepSimulator/deep_simulator.sh: Zeile 207: deactivate: Datei oder Verzeichnis nicht gefunden
Pre-process input genome done!
Executing the preprocessing step...
Traceback (most recent call last):
 File "/home/user/path/bin/DeepSimulator/util/genome_sampling.py", line 5, in <module>
 import scipy.stats as st
ImportError: No module named scipy.stats

share|improve this question

edited Mar 24 at 17:42

Michael

asked Mar 24 at 17:08

MichaelMichael

313320

share|improve this question

edited Mar 24 at 17:42

Michael

asked Mar 24 at 17:08

MichaelMichael

313320

asked Mar 24 at 17:08

MichaelMichael

313320

asked Mar 24 at 17:08

MichaelMichael

313320

1 Answer
1

active

oldest

votes

1

You can always call a particular install of python, including virtual environments, using the full path to the python executable. So that's your answer. Use a full path to a python binary that is in the actual Python installation you want to use to run the subprocesses, and you won't involve any virtual environments in running the subprocesses.

As an example, here's what two Python binary paths look like on my system:

> which python
/usr/local/bin/python
> venv development
> which python
/Users/stevenjohnson/envs/development/bin/python

So /usr/local/bin/python is my actual Python 2.7 installation, and /Users/stevenjohnson/envs/development/bin/python is my "development" virtual environment. So if I run the main program in my virtual environment, but if I call /usr/local/bin/python in my subprocess call, The subprocess will run using the base Python 2.7 installation.

share|improve this answer

edited Mar 24 at 17:52

answered Mar 24 at 17:46

SteveSteve

3,9941728

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thanks! What confuses me: I am calling a bash script and no python script. How do I tell the subprocess that I want to use a specific Python path inside this bash script? I mean, my call will NOT be like: "/path/to/python script.py -p some paramter -s secondparamter"
  
  – Michael
  Mar 24 at 18:22
  
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  If you can't modify the bash script, then you really do need to modify the runtime environment, which I was hoping you could avoid. What you probably then need to do is cause the subprocess to run with its PATH environment variable set so that the right python version is found. Mostly what virtualenv does when you switch environments is manipulate the PATH environment variable. So you could just add the path to the python binary you want to use, minus the '/python' at the end, to the front of PATH.
  
  – Steve
  Mar 24 at 18:34
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Unfortunately, it seems that subprocess calls like check_call and check_output don't take a set of environment variables as input. You'd have to use Popen, which is more complicated. It takes environment variables. Another way to go would be to write your own bash script and call that. the bash script could then set the PATH properly before running the real bash script you want to run.
  
  – Steve
  Mar 24 at 18:40
  
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Calling a wrapper script with specific python path like this: result = subprocess.call(["/home/my/propper/python_path", "wrapper_script.py"]). If I call "which python" in the wrapper I still get the python path from the Pycharm venv. Driving me nuts...
  
  – Michael
  Mar 24 at 19:37
  
  

  
  
  
  

add a comment | 

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1

You can always call a particular install of python, including virtual environments, using the full path to the python executable. So that's your answer. Use a full path to a python binary that is in the actual Python installation you want to use to run the subprocesses, and you won't involve any virtual environments in running the subprocesses.

As an example, here's what two Python binary paths look like on my system:

> which python
/usr/local/bin/python
> venv development
> which python
/Users/stevenjohnson/envs/development/bin/python

So /usr/local/bin/python is my actual Python 2.7 installation, and /Users/stevenjohnson/envs/development/bin/python is my "development" virtual environment. So if I run the main program in my virtual environment, but if I call /usr/local/bin/python in my subprocess call, The subprocess will run using the base Python 2.7 installation.

share|improve this answer

edited Mar 24 at 17:52

answered Mar 24 at 17:46

SteveSteve

3,9941728

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thanks! What confuses me: I am calling a bash script and no python script. How do I tell the subprocess that I want to use a specific Python path inside this bash script? I mean, my call will NOT be like: "/path/to/python script.py -p some paramter -s secondparamter"
  
  – Michael
  Mar 24 at 18:22
  
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  If you can't modify the bash script, then you really do need to modify the runtime environment, which I was hoping you could avoid. What you probably then need to do is cause the subprocess to run with its PATH environment variable set so that the right python version is found. Mostly what virtualenv does when you switch environments is manipulate the PATH environment variable. So you could just add the path to the python binary you want to use, minus the '/python' at the end, to the front of PATH.
  
  – Steve
  Mar 24 at 18:34
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Unfortunately, it seems that subprocess calls like check_call and check_output don't take a set of environment variables as input. You'd have to use Popen, which is more complicated. It takes environment variables. Another way to go would be to write your own bash script and call that. the bash script could then set the PATH properly before running the real bash script you want to run.
  
  – Steve
  Mar 24 at 18:40
  
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Calling a wrapper script with specific python path like this: result = subprocess.call(["/home/my/propper/python_path", "wrapper_script.py"]). If I call "which python" in the wrapper I still get the python path from the Pycharm venv. Driving me nuts...
  
  – Michael
  Mar 24 at 19:37
  
  

  
  
  
  

add a comment | 

1

You can always call a particular install of python, including virtual environments, using the full path to the python executable. So that's your answer. Use a full path to a python binary that is in the actual Python installation you want to use to run the subprocesses, and you won't involve any virtual environments in running the subprocesses.

As an example, here's what two Python binary paths look like on my system:

> which python
/usr/local/bin/python
> venv development
> which python
/Users/stevenjohnson/envs/development/bin/python

So /usr/local/bin/python is my actual Python 2.7 installation, and /Users/stevenjohnson/envs/development/bin/python is my "development" virtual environment. So if I run the main program in my virtual environment, but if I call /usr/local/bin/python in my subprocess call, The subprocess will run using the base Python 2.7 installation.

share|improve this answer

edited Mar 24 at 17:52

answered Mar 24 at 17:46

SteveSteve

3,9941728

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thanks! What confuses me: I am calling a bash script and no python script. How do I tell the subprocess that I want to use a specific Python path inside this bash script? I mean, my call will NOT be like: "/path/to/python script.py -p some paramter -s secondparamter"
  
  – Michael
  Mar 24 at 18:22
  
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  If you can't modify the bash script, then you really do need to modify the runtime environment, which I was hoping you could avoid. What you probably then need to do is cause the subprocess to run with its PATH environment variable set so that the right python version is found. Mostly what virtualenv does when you switch environments is manipulate the PATH environment variable. So you could just add the path to the python binary you want to use, minus the '/python' at the end, to the front of PATH.
  
  – Steve
  Mar 24 at 18:34
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Unfortunately, it seems that subprocess calls like check_call and check_output don't take a set of environment variables as input. You'd have to use Popen, which is more complicated. It takes environment variables. Another way to go would be to write your own bash script and call that. the bash script could then set the PATH properly before running the real bash script you want to run.
  
  – Steve
  Mar 24 at 18:40
  
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Calling a wrapper script with specific python path like this: result = subprocess.call(["/home/my/propper/python_path", "wrapper_script.py"]). If I call "which python" in the wrapper I still get the python path from the Pycharm venv. Driving me nuts...
  
  – Michael
  Mar 24 at 19:37
  
  

  
  
  
  

add a comment | 

You can always call a particular install of python, including virtual environments, using the full path to the python executable. So that's your answer. Use a full path to a python binary that is in the actual Python installation you want to use to run the subprocesses, and you won't involve any virtual environments in running the subprocesses.

As an example, here's what two Python binary paths look like on my system:

> which python
/usr/local/bin/python
> venv development
> which python
/Users/stevenjohnson/envs/development/bin/python

So /usr/local/bin/python is my actual Python 2.7 installation, and /Users/stevenjohnson/envs/development/bin/python is my "development" virtual environment. So if I run the main program in my virtual environment, but if I call /usr/local/bin/python in my subprocess call, The subprocess will run using the base Python 2.7 installation.

share|improve this answer

edited Mar 24 at 17:52

answered Mar 24 at 17:46

SteveSteve

3,9941728

> which python
/usr/local/bin/python
> venv development
> which python
/Users/stevenjohnson/envs/development/bin/python

share|improve this answer

edited Mar 24 at 17:52

answered Mar 24 at 17:46

SteveSteve

3,9941728

answered Mar 24 at 17:46

SteveSteve

3,9941728

answered Mar 24 at 17:46

SteveSteve

3,9941728