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Several Python runtimes are available for use inside Toolforge:
python3: Python 3.5.3 (3.7.3 on kubernetes)
python: Python 2.7.13 (2.7.9 on kubernetes; deprecated)
Deprecating Python 2
Many legacy tools and code examples use Python 2.x as a runtime. Use of Python 3.x is encouraged for new code as Python 2.7 stopped being maintained in 2020. Toolforge will provide some amount of support for Python 2.x through 2022 because Debian will be supporting Python 2.7 in Debian 10 (buster). This support will only extend to critical security patches however.
If you don't want to create one tool for each Python task you need specific environment for, that's when virtual environment comes handy. The advantages of virtual environments don't end there. Apart from packages you can also maintain several separated git/svn repositories, several command line profiles, etc. You basically create this small virtual unit in your folder system, set up its environment to your needs and then reach its contents when you need it.
The python3 venv must be created in the same execution environment that the venv will be used from. This means:
- if the tool uses a a kubernetes backend (recommended), the venv should be boostrapped inside a container.
- if the tool uses a grid engine backend, the venv should be bootstrapped directly on a Toolforge bastion filesystem like
Read below for more concrete information.
For Kubernetes backend
This is for tools that use the Toolforge Kubernetes backend (recommended).
Kubernetes python webservices
Kubernetes python jobs
Follow these instructions if your are using the Toolforge Jobs framework.
You need to bootstrap your python venv from inside a job itself (similar to what happens in kubernetes webservices).
Create a script similar to this:
#!/bin/bash # create the venv python3 -m venv pyvenv # activate it source pyvenv/bin/activate # upgrade pip inside the venv and add support for the wheel package format pip install -U pip wheel # install some concrete packages pip install requests pip install yaml # or, install all packages from src/requirements.txt # pip install -r src/requirements.txt
Then run it in the desired python container, selecting the python version you prefer, example:
tools.mytool@tools-sgebastion-11:~$ ls bootstrap_venv.sh bootstrap_venv.sh tools.mytool@tools-sgebastion-11:~$ chmod ug+x bootstrap_venv.sh tools.mytool@tools-sgebastion-11:~$ toolforge-jobs run bootstrap-venv --command "cd $PWD && ./bootstrap_venv.sh" --image tf-python39 --wait tools.mytool@tools-sgebastion-11:~$ ls pyvenv pyvenv
Now you can run your python tool using this venv, example:
tools.mytool@tools-sgebastion-11:~$ cat src/mytool.py import requests r = requests.get('https://www.wikidata.org/wiki/Q1') print(r.status_code) tools.mytool@tools-sgebastion-11:~$ toolforge-jobs run mytool --command "pyvenv/bin/python src/mytool.py" --image tf-python39 tools.mytool@tools-sgebastion-11:~$ cat mytool.out 200
For Grid Engine backend
|Please consider migrating your tool into the Kubernetes backend.|
This is for tools that use the Toolforge Grid Engine backend (not recommended).
Grid Engine python webservice
Grid Engine python jobs
|Please consider migrating your python jobs to Toolforge Jobs framework.|
Follow these instructions if you are using the Grid Engine backend to run your jobs.
You can create your first virtual environment using:
$ python3 -mvenv my_venv
This will install package manager, some basic tools, commands and prerequisites, everything into your new little unit. Once you created one, let's use it and play with it:
$ source my_venv/bin/activate (my_venv) $ pip install my_dream_package==7.0.3 ...
Once you are happy with it, you can always leave using:
(my_venv) $ deactivate
This way you can create as many separated Python environments as you wish.
You can reach it again from the inside the same way any time you want. This is handy when you want to update it for example. But for scheduled tasks, you would have to create a batch file with multiple commands to reach it, use it and leave it.
Use venv with scheduled tasks
Since it is saved in a folder in your Toolforge space, you can always use it from the outside just like any other folder. Well, you can not alter it this way, but for scheduled tasks you usually don't need to:
$ jsub -N my_task -once -quiet my_venv/bin/python3 my_script
Use your venv everywhere
You can also use your virtual environment everywhere by default. You can activate it using
$ echo "source my_venv/bin/activate" >> .profile
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