I can't seem to be able to set local python for a project, not even global python.
$ pyenv local 3.9.6
$ pyenv global 3.9.6
$ pyenv versions
system
* 3.9.6 (set by /home/cmap/c-map/.python-version)
In .python-version it is written 3.9.6
But when I type python -V I get 3.7.3 which is the original system installed python
What am I missing here?
I finally found what was missing. Had to add the following to .profile
export PYENV_ROOT="$HOME/.pyenv"
export PATH="$PYENV_ROOT/bin:$PATH"
Related
I have installed pyenv
After that I do exec $SHELL to restart the shell
However after I do this, this happens
pyenv versions
* system (set by /home/user/.pyenv/version)
3.9.16
:~$ pyenv global 3.9.16
:~$ python --version
Python 3.8.10
:-$ pyenv versions
system
* 3.9.16 (set by /home/aliaga/.pyenv/version)
So python does not change even though it shows as changed
When I open a new terminal this problem seems to disapear.
So I suppose the problem is with exec $SHELL. Why is not working?
I want to run a job on Slurm and my Python script needs the evaluate package which I have on my local machine. I don't know if I could change the Python path on the server to match the one on my local machine, and if I could I'm afraid I might break the system.
So I followed this answer, and included a requirements.txt file with just evaluate==0.1.2 in it, and I get even more errors:
load GCC/10.2.0 (PATH, MANPATH, INFOPATH, LIBRARY_PATH, LD_LIBRARY_PATH, STD COMP VARS)
load ROCM/5.1.1 (PATH, MANPATH, LD_LIBRARY_PATH, LIBRARY_PATH, C_INCLUDE_PATH)
Set INTEL compilers as MPI wrappers backend
load mkl/2018.4 (LD_LIBRARY_PATH)
load PYTHON/3.7.4 (PATH, MANPATH, LD_LIBRARY_PATH, LIBRARY_PATH, PKG_CONFIG_PATH, C_INCLUDE_PATH, CPLUS_INCLUDE_PATH, PYTHONHOME, PYTHONPATH)
/var/spool/slurmd/job216863/slurm_script: line 12: virtualenv: command not found
/var/spool/slurmd/job216863/slurm_script: line 16: /env/bin/activate: No such file or directory
ERROR: Could not find a version that satisfies the requirement evaluate==0.1.2 (from versions: none)
ERROR: No matching distribution found for evaluate==0.1.2
Traceback (most recent call last):
File "eval_comet.py", line 1, in <module>
from evaluate import load
ModuleNotFoundError: No module named 'evaluate'
Most of the time, the Python version on HPCs are old. My Uni's HPC cluster has Python 3.7. If you wish to create a Python virtual environment (not conda) with a newer version, then there is a trick.
Activate the Anaconda Module, some system uses Module load and some uses load depending on your organisation.
[s.1915438#sl2 ~]$ module load anaconda/2021.05
[s.1915438#sl2 ~]$ conda create -n surrogate python=3.8
Here I created a Conda environment named surrogate with Python 3.8. Here, you can choose any version of your choice. Now you can activate the Conda environment and check the Python version.
[s.1915438#sl2 ~]$ source activate surrogate
(modulus) [s.1915438#sl2 ~]$ which python
~/.conda/envs/surrogate/bin/python
(surrogate) [s.1915438#sl2 ~]$ python --version
Python 3.8.13
Now navigate to the directory where you want to install your Python virtual environment and install the virtual environment using the following command.
(surrogate) [s.1915438#sl2 s.1915438]$ mkdir modulus_pysdf
(surrogate) [s.1915438#sl2 s.1915438]$ cd modulus_pysdf/
(surrogate) [s.1915438#sl2 modulus_pysdf]$ python3 -m venv modulus_pysdf
Logout (ctrl + D) from the server to exit the Conda environment and then login again. Remember, in my case the path to the Python virtual environment was /scratch/s.1915438/modulus_pysdf.
This is how I will activate the Python virtual environment.
[s.1915438#sl2 ~]$ cd /scratch/s.1915438
[s.1915438#sl2 s.1915438]$ cd modulus_pysdf/
[s.1915438#sl2 modulus_pysdf]$ source modulus_pysdf/bin/activate
Now I can check the Python version and the path.
(modulus_pysdf) [s.1915438#sl2 modulus_pysdf]$ python --version
Python 3.8.13
(modulus_pysdf) [s.1915438#sl2 modulus_pysdf]$ which python
/scratch/s.1915438/modulus_pysdf/modulus_pysdf/bin/python
As usual, I can install any package using pip. For example, to install evaluate you can download it from PyPI
pip install evaluate
Or if you have a requirements.txt file then you can do this. See this for more details.
cat requirements.txt | grep -Eo '(^[^#]+)' | xargs -n 1 pip install
This seems pretty basic so why the no such command error:
$ pyenv shell
pyenv: no such command `shell`
https://github.com/pyenv/pyenv/blob/master/COMMANDS.md#pyenv-shell
pyenv shell switch your python locally (current shell session) to a specific version. You should run it by following the version you've already instlled.
To check the current python you are using and the versions installed:
pyenv version #return the version you are using
pyenv versions # return all versions installed
You can then set the python version for your current shell session
pyenv shell 3.6.4 #3.6.4 is one of the installed python version
I'm showing you the steps I use to create a virtualenv based on miniconda based on pyenv-virtualenv docs. Finally you will see that the virtualenv was created but I can't access to it.
1.0. Check my initial pyenv versions:
$ pyenv versions
* system (set by /home/oscar/.python-version)
2.7.9
3.5.1
1.1 Install miniconda:
$ pyenv install miniconda3-4.0.5
$ pyenv versions
* system (set by /home/oscar/.python-version)
2.7.9
3.5.1
miniconda3-4.0.5
1.2. Create the venvtest virtualenv based on miniconda:
$ pyenv virtualenv miniconda3-4.0.5 venvtest
$ pyenv versions
* system (set by /home/oscar/.python-version)
2.7.9
3.5.1
miniconda3-4.0.5
miniconda3-4.0.5/envs/venvtest
venvtest
When I want to check if the virtualenv was created, It doesn't show it. So I can't no access to it :(
$ pyenv virtualenvs
miniconda3-4.0.5 (created from /home/oscar/.pyenv/versions/miniconda3-4.0.5)
$ pyenv activate ... (autocompleting)
--help miniconda3-4.0.5 --unset
Please, I hope you can help me.
https://github.com/yyuu/pyenv-virtualenv/issues/178
A bit late answer. But a similar thing happened to me.
So I used
source /Users/<user_name>/Applications/anaconda3/bin/activate <env_name>
instead of
source activate <env_name>
My recommendation is to not install Miniconda or Anaconda (herein refereed to as *conda) via pyenv. Instead, download the installer from the applicable site and install it as follows.
Eg. I downloaded the installer from the website to ~/Downloads
% cd ~/Downloads
% ls | grep conda
Miniconda3-latest-Linux-x86_64.sh
Run the installer:
% bash Miniconda3-latest-Linux-x86_64.sh
Now most importantly, at the end of the installer when you are prompted Q) Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no], choose no.
Note: If you choose yes, Miniconda or Anaconda will deploy changes into your ~/.bashrc which will start up the *conda environment every time you open a bash session. This will corrupt pyenv.
After the installer is complete, add the following functions* to your ~/.bashrc:
function aconda {
eval "$(${HOME/miniconda3/bin/conda shell.bash hook)"
}
function dconda {
conda deactivate
}
* change the path to conda executable as required.
To launch the *conda environment, open any terminal and type aconda and to deactivate type dconda and that's it.
These instructions are for Linux but should port to Mac easily, not sure about windows though as I don't use it for my development.
I'm new to using the *conda environments and was surprised with the lack of simple instructions so I had to do a bunch of trial and error to get it so PyEnv, which I adore, working correctly. Hopefully this helps some others.
Now that it's 2022, it's time for a new answer...
It appears that the current method for installs of *conda via pyenv is to manage the conda virtual environment with conda's commands.
From the pyenv-virtualenv README:
"You can manage conda environments by conda create as same manner as standard Anaconda/Miniconda installations. To use those environments, you can use pyenv activate and pyenv deactivate... If conda is available, pyenv virtualenv will use it to create environment by conda create." See the Github repo README.md for a command walk-through.
I am on an Ubuntu machine, which has Python 2.7.6 as its default python. It also has Python 3.4.3, with both versions located in /usr/bin/.
I have downloaded virtualenv and virtualenvwrapper. I then downloaded the current version of Python, 3.5.1. In its directory I ran the following commands:
./configure
make
make test
sudo make altinstall
Python 3.5.1 is now installed in /usr/local/bin/.
I now run the following commands:
mkvirtualenv test1
mkvirtualenv test2 -p /usr/bin/python3
mkvirtualenv test3 -p /usr/local/bin/python3.5
Environment test1 successfully created with Python version 2.7.6, and environment test2 successfully created with Python version 3.4.3. However, test3 fails with the following error:
ImportError: No module named 'zlib'
I see mentioned that I need to have "zlib" installed when compiling python to begin with, though make test didn't seem to give any problems. Do I just need to download and compile zlib from www.zlib.net and recompile python3.5?
zlib is a built-in module for Python 3.5.
I think you just need re-compile Python 3.5...
Look that link for Python virtualenv :
https://www.reddit.com/r/linux4noobs/comments/3uwk76/help_using_python_in_linux/
Get python source and extract
wget https://www.python.org/ftp/python/3.5.0/Python-3.5.0.tgz
tar xvf Python-3.5.0.tgz
configure for local install
cd Python-3.5.0/
./configure --prefix=$HOME/python35
make
If it complains about missing dependencies, install them, make clean and repeat.
make install