Installing python packages in a virtual environment via bash script and pip - python

To clarify I have read these questions already:
How to source virtualenv activate in a Bash script
How to activate python virtual environment by shell script
Activating virtualenv in Bash script not working
Bash: How _best_ to include other scripts?
My goal is to create a script that will automate the process of installing several (roughly 27) python packages via pip in a virtual environment using (preferably) a bash script.
So far in bash scripts I have tried:
source env/bin/activate
pip install numpy Scipy ez_setup
As well as
activate() {
. ../.env/bin/activate
}
activate
pip install numpy Scipy ez_setup
Neither of which works. What is the best way to approach this problem given it must be executable as part of a larger bash (or python) script?

Update: So I figured out my problem. The solution for me is to force the script to pull from the correct pip directory with
/env/bin/pip install numpy Scipy ez_setup
The second part is to break down the install instructions into each line because the registries were not being updated properly.

Related

Create fresh python venv while local have some package installed [duplicate]

I am very new at command line usage. I am using python 3.7.2, Bash and VSCode Integrated Terminal. I am trying to create a virtual environment using venv and following python documentation:
https://docs.python.org/3/tutorial/venv.html#creating-virtual-environments
The command to use is this one:
$ python3 -m venv test-env
and I get:
bash: python3: command not found
Later I have found a similar answer in an stackoverflow post:
How to create and activate virtual environment in windows 10 using bash command
And I use the command:
py -m virtualenv test-env
and I get this:
No module named virtualenv
I am very new using the command line so i don´t really know what is going on and how to work it around.
Hi i can see that you are using two different tools to create your environment.
Those are "venv" and "virtualenv".
Venv is a library that already comes with your python installation.
Virtualenv is an external one.
I had the same problem before and the solution is very simple.
I recommend you to stick with venv because it works pretty ok and you don´t need to do extra job installing external libraries.
So for solving your problem the Bash Shell is telling you that the command Python3 has not been found.
So try instead just:
python -m venv test-env
Sometimes Python documentation is not accurate enough and I know when you start using commands, accuracy in the sintax is extremely important.
Try this steps,it'll helped you:
First, make a directory :
mkdir testing
Then, moved to this directory named testing :
cd testing
When you type following command in this directory:
python3 -m venv env (OR, python -m venv env)
You got error like :
The virtual environment was not created successfully because ensurepip is not
available. On Debian/Ubuntu systems, you need to install the python3-venv
package using the following command.
apt install python3.8-venv
Type the following command but before that keep an eye on the version of python you installed on the machine; in my case its python3.8
sudo apt install python3.8-venv
Now, we can create a virtual environment and store its tools in the "bhandari" folder .
python3 -m venv bhandari
Note: you can named this "bhandari" folder; anyname you like( Standard practice is to name it "env" ...)
Now to activate your virtual environment, from the directory of your folder, type the following command this will activate our virtual environment in the “bhandari” folder
source bhandari/bin/activate
If you have successfully activated your virtual environment, you should see the (bhandari) word indicating that we are working in a virtual environment.
After this, we can install anything that will be isolated from the rest of the system....

With Mamba, pypy cannot find modules installed using pip?

I'm testing using pypy for speeding up the execution time of a Python script I wrote. To install the dependencies of the script, I used both pip (some modules I need are not available via anaconda) and Mamba.
When I run the script using pypy script.py, I get an error message saying that the modules I installed using pip are not found (example: ImportError: No module named presidio_analyzer). Why does this happen? And do you have suggestions on how to fix this?
I'm running the tests on OSX. I installed Mamba using micromamba.
To make this work you should:
Create a conda environment that contains python and pip.
Activate the conda environment
Run pip install ...
Run pypy script.py
When you run pip install ... using an instance of pip that is part of your conda environment, then the python packages also get installed into the conda environment.
Your conda environment should also be activated when you run pypy script.py so that the python binary within the conda environment is utilized along with the packages you pip installed.

Django, Python 3.4, CentOS 6.4, virtualenv: ImportError: No module named Django

I am running a Linux server with CentOS 6.4. I need to run Django 1.8.2 with Python 3.4. I already have pip and virtualenv installed, and I am currently in a virtual env. I tried to install Django using the pip command but it has installed it in the Python 2.6 site packages, so when I run a python 3 interpreter and type import django I get ImportError: No module named Django. I need to find a way to install Django with Python 3.4. I do not have pip3 and cannot figure out how to install it. All of the help I have found on other sites deals with Ubuntu systems and do not work for me.
EDIT:
which pip outputs ~/MAP_VIO/bin/pip
which python3 outputs /usr/local/bin/python3
which python outputs ~/MAP_VIO/bin/python
MAP_VIO is my virtual env, so it looks like I don't have python 3 in my virtual env? If that's my problem, how do I solve it?
It seems you installed a Python 2 virtual environment. To get a Python 3 environment you need to do
virtualenv -p python3 venv_path
The -p flag tells it which interpreter you want. That should install both pip3 and setuptools into the environment. If you really don't have pip3 (which virtualenv can copy into the environment) and can't install it system wide for some reason, try doing
easy_install pip
inside the virtual environment. That should be able to fetch and install the right pip for the virtual environment you're in.
Please see that you are using the correct, virtualenv'ed, pip command.
You can verify this by running command:
which pip
... and it will tell you the absolute path of pip command (and Python installation) you are using.
Also do the same for python command you are trying to run Django with. If necessary edit your question and add the relevant information about virtualenv, python and pip paths.

Install python libraries using shell script

I'm very new in python, sorry if my question is very basic.I have a shell script that using it to run a .py file on a cluster. Here is my shell script:
#!/bin/bash
module add python/2.6
python Myfile.py
Python has been installed on the cluster but some of the libraries and packages needs to be installed. For example, I need to install Numpy package, is there any way that I can do it inside my shell script or my .py file before "import" it?
Thanks
For this (and similar) use case, I would recommend a combination of pip and virtualenv.
You would install pip into your system Python install (i.e. sudo apt-get install python-pip), and then install virtualenv via pip, i.e. pip install virtualenv).
You can then create a specific virtualenv for this project. This represents a sandboxed environment with specific versions of libraries that are specified traditionally through a requirements file (using the -r option), but can also be specified individually through the command line.
You would do this via command like virtualenv venv_test, which will create a virtualenv directory named venv_test in the current directory. You can then run pip from that virtualenv's bin dir to install packages.
For example, to install the flask package in that virutalenv, you would run:
venv_test/bin/pip install flask
You can then either run source venv_test/bin/activate to put the current shell into the virtualenv's, or invoke a script directly from the virtualenv's interpreter, i.e.:
venv_test/bin/python foo.py
Here's link to a virtualenv introduction for some additional details/steps.

Using Python 3 in virtualenv

Using virtualenv, I run my projects with the default version of Python (2.7). On one project, I need to use Python 3.4.
I used brew install python3 to install it on my Mac. Now, how do I create a virtualenv that uses the new version?
e.g. sudo virtualenv envPython3
If I try:
virtualenv -p python3 test
I get:
Running virtualenv with interpreter /usr/local/bin/python3
Using base prefix '/usr/local/Cellar/python3/3.4.0_1/Frameworks/Python.framework/Versions/3.4'
New python executable in test/bin/python3.4
Also creating executable in test/bin/python
Failed to import the site module
Traceback (most recent call last):
File "/Users/user/Documents/workspace/test/test/bin/../lib/python3.4/site.py", line 67, in <module>
import os
File "/Users/user/Documents/workspace/test/test/bin/../lib/python3.4/os.py", line 634, in <module>
from _collections_abc import MutableMapping
ImportError: No module named '_collections_abc'
ERROR: The executable test/bin/python3.4 is not functioning
ERROR: It thinks sys.prefix is '/Users/user/Documents/workspace/test' (should be '/Users/user/Documents/workspace/test/test')
ERROR: virtualenv is not compatible with this system or executable
simply run
virtualenv -p python3 envname
Update after OP's edit:
There was a bug in the OP's version of virtualenv, as described here. The problem was fixed by running:
pip install --upgrade virtualenv
Python 3 has a built-in support for virtual environments - venv. It might be better to use that instead. Referring to the docs:
Creation of virtual environments is done by executing the pyvenv
script:
pyvenv /path/to/new/virtual/environment
Update for Python 3.6 and newer:
As pawciobiel correctly comments, pyvenv is deprecated as of Python 3.6 and the new way is:
python3 -m venv /path/to/new/virtual/environment
I'v tried pyenv and it's very handy for switching python versions (global, local in folder or in the virtualenv):
brew install pyenv
then install Python version you want:
pyenv install 3.5.0
and simply create virtualenv with path to needed interpreter version:
virtualenv -p /Users/johnny/.pyenv/versions/3.5.0/bin/python3.5 myenv
That's it, check the version:
. ./myenv/bin/activate && python -V
There are also plugin for pyenv pyenv-virtualenv but it didn't work for me somehow.
Install prerequisites.
sudo apt-get install python3 python3-pip virtualenvwrapper
Create a Python3 based virtual environment. Optionally enable --system-site-packages flag.
mkvirtualenv -p /usr/bin/python3 <venv-name>
Set into the virtual environment.
workon <venv-name>
Install other requirements using pip package manager.
pip install -r requirements.txt
pip install <package_name>
When working on multiple python projects simultaneously it is usually recommended to install common packages like pdbpp globally and then reuse them in virtualenvs.
Using this technique saves a lot of time spent on fetching packages and installing them, apart from consuming minimal disk space and network bandwidth.
sudo -H pip3 -v install pdbpp
mkvirtualenv -p $(which python3) --system-site-packages <venv-name>
Django specific instructions
If there are a lot of system wide python packages then it is recommended to not use --system-site-packages flag especially during development since I have noticed that it slows down Django startup a lot. I presume Django environment initialisation is manually scanning and appending all site packages from the system path which might be the reason. Even python manage.py shell becomes very slow.
Having said that experiment which option works better. Might be safe to just skip --system-site-packages flag for Django projects.
virtualenv --python=/usr/bin/python3 <name of env>
worked for me.
This is all you need, in order to run a virtual environment in python / python3
First if virtualenv not installed, run
pip3 install virtualenv
Now Run:
virtualenv -p python3 <env name> # you can specify full path instead <env_name> to install the files in a different location other than the current location
Sometime the cmd virtualenv fails, if so use this:
python3 -m virtualenv <env_name> # you can specify full path instead <env_name> to install the files in a different location other than the current location
Now activate the virtual env:
source <env_name>/bin/activate
Or:
source `pwd`/<env_name>/bin/activate
Now run
which python
You should see the full path to your dir and <env_name>/bin/python suffix
To exit the virtualenv, run:
deactivate
To troubleshoot Python location got to here
You can specify specific Version of Python while creating environment.
It's mentioned in virtualenv.py
virtualenv --python=python3.5 envname
In some cases this has to be the full path to the executable:
virtualenv --python=/Users/username/.pyenv/versions/3.6.0/bin/python3.6 envname
How -p works
parser.add_option(
'-p', '--python',
dest='python',
metavar='PYTHON_EXE',
help='The Python interpreter to use, e.g., --python=python3.5 will use the python3.5 '
'interpreter to create the new environment. The default is the interpreter that '
'virtualenv was installed with (%s)' % sys.executable)
I had the same ERROR message. tbrisker's solution did not work in my case. Instead this solved the issue:
$ python3 -m venv .env
In addition to the other answers, I recommend checking what instance of virtualenv you are executing:
which virtualenv
If this turns up something in /usr/local/bin, then it is possible - even likely - that you installed virtualenv (possibly using an instance of easy_tools or pip) without using your system's package manager (brew in OP's case). This was my problem.
Years ago - when I was even more ignorant - I had installed virtualenv and it was masking my system's package-provided virtualenv.
After removing this old, broken virtualenv, my problems went away.
The below simple commands can create a virtual env with version 3.5
apt-get install python3-venv
python3.5 -m venv <your env name>
if you want virtual env version as 3.6
python3.6 -m venv <your env name>
Python now comes with its own implementation of virtual environment, by the name of "venv". I would suggest using that, instead of virtualenv.
Quoting from venv - docs,
Deprecated since version 3.6: pyvenv was the recommended tool for
creating virtual environments for Python 3.3 and 3.4, and is
deprecated in Python 3.6.
Changed in version 3.5: The use of venv is now recommended for
creating virtual environments.
For windows, to initiate venv on some project, open cmd:
python -m venv "c:\path\to\myenv"
(Would suggest using double quote around directory path if it contains any spaces. Ex: "C:/My Dox/Spaced Directory/Something")
Once venv is set up, you will see some new folders inside your project directory. One of them would be "Scripts".
To activate or invoke venv you need:
C:\> <venv>\Scripts\activate.bat
You can deactivate a virtual environment by typing “deactivate” in your shell. With this, you are now ready to install your project specific libraries, which will reside under the folder "Lib".
================================ Edit 1 ====================================
The scenario which will be discussed below is not what originally asked, just adding this in case someone use vscode with python extension
In case, you use vs code with its python extension, you might face an issue with its pylint which points to the global installation. In this case, pylint won't be able to see the modules that are installed in your virtual environment and hence will show errors while importing.
Here is a simple method to get past this.
cd Workspace\Scripts
.\Activate.ps1
code .
We are basically activating the environment first and then invoking vs-code so that pylint starts within the environment and can see all local packages.
In python3.6 I tried
python3 -m venv myenv,
as per the documentation, but it was taking so long. So the very simple and quick command is
python -m venv yourenv
It worked for me on python3.6.
On Mac I had to do the following to get it to work.
mkvirtualenv --python=/usr/bin/python3 YourEnvNameHere
If you install python3 (brew install python3) along with virtualenv burrito, you can then do mkvirtualenv -p $(which python3) env_name
Of course, I know virtualenv burrito is just a wrapper, but it has served me well over the years, reducing some learning curves.
virtualenv --python=/usr/local/bin/python3 <VIRTUAL ENV NAME>
this will add python3
path for your virtual enviroment.
It worked for me
virtualenv --no-site-packages --distribute -p /usr/bin/python3 ~/.virtualenvs/py3
For those having troubles while working with Anaconda3 (Python 3).
You could use
conda create -n name_of_your_virtualenv python=python_version
To activate the environment ( Linux, MacOS)
source activate name_of_your_virtualenv
For Windows
activate name_of_your_virtualenv
I tried all the above stuff, it still didn't work. So as a brute force, I just re-installed the anaconda, re-installed the virtualenv... and it worked.
Amans-MacBook-Pro:~ amanmadan$ pip install virtualenv
You are using pip version 6.1.1, however version 8.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Collecting virtualenv
Downloading virtualenv-15.0.3-py2.py3-none-any.whl (3.5MB)
100% |████████████████████████████████| 3.5MB 114kB/s
Installing collected packages: virtualenv
Successfully installed virtualenv-15.0.3
Amans-MacBook-Pro:python amanmadan$ virtualenv my_env
New python executable in /Users/amanmadan/Documents/HadoopStuff/python/my_env/bin/python
Installing setuptools, pip, wheel...done.
Amans-MacBook-Pro:python amanmadan$
I wanted to keep python 2.7.5 as default version on Centos 7 but have python 3.6.1 in a virtual environment running alongside other virtual environments in python 2.x
I found the below link the best solution for the newest python version ( python 3.6.1)
https://www.digitalocean.com/community/tutorial_series/how-to-install-and-set-up-a-local-programming-environment-for-python-3.
It shows the steps for different platforms but the basic steps are
Install python3.x (if not present) for your platform
Install python3.x-devel for your platform
Create virtual environment in python 3.x
(for example $ python3.6 -m venv virenv_test_p3/ )
Activate the testenvironment for python 3.x
(for example source virenv_test_p3/bin/activate)
Install the packages which you want to use in your new python 3 virtual environment and which are supported ( for example pip install Django==1.11.2)
On Windows command line, the following worked for me. First find out where your python executables are located:
where python
This will output the paths to the different python.exe on your system. Here were mine:
C:\Users\carandangc\Anaconda3\python.exe
C:\Python27\python.exe
So for Python3, this was located in the first path for me, so I cd to the root folder of the application where I want to create a virtual environment folder. Then I run the following which includes the path to my Python3 executable, naming my virtual environment 'venv':
virtualenv --python=/Users/carandangc/Anaconda3/python.exe venv
Next, activate the virtual environment:
call venv\Scripts\activate.bat
Finally, install the dependencies for this virtual environment:
pip install -r requirements.txt
This requirements.txt could be populated manually if you know the libraries/modules needed for your application in the virtual environment. If you had the application running in another environment, then you can automatically produce the dependencies by running the following (cd to the application folder in the environment where it is working):
pip freeze > requirements.txt
Then once you have the requirements.txt that you have 'frozen', then you can install the requirements on another machine or clean environment with the following (after cd to the application folder):
pip install -r requirements.txt
To see your python version in the virtual environment, run:
python --version
Then voila...you have your Python3 running in your virtual environment. Output for me:
Python 3.7.2
For those of you who are using pipenv and want to install specific version:
pipenv install --python 3.6
I got the same error due to it being a conflict with miniconda3 install so when you type "which virtualenv" and if you've installed miniconda and it's pointing to that install you can either remove it (if your like me and haven't moved to it yet) or change your environment variable to point to the install you want.

Categories

Resources