Develop Reference

Emacs and conda workaround

I'm using emacs and anaconda.
I have this in my init.el:
(setenv "WORKON_HOME" "/home/user/anaconda3/envs/")
And conda on my path:
# added by Anaconda3 installer
export PATH="/home/user/anaconda3/bin:$PATH"
but emacs can't find my conda environments, which I understand it is supposed to be able to do..
So, when I run C-c C-p to start a new session, and C-c C-c, it fails to import my packages which are installed in a conda environment, with ModuleNotFoundError.
Since I have added this to my path and it still doesn't work, I am trying to work around this, and still be able to run my conda applications from emacs.
I can open a shell in emacs with M-x shell, then source activate myenv, and run python.
I now want C-c C-c to copy into /this/ shell. How do I mark this shell buffer as a python process to send my file.py's text to on C-c C-c, rather than just a shell shell?
Update1
I've also looked at the following references:
https://emacs.stackexchange.com/questions/20092/using-conda-environments-in-emacs
How does conda-env list / conda info --envs find environments?
But neither package works for me. I still get, when I try:
conda-env-list
*Conda envs*
Produces a blank buffer.
And this for pyvenv-workon:
pyvenv-workon
Work on: (empty)
These environments very much exist, and it makes it impossible to use emacs as a python IDE if I can't run my code.

What I found works for me is to use the conda package from ELPA and set two of its configuration variables to point to my Conda directory. The following snippet does the trick in my .emacs:
(use-package conda
:ensure t
:init
(setq conda-anaconda-home (expand-file-name "~/miniconda3"))
(setq conda-env-home-directory (expand-file-name "~/miniconda3")))
conda-anaconda-home is the equivalent to the ANACONDA_HOME environment variable (i.e. contains all files of your Anaconda installation)
conda-env-home-directory - is the directory where your virtual environments get stored (within the envs subdirectory)
With this configuration I'm able to run M-x conda-env-activate and have access to all previously created envs.

Programs inherit the environment variables from the shell that spawned them. The way conda and virtualenv work is by overriding the shell's PATH variable. They do this so that the OS finds the new version of the app (conda's or virtualenv's) instead of the default one installed with the OS (Macs come with an ancient version of python).
So, what is happening here? If you start Emacs by double clicking on the OS icon it will inherit the default shell environment variables. So when you try to call a library that you installed with conda (or equivalently with virtualenv and pip), because you are using the default OS path, the OS is finding the default version of python (and crucially the default version's libraries). The default version of python is going to respond "I have no idea what library that is."
How to fix? One reliable way is to not start Emacs by double clicking on the OS Icon. Here is what I do most days:
1) start a console/terminal
2) switch to the conda environment `activate py37`
(or with virtualenv: `source .py37dev/bin/activate`)
3) start Emacs from that same shell that has the modified environment variables.
On a Mac its: `/Applications/Emacs.app/Contents/MacOS/Emacs`
(I use a installed version of Emacs on the Mac because the one that
comes with Mac is ancient).
On Linux and Windows the path to EMacs will be different but the idea is the same.
4) start a shell inside Emacs and you should see the shell looks the way it does
in your conda shell (or virtualenv shell)
here it what it looks like for me:
see how the version of python is not the default OS python? Its the one from the virtualenv + pip environment (conda works the exact same way, just the start envirmonment is a different command)

I tested the solutions given in the answers of Wojciech Gac, of Mittenchops and James Anderson.
While solution of James Anderson's solution is by far the easiest, it comes with a few problems:
First, you have to reactivate the environment in each shell process you spawn in emacs. There is also the possibility that emacs has a different pythonpath, therefor reluctantly using system python and not venv python.
The solution with conda.el is somehow weird. In Melpa it is listed as obsolete and with instructions of https://github.com/necaris/conda.el it won't recognize the environments on my certain machine.
On the same machine the solution with pyenv as mentioned in https://emacs.stackexchange.com/a/20093/28567 is working like a charm.
Therefor you only need to install with M-x package-install search for pyenv and then insert following two lines into .emacs:
(setenv "WORKON_HOME" "~/anaconda3/envs") ; /anaconda3 || /miniconda || wathever path your conda installation is located at
(pyvenv-mode 1)

This is my minimal solution to this problem:
create a batch file like this
conda activate <yourEnv>
python -i
set (local) python-shell-interpreter pointing to the batch-file
run-python as always (C-c C-p ...)

I know this is not exactly an answer to your question. But If you JUST want to run your code, open the directory in the terminal where your files are located (e.g. cd /Downloads/Chapter01/yourfile.py) . Then, activate the environment (conda activate *your env*) and pass this command (python yourfile.py). Your code will be executed within that environment by python.
I edit remote files with emacs and run code like this in another terminal window. You may wanna open the two terminal windows side by side while debugging your code.

With conda/anaconda should I work in (base) all the time?

This is a total newbie question, but I installed conda along with a bunch of other stuff like Tensorflow with a virtual environment, and now I'm a little confused. If I open a terminal my python is pointing to /usr/bin/python. If I go to the base environment ("conda activate base"), my path points to where I installed anaconda, /usr/local/anaconda2. Does conda expect that I always go into the base environment to use all the anaconda packages, or did I do something weird on my install that my non-environment still points to the original system python? Should I just change my path to point to anaconda? I'm on Ubuntu 18.10.

I am a fan of being explicit -- instead of running python at the command line, I use the full path to the python interpreter when running scripts (e.g. /usr/local/anaconda2/bin/python) -- this way I don't rely on the shell behavior or having to worry about which environment is currently active. Running the interpreter using its full path is no different than just running python while the environment is active.
But that's not everbody's cup of tea... So...
Even if anaconda did not prompt you to update your PATH variable, you can do it explicitly by updating your .bashrc or .bash_profile (or .zshrc or whatever else) by adding this line: PATH=/usr/local/anaconda2/bin${PATH}. Dont forget to re-source the .bashrc or close/reopen your shell for it to take effect.
Conda is capable of creating many virtual environments beyond the base, so if you have more than one and you want to set one as the default, then just update the line above for the appropriate path.

How to switch python version permanently, without "activating" environments?

I would like to be able to switch Python version permanently, in OS-wide manner and reboot tolerant, is it possible?
I don't want to use usual activate approach, which shows environment in command line prompt.

For windows, you can simply install a new version of anaconda and add it to the PATH before the old version (and any other python versions). Windows will then find this version of python first, and it will thus be your "OS-wise" python installation.

On windows, I think you just have to change your PATH environment variable and add the path to your favorite python.
I think you don't need to reboot your machine but you may have to restart your command line console (cmd.exe) to take it into account

Using linux console in pycharm

I'm new to pycharm, virtualenv, linux and git.
I've recently begun a journey of using djangoto make webapps. Before I used sublime to make scripts however now a more complex project management system such as pycarm was needed. I actually wanted to get a linux VM and go down that road but was advised that windows python IDE such as pycharm would be suitable
I recently learnt the importance of dependencies and how to use virtualenv. However in this tutorial, under the 'How do I use my shiny new virtual environment?' it starts using commands such as:
ls env
and
which python
Neither of which my pycharm console would understand.
I could use a console emulator such cmder to use the commands but then I would remove the convience of using the IDE's integrated one.
Should I upgrade to a linux VM ? Or can I install a package that allows me to use such commands in PyCharm.
As a bonus question, what are the commands in that tutorial ? are they linux commands? when ever i see $ .... is that the linux console ?

You can accomplish this using Vagrant: https://www.vagrantup.com/
You can use Vagrant and VirtualBox to setup a Linux VM (distro of your choice) and then install all of your Python dependencies in the VM. Once you have that setup, you can tell PyCharm to use the Python interpreter in your VM by following these steps:
Open the project settings dialog box in PyCharm.
Expand Project: (your project name) on the left side.
Click on Project Interpreter.
Click on the cog icon on the upper right side of the window and select Add Remote.
Click on the Vagrant radio button.
In the Vagrant Instance Folder box, select the directory your Vagrantfile is located in.
In the Vagrant Host URL box, make sure ssh://vagrant#127.0.0.1:2222 is specified.
Click OK.
Since Vagrant is compatible with Windows this solution should work for you. I have done it successfully using macOS and it works great. Good luck!
You might find this tutorial useful: https://developer.rackspace.com/blog/a-tutorial-on-application-development-using-vagrant-with-the-pycharm-ide/

I got this to work on Windows 10 with Anaconda Prompt. This terminal which comes with Anaconda, creates a "base" environment with a linux-like virtual machine and your Windows file system (C:\\) mounted to /c, and has bash installed with common Unix commands like cd, ls, chmod, echo, cat, ... Running programs from bash with access to environment variables is much nicer than Windows Powershell etc.
Now to get your Terminal in Pycharm to use Anaconda Prompt instead of cmd.exe, I followed this answer. After installing Anaconda and/or Anaconda Prompt, right-click -> Open File Location -> right-click the shortcut -> Properties -> copy file path. Then use your file path instead.
Conda is great for package environment management. Learn more about it here. For Django + Conda specifically, read here. You can also use pip to install from Python package indexes, github repos, and requirements.txt files instead. Unless you know how Anaconda Prompt works, I don't recommend creating your own environments from scratch. What worked for me was:
(base) C:\Users\wassadamo> conda create -n mynewenvironment --copy base
...
(base) C:\Users\wassadamo> conda activate mynewenvironment
(mynewenvironment) C:\Users\wassadamo> ls
folderA folderB file.txt
Works!
Whenever I try running conda deactivate to leave the base environment, my bash commands would stop working. So clone base as above.
Another tip: if you want to run shell scripts from Terminal within PyCharm with Anaconda Prompt this way, then execute them (e.g. "run.sh") on command line with
bash run.sh
I tried putting this on the first line of my run.sh
#!/usr/bin/bash
And running it with
./run.sh
But this had the effect of running it in an external Anaconda Prompt instance (add sleep, or some user input command to force it to wait and see for yourself). Explicitly running my .sh files with bash had the desired effect of running them in the same shell as I started them in PyCharm Terminal configured with Anaconda Prompt.

How to set the default python path for anaconda on Linux?

I have installed anaconda on a Linux machine. I noticed that after deactivating the anaconda environment with:
source deactivate
When running:
which python
I get:
/home/user/anaconda/bin/python
Instead of
/usr/bin/python
How can I restore this setting?

The comments somewhat cover the answer to the question, but to clarify:
When you installed Anaconda you must have agreed to have it added to your PATH. You'll want to check in your ~/.bash* files and look for any export PATH= lines to check this. So Anaconda is always on your path. The source deactivate command will only deactivate "sub" Conda environments. It will never remove what is called the "root" Conda environment (the one you originally installed). If you don't want Anaconda on your PATH by default then remove it from your ~/.bash* startup files. Then when you want to use Anaconda you'll need to add it to your PATH. Or just add the specific Conda environment you are interested in to your PATH directly, and don't worry about the activate and deactivate scripts. At their core all they do is modify PATH.
I hope that helps clarify things.

Anaconda comes with its own everything, and they ask if you wish to use their software as a default when you install it by adding their bin first to your PATH variable. If you do that, you can only manually remove it later from .bashrc to undo this action.
I chose not to do it, but i made a shell script to start spyder and use the anaconda distribution when i wish to, without altering my PATH by calling spyder like this from the shell script:
PATH=/home/<... path to where i installed anaconda>/bin:$PATH spyder &
This means that i am adding their distribution's bin to the path only for the extent of running that command (spyder), otherwise my environment is unaffected by anaconda.
If i wish to add things to it, i pass an option to the shell when i source it and that triggers these actions:
PATH=/home/<... path to where i installed anaconda>/bin:$PATH
PS1='\[\033[1;34m\](A)\w:\[\033[0m\] '
so that i see (with colors!) that in this terminal i am using an altered PATH, the one with python3 and such from anaconda, etc... When done, i kill the terminal! :)

To get back to the former default, I comment out the entry setting the pathbin the .bashrc file and get these results:
$ which python
/usr/bin/python
$ python -v
python 2.7.*

If you have installed something, you want to use it before older installs, in general.
Your path is well set: your install is searched before system install.
If you want to use system python, run % /usr/bin/python.
If you don't want anaconda, just trash it (or move it somewhere ouside of path).
This may help:
% which -a python.