Conda Environment README setup Instructions

[annakrystalli]

Feedback on #85 PR.

In all, the instructions are correct and appropriate. However, I ended up with installation issues and seemed to have bumped up against quite a few annoyances/bugs in working with Conda environments (with my limited experience of environments not really helping!).

I'm not sure that my feedback can and should be incorporated in the README. However, I thought I'd record them so we could at least review and discuss.

Installation issues

1. Environment not being prepended to the $PATH

This seems related to a still open issue in Conda (conda/conda#9392) where the path is not set by conda activate. This results (at least on my system on a mac) to resorting to using the user wide python 2.7 (/usr/bin/python annoying!). I followed the instruction to deactivate and then reactivate to get it to work but seems hacky. Anyways, something I certainly spent some time to figure given my limited familiarity with python.

2. Pip not installing python packages into environment.

When running pip install -r requirements/local.txt, the packages ended up being installed in my user level library (/usr/local/lib/python3.8/site-packages)

I had a look at this stackoverflow post to troubleshoot and tried:

• including conda install pip prior to pip install -r requirements/local.txt. This wan unsuccessful
• Using the explicit path to the environment pip (in my case /Users/Anna/miniconda3/envs/reprohack/bin/pip install -r requirements/local.txt). This was successful but again feels annoying, hacky and not easy to document.

---

Any suggestions on whether I should have handled this better / README instructions can/should be improved? @twinkarma @willfurnass

[twinkarma]

@annakrystalli Looks like I've missed out a few key commands in the readme for some reason, apologies

Normally you'd need to run

source activate my_conda_environment_name

(and not conda activate as that normally fails)

after running this command you should see your conda environment before your terminal carat e.g.

(my_conda_environment_name) myusername@mycomputername $ 

Then you'll know that you're inside the conda enviornment and any pip install that you run will be installed into your enviornment

[twinkarma]

Ah just had a re-read of installation instructions and the instructions to run source activate reprohack is there?

[annakrystalli]

Yup, I did all that and was in the activated environment yet the environment path had not prepended to the path. This seems to be a conda occasional bug. Have a look at the conda issue I linked to.

[twinkarma]

Strange, did you actually run source activate reprohack or conda activate reprohack?

[annakrystalli]

`source activate reprohack`

[twinkarma]

if you run

cat ~/.bashrc | grep conda

Do you see a line similar to below?, the myusername is meant to be your username:

export PATH="/home/myusername/miniconda3/bin:$PATH"

[twinkarma]

After installing conda, it adds the above line to your .bashrc but this only activates after you've restarted your terminal (or open a new terminal)

[annakrystalli]

OK, point 1 might be a VSCODE issue. I ran everything from terminal and it worked fine. However, pip install -r requirements/local.txt did not (still needed to explicitly specify the path to pip in the venv.)

[annakrystalli]

Looks like this is what problem 1 relates to in VSCODE 🙄 https://code.visualstudio.com/docs/supporting/faq#_resolving-shell-environment-is-slow-error-warning