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Python Env Setup

This document provides instructions for setting up a Python development environment on Mac. It discusses creating and managing conda environments, setting environment variables to avoid exposing secrets, and using Python within RMarkdown documents by calling Python code from R. Procedures are outlined for creating, activating, deactivating, updating, and removing conda environments. Best practices are described for separating environment variables among projects to prevent overwriting.

Uploaded by

Hieu Nguyen
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
11 views

Python Env Setup

This document provides instructions for setting up a Python development environment on Mac. It discusses creating and managing conda environments, setting environment variables to avoid exposing secrets, and using Python within RMarkdown documents by calling Python code from R. Procedures are outlined for creating, activating, deactivating, updating, and removing conda environments. Best practices are described for separating environment variables among projects to prevent overwriting.

Uploaded by

Hieu Nguyen
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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How to set up python development env

Hieu Nguyen
2/22/2019

Contents
1 Envs Set up procedures for mac: 2

2 Environment Variables 2

3 Use Python within Rmarkdown 3

1
hq2n 2 ENVIRONMENT VARIABLES

1 Envs Set up procedures for mac:


• conda create –name my_env python=3.x
• source activate
• source deactivate
• To view installed packages: conda list
• Search outdated packages: conda search –outdated
• To update packages: conda update –all
• Update the outdated packages: conda install -U
• To view which python: which python
• To view list of envs: conda env list
• To remove an env: conda remove –name my_env –all
• To create a new dir: mkdir my_project_env
• To Export an env to a YML file: conda env > env.yaml
• display the yaml file on the terminal: cat env.yaml
• To create a new env out of the above yaml file: conda create -f env.yaml. Make sure that the yaml
must be inside the newly create directory

2 Environment Variables
used in many different projects to set data base url, hold secret keys or set python path. It allows us to
access the data without putting it directly on our project codes for everyone to see. Some people just use
global env var that can be shared among all projects BUT you have to be very careful not to overwrite them.
It is better to separate them out
• After create a new env, do conda env list and cd env’s path
• Create an activate directory (-p means the dir does not have to curently exist):
mkdir -p etc/conda/activate.d
• Create an deactivate directory (-p means the dir does not have to curently exist):
mkdir -p etc/conda/deactivate.d
• In the activate dir, create a file:
touch etc/conda/activate.d/env_vars.sh
• In the deactivate dir, create a file:
touch etc/conda/deactivate.d/env_vars.sh
• In terminal, use sublime text editor to open up the newly created file:
subl .
• In sublime, for the activate/env_vars.sh:
#!/bin/sh
export DATABASE_URI=“postgresql://user:pass@db_server:5432/test_db” This way no one can see
the pw

Hieu Q Nguyen - University of Waterloo 2


hq2n 3 USE PYTHON WITHIN RMARKDOWN

• In sublime, for the deactivate/env_vars.sh:


#!/bin/sh
*unset DATABASE_URI
• Test: try to deactivate and activate the env
Once activated: echo DAT ABASEU RI should show “postgresql://user:pass@db_server:5432/test_db”
Once deactivated: echo DAT ABASEU RI should show NOTHING
• To look at all the files in a dir: ls -la
• DO NOT FORGET TO DEACTIVATE ENV WHEN MOVING FROM ONE PROJECT
TO ANOTHER

3 Use Python within Rmarkdown

library(reticulate)

# engine.path = '/Users/hq2nguye/anaconda3/bin/python' --> MAc


import sys
print("Hello World")

## Hello World
print(sys.version_info)

## sys.version_info(major=2, minor=7, micro=10, releaselevel='final', serial=0)

Hieu Q Nguyen - University of Waterloo 3

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