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Python notes

This is the section to include all notes related to python development.

Set up python conda environment

This notes are here just as a reference. Don't use anaconda. If I need a tool to manage environments, it's preferable to use pipenv or venv.

I have faced many problems within projects when trying to program in python with the virtual environments managed by anaconda. I didn't document the problems given that I though I wasn't understanding the process, but all the problems were gone when I uninstalled anaconda and started using pipenv.

  • Check if there are already envs:
conda info --envs

# conda environments:
base                  *  /home/ronny/anaconda3
gee                      /home/ronny/anaconda3/envs/gee
gpp                      /home/ronny/anaconda3/envs/gpp
satellite                /home/ronny/anaconda3/envs/satellite
  • To activate/deactivate:
conda activate
conda deactivate
  • There is a difference between:
apt install spyder
conda install spyder
  • To create a new env:
conda create --name gee python = 3.5

Environmental variables

If I have credentials that I need to use in one project, what I can do is to store them as a system environmental variable and then call them later in the python script. This can be achieve with the following steps:

  • In the terminal, create the variables:
export my_username=fulano
export my_password=123abc
  • Then, let's check if the step above was succesful:
echo $my_username
echo $my_password

They should print the values we stored.

  • Now, in the python script, let's access those values

This should return the values of the environmental variables.

There is one way to create the environmental variables in a file that we can include in the project and ignore it in the .gitignore. The steps for this are here

Working with pipenv

If I have a project already started by someone else, and it have a pip file + pipfile.lock I can follow the next steps:

  • I cloned the repo
  • There is a pip file + pipfile.lock
  • When on the directory, I run pipenv install
  • When everything was already installed, I ran pipenv shell
  • Then, I will see (CEOS-research) (base) ronny@ronny:~/Documents/repos/github/ceos/CEOS-research$ in my terminal

If I want to check where my virtualenv is: pipenv --venv

If I installed a package with pipenv, it will be shown in the Pipfile. If I need to uninstall it, I can run pipenv uninstall name_package. This will remove the package also from the Pip files.

To activate the environment, that we are working on, we need to run pipenv shell

To check the status of the packages pipenv check

Check arguments of a python function


How to debug on python?

First, I need to install pdbpp to run in sticky mode:

pip install pdbpp

Then I need to include breakpoint at the beginning of the code lines that I want to run the test.

Then, in the terminal, I can open the file with:

python -m pdb

These are the commands:

sticky start para iniciar

n(ext) para siguiente linea

s(tep) para entrar a depurar una funcion

si estoy en sticky no tengo que estar poniendo el list todo el tiempo

j(ump) para brincarme por numero de linea