valosekj

Simple workflow of collaboration in small team using git and GitHub

This gist describes example of simple workflow on repository whose changes are tracked by git and GitHub

1) Clone (download repository from GitHub to your computer)

# Go to directory where repository will be cloned (downloaded)
cd ~/Documents
# Clone repository from GitHub

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How to create and use virtual environments (venv and conda)

venv and conda are environment manager tools allowing to create virtual environments. Virtual environment separates the dependencies (Python packages) for different projects. This mean that each project can have its own dependencies. Usage of virtual environments allows you to avoid installing Python packages globally (to the system Python) which could break system tools or other projects.

venv environment

1. Create venv

MacOS or Linux (without or with site-packages)

valosekj

Run python script from shell (bash, zsh)

Sometimes, I need to call/run python script with arguments from shell. I use bash or zsh as my shell and following workaround works great for me.

Using shell wrapper

1. Some example python script which I need to run from bash:

my_python_script.py:

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Basic shell commands

A few basic shell (bash, zsh, ...) commands for UNIX (Linux, MacOS) CLI (command-line interface)

1. File and directory manipulation commands

cd - change directory:

# change directory to /home/username/Downloads:

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Useful shell commands

This gist contains several useful shell commands which I use frequently during my work.

$0 - Get current shell

$ echo $0
zsh

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Useful string manipulation examples for bash and zsh

I need very often to modify filenames or replace/delete their parts across huge number of files. I was using sed command for these purposes but recently I have found out that all these tasks can be easily done directly in bash (or zsh) because both of them support so called string manipulation operations.

String manipulations

Define some example string:

$ file=some_file_name.txt

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Convert photos from HEIF to JPEG

I use on my iPhone HEIF (High Efficiency Image File Format) format for storing my photos.

This format is widely supported throughout Apple ecosystem but sometimes I need to quickly convert photos from HEIF to JPG to be able to use these photos also elsewhere (Windows, some websites, etc.)

I use for this purpose convert command line tool from ImageMagick

Usage:

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My zsh configuration and tips

This gist contains some essential commands and configurations which I have included in my config files on my MacOS and Linux machines.

NOTE: on Linux, it may be necessary to install zsh (e.g., sudo apt install zsh zplug)

NOTE on MacOS:

• it is necessary to install nano from homebrew (using brew install nano)

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Run arbitrary application from terminal on MacOS

Sometimes, it is convenient to have possibility to start/run any application (like your internet browser or text editor) directly from your terminal. Most of these applications however do not create shortcut for easy run from terminal during their installation. Below is short manual how to create this shortcut manually.

Steps

1. Open terminal (cmd + space --> type terminal)

2. Navigate to /usr/local/bin:

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Run matlab function from python script

I needed to run matlab script from python script. I wanted to pass several input arguments from pandas DataFrame, perform calculation in matlab and return multiple output arguments back to python.

Steps (MacOS):

1. Install matlab engine API for python:

In your terminal, go to directory where matlab is install and run installation python script, e.g.: