Python#

Author: Fu Yin
Update: July 29, 2022
Reading: 30 min

Warning

Python is an interpreted language that requires the interpreter to execute Python code. Although the Python interpreter is built into Linux/macOS systems, it is recommended that users do not use it to avoid damaging the built-in Python and causing system problems.

Install#

It is recommended to install Miniconda and use its conda to manage and install Python and its packages.

Download Miniconda3 macOS Intel x86 64-bit bash.

Install Miniconda

bash Miniconda3-latest-MacOSX-x86_64.sh

Miniconda will be installed into ~/miniconda3 path in M1 by default. The installation package will write the initialization statement to the shell’s configuration file, e.g. ~/.zshrc in my Mac.

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/Users/yinfu/opt/miniconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/Users/yinfu/opt/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/Users/yinfu/opt/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/Users/yinfu/opt/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

Configuration#

Package Manager#

It is recommended to use mamba to manage packages. Sometimes mamba may not work, you can consider to use conda or pip.

Install mamba

Foreign

To get mamba via conda, just install it into the base environment from the conda-forge channel:

conda install mamba -n base -c conda-forge

China

mamba uses the configuration file of conda. Therefore, you need to configure ~/.condarc file before using Mamba. Use Tsinghua mirror to speed up the download of softwares. Here is my ~/.condarc file:

cat ~/.condarc

# output
channels:
  - defaults
show_channel_urls: true
default_channels:
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2
custom_channels:
  conda-forge: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  msys2: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  bioconda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  menpo: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  pytorch: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  pytorch-lts: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  simpleitk: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud

Then you can use conda to install mamba, and just install it into the base environment from the conda-forge channel:

conda install mamba -n base -c conda-forge

Now you can use mamba to manage your packages, e.g.:

mamba install numpy

Warning

Installing mamba into any other environment than base can cause unexpected behavior

VSCode#

Download the plugin, Python, in VSCode Extensions

Manual refer to Miscrosoft docs

Package#

scientific computation-related package:

Name	Purpose	Way
`mamba`	…	conda
`numpy`	…	conda
`matplotlib`	…	conda
`scipy`	…	conda
`pandas`	…	conda
`jupyter book`	…	conda
`jupyterlab`	…	conda
`jupyter notebook`	…	conda
`jupyterlab_myst`	…	pip
`h5py`	…	pip
`jill`	for installing Julia	pip
`openpyxl`	read excel	pip
``

geophysics package:

Name	Purpose	Way
`obspy`	…	conda
`pygmt`	… in (pygmt env)	-c conda-forge conda
`cartopy`	Geo-Map	conda
`pyfk`	…	pip
``
``

Resource#

Here are some resources for learning about Python and common scientific computing modules:

Programming Notebook

Python

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