Anaconda

Availability for OS: Linux, OS X, Windows Description: Distribution Notes: can be installed locally

Installation

• Follow instructions at Anaconda.com
• Once you started the anaconda.exe, tick the “Add anaconda to my PATH environment variable”.

conda-cheatsheet.pdf

Conda Set-up in VSCode

• Create a file under your working folder in VS Code (to do this, see: Visual Studio Code How-to)

• Open a new Terminal and select cmd on the RHS (not powershell!)

  

  Important note : if you are on mac, you should use zsh since cmd is windows specific

• In the terminal, type:

conda activate

• This will create a base conda environment. However, we want to create another environment where we can play around with Python code that is not the base one (here called blub). To do this, type:

conda create --name blub python=3.11

• To check that you have actually created a new environment:

conda env list

• To activate the newly created environment

conda activate blub 

• Before starting your project, you also want to select your interpreter at the bottom right of your terminal - we want to change from Python (version installed on your laptop) to the one you have in your conda environment

  

• By clicking on 3.11.2 64-bit etc, this window will pop up:

  

• We want to select the conda env that you are using

  

  If you did it right, you should now see the name of your conda environment

• Never work in the base environment! Always do things in the generated environment

  • Recommended: create an environment for every “big project” you work on.

Useful Packages

N.B.: It is recommended, when possible, to use conda (see table below) to install new packages. When conda does not have the package of interest, google other ways of doing this (make sure you trust what you find though)

General packages

Lab-specific packages

(install only in conda environment of the appropriate project !!)

• PyActigraphy
  • Link to installation here
  • Package manager: pip
  • Procedure

    1. PyActigraphy installition has to go through pip

    2. Problem is: installing pyActigraphy through pip will automatically install many packages which are better to be installed by conda

    3. Please install the following packages through conda before you install PyActigraphy

       • texttable, pytz, lml, tenacity, pyparsing, pyexcel-io, pillow, numpy, lxml, llvmlite, kiwisolver, joblib, future, fonttools, et-xmlfile, cycler, chardet, asteval, uncertainties, scipy, pyexcel-ezodf, pyexcel, plotly, patsy, pandas, openpyxl, numba, contourpy, stochastic, statsmodels, pyexcel-xlsx, pyexcel-ods3, matplotlib, lmfit, spm1d
       • You can to this in one go:

       conda install -c conda-forge package1 package2 package3
       

       separated by a single space

    4. Finally, we can download PyActigraphy:

    pip3 install pyActigraphy