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Setting up your system

Anaconda:

We recommend installing Python via the Anaconda Distribution. Be sure to use the "Python 3.6.x" version or later. We will use the Conda Package Management System within the Anaconda Distribution. From the documentation:

Conda is an open source package management system and environment management system that runs on Windows, macOS and Linux. Conda quickly installs, runs and updates packages and their dependencies. Conda easily creates, saves, loads and switches between environments on your local computer.

After the installation run python --version in a terminal window (in "Anaconda Prompt" if you are using Windows). If the output show "Python 3.6.x" or later (and "Anaconda") you are good to go.

GitHub:

The course code is hosted on the code-sharing platform GitHub (where you now are reading this). If you do not have a GitHub account already you should make one now. We recommend that you are using the platform for you own projects during the course. https://github.com/join.

Install and test the course environment:

After you have successfully installed Anaconda, go through the following steps (if you are using Windows, be at the "Anaconda Prompt").

Install Git:

conda install git

Download the repository:

git clone https://github.com/oercompbiomed/CBM101
cd CBM101

Configure the Python-environment:

conda env update

Activate the environment:

conda activate cbm101

If you are using Linux or MacOS and the command above fails, type

source ~/.bash_profile

and try conda activate cbm101 again. If this fails, activate the environment by typing source activate cbm101 instead.

Install a Jupyter kernel:

python -m ipykernel install --user --name cbm101 --display-name "CBM101"

Test you installation:

Go through the notebook 0.0-test.ipynb in the notebooks-directory:

cd notebooks
jupyter notebook

You can also use JupyterLab: jupyter lab.

Update:

The code and environment will be updated during the course. Run the following commands regularly:

  • Update code: git pull
  • Update environment:
conda activate cbm101
conda env update