Installation

First we must make sure we have the JII MultispeQ library installed:

pip install git+https://github.com/Jan-Ingenhousz-Institute/JII-MultispeQ.git --upgrade --no-cache-dir

Now you have all the tools available to download your Project data and information to get started.

Important

PhotosynQ Inc. is offering a library called PhotosynQ-Python which supports donwloading Project data and information as well. It is actually running in the background of this library.

JII MultispeQ is providing more functionality, including saving data locally, so you don’t have to download the Project every time or you can work offline. Also, it provides additional functions on viewing the Project’s information and gives you access to the measurement Protocol and all the information related to your analysis.

Jupyter Notebooks

The JII-MultispeQ library will work using a regular Python file you execute from your Terminal, but most users will probably want to use a more interactive approach like Jupyter Notebooks.

Most convinently, Jupyter Notebooks can be used in combination with Anaconda to manage packages and environments. You have two options, using the Anaconda Distribution including a GUI (Graphical User Interface) or Miniconda (without the GUI to be used with the Terminal): Download and Install.

Conda Environments

With Conda it is beneficial, to use an environment when performing your data analysis. This environment will contain all the libraries like JII MultispeQ including a specific version of Python. That way, you can keep exact track of all the dependencies needed for your analysis.

In case you want to share your work, you can export the environment as well, so the person you are sharing your work with can set it up on their computer, avoiding problems with different versions of the used libraries when setting everything up. Further, you don’t have to explain, which libraries need to be installed to run your analysis.

Hint

Find the detailed documentation on Environments in the Anaconda Documentation.

Miniconda (Terminal)

When you are using Conda and you open a Terminal, you will most likely see a (base) in your command prompt. That is the currently active environment. If it is not showing (base) or any other name, make sure to activate the environment, before installing any libraries.

To activate an environment use the following command:

## Activate the standard environment
conda activate

## Activate a specific environment
conda activate <environment name>

To deactivate an environment use the following command. You don’t have to add the name of the current envrionment, since there is only one active envrionment at a time.

conda deactivate

Tip

By default, conda is loading the base environment. To remove this default behavior when opening a terminal, use:

conda config --set auto_activate_base false

Anaconda (GUI)

For how to use environments with Anaconda, please refer to the official documentation.