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Note to participants of one of our courses

We provide online access to cloud resources. There is no need to follow any installation process therefore. Instructions below are for setting it up yourself.

Installation instructions

Author: Kris Thielemans

The exercises use Jupyter notebooks. These provide a nice GUI interface to Python. You need a few components: The jupyter notebook server and a web browser to open it, SIRF and the SIRF-Exercises.

An easy way to run the exercises is to use a GitHub Codespace, the SIRF Virtual Machine or a Docker image where SIRF has already been installed for you. Please read https://github.com/SyneRBI/SIRF/wiki/How-to-obtain-SIRF.

Alternatively you can install SIRF and the SIRF-Exercises yourself. Below are some brief instructions.

Installing SIRF and the exercises yourself

You will need SIRF of course. Please check the instructions on our wiki.

The SIRF-exercises themselves can just be downloaded, preferably via

mkdir ~/devel
cd ~/devel
git clone https://github.com/SyneRBI/SIRF-Exercises
cd SIRF-Exercises

adjusting the path to where you want to install the SIRF-Exercises of course.

You will need to install the additional Python dependencies needed for the exercises. This includes a Jupyter notebook server. If you've installed SIRF using a conda python environment, we recommend

conda env update -n <your_env_name> --file environment.yml
conda activate <your_env_name>
jupyter lab
# when done
conda deactivate

If you didn't use conda, we recommend using venv, i.e. something like this

$SIRF_PYTHON_EXECUTABLE -m venv ~/devel/SIRFenv
# Activate the venv. Use the appropriate line for your shell, see the venv doc
source ~/devel/SIRFenv/bin/activate
pip install -U pip
pip install -r requirements.txt
jupyter lab
# when done
deactivate

where we used the environment variable created when you follow the SIRF-SuperBuild instructions to make sure that you use a Python version which is compatible with how you compiled SIRF. Please note that the conda environment includes dependencies (in particular cil) which are not available with pip.

Warning: At present, SIRF is not yet available via conda or pip. The above instructions therefore do not install SIRF itself.

Next steps are in the DocForParticipants.md.

Updating the exercises after installation

You can repeat clone the repository again to get any updates. However, if you made any changes to the exercises, you might want to keep those. Merging your changes and any "upstream" ones is unfortunately a bit complicated due to the file format used by jupyter notebooks. The following should work

cd SIRF-Exercises
nbstripout --install
git config --global filter.nbstripout.extrakeys '
  metadata.celltoolbar 
  metadata.language_info.codemirror_mode.version
  metadata.language_info.pygments_lexer metadata.language_info.version'
git pull

(You do not have to write the nbstripout lines on the VM, and on other systems you have to write those only once).

Contributing to the SIRF-Exercises

Follow the guidelines given in https://github.com/SyneRBI/SIRF/blob/master/CONTRIBUTING.md. Please do follow the nbstripout instructions above before commiting any changes.