Jupyter notebooks with matchms tutorial.

Prerequisites

For running locally on Ubuntu:

sudo apt install jupyter-core
sudo apt install jupyter-notebook

Install Miniconda or Anaconda from https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html

Create a conda environment:

conda env create

Activate the conda environment:

conda activate matchms-notebooks

While matchms is being developed, we cannot yet install it from conda-forge, therefore matchms is not yet listed as a dependency in environment.yml. To circumvent this issue, we will check out a development copy of matchms, then use pip install with the --editable argument to add it to the matchms conda environment.

# (first, change to where you want to store the copy of matchms)
git clone https://github.com/matchms/matchms.git
cd matchms
pip install --editable .

Check to see if it all worked by listing the packages that are present in the conda environment named matchms:

conda list

This should yield a table of packages alongside where they were installed from, like so (excerp):

libsodium 1.0.17 h516909a_0 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
markupsafe 1.1.1 py38h1e0a361_1 conda-forge
matchms 0.1.0 dev_0 <develop>
mistune 0.8.4 py38h516909a_1000 conda-forge
nb_conda 2.2.1 py38_2 conda-forge
nb_conda_kernels 2.2.3 py38_0 conda-forge
nbconvert 5.6.1 py38_0 conda-forge
nbformat 5.0.4 py_0 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
notebook 6.0.3 py38_0 conda-forge

You can tell that matchms was not retrieved from conda-forge (the normal source of packages), but instead was installed from local disk as indicated by the <develop> label.

If everything looks OK, start the notebook server:

jupyter notebook

And open a browser to http://localhost:8888 to interact with the notebook.