Make tutorials interactive with binder

[create-issue-branch]

closes #80

[pablo-de-andres]

There are now 3 tutorials that can be run on binder (cuds_api, ontology_interface and wrapper_development)
I checked, and they should be working fine.
To check for yourselves, you can copy the link from the binder badge, and replace master with 80-Make_tutorials_interactive_with_binder

[kysrpex]

I checked and indeed they work fine. However, I am experiencing a strange problem with this branch: the CUDS API tutorial and the Ontology Interface tutorials do not show up on the table of contents. @pablo-de-andres Are you able to see them there?

[pablo-de-andres]

My bad. I renamed some files, because there was an inconsistency between - and _ in the namings

[kysrpex]

I have tracked down a bit better the error of the Binder badge not being displayed when using the Docker image. It happens because the python Docker image it is based on is itself based on Debian Buster, and at least one of the packages binutils binutils-common binutils-x86-64-linux-gnu cpp g++ gcc libatomic1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libgomp1 libitm1 liblsan0 libpython3-stdlib libquadmath0 libstdc++6 libtsan0 libubsan1 python3 python3-distutils python3-lib2to3 python3-minimal are causing this bug.

I have discovered this using this modified dockerfile, which installs Pandoc from Debian Bullseye. This triggers the update of the above mentioned packages.

FROM python:3.8-buster
RUN apt-get update
RUN apt-get install -y default-jre graphviz
RUN apt-get install -y texlive-latex-recommended \
                       texlive-latex-extra \
                       texlive-fonts-recommended \
                       latexmk

RUN sed -i 's/buster/bullseye/g' /etc/apt/sources.list
RUN sed -i 's\bullseye/updates\bullseye-security\g' /etc/apt/sources.list
RUN apt-get update
RUN apt-get install -y pandoc


WORKDIR /app
ADD . .

RUN pip install -r requirements.txt

CMD sphinx-autobuild --host 0.0.0.0 docs/source docs/build/html

# Build:
# $ docker build -f local_build.Dockerfile -t simphony-docs .

# Run:
# $ docker run --rm -v $PWD:/app -p 8000:8000 simphony-docs

For now I suggest that we do not do anything more in this regard, as whether the bug will be happening on readthedocs or not will depend on the software stack installed in there. We may put effort in fixing it in the end this actually happens.

[kysrpex]

I also centered the Binder badges.

[pablo-de-andres]

I believe they were centered by default (or so it showed on my vscode Notebook)
However, I can't test it right now because of the issue building the docs

[kysrpex]

About the tooltip of the Binder badges, I think that nbsphinx (the plugin that renders notebooks in the docs) is breaking it. It seems to keep only a handful of HTML tags after the conversion. See #468 on nbsphinx's repo. There is nothing we can do to fix this.

[kysrpex]

I believe they were centered by default (or so it showed on my vscode Notebook)
However, I can't test it right now because of the issue building the docs

Do not worry, I think it also has something to do with nbsphinx.