Fix pyyaml and docker-compose dependencies

[tcompa]

Close #813

[github-actions]

Coverage report

The coverage rate went from 91.83% to 91.76% ⬇️
The branch rate is 81%.

None of the new lines are part of the tested code. Therefore, there is no coverage data about them.

[tcompa]

CI failure with pytest-docker v2 -> to check.

Meanwhile, this PR would also have the nice effect of removing quite a few (dev) dependencies, which never hurts ;)

[tcompa]

Some details from a (local) CI failure:

    def execute(command, success_codes=(0,)):
        """Run a shell command."""
        try:
            output = subprocess.check_output(command, stderr=subprocess.STDOUT, shell=True)
            status = 0
        except subprocess.CalledProcessError as error:
            output = error.output or b""
            status = error.returncode
            command = error.cmd
    
        if status not in success_codes:
>           raise Exception(
                'Command {} returned {}: """{}""".'.format(
                    command, status, output.decode("utf-8")
                )
            )
E           Exception: Command docker compose -f "/home/tommaso/Fractal/fractal-server/tests/data/slurm_docker_images/docker-compose.yml" -p "pytest98522" up --build -d returned 125: """unknown shorthand flag: 'f' in -f

EDIT: this is most likely due to my own docker version

[tcompa]

The main issue was related to dash/underscore in the container name, see https://docs.docker.com/compose/migrate/#service-container-names.