CLI: do not except when --help is passed to sub command

[sphuber]

Fixes #97

The rocrate add workflow --help call would except because the add
command group would attempt to instantiate a research object crate. But
since no existing crate was defined through the -c option, the
instantiation of the crate would except.

There is no straightforward way in click to prevent the execution of
group command code when --help is passed. Instead, we move the
addition of the -c/--crate-dir option to those commands that actually
need it. Code duplication is prevented by defining the option once,
assigning it to OPTION_CRATE_PATH and using that decorator for each
command that requires the option.

This is a breaking change for the interface as the crate path should now
no longer be specified directly after the main command but rather after
the actual leaf command. So:

rocrate -c some/ro-crate add workflow

Now becomes

rocrate add workflow -c some/ro-crate

The advantage of this is that it doesn't enforce this option on all
commands, even those that don't need it and it is probably more
intuitive for the user to put the option closer to all other options.

[sphuber]

I ran into this problem and saw there was an open issue. I tried to find a solution first with keeping the place of the option as it was, but I think this is not possible with the current functionality of click.

[simleo]

Awesome, thanks! I've re-wrapped the docstrings to stay within 80 columns for readability

[simleo]

@sphuber I forgot: please add the relevant copyright info to the files you modified, in the boilerplate at the top

[sphuber]

I forgot: please add the relevant copyright info to the files you modified, in the boilerplate at the top

I am not sure I understand what you mean. What should I change or add?

[simleo]

At the top of code files there's a copyright notice that looks like this:

# Copyright 2019-2022 The University of Manchester, UK
[...]
# Licensed under the Apache License, Version 2.0 (the "License");
[...]

Please add a line like the following:

# Copyright 2022 <YOUR EMPLOYER>

[sphuber]

See #117

[simleo]

I just recalled that we're adding all copyright entries to all files, for simplicity. I've updated #117 accordingly.