Make ase,mdtraj and MDAnalysis optional extras

[oerc0122]

Description of work
Remove explicit dependency on optional external projects.

Fixes

• Remove dependency on ase, mdtraj and mdanalysis
• Disable jobs if not present.
• Add visible label to Configurable s to enable visibility without working.
• These should also have a requires_extras tuple to display a useful error message to users for disabled jobs.

To test
Try GUI, ensure jobs are disabled. Ensure tests pass.

[MBartkowiakSTFC]

Could we change the behaviour so the corresponding jobs are still listed in the GUI, but are not enabled if their underlying Python package is not installed? This would prevent the situation where a new user never realises that they had the option of installing external packages. What do you think?

[oerc0122]

This is exactly what Chi said, so it seems like a popular option. Do we want to change enabled to grey out the option rather than not list in general?

[MBartkowiakSTFC]

At the moment the enabled variable in MDANSE also controls if the job is visible. We probably need a distinction between enabled and visible.

On the GUI side, it should be possible to run .setEnabled(False) on the specific QStandardItem in the JobTree.

[MBartkowiakSTFC]

@oerc0122 @ChiCheng45 What phrasing do we prefer for this message?

I would consider emphasising in the text that the whole thing is optional, so the users don't wonder why we did not include the required dependency to start with. Something like:

                widget = QLabel(f"""<h1>{job_name} requires an external package.</h1>

                <h2>The following optional dependencies of MDANSE are needed here: {", ".join(job_instance.requires_extras)}.</h2>

                <h2>If you want to use {job_name}, please install the additional dependencies, e.g. by running:</h2>

                <h2><b>pip install "mdanse[{",".join(job_instance.requires_extras)}]"</b></h2>
                """)

Anyway, I'm also happy with the current version (especially since it tells the user what to do to enable the job).

[oerc0122]

I would probably combine the two to make:

Suggested change

	widget = QLabel(f"""<h1>Job {job_name} not available.</h1>
	<h2>Please install MDANSE with the following extras enabled: {", ".join(job_instance.requires_extras)}.</h2>
	<h2>To do this, install using, e.g.:</h2>
	<h2><b>pip install "mdanse[{",".join(job_instance.requires_extras)}]"</b></h2>
	widget = QLabel(f"""<h1>{job_name} requires an external package.</h1>
	<h2>Please install MDANSE with the following
	optional dependencies enabled:
	{", ".join(job_instance.requires_extras)}.</h2>
	<h2>To do this, install using, e.g.:</h2>
	<h2><b>pip install "mdanse[{",".join(job_instance.requires_extras)}]"</b></h2>