Laboratory name is always used as a path

[aidanheerdegen]

I thought I could set laboratory name, without a path, and that would allow a config to be shared without a hard coded path. I formed that belief based on this code block:

https://github.com/marshallward/payu/blob/master/payu/laboratory.py#L65-L69

That code is never reached, as this logic:

https://github.com/marshallward/payu/blob/master/payu/laboratory.py#L40-L44

means it isn't called, even if laboratory isn't a full path.

[aidanheerdegen]

I've "fixed" it by changing the logic to this:

        # If no lab path is set, generate a default path
        if not self.basepath or not os.path.isabs(self.basepath):
            self.basepath = self.get_default_lab_path(config)

should I then remove the isabs test in get_default_lab_path? Seems redundant now.

[marshallward]

So laboratory: some/rel/path is not working? that is the issue?

I'm confused because set_default_lab_path should not even be called if laboratory: ... is set.

[aidanheerdegen]

I want to be able to have this:

laboratory: access-esm
model: access

So when I share this config it will make a /short/$PROJECT/$USER/access-esm laboratory

[aidanheerdegen]

The code seems to suggest this is possible

[marshallward]

i think it's just not handled, i.e. a bug.

Maybe just convert laboratory: access-esm to an absolute path? set_default_lab_path is really supposed to be for when no lab is set.

[marshallward]

This seems equally relevant to PAYU_LAB_PATH, btw

[marshallward]

Seems like this whole block is presuming absolute paths (if that is the problem, still not clear):

        if lab_path:
            self.basepath = lab_path
        elif 'PAYU_LAB_PATH' in os.environ:
            self.basepath = os.environ.get('PAYU_LAB_PATH')
        else:
            self.basepath = config.get('laboratory')

maybe save to a temp variable then conditionally convert it to absolute path before saving to self.basepath

[marshallward]

Either way, I would not recommend calling set_default_lab_path if config['laboratory'] is set.

[aidanheerdegen]

So why does this check even exist?

        if os.path.isabs(lab_name):
            lab_path = lab_name
        else:
            user_name = config.get('user', default_user)
            lab_path = os.path.join(short_path, user_name, lab_name)

[aidanheerdegen]

That is literally what I want to do, but am prevented by the code above

[aidanheerdegen]

In a way, you can use the way the code currently works to sort of have what @nichannah would like, and make the laboratory local. I know, he doesn't want all the symlinks, but it is 70% of what he wants.

What I am suggesting would require something like

laboratory: ./local

to have a local laboratory

[aidanheerdegen]

I think what I am suggesting would make it behave the same way as input paths, absolute paths are respected, otherwise relative to the input dir.

I don't see why laboratory is an exception.

[aidanheerdegen]

Agreed that relative laboratory paths should be supported. Implemented here

https://github.com/marshallward/payu/pull/166

Will close this as a result.