error when not specifying validation sets?

[realmarcin]

When these two keys are missing in the yaml:

pos_validation
neg_validation

Then get the following error:

can't find key in YAML: 'pos_validation'
can't find key in YAML: 'neg_validation'
Traceback (most recent call last):
File "/global/scratch/marcin/N2V/NEAT/venv/bin/neat", line 10, in
sys.exit(cli())
File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 829, in call
return self.main(*args, **kwargs)
File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/neat/cli.py", line 61, in run
yhelp.edge_embedding_method())
File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/neat/link_prediction/model.py", line 71, in make_link_prediction_data
these_params.update(graph_args)
TypeError: 'NoneType' object is not iterable

[justaddcoffee]

It'd be helpful to have the YAML you are using

[justaddcoffee]

Also it'd be helpful to have the graphs if possible.

These are likely just harmless warnings:

can't find key in YAML: 'pos_validation'
can't find key in YAML: 'neg_validation'

The error is here:

File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/neat/link_prediction/model.py", line 71, in make_link_prediction_data
these_params.update(graph_args)
TypeError: 'NoneType' object is not iterable

[realmarcin]

Here is another potentially related error:

can't find key in YAML: 'pos_validation'
can't find key in YAML: 'neg_validation'
Traceback (most recent call last):
File "/global/scratch/marcin/N2V/NEAT/venv/bin/neat", line 10, in
sys.exit(cli())
File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 829, in call
return self.main(*args, **kwargs)
File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/neat/cli.py", line 61, in run
yhelp.edge_embedding_method())
File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/neat/link_prediction/model.py", line 71, in make_link_prediction_data
these_params.update(graph_args)
TypeError: 'NoneType' object is not iterable

[justaddcoffee]

I think I'd need the graph files (nodes and edges tsv) to figure out what the problem is here. Seems to be an issue parsing the callbacks for MLP here.

It's nothing to do with these warning messages:

can't find key in YAML: 'pos_validation'
can't find key in YAML: 'neg_validation'