running example from muscle3 training results in unexpected error

[meiertgrootes]

Running the coupled_model.py example produces the following error:

'(cws) c-001-001-002:model_coupling eslt0101$ python3 coupled_model.py
Traceback (most recent call last):
  File "/Users/eslt0101/Projects/REPOS/eScience/couplingWS/model_coupling/coupled_model.py", line 23, in <module>
    configuration = ymmsl.load(Path('reaction_diffusion.ymmsl'))
  File "/Users/eslt0101/mambaforge/envs/cws/lib/python3.10/site-packages/ymmsl/io.py", line 41, in load
    return _load(source)
  File "/Users/eslt0101/mambaforge/envs/cws/lib/python3.10/site-packages/yatiml/loader.py", line 394, in __call__
    return cast(T, yaml.load(f, Loader=self.loader))
  File "/Users/eslt0101/mambaforge/envs/cws/lib/python3.10/site-packages/ruamel/yaml/main.py", line 951, in load
    return loader._constructor.get_single_data()
  File "/Users/eslt0101/mambaforge/envs/cws/lib/python3.10/site-packages/ruamel/yaml/constructor.py", line 111, in get_single_data
    node = self.composer.get_single_node()
  File "/Users/eslt0101/mambaforge/envs/cws/lib/python3.10/site-packages/yatiml/loader.py", line 60, in get_single_node
    node = self.__process_node(node, type(self).document_type)
  File "/Users/eslt0101/mambaforge/envs/cws/lib/python3.10/site-packages/yatiml/loader.py", line 162, in __process_node
    node = self.__savorize(node, recognized_type)
  File "/Users/eslt0101/mambaforge/envs/cws/lib/python3.10/site-packages/yatiml/loader.py", line 127, in __savorize
    expected_type._yatiml_savorize(cnode)
  File "/Users/eslt0101/mambaforge/envs/cws/lib/python3.10/site-packages/ymmsl/configuration.py", line 155, in _yatiml_savorize
    node.map_attribute_to_index('resources', 'name')
  File "/Users/eslt0101/mambaforge/envs/cws/lib/python3.10/site-packages/yatiml/helpers.py", line 886, in map_attribute_to_index
    if isinstance(new_mapping, yaml.MappingNode):
UnboundLocalError: local variable 'new_mapping' referenced before assignment
`

the ymmsl file used is the following:

ymmsl_version: v0.1

model:
  name: reaction_diffusion

  components:
    macro:
      implementation: diffusion
      ports:
        o_i: state_out
        s: state_in
        o_f: final_state_out

    micro:
      implementation: reaction
      ports:
        f_init: initial_state
        o_f: final_state  

  conduits:
    macro.state_out: micro.initial_state
    micro.final_state: macro.state_in

settings:
  micro.t_max: 2.469136e-6
  micro.dt: 2.469136e-8
  micro.k: -4.05e4
  macro.t_max: 1.234568e-4
  macro.dt: 2.469136e-6
  x_max: 1.01
  dx: 0.01
  d: 4.05e-2


resources:
  macro:
    threads:1
  micro:
    threads:2

[LourensVeen]

Ah, this may be a bug in YAtiML that I fixed in April, but which fix only just got released. Should check this with YAtiML 0.10.0 to see if that's the case.

[LourensVeen]

YAtiML 0.10.0 gives a better error message, but it still does not accept the file. The problem is that there is no space after the colon for the threads keys in the resources section, so ruamel.yaml doesn't parse it as a mapping. Something for the next YAtiML to give a better hint on maybe.