Add AiiDA infrastructure

[GeigerJ2]

No description provided.

[jan-janssen]

@GeigerJ2 I adopted the changes to quantum_espresso_workflow.py in #12 and #13 , this helped me to update the jobflow and pyiron_base notebooks.

[jan-janssen]

I tried the jupyter notebook universal_simple_to_aiida.ipynb and it seems to require an updated aiida-workgraph version, as I get the following error message:

---------------------------------------------------------------------------
Exception                                 Traceback (most recent call last)
Cell In[2], line 1
----> 1 workgraph = load_workflow_json(filename='workflow_simple.json')

File [~/python_workflow_definition/src/python_workflow_definition/aiida.py:78](https://hub.2i2c.mybinder.org/user/geigerj2-python-flow-definition-t6m0v92n/python_workflow_definition/src/python_workflow_definition/aiida.py#line=77), in load_workflow_json(filename)
     75 # func = func_mapping[identifier]
     76 # I use the register_pickle_by_value, because the function is defined in a local file
     77 try:
---> 78     wg.add_task(func, register_pickle_by_value=True, name=m)
     79 except ValueError:
     80     if m in name_counter:

File [/srv/conda/envs/notebook/lib/python3.12/site-packages/aiida_workgraph/workgraph.py:512](https://hub.2i2c.mybinder.org/srv/conda/envs/notebook/lib/python3.12/site-packages/aiida_workgraph/workgraph.py#line=511), in WorkGraph.add_task(self, identifier, name, **kwargs)
    508 def add_task(
    509     self, identifier: Union[str, callable], name: str = None, **kwargs
    510 ) -> Task:
    511     """Add a task to the workgraph."""
--> 512     node = self.tasks._new(identifier, name, **kwargs)
    513     return node

File [/srv/conda/envs/notebook/lib/python3.12/site-packages/aiida_workgraph/collection.py:44](https://hub.2i2c.mybinder.org/srv/conda/envs/notebook/lib/python3.12/site-packages/aiida_workgraph/collection.py#line=43), in TaskCollection._new(self, identifier, name, uuid, **kwargs)
     42 if isinstance(identifier, WorkGraph):
     43     identifier = build_task_from_workgraph(identifier)
---> 44 return super()._new(identifier, name, uuid, **kwargs)

File [/srv/conda/envs/notebook/lib/python3.12/site-packages/node_graph/collection.py:200](https://hub.2i2c.mybinder.org/srv/conda/envs/notebook/lib/python3.12/site-packages/node_graph/collection.py#line=199), in decorator_check_identifier_name.<locals>.wrapper_func(*args, **kwargs)
    196 if kwargs.get("name", None) in args[0]._get_keys():
    197     raise ValueError(
    198         f"{kwargs.get('name')} already exists, please choose another name."
    199     )
--> 200 item = func(*args, **kwargs)
    201 return item

File [/srv/conda/envs/notebook/lib/python3.12/site-packages/node_graph/collection.py:246](https://hub.2i2c.mybinder.org/srv/conda/envs/notebook/lib/python3.12/site-packages/node_graph/collection.py#line=245), in NodeCollection._new(self, identifier, name, uuid, _metadata, _executor, **kwargs)
    237 item = ItemClass(
    238     list_index=list_index,
    239     name=name,
   (...)
    243     executor=_executor,
    244 )
    245 self._append(item)
--> 246 item.set(kwargs)
    247 # Execute post creation hooks
    248 self._execute_post_creation_hooks(item)

File [/srv/conda/envs/notebook/lib/python3.12/site-packages/node_graph/node.py:562](https://hub.2i2c.mybinder.org/srv/conda/envs/notebook/lib/python3.12/site-packages/node_graph/node.py#line=561), in Node.set(self, data)
    560     self.inputs[key]._set_socket_value(value)
    561 else:
--> 562     raise Exception(
    563         "No property named {}. Accept name are {}".format(
    564             key,
    565             list(self.get_property_names() + list(self.get_input_names())),
    566         )
    567     )

Exception: No property named register_pickle_by_value. Accept name are ['x', 'y', '_wait', 'computer', 'command_info', 'metadata', 'code', 'monitors', 'remote_folder', 'function_data', 'process_label', 'function_inputs', 'parent_folder', 'parent_folder_name', 'parent_output_folder', 'upload_files', 'copy_files', 'additional_retrieve_list']

[GeigerJ2]

Hi @jan-janssen, I just ran the universal_simple_to_aiida.ipynb notebook and couldn't reproduce your issue. Though, at this point, I also have editable installs of all the required packages (aiida-workgraph, node-graph, aiida-pythonjob) in my venv, as @superstar54 is actively developing them, so it might indeed just be that you have the released versions installed?

[jan-janssen]

@GeigerJ2 I was able to fix the pyiron_base related errors, by updating the environment variable but there still seem to be issues with the exported workflows.

[jan-janssen]

@GeigerJ2 From my perspective this is ready to be merged.

[GeigerJ2]

Thanks for the fix and merge, @jan-janssen!

[GeigerJ2]

Doesn't this apply for all the tasks, rather than just the generate_structures one? 🤔

[jan-janssen]

Yes, all lists