Replace the dict-based way of declaring sockets and namespaces with the spec API

[superstar54]

This PR replaces the old dict-based way of declaring sockets and namespaces with the spec API from node-graph.

In this way, one can declare the

• top-level dynamic outputs, output_sepc=spec.dynamic(any)
• dynamic of namespace, output_spec=spec.dynamic(spec.namespace(sum=int))

Before

@pyfunction(outputs=[{"name": "sum"}, {"name": "diff"}])
def add(x, y):
    return {"sum": x + y, "diff": x - y}

After

@pyfunction(outputs=spec.namespace(sum=any, diff=any))
def add(x, y):
    return {"sum": x + y, "diff": x - y}

Or, one can use type annotation directly:

@pyfunction()
def add(x, y) -> spec.namespace(sum=any, diff=any):
    return {"sum": x + y, "diff": x - y}

[codecov-commenter]

Codecov Report

❌ Patch coverage is 92.14660% with 15 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.15%. Comparing base (a70e9a0) to head (a89a8a7).

Files with missing lines	Patch %	Lines
src/aiida_pythonjob/utils.py	89.88%	9 Missing ⚠️
src/aiida_pythonjob/ports_adapter.py	94.02%	4 Missing ⚠️
src/aiida_pythonjob/calculations/pyfunction.py	77.77%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #35      +/-   ##
==========================================
+ Coverage   83.72%   84.15%   +0.42%     
==========================================
  Files          19       20       +1     
  Lines        1063     1136      +73     
==========================================
+ Hits          890      956      +66     
- Misses        173      180       +7     

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[edan-bainglass]

Just for future reference, it only needs to be as long as the title (less raises an issue, more is unnecessary) 🙂

[edan-bainglass]

Because ._func is no longer guaranteed?

[superstar54]

I encountered _func does not exist one time, but I can not reproduce, maybe when reloading the process (e.g., when the daemon restarts). But this should be fixed in another method. I have update it in this commit

[edan-bainglass]

Can you explain this file?

[superstar54]

Yes, the spec API and its related utilities are defined in node-graph and reused by WorkGraph and PythonJob, which keeps this API as the single source of truth. To avoid exposing the "socket" concept to PythonJob users (since it's an AiiDA plugin that can be used independently of WorkGraph), a simple adapter is used to convert "socket" to "port".
It's hard to decide where we put the spec API, we keep it in the node-graph for now.

[superstar54]

Socket and Port are very similar schemas, but Socket has more metadata (e.g., links).

[edan-bainglass]

Okay. Thanks 🙏

[edan-bainglass]

Got a few questions

[edan-bainglass]

LGTM!