Refactor parser

[superstar54]

• rename function_outputs to output_ports
• add support for input_ports
• PyFunction and PythonJob share the helper parser function.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 91.62562% with 17 lines in your changes missing coverage. Please review.

Project coverage is 87.71%. Comparing base (81f97f9) to head (c6f9fa8).

Files with missing lines	Patch %	Lines
src/aiida_pythonjob/utils.py	90.90%	11 Missing ⚠️
src/aiida_pythonjob/calculations/pyfunction.py	85.18%	4 Missing ⚠️
src/aiida_pythonjob/data/utils.py	77.77%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #25      +/-   ##
==========================================
+ Coverage   85.57%   87.71%   +2.13%     
==========================================
  Files          16       17       +1     
  Lines         929      944      +15     
==========================================
+ Hits          795      828      +33     
+ Misses        134      116      -18     

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[Copilot]

Pull Request Overview

This PR refactors the parser interface by renaming the output‐related keys from function_outputs to output_ports and adding support for input_ports. In addition, it shares the helper parser function between PyFunction and PythonJob and updates related tests and documentation for consistency.

Reviewed Changes

Copilot reviewed 16 out of 16 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
src/aiida_pythonjob/utils.py	Introduces helper functions for formatting and serializing input/output ports.
src/aiida_pythonjob/calculations/pyfunction.py	Updates process specification to use output_ports instead of deprecated outputs key.
tests/test_pyfunction.py	Adjusts tests to use the new output_ports parameter instead of function_outputs.
tests/test_parser.py	Modifies tests to validate output_ports handling in the parser.
docs/gallery/autogen/*	Updates documentation examples replacing function_outputs with output_ports.
Other files	Various helper functions, decorators, and utilities updated accordingly for consistency.

Comments suppressed due to low confidence (3)

src/aiida_pythonjob/utils.py:259

• [nitpick] Consider using a consistent uppercase default for 'identifier' (e.g., 'ANY') to match comparisons elsewhere in the code.

item.setdefault("identifier", "any")

tests/test_pyfunction.py:55

• Ensure test inputs consistently use 'output_ports' instead of the deprecated 'function_outputs' to align with the updated API.

output_ports=[{"name": "sum"}, ...]

src/aiida_pythonjob/calculations/pyfunction.py:46

• The change from 'function_data.outputs' to 'function_data.output_ports' improves clarity; ensure that corresponding documentation and error messages are updated accordingly.

spec.input("function_data.output_ports", valid_type=Dict, serializer=to_aiida_type, required=False)