Add transPath to input

[samwaseda]

This pull request adds support for the transPath group to the ricTS section in the Sphinx input parser. The transPath group allows users to specify an initial guess for the atomic displacement pattern along the transition direction, which is important for transition state searches. The changes include updates to both the Python parser logic and the YAML schema.

New feature: transPath support in ricTS:

• Added an optional transPath parameter to the _sphinx__main__ricTS function, updated its docstring, and ensured it is passed to the underlying value filler. (sphinx_parser/input.py) [1] [2] [3]
• Implemented the _sphinx__main__ricTS__transPath helper function to handle the transPath group, including its arguments (dir_, atomId, atomIds) and documentation. (sphinx_parser/input.py)

Schema update:

• Added the transPath group to the sphinx.main.ricTS section in the YAML schema, with fields for atomId, atomIds, and dir, along with descriptions and data types. (sphinx_parser/src/input_data.yml)

[github-actions]

👈 Launch a binder notebook on branch pyiron/sphinx_parser/transpath

[codacy-production]

Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

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🟢 Metrics 0 complexity · 5 duplication

Metric	Results
Complexity	0
Duplication	5

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[codecov]

Codecov Report

❌ Patch coverage is 75.00000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 88.63%. Comparing base (ef195f2) to head (134cdd7).

Files with missing lines	Patch %	Lines
sphinx_parser/input.py	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #77      +/-   ##
==========================================
- Coverage   88.70%   88.63%   -0.07%     
==========================================
  Files           8        8              
  Lines         841      845       +4     
==========================================
+ Hits          746      749       +3     
- Misses         95       96       +1     

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[Copilot]

Pull request overview

Adds support for the transPath group under sphinx.main.ricTS so users can provide an initial transition-direction displacement pattern for transition state searches.

Changes:

• Extended sphinx.main.ricTS(...) to accept an optional transPath group and pass it through to the generated input dictionary.
• Added a new sphinx.main.ricTS.transPath(...) helper for constructing the transPath group.
• Updated the YAML schema to include ricTS.transPath with atomId / atomIds and required dir.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 4 comments.

File	Description
sphinx_parser/src/input_data.yml	Adds transPath schema under sphinx.main.ricTS (fields + descriptions).
sphinx_parser/input.py	Adds transPath parameter to ricTS and introduces the ricTS.transPath group helper.

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