docs: add PIPELINE_SETTINGS.md — how to configure the LNG + DeltaSign…

[adamjohnwright]

…al run

Aimed at operators standing the pipeline up (not tuning the model). Core message: the LNG_/DS_ tuning flags are the validated winning config as code defaults — leave them. The only things to configure per environment are the Neo4j connection, Reactome release alignment (Release97; LNG defaults to 97), and the diagram/catalog paths. Also documents the 0-100-in / 0-1-out solver scale and the parse-once/solve-many network_id flow (see deltasignal/docs/API.md).

Description

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Type of Change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Code quality improvement (refactoring, performance, etc.)

Related Issue

Fixes #(issue number)

Changes Made

• Change 1
• Change 2
• Change 3

Testing

Unit Tests

• All existing unit tests pass locally (poetry run pytest tests/ -v -m "not database")
• Added new unit tests for changes (if applicable)

Integration Tests (Optional - requires Neo4j)

• All integration tests pass locally (poetry run pytest tests/ -v)

Manual Testing

Describe any manual testing performed:

• Tested with pathway ID(s):
• Verified output files:

Code Quality

• Code follows project style guidelines (ruff)
• Ran poetry run ruff check src/ with no errors
• Ran poetry run ruff format src/
• Type hints added/updated where applicable
• Ran poetry run mypy --ignore-missing-imports src/ (optional)

Documentation

• Updated README.md (if needed)
• Added/updated docstrings
• Updated relevant documentation in docs/

Checklist

• Self-review completed
• Code is well-commented, particularly in complex areas
• No debugging code left in (print statements, breakpoints, etc.)
• No credentials or sensitive information in code
• Git commit messages are clear and descriptive

Screenshots (if applicable)

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Additional Notes

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