refactor: reorganize repository to src/ layout
Move 6 packages (core, config, data_processing, analysis, visualization, cli) into src/ to reduce root clutter. Merge tools/data.py into data_processing/transforms.py. Move docs to docs/. Path resolution via .pth file (setup_dev.py), pytest pythonpath config, and sys.path bootstrap in rxconfig.py and CLI entry points. Clean up pyproject.toml deps (remove stale pins, add snowflake-connector-python). Fix tomllib import for Python 3.10 compatibility. All 113 tests pass.
This commit is contained in:
Andrew Charlwood
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"""
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Data models for NHS High-Cost Drug Patient Pathway Analysis Tool.
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Contains dataclasses for encapsulating application state and filter parameters.
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"""
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from dataclasses import dataclass, field
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from datetime import date
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from pathlib import Path
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from typing import Optional
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@dataclass
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class AnalysisFilters:
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"""
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Encapsulates all filter state for the analysis pipeline.
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Replaces the individual parameters currently passed to generate_graph()
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and the global state managed in the GUI. This provides:
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- Type safety for filter values
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- Validation of filter combinations
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- Easy serialization for caching/persistence
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- Clear interface between GUI and analysis engine
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Attributes:
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start_date: Patient initiated start date (treatment pathway start)
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end_date: Patient initiated end date (treatment pathway start cutoff)
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last_seen_date: Minimum last seen date (filters out patients not seen recently)
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trusts: List of NHS Trust names to include (empty = all)
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drugs: List of drug names to include (empty = all)
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directories: List of medical directories/specialties to include (empty = all)
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custom_title: Optional custom title for the graph (blank = auto-generated)
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minimum_patients: Minimum number of patients for a pathway to be included
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output_dir: Directory where output files should be saved
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"""
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start_date: date
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end_date: date
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last_seen_date: date
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trusts: list[str] = field(default_factory=list)
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drugs: list[str] = field(default_factory=list)
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directories: list[str] = field(default_factory=list)
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custom_title: str = ""
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minimum_patients: int = 0
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output_dir: Optional[Path] = None
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def validate(self) -> list[str]:
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"""
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Validate filter configuration for logical consistency.
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Returns:
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List of error messages. Empty list means all validations passed.
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"""
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errors = []
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# Date range validation
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if self.end_date < self.start_date:
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errors.append(
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f"End date ({self.end_date}) cannot be before start date ({self.start_date})"
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)
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if self.last_seen_date > self.end_date:
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errors.append(
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f"Last seen date ({self.last_seen_date}) is after end date ({self.end_date}), "
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"which would exclude all patients"
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)
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# Minimum patients validation
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if self.minimum_patients < 0:
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errors.append(
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f"Minimum patients ({self.minimum_patients}) cannot be negative"
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)
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# Output directory validation
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if self.output_dir is not None and not self.output_dir.exists():
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errors.append(f"Output directory does not exist: {self.output_dir}")
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# Filter list validation (warn if empty but don't error)
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# Empty lists are valid and mean "include all"
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return errors
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@property
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def has_trust_filter(self) -> bool:
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"""Check if any trust filter is applied."""
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return len(self.trusts) > 0
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@property
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def has_drug_filter(self) -> bool:
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"""Check if any drug filter is applied."""
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return len(self.drugs) > 0
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@property
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def has_directory_filter(self) -> bool:
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"""Check if any directory filter is applied."""
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return len(self.directories) > 0
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@property
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def title(self) -> str:
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"""
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Return the display title for the graph.
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If custom_title is set, use it. Otherwise, generate a default title
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based on the date range.
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"""
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if self.custom_title:
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return self.custom_title
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return f"Patients initiated from {self.start_date} to {self.end_date}"
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def summary(self) -> str:
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"""
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Return a human-readable summary of the filter configuration.
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Useful for logging and display in the GUI.
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"""
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lines = [
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f"Date range: {self.start_date} to {self.end_date}",
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f"Last seen after: {self.last_seen_date}",
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f"Minimum patients: {self.minimum_patients}",
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]
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if self.trusts:
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lines.append(f"Trusts: {len(self.trusts)} selected")
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else:
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lines.append("Trusts: All")
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if self.drugs:
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lines.append(f"Drugs: {len(self.drugs)} selected")
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else:
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lines.append("Drugs: All")
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if self.directories:
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lines.append(f"Directories: {len(self.directories)} selected")
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else:
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lines.append("Directories: All")
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if self.custom_title:
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lines.append(f"Custom title: {self.custom_title}")
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return "\n".join(lines)
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