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.
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Andrew Charlwood
-197
@@ -1,197 +0,0 @@
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"""
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Configuration module for NHS High-Cost Drug Patient Pathway Analysis Tool.
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Contains PathConfig dataclass for centralizing all file path references.
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"""
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from dataclasses import dataclass, field
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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 PathConfig:
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"""
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Centralizes all file paths used across the application.
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Provides a single source of truth for file locations, making it easier to:
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- Change the data directory location
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- Support different environments (development, production)
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- Validate that required files exist
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Attributes:
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base_dir: Root directory of the application (defaults to current working directory)
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data_dir: Directory containing reference data files
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images_dir: Directory containing UI assets and fonts
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"""
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base_dir: Path = field(default_factory=Path.cwd)
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_data_dir: Optional[Path] = field(default=None, repr=False)
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_images_dir: Optional[Path] = field(default=None, repr=False)
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def __post_init__(self) -> None:
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"""Set default subdirectories relative to base_dir if not provided."""
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if self._data_dir is None:
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self._data_dir = self.base_dir / "data"
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if self._images_dir is None:
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self._images_dir = self.base_dir / "images"
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@property
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def data_dir(self) -> Path:
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"""Directory containing reference data files."""
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# _data_dir is always set after __post_init__
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assert self._data_dir is not None
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return self._data_dir
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@property
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def images_dir(self) -> Path:
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"""Directory containing UI assets and fonts."""
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# _images_dir is always set after __post_init__
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assert self._images_dir is not None
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return self._images_dir
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# Reference data files (read-only lookups)
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@property
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def drugnames_csv(self) -> Path:
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"""Drug name standardization mapping."""
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return self.data_dir / "drugnames.csv"
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@property
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def directory_list_csv(self) -> Path:
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"""Medical specialties/directories list."""
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return self.data_dir / "directory_list.csv"
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@property
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def treatment_function_codes_csv(self) -> Path:
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"""NHS treatment function code mappings."""
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return self.data_dir / "treatment_function_codes.csv"
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@property
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def drug_directory_list_csv(self) -> Path:
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"""Valid drug-to-directory mappings (pipe-separated)."""
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return self.data_dir / "drug_directory_list.csv"
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@property
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def org_codes_csv(self) -> Path:
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"""Provider code to organization name mapping."""
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return self.data_dir / "org_codes.csv"
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@property
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def include_csv(self) -> Path:
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"""Drug filter list with default selections."""
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return self.data_dir / "include.csv"
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@property
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def default_trusts_csv(self) -> Path:
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"""NHS Trust list for filter."""
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return self.data_dir / "defaultTrusts.csv"
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# Output/diagnostic files
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@property
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def na_directory_rows_csv(self) -> Path:
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"""Exported rows with unresolved Directory for diagnostics."""
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return self.data_dir / "na_directory_rows.csv"
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@property
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def ta_recommendations_xlsx(self) -> Path:
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"""NICE TA recommendations (downloaded from web)."""
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return self.data_dir / "ta-recommendations.xlsx"
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# UI assets
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@property
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def font_medium(self) -> Path:
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"""AvenirLTStd-Medium font file."""
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return self.images_dir / "AvenirLTStd-Medium.ttf"
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@property
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def font_roman(self) -> Path:
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"""AvenirLTStd-Roman font file."""
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return self.images_dir / "AvenirLTStd-Roman.ttf"
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@property
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def logo_ico(self) -> Path:
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"""Application icon."""
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return self.images_dir / "logo.ico"
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@property
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def logo_png(self) -> Path:
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"""Application logo."""
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return self.images_dir / "logo.png"
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def validate(self) -> list[str]:
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"""
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Validate that required files and directories exist.
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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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# Check directories exist
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if not self.data_dir.exists():
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errors.append(f"Data directory not found: {self.data_dir}")
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if not self.images_dir.exists():
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errors.append(f"Images directory not found: {self.images_dir}")
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# Check required reference files
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required_files = [
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(self.drugnames_csv, "Drug names mapping"),
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(self.directory_list_csv, "Directory list"),
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(self.treatment_function_codes_csv, "Treatment function codes"),
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(self.drug_directory_list_csv, "Drug-directory mapping"),
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(self.org_codes_csv, "Organization codes"),
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(self.include_csv, "Drug include list"),
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(self.default_trusts_csv, "Default trusts"),
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]
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for file_path, description in required_files:
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if not file_path.exists():
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errors.append(f"{description} not found: {file_path}")
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return errors
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def validate_fonts(self) -> list[str]:
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"""
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Validate that font files exist (for GUI mode).
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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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font_files = [
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(self.font_medium, "Medium font"),
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(self.font_roman, "Roman font"),
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]
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for file_path, description in font_files:
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if not file_path.exists():
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errors.append(f"{description} not found: {file_path}")
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return errors
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def as_legacy_paths(self) -> dict[str, str]:
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"""
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Return paths as strings with './' prefix for backwards compatibility.
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This method eases migration by providing paths in the format
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currently used throughout the codebase.
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Returns:
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Dictionary mapping path names to legacy-format string paths.
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"""
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return {
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"drugnames_csv": f"./{self.drugnames_csv.relative_to(self.base_dir)}",
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"directory_list_csv": f"./{self.directory_list_csv.relative_to(self.base_dir)}",
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"treatment_function_codes_csv": f"./{self.treatment_function_codes_csv.relative_to(self.base_dir)}",
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"drug_directory_list_csv": f"./{self.drug_directory_list_csv.relative_to(self.base_dir)}",
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"org_codes_csv": f"./{self.org_codes_csv.relative_to(self.base_dir)}",
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"include_csv": f"./{self.include_csv.relative_to(self.base_dir)}",
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"default_trusts_csv": f"./{self.default_trusts_csv.relative_to(self.base_dir)}",
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"na_directory_rows_csv": f"./{self.na_directory_rows_csv.relative_to(self.base_dir)}",
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"ta_recommendations_xlsx": f"./{self.ta_recommendations_xlsx.relative_to(self.base_dir)}",
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}
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# Default instance for application-wide use
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default_paths = PathConfig()
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