Principal Processing Code/_common.py

"""Shared CSV validation and non-overwriting output helpers."""
import argparse
import os
from contextlib import contextmanager
from pathlib import Path
import tempfile

import numpy as np
import pandas as pd


def parser(description):
    return argparse.ArgumentParser(description=description)


def require(df, columns):
    missing = set(columns) - set(df.columns)
    if missing:
        raise ValueError(f"Missing columns: {sorted(missing)}")


def numeric(df, columns, integer=False):
    require(df, columns)
    for col in columns:
        values = pd.to_numeric(df[col], errors="raise")
        if not np.isfinite(values.to_numpy(dtype=float)).all():
            raise ValueError(f"Non-finite values in {col}")
        if integer:
            if not (values == np.floor(values)).all():
                raise ValueError(f"Non-integer values in {col}")
            values = values.astype("int64")
        df[col] = values


def unique(df, keys):
    require(df, keys)
    if df[keys].isna().any().any() or df.duplicated(keys).any():
        raise ValueError(f"Missing or duplicate keys: {keys}")


def read_csv(path):
    df = pd.read_csv(path, encoding="utf-8-sig")
    if df.empty:
        raise ValueError(f"Empty input: {path}")
    return df


@contextmanager
def output_path(path):
    path = Path(path)
    if path.exists():
        raise FileExistsError(f"Output exists; choose a new filename: {path}")
    path.parent.mkdir(parents=True, exist_ok=True)
    handle, temporary = tempfile.mkstemp(prefix=path.name + ".", dir=path.parent)
    os.close(handle)
    try:
        yield temporary
        if path.exists():
            raise FileExistsError(path)
        os.replace(temporary, path)
    finally:
        if os.path.exists(temporary):
            os.unlink(temporary)


def save_csv(df, path):
    with output_path(path) as temporary:
        df.to_csv(temporary, index=False, encoding="utf-8-sig")
    print(f"Saved {len(df):,} rows: {path}")