touchpycli.sh

#!/usr/bin/bash

filename=$1

if [[ $# -eq 0 ]]; then
    >&2 echo "Error: no arguments provided"
    >&2 echo "USAGE: $(basename $0) [NEW_FILE_NAME]"
    exit 1
fi

touch "${filename}.py"
chmod +x "${filename}.py"

template() {
    cat <<'EOF'
#!/usr/bin/env python3
"""
Description

Input:
    ...
Output:
    ...
Purpose:
    ...
Prerequisites:
    ...
\033[1m\033[31mWARNING:\033[0m
    ...

"""
# TODO:
# - [ ]

from Bio import SeqIO
from itertools import combinations
from pathlib import Path
from typing import TextIO, NamedTuple
from dataclasses import dataclass
import argparse
import gzip
import logging
import numpy as np
import polars as pl
import shutil
import subprocess
import sys


# =============================================================================
# logger
logging.basicConfig(
    level=logging.INFO,
    format="[%(asctime)s] %(levelname)s -- %(message)s",
    datefmt="%H:%M:%S",
)
logger = logging.getLogger(__name__)


# =============================================================================
# CLI args
# =============================================================================
@dataclass
class Args:
    infile: Path
    outdir: Path


def collect_args() -> Args:
    """Argument parsing"""
    parser = argparse.ArgumentParser(
        description=__doc__,
        formatter_class=argparse.RawDescriptionHelpFormatter,
    )

    parser.add_argument(
        "-i",
        "--infile",
        type=Path,
        metavar="FILE",
        required=True,
        help="Path to input [Required]",
    )

    parser.add_argument(
        "-o",
        "--outdir",
        type=Path,
        required=False,
        default=".",
        metavar="DIR",
        help="Output target directory [Optional][Default: cwd]",
    )

    args = Args(**vars(parser.parse_args()))

    return args


# =============================================================================
# Core func.
# =============================================================================
def funca(args):
    """Description

    ---
    Args:
        arg1 (dtype): description

    Returns:
        dtype: description
    """
    # stuff
    print("Hello world")


# =============================================================================
def main() -> None:
    """Workflow:
    ---
    main
     ├── args
     └── func
     │
    """
    # get args
    args = collect_args()

    # func
    funca(args)


# =============================================================================
if __name__ == "__main__":
    sys.exit(main())
EOF
}

template >"${filename}.py"