Run as follows: `python clip_to_same.py source.tif raster_with_desired_shape.tif outputfile.tif`

clip_to_same.py

import sys

import numpy as np
import rasterio as rio
from rasterio.warp import reproject, Resampling


def make_same(src_path: str, like_path: str, out_path: str) -> None:
    with rio.open(like_path) as ds:
        like_arr = ds.read(1)
        like_aff = ds.transform
        like_crs = ds.crs

    with rio.open(src_path) as ds:
        src_arr = ds.read(1)
        src_aff = ds.transform
        src_crs = ds.crs

    dest_arr = np.empty_like(like_arr, dtype=src_arr.dtype)

    with rio.Env():
        reproject(
            source=src_arr,
            destination=dest_arr,
            src_transform=src_aff,
            dst_transform=like_aff,
            src_crs=src_crs,
            dst_crs=like_crs,
            resampling=Resampling.nearest,
        )

    with rio.open(
        out_path,
        "w",
        driver="GTiff",
        count=1,
        width=dest_arr.shape[0],
        height=dest_arr.shape[1],
        transform=like_aff,
        crs=like_crs,
        dtype=dest_arr.dtype,
    ) as ds:
        ds.write(dest_arr, indexes=1)


if __name__ == "__main__":
    src_path = sys.argv[1]
    like_path = sys.argv[2]
    out_path = sys.argv[3]
    make_same(src_path, like_path, out_path)