script.py

#!/usr/bin/env python
"""Use docstrings at the top of the file to document scripts' purpose."""
import datetime as dt
import json
import logging
import pickle

import navis
import pymaid

from utils.constants import CACHE_DIR, CREDENTIALS_DIR, OUTPUT_DIR

logger = logging.getLogger(__name__)
logger.info("Using navis version %s", navis.__version__)


# change "example.json" to match your credentials file's name
with open(CREDENTIALS_DIR / "example.json") as f:
    CREDS = json.load(f)

catmaid = pymaid.CatmaidInstance(**CREDS)


def example_function(some_arg, another_arg):
    """Use docstrings like this to describe functions.

    Here, some_arg and another_arg would be something like a name (str) or number
    which inform a query from CATMAID.
    """
    return {"some_arg": some_arg, "another_arg": another_arg}


def example_function_with_cache(some_arg, another_arg, force=False):
    """A wrapper around the above with a cache.

    You may want to cache raw data which takes a long time to fetch/generate
    or can change beneath your feet.
    Where possible, don't mix cached and fresh data.

    Cached data should not be shared, or kept for a long time.

    force=True ignores the cache and generates (then caches) new data.
    """
    cache_file = CACHE_DIR / f"example_{some_arg}_{another_arg}.pickle"
    if cache_file.is_file() and not force:
        logger.info("Loading cached output from %s", cache_file)
        return pickle.loads(cache_file.read_bytes())

    # do whatever data wrangling you were planning on...
    data = example_function(some_arg, another_arg)

    logger.info("Writing result to cache at %s", cache_file)
    cache_file.write_bytes(pickle.dumps(data))
    return data


# write your output to a timestamped file like
datestamp = dt.date.today().isoformat()
with open(OUTPUT_DIR / f"output_{datestamp}.txt", "w") as f:
    f.write("Hello, world!")