PR for whole code first CR #1
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istarmap.py
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| import multiprocessing.pool as mp | |||
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Add module level documentation for this file.
"""Summary line
More details...
"""
istarmap.py
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| import multiprocessing.pool as mp | ||
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| def istarmap(self, func, iterable, chunksize=1): |
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prefer creating a class that extends mp.Pool and adds this method. in your code you'll be using this class instead of mp.Pool.
istarmap.py
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| import multiprocessing.pool as mp | ||
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| def istarmap(self, func, iterable, chunksize=1): |
istarmap.py
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| def istarmap(self, func, iterable, chunksize=1): | ||
| """starmap-version of imap |
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Summary line. Starts with capital, end with period.
main.py
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| FLAGS = flags.FLAGS | ||
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| flags.DEFINE_integer('cpus', None, 'Number of CPUs to use in parallel. \ |
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for readability prefer breaking the string without slash:
flags.DEFINE_integer(
'cpus', None,
('Number of CPUs to use in parallel. default: all available cpus are used '
'bla blab bla.'))
main.py
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| logging.debug('MicroRNA list: %s', miR_list) | ||
| if FLAGS.species == 'homo_sapiens' and 'hsa' not in miR_list[0]: | ||
| logging.exception('species is \'homo_sapiens\' but some of the microRNAs in the list do not belong to humans') | ||
| raise Exception('species is \'homo_sapiens\' but some of the microRNAs in the list do not belong to humans') |
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Try using a less broad exception (maybe ValueError, or define your own exceptions as needed).
utils.py
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| import istarmap | ||
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| warnings.simplefilter(action='ignore', category=FutureWarning) |
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should be part of main? not sure anyone that imports this module would be interested in this filter
utils.py
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| the detected file name. | ||
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| Raises: | ||
| Exception if more than one file was detected. |
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use (existing or custom) less broad exceptions.
if only one type is raised, keep it in a single declaration: BlaBlaError if this happened or if that happened.
utils.py
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| pkl_file = glob.glob(data_path + '/*.pkl') | ||
| txt_files = glob.glob(data_path + '/*.txt') | ||
| tsv_files = glob.glob(data_path + '/*.tsv') | ||
| if pkl_file: |
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this code repeats and can be extracted into a method. something like:
def get_data_file(data_path:str, file_extension:str) -> Optional[str]:
"""..."""
files = glob.glob(os.path.join(data_path, '*.%s' extension))
if len(files) > 1:
raise ...
return next(iter(files), None)
and then you can do:
data_file = (
get_data_file(data_path, 'pkl') or
get_data_file(data_path, 'txt') or
get_data_file(data_path, 'tsv')
)
if not data_file:
raise BlaError(...)
return data_file
utils.py
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| logging.error('Type of species not recognized, either "homo_sapiens" or \ | ||
| "mus_musculus" are supported. For other species type, \ | ||
| please download the mti data file and update mti_loader function') | ||
| raise Exception('Type of species not recognized, either "homo_sapiens" or \ |
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replace all the \ line breakers with breaking strings into lines
… well as scientific notation in html
fix typos
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