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jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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atropos does not work with python 3.8 because of clock module #87

Closed kingralph80 closed 4 years ago

kingralph80 commented 4 years ago

Dear authors,

when I run atropos I get: self.start_time = Timestamp() File "/netscratch/dep_psl/grp_frommer/Thomas/bin/miniconda3/envs/atropos/lib/python3.8/site-packages/atropos-1.1.23-py3.8-linux-x86_64.egg/atropos/util/init.py", line 227, in init self.clock = time.clock() AttributeError: module 'time' has no attribute 'clock'

After checking online i found that the time module has been removed from python 3.8:

From the Python 3.8 doc:

The function time.clock() has been removed, after having been deprecated since Python 3.3: use time.perf_counter() or time.process_time() instead, depending on your requirements, to have well-defined behavior. (Contributed by Matthias Bussonnier in bpo-36895.)

jdidion commented 4 years ago

Thanks for reporting this. I should be able to get a new version out shortly with this resolved.

jdidion commented 4 years ago

Fixed in 1.1.24