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Updated some inline documentation for prepare decoding #10

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Updated some inline documentation for prepare decoding #10

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18 changes: 11 additions & 7 deletions src/__init__.py
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Expand Up @@ -51,13 +51,17 @@ def prepare_decoding(
Calculate decoding quantities. If a csfs_file is specified, the precalculated CSFS will be used. If no csfs_file is
specified, CSFS will be calculated.

:param demography: the demographic file or code (e.g. 'CEU')
:param discretization: the discretization file or discretization quantile information
:param frequencies: the frequencies file, or built-in (e.g. 'UKBB')
:param csfs_file: optional file containing precalculated CSFS (default, CSFS will be calculated at runtime)
:param file_root: optional file root containing data from which frequencies may be calculated
:param samples: number of samples (default 300)
:param mutation_rate: the mutation rate (default 1.65e-8)
:param str demography: the demographic file or code (e.g. 'CEU'),
NOTE: Effective population size is specified as haploid.
:param discretization: a discretization file or discretization quantile information,
for example `[[30.0, 10], [100.0, 8], 25]` specifies a discretization with
10 intervals of size 30 generations, followed by 8 intervals of size 100,
followed by 25 additional quantiles from the coalescent distribution
:param str frequencies: the frequencies file, or built-in (e.g. 'UKBB')
:param str csfs_file: optional file containing precalculated CSFS (default, CSFS will be calculated at runtime)
:param str file_root: optional file root containing data from which frequencies may be calculated
:param int samples: number of haploid samples (default: 300)
:param float mutation_rate: the mutation rate per basepair per generation (default: 1.65e-8)
:return: a decoding quantities object
"""
return prepareDecoding(
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