I've identified 59 candidate undocumented functions to potentially get an underscore prefix to mark it as "private":

add_frequency_ci

apply_allele_mapping

biallelic_diplotype_cityblock

biallelic_diplotype_euclidean

biallelic_diplotype_pdist

biallelic_diplotype_sqeuclidean

build_cohorts_from_sample_grouping

check_colab_location

check_types

compare_series_like

da_compress

da_concat

da_from_zarr

dask_apply_allele_mapping

dask_compress_dataset

dask_genotype_array_map_alleles

diplotype_frequencies

distributed_client

garud_g123

garud_h12

genotype_array_map_alleles

get_gcp_region

gff3_parse_attributes

h1x

haplotype_frequencies

haplotype_joint_frequencies

hash_columns

hash_params

init_filesystem

init_zarr_store

jackknife_ci

jitter

locate_cohorts

locate_region

median_joining_network

mjn_graph

moving_h1x

multiallelic_diplotype_mean_cityblock

multiallelic_diplotype_mean_euclidean

multiallelic_diplotype_mean_sqeuclidean

multiallelic_diplotype_pdist

multiallelic_diplotype_sqeuclidean

pandas_apply

parse_multi_region

parse_single_region

pdist_abs_hamming

plot_dendrogram

plotly_discrete_legend

prep_samples_for_cohort_grouping

read_gff3

region_str

resolve_region

simple_xarray_concat

square_to_condensed

trim_alleles

true_runs

unpack_gff3_attributes

validate_sample_selection_params

value_error

@jonbrenas Do we want to document any of those instead? I.e. Add any of those to the docs/source/*.rst files instead? The consideration for "documented" functions is that we would want/need them to honour any of the new constructor params, unrestricted_use_only and surveillance_use_only, which would require checking and maybe substantial work.

I'll try to identify which of these "undocumented" functions look safe to make markedly "private", and perhaps which look like they really should be "public" and perhaps "documented" instead.

Rename functions that are not publicly documented to include an underscore prefix, to mark them as private #796

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