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Prefix undocumented functions with an underscore to indicate that they're private#833

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leehart merged 70 commits intomasterfrom
GH796_prefix_private_functions
Dec 5, 2025
Merged

Prefix undocumented functions with an underscore to indicate that they're private#833
leehart merged 70 commits intomasterfrom
GH796_prefix_private_functions

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@leehart leehart commented Dec 1, 2025

Re: issue #796

leehart added 30 commits December 1, 2025 09:51
@leehart
Remove obsolete duplicate add_frequency_ci function from util.py (was…
e55906c 
… previously moved to frq_base.py)
@leehart
Merge branch 'master' into GH796_prefix_private_functions
49cd651
@leehart
Rename to _add_frequency_ci and update uses
6c65f49
@leehart
Rename to _apply_allele_mapping and update uses
83bf319
@leehart
Update to _add_frequency_ci, update uses. Reorder imports (Pylint)
3d01aaf
@leehart
Update use of _apply_allele_mapping
162ad3e
@leehart
Rename to _biallelic_diplotype_cityblock, update uses
86dc5c6
@leehart
Rename to _biallelic_diplotype_euclidean, update uses
15dec3b
@leehart
Rename to _biallelic_diplotype_pdist, update uses
58b2f66
@leehart
Rename to _biallelic_diplotype_sqeuclidean, update uses
2dbeb1d
@leehart
Rename to _build_cohorts_from_sample_grouping, update uses
f7000f2
@leehart
Rename to _check_colab_location, update uses
eb15ea7
@leehart
Rename to _compare_series_like, update uses
b597aa0
@leehart
Rename to _da_compress, update uses
cdbf3fa
@leehart
Rename to _da_concat, update uses
0bed276
@leehart
Rename to _da_from_zarr, update uses
0770754
@leehart
Rename to _dask_apply_allele_mapping, update uses
0407f49
@leehart
Rename to _dask_compress_dataset, update uses
f08be92
@leehart
Rename to _dask_genotype_array_map_alleles, update uses
179d432
@leehart
Rename to _diplotype_frequencies, update uses
2152380
@leehart
Rename to _distributed_client, update uses
ccf9b42
@leehart
Rename to _garud_g123, update uses
ebb03e7
@leehart
Rename to _garud_h12, update uses
7222ae1
@leehart
Rename to _genotype_array_map_alleles, update uses
f86acf9
@leehart
Rename to _get_gcp_region, update uses
6d545a2
@leehart
Rename to _gff3_parse_attributes, update uses
2a87710
@leehart
Rename to _h1x, update uses
fbe1ad9
@leehart
Rename to _haplotype_frequencies, update uses
5a3b793
@leehart
Rename to _haplotype_joint_frequencies, update uses
61a7fb1
@leehart
Rename to _hash_columns, update uses
0d52f41
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codecov bot commented Dec 1, 2025

Codecov Report

❌ Patch coverage is 99.00000% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.68%. Comparing base (4c9100b) to head (6168f4c).

Files with missing lines Patch % Lines
malariagen_data/anoph/distance.py 85.71% 2 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##           master     #833      +/-   ##
==========================================
+ Coverage   90.66%   90.68%   +0.02%     
==========================================
  Files          49       49              
  Lines        5174     5175       +1     
==========================================
+ Hits         4691     4693       +2     
+ Misses        483      482       -1

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

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leehart commented Dec 2, 2025

A couple of functions do not appear to be used anywhere in the package:

  • _multiallelic_diplotype_mean_euclidean (formerly multiallelic_diplotype_mean_euclidean)
  • _value_error (formerly value_error)

A curiosity: plasmodium.py overrides the _resolve_region (formerly resolve_region) from util.py but does nothing except provide a different docstring.

The only undocumented function so far (afaik) that doesn't get the private underscore treatment is check_types in util.py, which is a decorator function, used throughout the codebase as @check_types. There appears to be a problem converting this to a private function and using a @_check_types decorator instead, which I'm still investigating.

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leehart commented Dec 2, 2025

Somewhere along the way, some expected NaNs became Nones.
Investigating...

=========================== short test summary info ============================
FAILED tests/anoph/test_snp_frq.py::test_allele_frequencies_advanced_with_area_by[ag3_sim-admin1_iso] - AssertionError: 
Arrays are not equal

Mismatched elements: 14702 / 14908 (98.6%)
 x: array([None, None, None, ..., None, None, None], dtype=object)
 y: array([nan, nan, nan, ..., nan, nan, nan], dtype=object)
FAILED tests/anoph/test_snp_frq.py::test_allele_frequencies_advanced_with_area_by[af1_sim-admin1_iso] - AssertionError: 
Arrays are not equal

Mismatched elements: 1189 / 1422 (83.6%)
 x: array([None, None, None, ..., None, None, None], dtype=object)
 y: array([nan, nan, nan, ..., nan, nan, nan], dtype=object)
FAILED tests/anoph/test_snp_frq.py::test_allele_frequencies_advanced_with_area_by[adir1_sim-admin1_iso] - AssertionError: 
Arrays are not equal

Mismatched elements: 3297 / 3400 (97%)
 x: array([None, None, None, ..., None, None, None], dtype=object)
 y: array([nan, nan, nan, ..., nan, nan, nan], dtype=object)
FAILED tests/anoph/test_snp_frq.py::test_allele_frequencies_advanced_with_period_by[ag3_sim-year] - AssertionError: 
Arrays are not equal

[...more of the same...]

Mismatched elements: 2802 / 3153 (88.9%)
 x: array([None, None, None, ..., None, None, None], dtype=object)
 y: array([nan, nan, nan, ..., nan, nan, nan], dtype=object)
FAILED tests/anoph/test_snp_frq.py::test_allele_frequencies_advanced_with_dup_samples[af1_sim] - AssertionError: 
Arrays are not equal

Mismatched elements: 9399 / 9567 (98.2%)
 x: array([None, None, None, ..., None, None, None], dtype=object)
 y: array([nan, nan, nan, ..., nan, nan, nan], dtype=object)
FAILED tests/anoph/test_snp_frq.py::test_allele_frequencies_advanced_with_dup_samples[adir1_sim] - AssertionError: 
Arrays are not equal

Mismatched elements: 2521 / 3016 (83.6%)
 x: array([None, None, None, ..., None, None, None], dtype=object)
 y: array([nan, nan, nan, ..., nan, nan, nan], dtype=object)
=========== 24 failed, 631 passed, 194 warnings in 720.47s (0:12:00) ===========

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leehart commented Dec 4, 2025

Requires resolution of the segmentation fault issue in CI checks: #835

@leehart leehart marked this pull request as ready for review December 4, 2025 11:48
@leehart leehart requested a review from jonbrenas December 4, 2025 11:48
@leehart leehart mentioned this pull request Dec 4, 2025
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jonbrenas approved these changes Dec 5, 2025
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LGTM

@leehart leehart merged commit 57d6b5d into master Dec 5, 2025
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@leehart leehart deleted the GH796_prefix_private_functions branch December 5, 2025 13:08
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