From aab1337c811fdf8c35d6c946447316384c79c426 Mon Sep 17 00:00:00 2001 From: Jon Brenas Date: Thu, 16 Jul 2026 15:45:39 +0200 Subject: [PATCH 1/2] Updated pca and _pca --- malariagen_data/anoph/pca.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/malariagen_data/anoph/pca.py b/malariagen_data/anoph/pca.py index d18e2842d..dda4a030c 100644 --- a/malariagen_data/anoph/pca.py +++ b/malariagen_data/anoph/pca.py @@ -145,6 +145,7 @@ def pca( sample_query_options=sample_query_options, sample_indices=sample_indices, ) + print(prepared_sample_indices) prepared_region = self._prep_region_cache_param(region=region) prepared_site_mask = self._prep_optional_site_mask_param(site_mask=site_mask) @@ -171,7 +172,6 @@ def pca( cohorts=cohorts, cohort_size=cohort_size, min_cohort_size=min_cohort_size, - max_cohort_size=max_cohort_size, exclude_samples=exclude_samples, fit_exclude_samples=fit_exclude_samples, random_seed=random_seed, @@ -236,7 +236,6 @@ def _pca( n_components, cohort_size, min_cohort_size, - max_cohort_size, exclude_samples, fit_exclude_samples, random_seed, @@ -257,7 +256,7 @@ def _pca( site_class=site_class, cohort_size=cohort_size, min_cohort_size=min_cohort_size, - max_cohort_size=max_cohort_size, + max_cohort_size=None, random_seed=random_seed, chunks=chunks, inline_array=inline_array, From 0863b95fc4b05dac9a5d08a3481b3e479d4f7140 Mon Sep 17 00:00:00 2001 From: Jon Brenas Date: Thu, 16 Jul 2026 15:49:12 +0200 Subject: [PATCH 2/2] Forgot a debugging comment --- malariagen_data/anoph/pca.py | 1 - 1 file changed, 1 deletion(-) diff --git a/malariagen_data/anoph/pca.py b/malariagen_data/anoph/pca.py index dda4a030c..e51d61a69 100644 --- a/malariagen_data/anoph/pca.py +++ b/malariagen_data/anoph/pca.py @@ -145,7 +145,6 @@ def pca( sample_query_options=sample_query_options, sample_indices=sample_indices, ) - print(prepared_sample_indices) prepared_region = self._prep_region_cache_param(region=region) prepared_site_mask = self._prep_optional_site_mask_param(site_mask=site_mask)