From b61db654c94b2ebbdab2b9c24b1b38acaba3776f Mon Sep 17 00:00:00 2001
From: chris <kai.clarkson@gmail.com>
Date: Thu, 7 Oct 2021 15:18:04 +0100
Subject: [PATCH] new cohort analysis is default

---
 malariagen_data/ag3.py |  6 +++---
 tests/test_ag3.py      | 10 +++++-----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/malariagen_data/ag3.py b/malariagen_data/ag3.py
index fa4448407..ce1031c78 100644
--- a/malariagen_data/ag3.py
+++ b/malariagen_data/ag3.py
@@ -771,7 +771,7 @@ def snp_allele_frequencies(
         self,
         transcript,
         cohorts,
-        cohorts_analysis="20210702",
+        cohorts_analysis="20210927",
         min_cohort_size=10,
         site_mask=None,
         site_filters="dt_20200416",
@@ -1661,7 +1661,7 @@ def gene_cnv_frequencies(
         self,
         contig,
         cohorts,
-        cohorts_analysis="20210702",
+        cohorts_analysis="20210927",
         min_cohort_size=10,
         species_calls=("20200422", "aim"),
         sample_sets="v3_wild",
@@ -1962,7 +1962,7 @@ def _read_cohort_metadata(self, *, sample_set, cohorts_analysis):
             self._cache_cohort_metadata[(sample_set, cohorts_analysis)] = df
             return df
 
-    def sample_cohorts(self, sample_sets="v3_wild", cohorts_analysis="20210702"):
+    def sample_cohorts(self, sample_sets="v3_wild", cohorts_analysis="20210927"):
         """Access cohorts metadata for one or more sample sets.
 
         Parameters
diff --git a/tests/test_ag3.py b/tests/test_ag3.py
index 2089618b3..5e45fd3bd 100644
--- a/tests/test_ag3.py
+++ b/tests/test_ag3.py
@@ -617,20 +617,20 @@ def test_snp_allele_frequencies__str_cohorts():
     df = ag3.snp_allele_frequencies(
         transcript="AGAP004707-RD",
         cohorts=cohorts,
-        cohorts_analysis="20210702",
+        cohorts_analysis="20210927",
         min_cohort_size=10,
         site_mask="gamb_colu",
         sample_sets="v3_wild",
         drop_invariant=True,
     )
-    df_coh = ag3.sample_cohorts(sample_sets="v3_wild", cohorts_analysis="20210702")
+    df_coh = ag3.sample_cohorts(sample_sets="v3_wild", cohorts_analysis="20210927")
     coh_nm = "cohort_" + cohorts
     all_uni = df_coh[coh_nm].dropna().unique().tolist()
     expected_fields = universal_fields + all_uni + ["max_af"]
 
     assert df.columns.tolist() == expected_fields
     assert isinstance(df, pd.DataFrame)
-    assert df.shape == (16639, 101)
+    assert df.shape == (16524, 103)
 
 
 def test_snp_allele_frequencies__dict_cohorts():
@@ -1049,7 +1049,7 @@ def test_gene_cnv_frequencies(contig, cohorts):
             cohort_labels = cohorts.keys()
         if isinstance(cohorts, str):
             df_coh = ag3.sample_cohorts(
-                sample_sets="v3_wild", cohorts_analysis="20210702"
+                sample_sets="v3_wild", cohorts_analysis="20210927"
             )
             coh_nm = "cohort_" + cohorts
             cohort_labels = list(df_coh[coh_nm].dropna().unique())
@@ -1173,7 +1173,7 @@ def test_sample_cohorts(sample_sets):
     )
 
     ag3 = setup_ag3()
-    df_coh = ag3.sample_cohorts(sample_sets=sample_sets, cohorts_analysis="20210702")
+    df_coh = ag3.sample_cohorts(sample_sets=sample_sets, cohorts_analysis="20210927")
     df_meta = ag3.sample_metadata(sample_sets=sample_sets)
 
     assert tuple(df_coh.columns) == expected_cols