From 09aeeee0c0973b2811210833fb511cc1f8eeafe7 Mon Sep 17 00:00:00 2001 From: John Huddleston Date: Mon, 9 Jan 2023 14:40:27 -0800 Subject: [PATCH] Ignore scipy warnings Ignores spurious scipy warnings that cause CI to fail. See PR 1120 [1] for a long-term solution to this issue. This short-term solution allows us to run CI on new code and ensure tests pass. [1] https://github.com/nextstrain/augur/pull/1120 --- tests/builds/zika.t | 2 +- tests/functional/refine.t | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/builds/zika.t b/tests/builds/zika.t index 55f8b2c93..745ab7453 100644 --- a/tests/builds/zika.t +++ b/tests/builds/zika.t @@ -86,7 +86,7 @@ Build a time tree from the existing tree topology, the multiple sequence alignme > --date-confidence \ > --date-inference marginal \ > --clock-filter-iqd 4 \ - > --seed 314159 > /dev/null + > --seed 314159 &> /dev/null Confirm that TreeTime trees match expected topology and branch lengths. diff --git a/tests/functional/refine.t b/tests/functional/refine.t index 7ceeb3614..3980c4d2c 100644 --- a/tests/functional/refine.t +++ b/tests/functional/refine.t @@ -16,7 +16,7 @@ Try building a time tree. > --date-confidence \ > --date-inference marginal \ > --clock-filter-iqd 4 \ - > --seed 314159 > /dev/null + > --seed 314159 &> /dev/null Confirm that TreeTime trees match expected topology and branch lengths. @@ -37,7 +37,7 @@ Build a time tree with mutations as the reported divergence unit. > --date-inference marginal \ > --clock-filter-iqd 4 \ > --seed 314159 \ - > --divergence-units mutations > /dev/null + > --divergence-units mutations &> /dev/null Confirm that TreeTime trees match expected topology and branch lengths. @@ -57,7 +57,7 @@ This is one way to get named internal nodes for downstream analyses and does not > --date-inference marginal \ > --clock-filter-iqd 4 \ > --seed 314159 \ - > --divergence-units mutations-per-site > /dev/null + > --divergence-units mutations-per-site &> /dev/null Confirm that trees match expected topology and branch lengths, given that the output should not be a time tree. @@ -80,7 +80,7 @@ This approach only works when we provide an alignment FASTA. > --date-inference marginal \ > --clock-filter-iqd 4 \ > --seed 314159 \ - > --divergence-units mutations > /dev/null + > --divergence-units mutations &> /dev/null Confirm that trees match expected topology and branch lengths, given that the output should not be a time tree. @@ -102,7 +102,7 @@ This approach does not make sense and should not work without an alignment FASTA > --date-inference marginal \ > --clock-filter-iqd 4 \ > --seed 314159 \ - > --divergence-units mutations > /dev/null + > --divergence-units mutations &> /dev/null *ERROR: alignment is required* (glob) [1]