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Ignore scipy warnings
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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] #1120
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huddlej committed Jan 9, 2023
1 parent 6a3d7c0 commit 09aeeee
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2 changes: 1 addition & 1 deletion tests/builds/zika.t
Original file line number Diff line number Diff line change
Expand Up @@ -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.

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10 changes: 5 additions & 5 deletions tests/functional/refine.t
Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand All @@ -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.

Expand All @@ -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.

Expand All @@ -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.

Expand All @@ -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]

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