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chore: bump required treetime version to 0.8.0 #633

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merged 4 commits into from
Nov 16, 2020
Merged

chore: bump required treetime version to 0.8.0 #633

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bddeaf4
chore: bump required treetime version to 0.8.0
rneher Nov 15, 2020
821d33c
chore: treetime new requires biopython <1.77 because of a bug in nexu…
rneher Nov 15, 2020
f022f09
tests: remove VisibleDeprecationWarning from test output since treeti…
rneher Nov 15, 2020
6b9cc9c
tests: update more test outputs
rneher Nov 15, 2020
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4 changes: 2 additions & 2 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,11 +49,11 @@
python_requires = '>={}'.format('.'.join(str(n) for n in min_version)),
install_requires = [
"bcbio-gff >=0.6.0, ==0.6.*",
"biopython >=1.67, <=1.78",
"biopython >=1.67, <=1.76",
"jsonschema >=3.0.0, ==3.*",
"packaging >=19.2",
"pandas >=1.0.0, ==1.*",
"phylo-treetime >=0.7.4, ==0.7.*"
"phylo-treetime ==0.8.*"
],
extras_require = {
'full': [
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4 changes: 0 additions & 4 deletions tests/builds/zika.t
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Original file line number Diff line number Diff line change
Expand Up @@ -75,8 +75,6 @@ Build a time tree from the existing tree topology, the multiple sequence alignme
> --date-inference marginal \
> --clock-filter-iqd 4 \
> --seed 314159 > /dev/null
*/treetime/aa_models.py:108: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray (glob)
[0.800038509951648, 1.20274751778601, 1.55207513886163, 1.46600946033173, 0.830022143283238, 1.5416250309563, 1.53255698189437, 1.41208067821187, 1.47469999960758, 0.351200119909572, 0.570542199221932, 1.21378822764856, 0.609532859331199, 0.692733248746636, 1.40887880416009, 1.02015839286433, 0.807404666228614, 1.268589159299, 0.933095433689795]

Confirm that TreeTime trees match expected topology and branch lengths.

Expand Down Expand Up @@ -107,8 +105,6 @@ Infer ancestral sequences from the tree.
> --infer-ambiguous \
> --output-node-data "$TMP/out/nt_muts.json" \
> --inference joint > /dev/null
*/treetime/aa_models.py:108: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray (glob)
[0.800038509951648, 1.20274751778601, 1.55207513886163, 1.46600946033173, 0.830022143283238, 1.5416250309563, 1.53255698189437, 1.41208067821187, 1.47469999960758, 0.351200119909572, 0.570542199221932, 1.21378822764856, 0.609532859331199, 0.692733248746636, 1.40887880416009, 1.02015839286433, 0.807404666228614, 1.268589159299, 0.933095433689795]

$ diff -u --ignore-matching-lines version "results/nt_muts.json" "$TMP/out/nt_muts.json"

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6 changes: 0 additions & 6 deletions tests/functional/ancestral.t
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Expand Up @@ -11,8 +11,6 @@ The default is to infer ambiguous bases, so there should not be N bases in the i
> --alignment ancestral/aligned.fasta \
> --output-node-data "$TMP/ancestral_mutations.json" \
> --output-sequences "$TMP/ancestral_sequences.fasta" > /dev/null
*/treetime/aa_models.py:108: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray (glob)
[0.800038509951648, 1.20274751778601, 1.55207513886163, 1.46600946033173, 0.830022143283238, 1.5416250309563, 1.53255698189437, 1.41208067821187, 1.47469999960758, 0.351200119909572, 0.570542199221932, 1.21378822764856, 0.609532859331199, 0.692733248746636, 1.40887880416009, 1.02015839286433, 0.807404666228614, 1.268589159299, 0.933095433689795]

$ grep N "$TMP/ancestral_sequences.fasta"
>NODE_0000000
Expand All @@ -26,8 +24,6 @@ There should not be N bases in the inferred output sequences.
> --infer-ambiguous \
> --output-node-data "$TMP/ancestral_mutations.json" \
> --output-sequences "$TMP/ancestral_sequences.fasta" > /dev/null
*/treetime/aa_models.py:108: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray (glob)
[0.800038509951648, 1.20274751778601, 1.55207513886163, 1.46600946033173, 0.830022143283238, 1.5416250309563, 1.53255698189437, 1.41208067821187, 1.47469999960758, 0.351200119909572, 0.570542199221932, 1.21378822764856, 0.609532859331199, 0.692733248746636, 1.40887880416009, 1.02015839286433, 0.807404666228614, 1.268589159299, 0.933095433689795]

$ grep N "$TMP/ancestral_sequences.fasta"
>NODE_0000000
Expand All @@ -41,8 +37,6 @@ There be N bases in the inferred output sequences.
> --keep-ambiguous \
> --output-node-data "$TMP/ancestral_mutations.json" \
> --output-sequences "$TMP/ancestral_sequences.fasta" > /dev/null
*/treetime/aa_models.py:108: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray (glob)
[0.800038509951648, 1.20274751778601, 1.55207513886163, 1.46600946033173, 0.830022143283238, 1.5416250309563, 1.53255698189437, 1.41208067821187, 1.47469999960758, 0.351200119909572, 0.570542199221932, 1.21378822764856, 0.609532859331199, 0.692733248746636, 1.40887880416009, 1.02015839286433, 0.807404666228614, 1.268589159299, 0.933095433689795]

$ grep N "$TMP/ancestral_sequences.fasta"
>NODE_0000000
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8 changes: 0 additions & 8 deletions tests/functional/refine.t
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Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,6 @@ Try building a time tree.
> --date-inference marginal \
> --clock-filter-iqd 4 \
> --seed 314159 > /dev/null
*/treetime/aa_models.py:108: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray (glob)
[0.800038509951648, 1.20274751778601, 1.55207513886163, 1.46600946033173, 0.830022143283238, 1.5416250309563, 1.53255698189437, 1.41208067821187, 1.47469999960758, 0.351200119909572, 0.570542199221932, 1.21378822764856, 0.609532859331199, 0.692733248746636, 1.40887880416009, 1.02015839286433, 0.807404666228614, 1.268589159299, 0.933095433689795]

Confirm that TreeTime trees match expected topology and branch lengths.

Expand All @@ -40,8 +38,6 @@ Build a time tree with mutations as the reported divergence unit.
> --clock-filter-iqd 4 \
> --seed 314159 \
> --divergence-units mutations > /dev/null
*/treetime/aa_models.py:108: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray (glob)
[0.800038509951648, 1.20274751778601, 1.55207513886163, 1.46600946033173, 0.830022143283238, 1.5416250309563, 1.53255698189437, 1.41208067821187, 1.47469999960758, 0.351200119909572, 0.570542199221932, 1.21378822764856, 0.609532859331199, 0.692733248746636, 1.40887880416009, 1.02015839286433, 0.807404666228614, 1.268589159299, 0.933095433689795]

Confirm that TreeTime trees match expected topology and branch lengths.

Expand All @@ -62,8 +58,6 @@ This is one way to get named internal nodes for downstream analyses and does not
> --clock-filter-iqd 4 \
> --seed 314159 \
> --divergence-units mutations-per-site > /dev/null
*/treetime/aa_models.py:108: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray (glob)
[0.800038509951648, 1.20274751778601, 1.55207513886163, 1.46600946033173, 0.830022143283238, 1.5416250309563, 1.53255698189437, 1.41208067821187, 1.47469999960758, 0.351200119909572, 0.570542199221932, 1.21378822764856, 0.609532859331199, 0.692733248746636, 1.40887880416009, 1.02015839286433, 0.807404666228614, 1.268589159299, 0.933095433689795]

Confirm that trees match expected topology and branch lengths, given that the output should not be a time tree.

Expand All @@ -87,8 +81,6 @@ This approach only works when we provide an alignment FASTA.
> --clock-filter-iqd 4 \
> --seed 314159 \
> --divergence-units mutations > /dev/null
*/treetime/aa_models.py:108: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray (glob)
[0.800038509951648, 1.20274751778601, 1.55207513886163, 1.46600946033173, 0.830022143283238, 1.5416250309563, 1.53255698189437, 1.41208067821187, 1.47469999960758, 0.351200119909572, 0.570542199221932, 1.21378822764856, 0.609532859331199, 0.692733248746636, 1.40887880416009, 1.02015839286433, 0.807404666228614, 1.268589159299, 0.933095433689795]

Confirm that trees match expected topology and branch lengths, given that the output should not be a time tree.

Expand Down