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Replace lazy loading of vectorize_counts_and_tree #115

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Replace lazy loading of vectorize_counts_and_tree #115

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13 changes: 11 additions & 2 deletions gemelli/preprocessing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@
from inspect import getfullargspec
from gemelli._defaults import DEFAULT_MTD
from skbio.stats.composition import clr
from skbio.diversity._util import _vectorize_counts_and_tree
from bp import parse_newick, to_skbio_treenode
from scipy.sparse.linalg import svds
# import QIIME2 if in a Q2env otherwise set type to str
Expand Down Expand Up @@ -627,13 +626,23 @@ def fast_unifrac(table, tree):
TODO

"""

# Lazy Loading
try:
from skbio.diversity._util import vectorize_counts_and_tree
except ImportError:
raise ImportError(
"Could not import vectorize_counts_and_tree from skbio.diversity._util. "
"This function was made public in scikit-bio >= 0.6. "
"Please upgrade scikit-bio: pip install 'scikit-bio>=0.6'"
)

# original table
bt_array = table.matrix_data.toarray()
otu_ids = table.ids('observation')
# expand the vectorized table
counts_by_node, tree_index, branch_lengths \
= _vectorize_counts_and_tree(bt_array.T, otu_ids, tree)
= vectorize_counts_and_tree(bt_array.T, otu_ids, tree)
# check branch lengths
if sum(branch_lengths) == 0:
raise ValueError('All tree branch lengths are zero. '
Expand Down