Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update arguments name used in beta_diversity in tests #160

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Update arguments name used in beta_diversity in tests #160

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
1837e00
Update arguments name used in beta_diversity in tests
eamanu Jun 27, 2024
41d2e0d
Pin scikit-bio to >= 0.6.0 in setup.py
eamanu Jun 28, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
PREFIX = os.environ.get('PREFIX', "")

base = ["cython >= 0.26", "biom-format", "numpy", "h5py >= 3.3.0",
"scikit-bio >= 0.5.8", "iow"]
"scikit-bio >= 0.6.0", "iow"]

test = ["nose", "flake8"]

Expand Down
8 changes: 4 additions & 4 deletions unifrac/tests/test_api.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ def test_unweighted_inmem(self):
otu_ids = table.ids(axis='observation')
cnts = table.matrix_data.astype(int).toarray().T
exp = skbio.diversity.beta_diversity('unweighted_unifrac', cnts,
ids=ids, otu_ids=otu_ids,
ids=ids, taxa=otu_ids,
tree=tree)
obs = ssu_inmem(table, tree, 'unweighted', False, 1.0,
False, 1)
Expand All @@ -57,7 +57,7 @@ def test_unweighted_fp32_inmem(self):
otu_ids = table.ids(axis='observation')
cnts = table.matrix_data.astype(int).toarray().T
exp = skbio.diversity.beta_diversity('unweighted_unifrac', cnts,
ids=ids, otu_ids=otu_ids,
ids=ids, taxa=otu_ids,
tree=tree)
obs = ssu_inmem(table, tree, 'unweighted_fp32', False, 1.0,
False, 1)
Expand All @@ -77,7 +77,7 @@ def test_unweighted_fp64_inmem(self):
otu_ids = table.ids(axis='observation')
cnts = table.matrix_data.astype(int).toarray().T
exp = skbio.diversity.beta_diversity('unweighted_unifrac', cnts,
ids=ids, otu_ids=otu_ids,
ids=ids, taxa=otu_ids,
tree=tree)
obs = ssu_inmem(table, tree, 'unweighted_fp64', False, 1.0,
False, 1)
Expand All @@ -102,7 +102,7 @@ def test_unweighted_root_eval_issue_46(self):
otu_ids = table_inmem.ids(axis='observation')
cnts = table_inmem.matrix_data.astype(int).toarray().T
exp = skbio.diversity.beta_diversity('unweighted_unifrac', cnts,
ids=ids, otu_ids=otu_ids,
ids=ids, taxa=otu_ids,
tree=tree_inmem)
obs = ssu(table, tree, 'unweighted', False, 1.0, False, 1)
npt.assert_almost_equal(obs.data, exp.data, decimal=6)
Expand Down
Loading