Skip to content

Commit

Permalink
Merge black-applied python test files
Browse files Browse the repository at this point in the history
  • Loading branch information
@olgabot
olgabot committed Oct 29, 2024
1 parent 1fd5687 commit e42440e
Show file tree
Hide file tree
Showing 4 changed files with 148 additions and 0 deletions.
13 changes: 13 additions & 0 deletions .github/workflows/black.yml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
name: Lint

on: [push, pull_request]

jobs:
lint:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: psf/black@stable
with:
src: "./src/python"
options: "--check --verbose"
9 changes: 9 additions & 0 deletions src/python/sourmash_plugin_branchwater/__init__.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -456,12 +456,15 @@ def __init__(self, p):
p.add_argument(
"-a", "--ani", action="store_true", help="estimate ANI from containment"
)
<<<<<<< HEAD
p.add_argument(
"-p",
"--prob",
action="store_true",
help="estimate probability of overlap for significance ranking of search results",
)
=======
>>>>>>> 31d3056 (Python Black Formatting (#492))

def main(self, args):
print_version()
Expand All @@ -474,9 +477,12 @@ def main(self, args):
notify(
f"searching all sketches in '{args.query_paths}' against '{args.against_paths}' using {num_threads} threads"
)
<<<<<<< HEAD
notify(
f"estimate ani? {args.ani} / estimate probability of overlap? {args.prob}"
)
=======
>>>>>>> 31d3056 (Python Black Formatting (#492))

super().main(args)
status = sourmash_plugin_branchwater.do_multisearch(
Expand All @@ -487,7 +493,10 @@ def main(self, args):
args.scaled,
args.moltype,
args.ani,
<<<<<<< HEAD
args.prob,
=======
>>>>>>> 31d3056 (Python Black Formatting (#492))
args.output,
)
if status == 0:
Expand Down
115 changes: 115 additions & 0 deletions src/python/tests/test_multisearch.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,13 @@
zip_siglist,
index_siglist,
)
<<<<<<< HEAD


def float_round(string: str, ndigits=None):
return round(float(string), ndigits)
=======
>>>>>>> 31d3056 (Python Black Formatting (#492))


def test_installed(runtmp):
Expand Down Expand Up @@ -61,9 +64,12 @@ def test_simple_no_ani(runtmp, zip_query, zip_db):
assert float(row["containment"] == 1.0)
assert float(row["jaccard"] == 1.0)
assert float(row["max_containment"] == 1.0)
<<<<<<< HEAD
# assert float(row['prob_overlap'] == 1.0)
# assert float(row['prob_overlap_adjusted'] == 1.0)
# assert float(row['containment_adjusted'] == 1.0)
=======
>>>>>>> 31d3056 (Python Black Formatting (#492))
assert "query_containment_ani" not in row
assert "match_containment_ani" not in row
assert "average_containment_ani" not in row
Expand All @@ -73,9 +79,15 @@ def test_simple_no_ani(runtmp, zip_query, zip_db):
# confirm hand-checked numbers
q = row["query_name"].split()[0]
m = row["match_name"].split()[0]
<<<<<<< HEAD
cont = float_round(row["containment"], 4)
jaccard = float_round(row["jaccard"], 4)
maxcont = float_round(row["max_containment"], 4)
=======
cont = float(row["containment"])
jaccard = float(row["jaccard"])
maxcont = float(row["max_containment"])
>>>>>>> 31d3056 (Python Black Formatting (#492))
intersect_hashes = int(row["intersect_hashes"])

print(q, m, f"{jaccard:.04}", f"{cont:.04}", f"{maxcont:.04}")
Expand Down Expand Up @@ -109,6 +121,10 @@ def test_simple_prob_overlap(runtmp, zip_query, zip_db, indexed_query, indexed_a

if zip_db:
against_list = zip_siglist(runtmp, against_list, runtmp.output("db.zip"))
<<<<<<< HEAD
=======

>>>>>>> 31d3056 (Python Black Formatting (#492))
if zip_query:
query_list = zip_siglist(runtmp, query_list, runtmp.output("query.zip"))

Expand All @@ -119,7 +135,11 @@ def test_simple_prob_overlap(runtmp, zip_query, zip_db, indexed_query, indexed_a
against_list = index_siglist(runtmp, against_list, runtmp.output("db"))

runtmp.sourmash(
<<<<<<< HEAD
"scripts", "multisearch", query_list, against_list, "-o", output, "--prob"
=======
"scripts", "multisearch", query_list, against_list, "-o", output, "--ani"
>>>>>>> 31d3056 (Python Black Formatting (#492))
)
assert os.path.exists(output)

Expand All @@ -136,6 +156,7 @@ def test_simple_prob_overlap(runtmp, zip_query, zip_db, indexed_query, indexed_a
assert float(row["containment"] == 1.0)
assert float(row["jaccard"] == 1.0)
assert float(row["max_containment"] == 1.0)
<<<<<<< HEAD
assert "query_containment_ani" not in row
assert "match_containment_ani" not in row
assert "average_containment_ani" not in row
Expand All @@ -147,11 +168,18 @@ def test_simple_prob_overlap(runtmp, zip_query, zip_db, indexed_query, indexed_a
assert float_round(row["containment_adjusted"], 4) == 2377.5947
assert float_round(row["containment_adjusted_log10"], 4) == 2377.5947
assert float_round(row["tf_idf_score"], 4) == 1.4974
=======
assert float(row["query_containment_ani"] == 1.0)
assert float(row["match_containment_ani"] == 1.0)
assert float(row["average_containment_ani"] == 1.0)
assert float(row["max_containment_ani"] == 1.0)
>>>>>>> 31d3056 (Python Black Formatting (#492))

else:
# confirm hand-checked numbers
q = row["query_name"].split()[0]
m = row["match_name"].split()[0]
<<<<<<< HEAD
cont = float_round(row["containment"], 4)
jaccard = float_round(row["jaccard"], 4)
maxcont = float_round(row["max_containment"], 4)
Expand Down Expand Up @@ -264,6 +292,36 @@ def test_simple_ani(runtmp, zip_query, zip_db, indexed_query, indexed_against):
f"{max_ani:.04}",
)

=======
cont = float(row["containment"])
jaccard = float(row["jaccard"])
maxcont = float(row["max_containment"])
intersect_hashes = int(row["intersect_hashes"])
q1_ani = float(row["query_containment_ani"])
q2_ani = float(row["match_containment_ani"])
avg_ani = float(row["average_containment_ani"])
max_ani = float(row["max_containment_ani"])

jaccard = round(jaccard, 4)
cont = round(cont, 4)
maxcont = round(maxcont, 4)
q1_ani = round(q1_ani, 4)
q2_ani = round(q2_ani, 4)
avg_ani = round(avg_ani, 4)
max_ani = round(max_ani, 4)
print(
q,
m,
f"{jaccard:.04}",
f"{cont:.04}",
f"{maxcont:.04}",
f"{q1_ani:.04}",
f"{q2_ani:.04}",
f"{avg_ani:.04}",
f"{max_ani:.04}",
)

>>>>>>> 31d3056 (Python Black Formatting (#492))
if q == "NC_011665.1" and m == "NC_009661.1":
assert jaccard == 0.3207
assert cont == 0.4828
Expand Down Expand Up @@ -994,6 +1052,7 @@ def test_simple_prot(runtmp):
# confirm hand-checked numbers
q = row["query_name"].split()[0]
m = row["match_name"].split()[0]
<<<<<<< HEAD
cont = float_round(row["containment"], 4)
jaccard = float_round(row["jaccard"], 4)
maxcont = float_round(row["max_containment"], 4)
Expand All @@ -1003,6 +1062,24 @@ def test_simple_prot(runtmp):
avg_ani = float_round(row["average_containment_ani"], 4)
max_ani = float_round(row["max_containment_ani"], 4)

=======
cont = float(row["containment"])
jaccard = float(row["jaccard"])
maxcont = float(row["max_containment"])
intersect_hashes = int(row["intersect_hashes"])
q1_ani = float(row["query_containment_ani"])
q2_ani = float(row["match_containment_ani"])
avg_ani = float(row["average_containment_ani"])
max_ani = float(row["max_containment_ani"])

jaccard = round(jaccard, 4)
cont = round(cont, 4)
maxcont = round(maxcont, 4)
q1_ani = round(q1_ani, 4)
q2_ani = round(q2_ani, 4)
avg_ani = round(avg_ani, 4)
max_ani = round(max_ani, 4)
>>>>>>> 31d3056 (Python Black Formatting (#492))
print(
q,
m,
Expand Down Expand Up @@ -1209,6 +1286,7 @@ def test_simple_dayhoff(runtmp):
# confirm hand-checked numbers
q = row["query_name"].split()[0]
m = row["match_name"].split()[0]
<<<<<<< HEAD
cont = float_round(row["containment"], 4)
jaccard = float_round(row["jaccard"], 4)
maxcont = float_round(row["max_containment"], 4)
Expand All @@ -1218,6 +1296,24 @@ def test_simple_dayhoff(runtmp):
avg_ani = float_round(row["average_containment_ani"], 4)
max_ani = float_round(row["max_containment_ani"], 4)

=======
cont = float(row["containment"])
jaccard = float(row["jaccard"])
maxcont = float(row["max_containment"])
intersect_hashes = int(row["intersect_hashes"])
q1_ani = float(row["query_containment_ani"])
q2_ani = float(row["match_containment_ani"])
avg_ani = float(row["average_containment_ani"])
max_ani = float(row["max_containment_ani"])

jaccard = round(jaccard, 4)
cont = round(cont, 4)
maxcont = round(maxcont, 4)
q1_ani = round(q1_ani, 4)
q2_ani = round(q2_ani, 4)
avg_ani = round(avg_ani, 4)
max_ani = round(max_ani, 4)
>>>>>>> 31d3056 (Python Black Formatting (#492))
print(
q,
m,
Expand Down Expand Up @@ -1297,6 +1393,7 @@ def test_simple_hp(runtmp):
# confirm hand-checked numbers
q = row["query_name"].split()[0]
m = row["match_name"].split()[0]
<<<<<<< HEAD
cont = float_round(row["containment"], 4)
jaccard = float_round(row["jaccard"], 4)
maxcont = float_round(row["max_containment"], 4)
Expand All @@ -1306,6 +1403,24 @@ def test_simple_hp(runtmp):
avg_ani = float_round(row["average_containment_ani"], 4)
max_ani = float_round(row["max_containment_ani"], 4)

=======
cont = float(row["containment"])
jaccard = float(row["jaccard"])
maxcont = float(row["max_containment"])
intersect_hashes = int(row["intersect_hashes"])
q1_ani = float(row["query_containment_ani"])
q2_ani = float(row["match_containment_ani"])
avg_ani = float(row["average_containment_ani"])
max_ani = float(row["max_containment_ani"])

jaccard = round(jaccard, 4)
cont = round(cont, 4)
maxcont = round(maxcont, 4)
q1_ani = round(q1_ani, 4)
q2_ani = round(q2_ani, 4)
avg_ani = round(avg_ani, 4)
max_ani = round(max_ani, 4)
>>>>>>> 31d3056 (Python Black Formatting (#492))
print(
q,
m,
Expand Down
11 changes: 11 additions & 0 deletions src/python/tests/test_sketch.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -961,7 +961,11 @@ def test_manysketch_prefix2(runtmp, capfd):
dna_prefix = os.path.join(
fa_path, "short"
) # need to avoid matching short-protein.fa
<<<<<<< HEAD
prot_prefix = os.path.join(fa_path, "*protein.fa")
=======
prot_prefix = os.path.join(fa_path, "*protein")
>>>>>>> 31d3056 (Python Black Formatting (#492))
zip_exclude = os.path.join(fa_path, "*zip")

# make prefix input file
Expand Down Expand Up @@ -1042,7 +1046,10 @@ def test_manysketch_prefix2(runtmp, capfd):
for sig in sigs:
assert sig.name in expected_signames
if sig.name == "short":
<<<<<<< HEAD
# minhash is not defined? How does this test work?
=======
>>>>>>> 31d3056 (Python Black Formatting (#492))
assert sig, minhash.hashes == sig1.minhash.hashes
if sig.name == "short_protein":
assert sig == sig2
Expand Down Expand Up @@ -1119,7 +1126,11 @@ def test_manysketch_prefix_duplicated_force(runtmp, capfd):
dna_prefix = os.path.join(
fa_path, "short"
) # need to avoid matching short-protein.fa
<<<<<<< HEAD
prot_prefix = os.path.join(fa_path, "*protein*fa")
=======
prot_prefix = os.path.join(fa_path, "*protein")
>>>>>>> 31d3056 (Python Black Formatting (#492))
zip_exclude = os.path.join(fa_path, "*zip")

# make prefix input file
Expand Down

0 comments on commit e42440e

Please sign in to comment.