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Merged
alpae merged 2 commits into from
Oct 29, 2026
Merged

Run the darwin reference tests in CI #32

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2df3c98
Run the darwin reference tests in CI
alpae Oct 29, 2026
9538a94
Run the full darwin tests on pull requests changing computations
alpae Oct 29, 2026
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47 changes: 47 additions & 0 deletions .github/workflows/full-tests.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,47 @@
name: Full darwin tests

# compares with all darwin reference results, which takes too long for every
# pull request (the regular tests use a subsample). Runs on pull requests that
# change the computations or the reference tests.
on:
push:
branches: [ master ]
pull_request:
branches: [ master ]
paths:
- "c_source/**"
- "pyopa/backend/**"
- "setup.py"
- "test/test_darwin.py"
- "test/data/**"
- ".github/workflows/full-tests.yml"
schedule:
- cron: "0 3 * * 1"
workflow_dispatch:

permissions:
contents: read

jobs:
full-tests:
runs-on: ubuntu-latest
timeout-minutes: 120
steps:
- uses: actions/checkout@v7
with:
submodules: true
- name: Set up uv and Python
uses: astral-sh/setup-uv@v10.3.2
with:
python-version: "3.14"
activate-environment: true
- name: Installation
env:
PYOPA_REQUIRE_OPENMP: "1"
run: |
uv pip install -v .
uv pip install --group test
- name: Test with pytest
env:
PYOPA_TEST_FULL: "1"
run: pytest -v test/test_darwin.py
42 changes: 23 additions & 19 deletions test/test_darwin.py
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Expand Up @@ -98,21 +98,25 @@ def setUp(self):
self.alignment_profiles[curr.s1_id] = p
'''

#def test_align(self):
# threading.stack_size(67104768)
# t = threading.Thread(None, self._align_t, 'Aligning Thread')
# t.start()
# t.join()

#def _align_t(self):
@unittest.skip("skip long runningtest")
def sample_results(self):
"""
All darwin results if PYOPA_TEST_FULL is set (takes several minutes), otherwise a
fixed subsample: every 20th result with an alignment (which also checks
estimate_pam) and every 200th of the others.
"""
if os.environ.get('PYOPA_TEST_FULL'):
return list(enumerate(self.darwin_results))
with_al = [(i, r) for i, r in enumerate(self.darwin_results) if r.als1 != '']
without_al = [(i, r) for i, r in enumerate(self.darwin_results) if r.als1 == '']
return sorted(with_al[::20] + without_al[::200], key=lambda x: x[0])

def test_align(self):
print('Running alignment tests...')
results = self.sample_results()
print('Running alignment tests on %d of %d results...' % (len(results), len(self.darwin_results)))
completed = 0
max_alignments = len(self.darwin_results)
progress_step = int(np.ceil(max_alignments / 100))
progress_step = int(np.ceil(len(results) / 100))

for r in self.darwin_results:
for test_id, r in results:
s1 = self.sequences[r.s1_id - 1]
s2 = self.sequences[r.s2_id - 1]
env = self.alignment_environments[r.matrix_nr - 1]
Expand All @@ -138,46 +142,46 @@ def test_align(self):
delta=r.ep_sim *10**(1-self.precision),
msg='Incorrect EstimatePam similarity score: %.10f != %.10f.'
'Test id: %d' %
(ep_result[0], r.ep_sim, completed + 1))
(ep_result[0], r.ep_sim, test_id + 1))
self.assertAlmostEqual(ep_result[1], r.ep_pamn, delta=r.ep_pamn*10**(1-self.precision))
self.assertAlmostEqual(ep_result[2], r.ep_var, delta=r.ep_var*10**(1-self.precision))

self.assertAlmostEqual(scalar_result_reference, r.score_double, places=self.precision,
msg='Incorrect reference double score: %.8f. The correct score is: %.8f, test id: %d'
% (scalar_result_reference, r.score_double, completed + 1))
% (scalar_result_reference, r.score_double, test_id + 1))
self.assertGreaterEqual(short_result, r.score_double,
msg="Short score (%f) must be greater or equal"
" than double score (%f), test id: %d'."
% (short_result, r.score_double, completed + 1)
% (short_result, r.score_double, test_id + 1)
)
self.assertGreaterEqual(byte_result, r.score_double,
msg="Byte score must be greater or equal than double score.")
self.assertAlmostEqual(double_result, r.score_double,
places=self.precision,
msg='Incorrect double score: %.8f. The correct score is: %.8f, test id: %d' %
(double_result, r.score_double, completed + 1))
(double_result, r.score_double, test_id + 1))
'''
if byte_result > r.threshold:
self.assertGreaterEqual(byte_result, sys.float_info.max)
else:
self.assertAlmostEqual(byte_result, r.score_byte,
places=7,
msg='Incorrect byte score: %.8f. The correct score is: %.8f, test id: %d' %
(byte_result, r.score_byte, completed + 1))
(byte_result, r.score_byte, test_id + 1))
'''
if short_result > r.threshold:
self.assertGreaterEqual(short_result, sys.float_info.max)
else:
if short_result < r.score_short and (r.score_short - short_result) > 0.01:
#print("Warning: python short score(%f) is less than darwin's, but still bigger" \
# " than the double score(%f) at id: %d!" \
# % (short_result, r.score_double, completed + 1))
# % (short_result, r.score_double, test_id + 1))
pass
else:
self.assertAlmostEqual(short_result, r.score_short,
places=self.precision,
msg='Incorrect short score: %.8f. The correct score is: %.8f, test id: %d' %
(short_result, r.score_short, completed + 1))
(short_result, r.score_short, test_id + 1))

completed += 1
if (completed % progress_step == 0):
Expand Down
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