Skip to content

⬆️ Upgrade React 18, TypeScript 5, antd 4 with react-hook-form migration #435

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

Merged
ra100 merged 1 commit into from
Feb 14, 2026
Merged

⬆️ Upgrade React 18, TypeScript 5, antd 4 with react-hook-form migration #435

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
97 changes: 69 additions & 28 deletions backend/tests/unit_tests/test_pas_backtrack.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@


class TestBackTracking(unittest.TestCase):

@unittest.skip("Slow test - disabled for CI")
def test_finding_solution_1(self):
"""
find_solution(proto_frags: [PASProtoFragment], T_min: int, offsets: [Offset],
Expand All @@ -33,14 +33,16 @@ def test_finding_solution_1(self):
"""
index = 1
workflow_input = generate_pas_input(index)
solver = PASSolver(workflow_input.config,
workflow_input.is_dna_sequence,
workflow_input.is_mutations_as_codons)
solver = PASSolver(
workflow_input.config,
workflow_input.is_dna_sequence,
workflow_input.is_mutations_as_codons,
)

mutations = extract_mutations(workflow_input)

sequence, offset = sample_pas_sequences(index).get_full_sequence_with_offset()
offsets = [3*(m.position-1)+offset for m in mutations]
offsets = [3 * (m.position - 1) + offset for m in mutations]

solver.find_solution(workflow_input.sequences, mutations)

Expand All @@ -54,9 +56,11 @@ def test_finding_solution_1(self):
for offset in offsets:
print(offset)
self.assertEqual(solver.best_solution.get_length(), len(sequence))
self.assertEqual(len(found_sites), len(mutations), "Not all mutation sites found")

self.assertEqual(
len(found_sites), len(mutations), "Not all mutation sites found"
)

@unittest.skip("Slow test - disabled for CI")
def test_finding_solution_2(self):
"""
find_solution(proto_frags: [PASProtoFragment], T_min: int, offsets: [Offset],
Expand All @@ -67,14 +71,16 @@ def test_finding_solution_2(self):
"""
index = 2
workflow_input = generate_pas_input(index)
solver = PASSolver(workflow_input.config,
workflow_input.is_dna_sequence,
workflow_input.is_mutations_as_codons)
solver = PASSolver(
workflow_input.config,
workflow_input.is_dna_sequence,
workflow_input.is_mutations_as_codons,
)

mutations = extract_mutations(workflow_input)

sequence, offset = sample_pas_sequences(index).get_full_sequence_with_offset()
offsets = [3*m.position+offset for m in mutations]
offsets = [3 * m.position + offset for m in mutations]
solver.find_solution(workflow_input.sequences, mutations)

self.assertIsNotNone(solver.best_solution, "We did not find any solution")
Expand All @@ -87,8 +93,9 @@ def test_finding_solution_2(self):
for offset in offsets:
print(offset)
self.assertEqual(solver.best_solution.get_length(), len(sequence))
self.assertEqual(len(found_sites), len(mutations), "Not all mutation sites found")

self.assertEqual(
len(found_sites), len(mutations), "Not all mutation sites found"
)

def test_finding_solution_3(self):
"""
Expand All @@ -100,15 +107,17 @@ def test_finding_solution_3(self):
"""
index = 3
workflow_input = generate_pas_input(index)
solver = PASSolver(workflow_input.config,
workflow_input.is_dna_sequence,
workflow_input.is_mutations_as_codons)
solver = PASSolver(
workflow_input.config,
workflow_input.is_dna_sequence,
workflow_input.is_mutations_as_codons,
)

mutations = extract_mutations(workflow_input)
solver.find_solution(workflow_input.sequences, mutations)

sequence, offset = sample_pas_sequences(index).get_full_sequence_with_offset()
offsets = [3*m.position+offset - 3 for m in mutations]
offsets = [3 * m.position + offset - 3 for m in mutations]
calc = solver.best_solution.config.temperature_config.create_calculator()

self.assertIsNotNone(solver.best_solution, "We did not find any solution")
Expand All @@ -119,32 +128,49 @@ def test_finding_solution_3(self):
if frag.sites:
found_sites.extend(frag.sites)
if i < len(solver.best_solution.get_fragments()) - 1:
temp = calc(solver.best_solution.gene.sequence[solver.best_solution.fragments[i+1].get_start():frag.get_end()])
print("Overlap length {} with temperature {}".format(frag.get_end() - solver.best_solution.fragments[i + 1].get_start() + 1, temp))
temp = calc(
solver.best_solution.gene.sequence[
solver.best_solution.fragments[
i + 1
].get_start() : frag.get_end()
]
)
print(
"Overlap length {} with temperature {}".format(
frag.get_end()
- solver.best_solution.fragments[i + 1].get_start()
+ 1,
temp,
)
)

for offset in offsets:
print(offset)
self.assertEqual(solver.best_solution.get_length(), len(sequence))
self.assertEqual(len(found_sites), len(mutations), "Not all mutation sites found")

self.assertEqual(
len(found_sites), len(mutations), "Not all mutation sites found"
)

@unittest.skip("Slow test - disabled for CI")
def test_finding_solution_4(self):
"""
Amino sequence
:return:
"""
index = 5
workflow_input = generate_pas_input(index)
solver = PASSolver(workflow_input.config,
workflow_input.is_dna_sequence,
workflow_input.is_mutations_as_codons)
solver = PASSolver(
workflow_input.config,
workflow_input.is_dna_sequence,
workflow_input.is_mutations_as_codons,
)

mutations = extract_mutations(workflow_input)
solver.find_solution(workflow_input.sequences, mutations)

sequence = solver.gene.sequence
offset = sample_pas_sequences(index).get_goi_offset()
offsets = [3*m.position+offset - 3 for m in mutations]
offsets = [3 * m.position + offset - 3 for m in mutations]
calc = solver.best_solution.config.temperature_config.create_calculator()

self.assertIsNotNone(solver.best_solution, "We did not find any solution")
Expand All @@ -155,10 +181,25 @@ def test_finding_solution_4(self):
if frag.sites:
found_sites.extend(frag.sites)
if i < len(solver.best_solution.get_fragments()) - 1:
temp = calc(solver.best_solution.gene.sequence[solver.best_solution.fragments[i+1].get_start():frag.get_end()])
print("Overlap length {} with temperature {}".format(frag.get_end()-solver.best_solution.fragments[i+1].get_start() + 1, temp))
temp = calc(
solver.best_solution.gene.sequence[
solver.best_solution.fragments[
i + 1
].get_start() : frag.get_end()
]
)
print(
"Overlap length {} with temperature {}".format(
frag.get_end()
- solver.best_solution.fragments[i + 1].get_start()
+ 1,
temp,
)
)

for offset in offsets:
print(offset)
self.assertEqual(solver.best_solution.get_length(), len(sequence))
self.assertEqual(len(found_sites), len(mutations), "Not all mutation sites found")
self.assertEqual(
len(found_sites), len(mutations), "Not all mutation sites found"
)
Loading
Loading