repo_id stringclasses 400
values | commit_sha stringclasses 400
values | commit_index int32 0 951 | in_repo_split stringclasses 1
value | cross_repo_split stringclasses 1
value | test_file stringlengths 7 121 | test_function stringlengths 1 108 | assertion_type stringclasses 32
values | difficulty stringclasses 8
values | context_lines int32 3 600 | prefix large_stringlengths 44 113k | target large_stringlengths 1 498 | anchor_sha stringclasses 400
values | anchor_index int32 0 951 | qna_source stringclasses 1
value |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
MinishLab/semhash | feccbb996fb29193929bcfd98ee6ad24a8855b9d | 15 | train | train | tests/test_utils.py | test_to_frozendict | assert | func_call | 19 | import numpy as np
import pytest
from frozendict import frozendict
from semhash.utils import (
Encoder,
compute_candidate_limit,
featurize,
prepare_records,
remove_exact_duplicates,
to_frozendict,
)
def test_to_frozendict() -> None:
"""Test converting dict to frozendict."""
record = {"... | frozendict({"a": "1", "c": "3"}) | feccbb996fb29193929bcfd98ee6ad24a8855b9d | 15 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/breadth_first/test_nodes.py | test_create_stub | assert | numeric_literal | 20 | import pytest
from aizynthfinder.search.breadth_first.nodes import MoleculeNode
from aizynthfinder.chem.serialization import MoleculeSerializer, MoleculeDeserializer
def setup_root(default_config):
def wrapper(smiles):
return MoleculeNode.create_root(smiles, config=default_config)
return wrapper
def... | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/breadth_first/test_nodes.py | test_create_stub | assert | numeric_literal | 21 | import pytest
from aizynthfinder.search.breadth_first.nodes import MoleculeNode
from aizynthfinder.chem.serialization import MoleculeSerializer, MoleculeDeserializer
def setup_root(default_config):
def wrapper(smiles):
return MoleculeNode.create_root(smiles, config=default_config)
return wrapper
def... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/breadth_first/test_search.py | test_one_iteration | assert | numeric_literal | 26 | import random
import pytest
from aizynthfinder.search.breadth_first.search_tree import SearchTree
def test_one_iteration(default_config, setup_policies, setup_stock):
root_smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1"
child1_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F", "O"]
child2_sm... | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/breadth_first/test_search.py | test_one_iteration | assert | numeric_literal | 30 | import random
import pytest
from aizynthfinder.search.breadth_first.search_tree import SearchTree
def test_one_iteration(default_config, setup_policies, setup_stock):
root_smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1"
child1_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F", "O"]
child2_sm... | 6 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/breadth_first/test_search.py | test_search_incomplete | assert | numeric_literal | 32 | import random
import pytest
from aizynthfinder.search.breadth_first.search_tree import SearchTree
def test_search_incomplete(default_config, setup_policies, setup_stock):
root_smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1"
child1_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F", "O"]
child... | 8 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/breadth_first/test_search.py | test_routes | assert | numeric_literal | 34 | import random
import pytest
from aizynthfinder.search.breadth_first.search_tree import SearchTree
def test_routes(default_config, setup_policies, setup_stock):
random.seed(666)
root_smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1"
child1_smi = ["O", "CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F"]... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/chem/test_mol.py | test_fingerprint | assert | numeric_literal | 10 | import pytest
from rdkit import Chem
from aizynthfinder.chem import MoleculeException, Molecule
def test_fingerprint():
mol = Molecule(smiles="O")
assert sum(mol.fingerprint(2)) == | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/chem/test_reaction.py | test_fwd_reaction | assert | numeric_literal | 24 | from aizynthfinder.chem import (
Molecule,
UniqueMolecule,
TreeMolecule,
Reaction,
TemplatedRetroReaction,
FixedRetroReaction,
SmilesBasedRetroReaction,
hash_reactions,
MoleculeException,
)
from aizynthfinder.reactiontree import ReactionTree
def test_fwd_reaction():
mol1 = Molec... | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/chem/test_serialization.py | test_deserialize_tree_mols | assert | numeric_literal | 22 | from aizynthfinder.chem.serialization import MoleculeSerializer, MoleculeDeserializer
from aizynthfinder.chem import Molecule, TreeMolecule
def test_deserialize_tree_mols():
store = {
123: {
"smiles": "CCC",
"class": "TreeMolecule",
"parent": None,
"transform... | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/chem/test_serialization.py | test_deserialize_tree_mols | assert | numeric_literal | 23 | from aizynthfinder.chem.serialization import MoleculeSerializer, MoleculeDeserializer
from aizynthfinder.chem import Molecule, TreeMolecule
def test_deserialize_tree_mols():
store = {
123: {
"smiles": "CCC",
"class": "TreeMolecule",
"parent": None,
"transform... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_collection.py | test_empty_collection | assert | numeric_literal | 9 | import pytest
from aizynthfinder.context.collection import ContextCollection
def test_empty_collection():
collection = StringCollection()
assert len(collection) == | 0 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_collection.py | test_add_single_item | assert | numeric_literal | 11 | import pytest
from aizynthfinder.context.collection import ContextCollection
def test_add_single_item():
collection = StringCollection()
collection.load("key1", "value1")
assert len(collection) == | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_collection.py | test_deselect_all | assert | numeric_literal | 12 | import pytest
from aizynthfinder.context.collection import ContextCollection
def test_deselect_all():
collection = StringCollection()
collection.load("key1", "value1")
collection.load("key2", "value2")
collection.selection = ("key1", "key2")
assert len(collection) == | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_mcts_config.py | test_get_properties | assert | numeric_literal | 15 | import pytest
from aizynthfinder.context.config import Configuration
from aizynthfinder.aizynthfinder import AiZynthFinder
def test_get_properties(default_config):
config = default_config
props = config.properties
# Just check a few properties
assert props["C"] == 1.4
assert props["time_limit"] ... | 6 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_mol_cost.py | test_load_cost | assert | numeric_literal | 12 | from aizynthfinder.context.cost import (
ZeroMoleculeCost,
MoleculeCost,
)
from aizynthfinder.chem import Molecule
def test_load_cost():
cost = MoleculeCost()
cost.load(ZeroMoleculeCost())
assert len(cost) == | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_policy.py | test_load_templated_expansion_policy | assert | numeric_literal | 22 | import pytest
import numpy as np
from aizynthfinder.chem import (
TreeMolecule,
SmilesBasedRetroReaction,
TemplatedRetroReaction,
)
from aizynthfinder.context.policy import (
TemplateBasedExpansionStrategy,
QuickKerasFilter,
ReactantsCountFilter,
)
from aizynthfinder.utils.exceptions import Rej... | 3 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_policy.py | test_reactants_count_rejection | assert | numeric_literal | 26 | import pytest
import numpy as np
from aizynthfinder.chem import (
TreeMolecule,
SmilesBasedRetroReaction,
TemplatedRetroReaction,
)
from aizynthfinder.context.policy import (
TemplateBasedExpansionStrategy,
QuickKerasFilter,
ReactantsCountFilter,
)
from aizynthfinder.utils.exceptions import Rej... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_score.py | test_template_occurrence_scorer_no_metadata | assert | numeric_literal | 24 | import pytest
import numpy as np
from aizynthfinder.context.scoring import (
StateScorer,
NumberOfReactionsScorer,
AverageTemplateOccurrenceScorer,
NumberOfPrecursorsScorer,
NumberOfPrecursorsInStockScorer,
PriceSumScorer,
RouteCostScorer,
ScorerCollection,
ScorerException,
)
from a... | 0 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_score.py | test_template_occurrence_scorer | assert | numeric_literal | 28 | import pytest
import numpy as np
from aizynthfinder.context.scoring import (
StateScorer,
NumberOfReactionsScorer,
AverageTemplateOccurrenceScorer,
NumberOfPrecursorsScorer,
NumberOfPrecursorsInStockScorer,
PriceSumScorer,
RouteCostScorer,
ScorerCollection,
ScorerException,
)
from a... | 5 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_score.py | test_scorers_one_mcts_node | assert | numeric_literal | 26 | import pytest
import numpy as np
from aizynthfinder.context.scoring import (
StateScorer,
NumberOfReactionsScorer,
AverageTemplateOccurrenceScorer,
NumberOfPrecursorsScorer,
NumberOfPrecursorsInStockScorer,
PriceSumScorer,
RouteCostScorer,
ScorerCollection,
ScorerException,
)
from a... | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_score.py | test_scoring_branched_mcts_tree | assert | numeric_literal | 24 | import pytest
import numpy as np
from aizynthfinder.context.scoring import (
StateScorer,
NumberOfReactionsScorer,
AverageTemplateOccurrenceScorer,
NumberOfPrecursorsScorer,
NumberOfPrecursorsInStockScorer,
PriceSumScorer,
RouteCostScorer,
ScorerCollection,
ScorerException,
)
from a... | 4 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_stock.py | test_load_stock | assert | numeric_literal | 21 | import pytest
import sys
from aizynthfinder.chem import Molecule
from aizynthfinder.context.stock import (
StockException,
)
from aizynthfinder.tools.make_stock import (
extract_plain_smiles,
extract_smiles_from_module,
make_hdf5_stock,
make_mongo_stock,
)
def test_load_stock(default_config, creat... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_stock.py | test_extract_smiles_from_plain_file | assert | numeric_literal | 21 | import pytest
import sys
from aizynthfinder.chem import Molecule
from aizynthfinder.context.stock import (
StockException,
)
from aizynthfinder.tools.make_stock import (
extract_plain_smiles,
extract_smiles_from_module,
make_hdf5_stock,
make_mongo_stock,
)
def test_extract_smiles_from_plain_file(c... | 8 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_stock.py | test_extract_smiles_from_module | assert | numeric_literal | 28 | import pytest
import sys
from aizynthfinder.chem import Molecule
from aizynthfinder.context.stock import (
StockException,
)
from aizynthfinder.tools.make_stock import (
extract_plain_smiles,
extract_smiles_from_module,
make_hdf5_stock,
make_mongo_stock,
)
def test_extract_smiles_from_module(creat... | 4 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/dfpn/test_nodes.py | test_create_root_node | assert | numeric_literal | 19 | import pytest
from aizynthfinder.search.dfpn.nodes import MoleculeNode, BIG_INT
from aizynthfinder.search.dfpn import SearchTree
def setup_root(default_config):
def wrapper(smiles):
owner = SearchTree(default_config)
return MoleculeNode.create_root(smiles, config=default_config, owner=owner)
... | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/dfpn/test_nodes.py | test_expand_reaction_node | assert | numeric_literal | 24 | import pytest
from aizynthfinder.search.dfpn.nodes import MoleculeNode, BIG_INT
from aizynthfinder.search.dfpn import SearchTree
def setup_root(default_config):
def wrapper(smiles):
owner = SearchTree(default_config)
return MoleculeNode.create_root(smiles, config=default_config, owner=owner)
... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/dfpn/test_search.py | test_search | assert | numeric_literal | 30 | import random
import pytest
from aizynthfinder.search.dfpn.search_tree import SearchTree
def test_search(default_config, setup_policies, setup_stock):
root_smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1"
child1_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F", "O"]
child2_smi = ["CN1CCC(Cl)... | 4 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/dfpn/test_search.py | test_search | assert | numeric_literal | 39 | import random
import pytest
from aizynthfinder.search.dfpn.search_tree import SearchTree
def test_search(default_config, setup_policies, setup_stock):
root_smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1"
child1_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F", "O"]
child2_smi = ["CN1CCC(Cl)... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/mcts/test_node.py | test_expand_root_node | assert | numeric_literal | 8 | def test_expand_root_node(setup_mcts_search):
root, _, _ = setup_mcts_search
root.expand()
view = root.children_view()
assert len(view["actions"]) == | 3 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/mcts/test_node.py | test_promising_child_of_root | assert | numeric_literal | 11 | def test_promising_child_of_root(setup_mcts_search):
root, _, _ = setup_mcts_search
root.expand()
child = root.promising_child()
view = root.children_view()
assert view["objects"][0] is child
assert root.children == [child]
assert root[child]["visitations"] == | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/mcts/test_serialization.py | test_serialize_deserialize_state | assert | numeric_literal | 15 | from aizynthfinder.chem.serialization import MoleculeSerializer, MoleculeDeserializer
from aizynthfinder.chem import TreeMolecule
from aizynthfinder.search.mcts import MctsState
from aizynthfinder.search.mcts import MctsNode
from aizynthfinder.search.mcts import MctsSearchTree
def test_serialize_deserialize_state(defa... | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/mcts/test_tree.py | test_route_to_node | assert | numeric_literal | 7 | def test_route_to_node(setup_complete_mcts_tree):
tree, nodes = setup_complete_mcts_tree
actions, route_nodes = nodes[2].path_to()
assert len(actions) == | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/mcts/test_tree.py | test_route_to_node | assert | numeric_literal | 8 | def test_route_to_node(setup_complete_mcts_tree):
tree, nodes = setup_complete_mcts_tree
actions, route_nodes = nodes[2].path_to()
assert len(actions) == 2
assert len(nodes) == | 3 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/retrostar/test_retrostar.py | test_one_iteration | assert | numeric_literal | 12 | import numpy as np
from aizynthfinder.search.retrostar.search_tree import SearchTree
from aizynthfinder.chem.serialization import MoleculeSerializer
def test_one_iteration(setup_search_tree):
tree = setup_search_tree
tree.one_iteration()
assert len(tree.root.children) == | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/retrostar/test_retrostar.py | test_one_iteration | assert | numeric_literal | 13 | import numpy as np
from aizynthfinder.search.retrostar.search_tree import SearchTree
from aizynthfinder.chem.serialization import MoleculeSerializer
def test_one_iteration(setup_search_tree):
tree = setup_search_tree
tree.one_iteration()
assert len(tree.root.children) == 1
assert len(tree.root.chil... | 3 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/retrostar/test_retrostar.py | test_one_iteration_filter_unfeasible | assert | numeric_literal | 13 | import numpy as np
from aizynthfinder.search.retrostar.search_tree import SearchTree
from aizynthfinder.chem.serialization import MoleculeSerializer
def test_one_iteration_filter_unfeasible(setup_search_tree):
tree = setup_search_tree
smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1>>CN1CCC(Cl)CC1.N#Cc1ccc... | 0 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/retrostar/test_retrostar.py | test_one_expansion_with_finder | assert | numeric_literal | 24 | import numpy as np
from aizynthfinder.search.retrostar.search_tree import SearchTree
from aizynthfinder.chem.serialization import MoleculeSerializer
def test_one_expansion_with_finder(setup_aizynthfinder):
"""
Test the building of this tree:
root
|
child 1
... | 4 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/retrostar/test_retrostar.py | test_one_expansion_with_finder | assert | numeric_literal | 38 | import numpy as np
from aizynthfinder.search.retrostar.search_tree import SearchTree
from aizynthfinder.chem.serialization import MoleculeSerializer
def test_one_expansion_with_finder(setup_aizynthfinder):
"""
Test the building of this tree:
root
|
child 1
... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/retrostar/test_retrostar_cost.py | test_load_cost_from_config | assert | numeric_literal | 18 | import numpy as np
import pytest
from aizynthfinder.context.cost import MoleculeCost
from aizynthfinder.search.retrostar.cost import RetroStarCost
from aizynthfinder.chem import Molecule
def test_load_cost_from_config(setup_mocked_model):
cost = MoleculeCost()
dict_ = {
"aizynthfinder.search.retrost... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/retrostar/test_retrostar_nodes.py | test_create_root_node | assert | numeric_literal | 12 | import numpy as np
import networkx as nx
from aizynthfinder.search.retrostar.nodes import MoleculeNode
from aizynthfinder.chem.serialization import MoleculeSerializer, MoleculeDeserializer
from aizynthfinder.search.andor_trees import ReactionTreeFromAndOrTrace
def test_create_root_node(setup_star_root):
node = se... | 0 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/retrostar/test_retrostar_nodes.py | test_create_stub | assert | numeric_literal | 16 | import numpy as np
import networkx as nx
from aizynthfinder.search.retrostar.nodes import MoleculeNode
from aizynthfinder.chem.serialization import MoleculeSerializer, MoleculeDeserializer
from aizynthfinder.search.andor_trees import ReactionTreeFromAndOrTrace
def test_create_stub(setup_star_root, get_action):
ro... | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/retrostar/test_retrostar_nodes.py | test_create_stub | assert | numeric_literal | 17 | import numpy as np
import networkx as nx
from aizynthfinder.search.retrostar.nodes import MoleculeNode
from aizynthfinder.chem.serialization import MoleculeSerializer, MoleculeDeserializer
from aizynthfinder.search.andor_trees import ReactionTreeFromAndOrTrace
def test_create_stub(setup_star_root, get_action):
ro... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/retrostar/test_retrostar_nodes.py | test_converstion_to_reaction_tree | assert | numeric_literal | 27 | import numpy as np
import networkx as nx
from aizynthfinder.search.retrostar.nodes import MoleculeNode
from aizynthfinder.chem.serialization import MoleculeSerializer, MoleculeDeserializer
from aizynthfinder.search.andor_trees import ReactionTreeFromAndOrTrace
def test_converstion_to_reaction_tree(
setup_star_roo... | 3 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_analysis.py | test_sort_nodes | assert | numeric_literal | 19 | import os
from tarfile import TarFile
import numpy as np
import pytest
from aizynthfinder.analysis import TreeAnalysis, RouteCollection
from aizynthfinder.analysis.utils import RouteSelectionArguments
from aizynthfinder.reactiontree import ReactionTree, SUPPORT_DISTANCES
from aizynthfinder.search.mcts import MctsSear... | 5 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_analysis.py | test_sort_nodes | assert | numeric_literal | 24 | import os
from tarfile import TarFile
import numpy as np
import pytest
from aizynthfinder.analysis import TreeAnalysis, RouteCollection
from aizynthfinder.analysis.utils import RouteSelectionArguments
from aizynthfinder.reactiontree import ReactionTree, SUPPORT_DISTANCES
from aizynthfinder.search.mcts import MctsSear... | 0 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_analysis.py | test_sort_nodes_return_all | assert | numeric_literal | 19 | import os
from tarfile import TarFile
import numpy as np
import pytest
from aizynthfinder.analysis import TreeAnalysis, RouteCollection
from aizynthfinder.analysis.utils import RouteSelectionArguments
from aizynthfinder.reactiontree import ReactionTree, SUPPORT_DISTANCES
from aizynthfinder.search.mcts import MctsSear... | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_analysis.py | test_sort_nodes_scorer | assert | numeric_literal | 20 | import os
from tarfile import TarFile
import numpy as np
import pytest
from aizynthfinder.analysis import TreeAnalysis, RouteCollection
from aizynthfinder.analysis.utils import RouteSelectionArguments
from aizynthfinder.reactiontree import ReactionTree, SUPPORT_DISTANCES
from aizynthfinder.search.mcts import MctsSear... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_analysis.py | test_tree_statistics | assert | numeric_literal | 20 | import os
from tarfile import TarFile
import numpy as np
import pytest
from aizynthfinder.analysis import TreeAnalysis, RouteCollection
from aizynthfinder.analysis.utils import RouteSelectionArguments
from aizynthfinder.reactiontree import ReactionTree, SUPPORT_DISTANCES
from aizynthfinder.search.mcts import MctsSear... | 6 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_analysis.py | test_tree_statistics | assert | numeric_literal | 27 | import os
from tarfile import TarFile
import numpy as np
import pytest
from aizynthfinder.analysis import TreeAnalysis, RouteCollection
from aizynthfinder.analysis.utils import RouteSelectionArguments
from aizynthfinder.reactiontree import ReactionTree, SUPPORT_DISTANCES
from aizynthfinder.search.mcts import MctsSear... | 4 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_analysis.py | test_tree_statistics_andor_tree | assert | numeric_literal | 26 | import os
from tarfile import TarFile
import numpy as np
import pytest
from aizynthfinder.analysis import TreeAnalysis, RouteCollection
from aizynthfinder.analysis.utils import RouteSelectionArguments
from aizynthfinder.reactiontree import ReactionTree, SUPPORT_DISTANCES
from aizynthfinder.search.mcts import MctsSear... | 3 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_analysis.py | test_create_route_collection_full | assert | numeric_literal | 22 | import os
from tarfile import TarFile
import numpy as np
import pytest
from aizynthfinder.analysis import TreeAnalysis, RouteCollection
from aizynthfinder.analysis.utils import RouteSelectionArguments
from aizynthfinder.reactiontree import ReactionTree, SUPPORT_DISTANCES
from aizynthfinder.search.mcts import MctsSear... | 8 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_cli.py | test_app_main_no_output | assert | numeric_literal | 34 | import os
import glob
import sys
import pandas as pd
import yaml
import pytest
from aizynthfinder.interfaces import AiZynthApp
from aizynthfinder.interfaces.aizynthapp import main as app_main
from aizynthfinder.interfaces.aizynthcli import main as cli_main
from aizynthfinder.tools.make_stock import main as make_stock... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_cli.py | test_cli_multiple_smiles | assert | numeric_literal | 49 | import os
import glob
import sys
import pandas as pd
import yaml
import pytest
from aizynthfinder.interfaces import AiZynthApp
from aizynthfinder.interfaces.aizynthapp import main as app_main
from aizynthfinder.interfaces.aizynthcli import main as cli_main
from aizynthfinder.tools.make_stock import main as make_stock... | 4 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_cli.py | test_cli_multiple_smiles_unsanitizable | assert | numeric_literal | 39 | import os
import glob
import sys
import pandas as pd
import yaml
import pytest
from aizynthfinder.interfaces import AiZynthApp
from aizynthfinder.interfaces.aizynthapp import main as app_main
from aizynthfinder.interfaces.aizynthcli import main as cli_main
from aizynthfinder.tools.make_stock import main as make_stock... | 0 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_cli.py | test_make_stock_from_plain_file | assert | numeric_literal | 31 | import os
import glob
import sys
import pandas as pd
import yaml
import pytest
from aizynthfinder.interfaces import AiZynthApp
from aizynthfinder.interfaces.aizynthapp import main as app_main
from aizynthfinder.interfaces.aizynthcli import main as cli_main
from aizynthfinder.tools.make_stock import main as make_stock... | 3 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_cli.py | test_preprocess_expansion | assert | numeric_literal | 37 | import os
import glob
import sys
import pandas as pd
import yaml
import pytest
from aizynthfinder.interfaces import AiZynthApp
from aizynthfinder.interfaces.aizynthapp import main as app_main
from aizynthfinder.interfaces.aizynthcli import main as cli_main
from aizynthfinder.tools.make_stock import main as make_stock... | 6 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_cli.py | test_preprocess_expansion_csv_headers | assert | numeric_literal | 42 | import os
import glob
import sys
import pandas as pd
import yaml
import pytest
from aizynthfinder.interfaces import AiZynthApp
from aizynthfinder.interfaces.aizynthapp import main as app_main
from aizynthfinder.interfaces.aizynthcli import main as cli_main
from aizynthfinder.tools.make_stock import main as make_stock... | 7 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_expander.py | test_expander_defaults | assert | numeric_literal | 11 | from aizynthfinder.aizynthfinder import AiZynthExpander
def test_expander_defaults(get_one_step_expansion, setup_policies):
expander = AiZynthExpander()
setup_policies(get_one_step_expansion, config=expander.config)
smi = "CCCCOc1ccc(CC(=O)N(C)O)cc1"
reactions = expander.do_expansion(smi)
assert... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_expander.py | test_expander_defaults | assert | numeric_literal | 12 | from aizynthfinder.aizynthfinder import AiZynthExpander
def test_expander_defaults(get_one_step_expansion, setup_policies):
expander = AiZynthExpander()
setup_policies(get_one_step_expansion, config=expander.config)
smi = "CCCCOc1ccc(CC(=O)N(C)O)cc1"
reactions = expander.do_expansion(smi)
assert ... | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_finder.py | test_dead_end_expansion | assert | numeric_literal | 22 | import logging
from aizynthfinder.aizynthfinder import AiZynthFinder
def state_smiles(state):
return [mol.smiles for mol in state.mols]
def test_dead_end_expansion(setup_aizynthfinder):
"""
Test the building of this tree:
root
root cannot be expanded
"""
root_smi = "CN1CCC(C(=... | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_finder.py | test_dead_end_expansion | assert | numeric_literal | 25 | import logging
from aizynthfinder.aizynthfinder import AiZynthFinder
def state_smiles(state):
return [mol.smiles for mol in state.mols]
def test_dead_end_expansion(setup_aizynthfinder):
"""
Test the building of this tree:
root
root cannot be expanded
"""
root_smi = "CN1CCC(C(=... | 0 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_finder.py | test_one_expansion | assert | numeric_literal | 26 | import logging
from aizynthfinder.aizynthfinder import AiZynthFinder
def state_smiles(state):
return [mol.smiles for mol in state.mols]
def test_one_expansion(setup_aizynthfinder):
"""
Test the building of this tree:
root
|
child 1
"""
root_smi = ... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_finder.py | test_two_expansions | assert | numeric_literal | 31 | import logging
from aizynthfinder.aizynthfinder import AiZynthFinder
def state_smiles(state):
return [mol.smiles for mol in state.mols]
def test_two_expansions(setup_aizynthfinder):
"""
Test the building of this tree:
root
|
child 1
|
... | 3 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_finder.py | test_two_expansions_two_children | assert | numeric_literal | 37 | import logging
from aizynthfinder.aizynthfinder import AiZynthFinder
def state_smiles(state):
return [mol.smiles for mol in state.mols]
def test_two_expansions_two_children(setup_aizynthfinder):
"""
Test the building of this tree:
root
/ \
child 1 chil... | 5 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_finder.py | test_three_expansions | assert | numeric_literal | 38 | import logging
from aizynthfinder.aizynthfinder import AiZynthFinder
def state_smiles(state):
return [mol.smiles for mol in state.mols]
def test_three_expansions(setup_aizynthfinder):
"""
Test the building of this tree:
root
|
child 1
|
... | 4 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_reactiontree.py | test_mcts_route_to_reactiontree | assert | numeric_literal | 20 | import pytest
from aizynthfinder.reactiontree import ReactionTree, SUPPORT_DISTANCES
def test_mcts_route_to_reactiontree(setup_linear_mcts, load_reaction_tree):
def remove_metadata(tree_dict):
if "metadata" in tree_dict:
tree_dict["metadata"] = {}
for child in tree_dict.get("children",... | 5 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_reactiontree.py | test_mcts_route_to_reactiontree | assert | numeric_literal | 23 | import pytest
from aizynthfinder.reactiontree import ReactionTree, SUPPORT_DISTANCES
def test_mcts_route_to_reactiontree(setup_linear_mcts, load_reaction_tree):
def remove_metadata(tree_dict):
if "metadata" in tree_dict:
tree_dict["metadata"] = {}
for child in tree_dict.get("children",... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_reactiontree.py | test_mcts_route_to_reactiontree | assert | numeric_literal | 26 | import pytest
from aizynthfinder.reactiontree import ReactionTree, SUPPORT_DISTANCES
def test_mcts_route_to_reactiontree(setup_linear_mcts, load_reaction_tree):
def remove_metadata(tree_dict):
if "metadata" in tree_dict:
tree_dict["metadata"] = {}
for child in tree_dict.get("children",... | 3 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_reactiontree.py | test_route_node_depth_from_mcts | assert | numeric_literal | 10 | import pytest
from aizynthfinder.reactiontree import ReactionTree, SUPPORT_DISTANCES
def test_route_node_depth_from_mcts(setup_branched_reaction_tree):
rt = setup_branched_reaction_tree()
mols = list(rt.molecules())
assert rt.depth(mols[0]) == | 0 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_reactiontree.py | test_route_node_depth_from_mcts | assert | numeric_literal | 13 | import pytest
from aizynthfinder.reactiontree import ReactionTree, SUPPORT_DISTANCES
def test_route_node_depth_from_mcts(setup_branched_reaction_tree):
rt = setup_branched_reaction_tree()
mols = list(rt.molecules())
assert rt.depth(mols[0]) == 0
assert rt.depth(mols[1]) == 2
assert rt.depth(mols[... | 4 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_reactiontree.py | test_route_node_depth_from_json | assert | numeric_literal | 17 | import pytest
from aizynthfinder.reactiontree import ReactionTree, SUPPORT_DISTANCES
def test_route_node_depth_from_json(load_reaction_tree):
dict_ = load_reaction_tree("branched_route.json")
rt = ReactionTree.from_dict(dict_)
# Molecules loaded in a different order than when created from MCTS
mols ... | 6 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_training.py | test_split_and_save_data_frame | assert | numeric_literal | 62 | import os
import pytest
import pandas as pd
import numpy as np
from aizynthfinder.chem import Molecule
def default_config():
return Config()
def filter_model_sequence(mocker, default_config):
mocked_load_npz = mocker.patch(
"aizynthfinder.training.keras_models.sparse.load_npz"
)
input_array ... | 5 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_training.py | test_smiles_to_fingerprint | assert | numeric_literal | 43 | import os
import pytest
import pandas as pd
import numpy as np
from aizynthfinder.chem import Molecule
def default_config():
return Config()
def filter_model_sequence(mocker, default_config):
mocked_load_npz = mocker.patch(
"aizynthfinder.training.keras_models.sparse.load_npz"
)
input_array ... | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_training.py | test_reactants_molecules | assert | numeric_literal | 43 | import os
import pytest
import pandas as pd
import numpy as np
from aizynthfinder.chem import Molecule
def default_config():
return Config()
def filter_model_sequence(mocker, default_config):
mocked_load_npz = mocker.patch(
"aizynthfinder.training.keras_models.sparse.load_npz"
)
input_array ... | 2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/utils/test_file_utils.py | test_cat_hdf | assert | numeric_literal | 41 | import os
import gzip
import json
import pytest
import pandas as pd
from aizynthfinder.utils.files import (
cat_datafiles,
split_file,
start_processes,
read_datafile,
save_datafile,
)
def create_dummy_file(tmpdir, mocker):
patched_tempfile = mocker.patch("aizynthfinder.utils.files.tempfile.mk... | 4 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/utils/test_image.py | test_graphviz_usage | assert | numeric_literal | 40 | import os
import shutil
import json
from tarfile import TarFile
from pathlib import Path
import pytest
from PIL import Image, ImageDraw
from aizynthfinder.utils import image
from aizynthfinder.chem import TreeMolecule, TemplatedRetroReaction
def new_image():
img = Image.new(mode="RGB", size=(300, 300), color="wh... | 0 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/utils/test_image.py | test_visjs_page | assert | numeric_literal | 38 | import os
import shutil
import json
from tarfile import TarFile
from pathlib import Path
import pytest
from PIL import Image, ImageDraw
from aizynthfinder.utils import image
from aizynthfinder.chem import TreeMolecule, TemplatedRetroReaction
def new_image():
img = Image.new(mode="RGB", size=(300, 300), color="wh... | 1 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/breadth_first/test_search.py | test_one_iteration | assert | numeric_literal | 36 | import random
import pytest
from aizynthfinder.search.breadth_first.search_tree import SearchTree
def test_one_iteration(default_config, setup_policies, setup_stock):
root_smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1"
child1_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F", "O"]
child2_sm... | 10 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_mcts_config.py | test_load_stop_criteria | assert | numeric_literal | 17 | import pytest
from aizynthfinder.context.config import Configuration
from aizynthfinder.aizynthfinder import AiZynthFinder
def test_load_stop_criteria(write_yaml):
filename = write_yaml(
{"stock": {"stop_criteria": {"price": 100, "counts": {"C": 10}}}}
)
config = Configuration.from_file(filename)... | 10 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_stock.py | test_price_with_price | assert | numeric_literal | 21 | import pytest
import sys
from aizynthfinder.chem import Molecule
from aizynthfinder.context.stock import (
StockException,
)
from aizynthfinder.tools.make_stock import (
extract_plain_smiles,
extract_smiles_from_module,
make_hdf5_stock,
make_mongo_stock,
)
def test_price_with_price(setup_stock_wit... | 14 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/retrostar/test_retrostar.py | test_split_andor_tree | assert | numeric_literal | 14 | import numpy as np
from aizynthfinder.search.retrostar.search_tree import SearchTree
from aizynthfinder.chem.serialization import MoleculeSerializer
def test_split_andor_tree(shared_datadir, default_config):
tree = SearchTree.from_json(
str(shared_datadir / "andor_tree_for_clustering.json"), default_confi... | 97 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/retrostar/test_retrostar_cost.py | test_retrostar_cost | assert | numeric_literal | 14 | import numpy as np
import pytest
from aizynthfinder.context.cost import MoleculeCost
from aizynthfinder.search.retrostar.cost import RetroStarCost
from aizynthfinder.chem import Molecule
def test_retrostar_cost(setup_mocked_model):
mol = Molecule(smiles="CCCC")
cost = RetroStarCost(model_path="dummy", finge... | 30 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_training.py | test_update_single_setting | assert | numeric_literal | 43 | import os
import pytest
import pandas as pd
import numpy as np
from aizynthfinder.chem import Molecule
def default_config():
return Config()
def filter_model_sequence(mocker, default_config):
mocked_load_npz = mocker.patch(
"aizynthfinder.training.keras_models.sparse.load_npz"
)
input_array ... | 10 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/test_training.py | test_split_and_save_data_frame | assert | numeric_literal | 59 | import os
import pytest
import pandas as pd
import numpy as np
from aizynthfinder.chem import Molecule
def default_config():
return Config()
def filter_model_sequence(mocker, default_config):
mocked_load_npz = mocker.patch(
"aizynthfinder.training.keras_models.sparse.load_npz"
)
input_array ... | 90 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_mcts_config.py | test_load_from_file | assert | numeric_literal | 21 | import pytest
from aizynthfinder.context.config import Configuration
from aizynthfinder.aizynthfinder import AiZynthFinder
def test_load_from_file(write_yaml):
filename = write_yaml(
{
"properties": {
"cutoff_number": 300,
"post_processing": {"all_routes": True}... | 300 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_mcts_config.py | test_load_from_file | assert | numeric_literal | 22 | import pytest
from aizynthfinder.context.config import Configuration
from aizynthfinder.aizynthfinder import AiZynthFinder
def test_load_from_file(write_yaml):
filename = write_yaml(
{
"properties": {
"cutoff_number": 300,
"post_processing": {"all_routes": True}... | 1.9 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_mcts_config.py | test_load_from_file | assert | numeric_literal | 23 | import pytest
from aizynthfinder.context.config import Configuration
from aizynthfinder.aizynthfinder import AiZynthFinder
def test_load_from_file(write_yaml):
filename = write_yaml(
{
"properties": {
"cutoff_number": 300,
"post_processing": {"all_routes": True}... | 200 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_mcts_config.py | test_get_properties | assert | numeric_literal | 13 | import pytest
from aizynthfinder.context.config import Configuration
from aizynthfinder.aizynthfinder import AiZynthFinder
def test_get_properties(default_config):
config = default_config
props = config.properties
# Just check a few properties
assert props["C"] == | 1.4 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/chem/test_serialization.py | test_chaining | assert | variable | 16 | from aizynthfinder.chem.serialization import MoleculeSerializer, MoleculeDeserializer
from aizynthfinder.chem import Molecule, TreeMolecule
def test_chaining():
serializer = MoleculeSerializer()
mol1 = TreeMolecule(parent=None, smiles="CCC", transform=1)
mol2 = TreeMolecule(smiles="CCO", parent=mol1)
... | id_ | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/chem/test_mol.py | test_equality | assert | variable | 11 | import pytest
from rdkit import Chem
from aizynthfinder.chem import MoleculeException, Molecule
def test_equality():
mol1 = Molecule(smiles="CCCCO")
mol2 = Molecule(smiles="OCCCC")
assert mol1 == | mol2 | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/context/test_stock.py | test_mol_in_stock | assert | variable | 20 | import pytest
import sys
from aizynthfinder.chem import Molecule
from aizynthfinder.context.stock import (
StockException,
)
from aizynthfinder.tools.make_stock import (
extract_plain_smiles,
extract_smiles_from_module,
make_hdf5_stock,
make_mongo_stock,
)
def test_mol_in_stock(setup_stock_with_qu... | stock | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/mcts/test_node.py | test_promising_child_of_root | assert | variable | 9 | def test_promising_child_of_root(setup_mcts_search):
root, _, _ = setup_mcts_search
root.expand()
child = root.promising_child()
view = root.children_view()
assert view["objects"][0] is | child | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/utils/test_image.py | test_rounded_rectangle | assert | variable | 30 | import os
import shutil
import json
from tarfile import TarFile
from pathlib import Path
import pytest
from PIL import Image, ImageDraw
from aizynthfinder.utils import image
from aizynthfinder.chem import TreeMolecule, TemplatedRetroReaction
def new_image():
img = Image.new(mode="RGB", size=(300, 300), color="wh... | color | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/chem/test_reaction.py | test_create_fixed_reaction | assert | variable | 21 | from aizynthfinder.chem import (
Molecule,
UniqueMolecule,
TreeMolecule,
Reaction,
TemplatedRetroReaction,
FixedRetroReaction,
SmilesBasedRetroReaction,
hash_reactions,
MoleculeException,
)
from aizynthfinder.reactiontree import ReactionTree
def test_create_fixed_reaction():
smi... | smiles | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/mcts/test_tree.py | test_backpropagation | assert_* | variable | 10 | def test_backpropagation(setup_complete_mcts_tree, mocker):
tree, nodes = setup_complete_mcts_tree
for node in nodes:
node.backpropagate = mocker.MagicMock()
score = 1.5
tree.backpropagate(nodes[2], score)
nodes[0].backpropagate.assert_called_once_with(nodes[1], | score) | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/dfpn/test_nodes.py | test_promising_child | assert | variable | 25 | import pytest
from aizynthfinder.search.dfpn.nodes import MoleculeNode, BIG_INT
from aizynthfinder.search.dfpn import SearchTree
def setup_root(default_config):
def wrapper(smiles):
owner = SearchTree(default_config)
return MoleculeNode.create_root(smiles, config=default_config, owner=owner)
... | BIG_INT | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/breadth_first/test_nodes.py | test_create_stub | assert | variable | 23 | import pytest
from aizynthfinder.search.breadth_first.nodes import MoleculeNode
from aizynthfinder.chem.serialization import MoleculeSerializer, MoleculeDeserializer
def setup_root(default_config):
def wrapper(smiles):
return MoleculeNode.create_root(smiles, config=default_config)
return wrapper
def... | reaction | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/retrostar/test_retrostar.py | test_one_expansion_with_finder | assert | variable | 25 | import numpy as np
from aizynthfinder.search.retrostar.search_tree import SearchTree
from aizynthfinder.chem.serialization import MoleculeSerializer
def test_one_expansion_with_finder(setup_aizynthfinder):
"""
Test the building of this tree:
root
|
child 1
... | root_smi | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
MolecularAI/aizynthfinder | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | train | train | tests/retrostar/test_retrostar_nodes.py | test_create_stub | assert | variable | 19 | import numpy as np
import networkx as nx
from aizynthfinder.search.retrostar.nodes import MoleculeNode
from aizynthfinder.chem.serialization import MoleculeSerializer, MoleculeDeserializer
from aizynthfinder.search.andor_trees import ReactionTreeFromAndOrTrace
def test_create_stub(setup_star_root, get_action):
ro... | reaction | 9e44989213c11f1bb647a00b8756e0c76a8f4b52 | 21 | v2_extractor_at_anchor |
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