repo_id stringclasses 409
values | prefix large_stringlengths 34 36.3k | target large_stringlengths 1 498 | assertion_type stringclasses 31
values | difficulty stringclasses 8
values | test_file stringlengths 10 121 | test_function stringlengths 1 104 | test_class stringlengths 0 51 | lineno int32 2 11.3k | commit_idx int32 |
|---|---|---|---|---|---|---|---|---|---|
MolecularAI/aizynthfinder | def test_create_graph(setup_complete_mcts_tree):
tree, nodes = setup_complete_mcts_tree
graph = tree.graph()
assert len(graph) == 3
assert list(graph.successors(nodes[0])) == [nodes[1]]
assert list(graph.successors(nodes[1])) == | [nodes[2]] | assert | collection | tests/mcts/test_tree.py | test_create_graph | 50 | null | |
MolecularAI/aizynthfinder | 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 | assert | numeric_literal | tests/breadth_first/test_search.py | test_routes | 102 | null | |
MolecularAI/aizynthfinder | 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 | assert | numeric_literal | tests/chem/test_serialization.py | test_deserialize_tree_mols | 71 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import TreeMolecule
from aizynthfinder.chem.serialization import MoleculeDeserializer, MoleculeSerializer
from aizynthfinder.search.mcts import MctsNode, MctsSearchTree, MctsState
def test_serialize_node(setup_mcts_search):
serializer = MoleculeSerializer()
root, _, _ = setup_mcts_searc... | [] | assert | collection | tests/mcts/test_serialization.py | test_serialize_node | 39 | null | |
MolecularAI/aizynthfinder | 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... | None | assert | none_literal | tests/chem/test_serialization.py | test_deserialize_tree_mols | 68 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.context.collection import ContextCollection
def test_select_single_collection():
collection = SingleStringCollection()
collection.load("key1", "value1")
collection.load("key2", "value2")
collection.selection = "key1"
assert collection.selection == | "key1" | assert | string_literal | tests/context/test_collection.py | test_select_single_collection | 176 | null | |
MolecularAI/aizynthfinder | 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 | assert | numeric_literal | tests/retrostar/test_retrostar.py | test_one_iteration | 13 | null | |
MolecularAI/aizynthfinder | 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... | grandchild2.mol | assert | complex_expr | tests/breadth_first/test_nodes.py | test_serialization_deserialization | 75 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import (
FixedRetroReaction,
SmilesBasedRetroReaction,
TemplatedRetroReaction,
TreeMolecule,
UniqueMolecule,
hash_reactions,
)
def test_create_fixed_reaction():
smiles = "[C:1](=[O:2])([cH3:3])[N:4][cH3:5]>>Cl[C:1](=[O:2])[cH3:3].[N:4][cH3:5]"
mol = UniqueMolecul... | smiles | assert | variable | tests/chem/test_reaction.py | test_create_fixed_reaction | 122 | null | |
MolecularAI/aizynthfinder | 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... | "d\ne" | assert | string_literal | tests/utils/test_file_utils.py | test_split_file_odd | 62 | null | |
MolecularAI/aizynthfinder | import pytest
import sys
import pandas as pd
from aizynthfinder.chem import Molecule
from aizynthfinder.context.stock import (
StockException,
)
from aizynthfinder.context.stock.queries import HAS_MOLBLOOM
from aizynthfinder.tools.make_stock import (
extract_plain_smiles,
extract_smiles_from_module,
m... | 2 | assert | numeric_literal | tests/context/test_stock.py | test_load_csv_stock | 37 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import (
FixedRetroReaction,
SmilesBasedRetroReaction,
TemplatedRetroReaction,
TreeMolecule,
UniqueMolecule,
hash_reactions,
)
def test_mapped_atom_bonds():
mol = TreeMolecule(smiles="[CH3:1][NH:2][C:3](C)=[O:4]", parent=None)
reaction = SmilesBasedRetroReaction(... | [(1, 2)] | assert | collection | tests/chem/test_reaction.py | test_mapped_atom_bonds | 199 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import (
FixedRetroReaction,
SmilesBasedRetroReaction,
TemplatedRetroReaction,
TreeMolecule,
UniqueMolecule,
hash_reactions,
)
def test_fixed_retroreaction_to_smiles_based_retroreaction_no_metadata():
mol = UniqueMolecule(smiles="CNC(C)=O")
reactant1 = UniqueMole... | "CNC(C)=O" | assert | string_literal | tests/chem/test_reaction.py | test_fixed_retroreaction_to_smiles_based_retroreaction_no_metadata | 168 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.search.mcts.node import ParetoMctsNode
from aizynthfinder.search.mcts import MctsSearchTree
def generate_root(default_config):
def wrapper(smiles, config=None):
return ParetoMctsNode.create_root(
smiles, tree=None, config=config or default_config
)
... | view_post["values"] | assert | complex_expr | tests/mcts/test_multiobjective.py | test_backpropagate | 72 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.chem import TreeMolecule
from aizynthfinder.context.policy import (
MultiExpansionStrategy,
TemplateBasedExpansionStrategy,
)
from aizynthfinder.utils.exceptions import PolicyException
def test_load_templated_expansion_strategy_from_csv(
default_config, mock_onnx_model, tm... | ["template", "metadata"] | assert | collection | tests/context/test_expansion_strategies.py | test_load_templated_expansion_strategy_from_csv | 195 | null | |
MolecularAI/aizynthfinder | import os
from tarfile import TarFile
import numpy as np
import pytest
from aizynthfinder.analysis import TreeAnalysis, RouteCollection
from aizynthfinder.analysis.routes import SUPPORT_CLUSTERING
from aizynthfinder.analysis.utils import RouteSelectionArguments
from aizynthfinder.reactiontree import ReactionTree
from... | 2 | assert | numeric_literal | tests/test_analysis.py | test_sort_nodes_scorer | 62 | null | |
MolecularAI/aizynthfinder | 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_conversion_to_reaction_tree(
setup_star_root... | 3 | assert | numeric_literal | tests/retrostar/test_retrostar_nodes.py | test_conversion_to_reaction_tree | 136 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.context.collection import ContextCollection
def test_empty_collection():
collection = StringCollection()
assert len(collection) == 0
assert collection.selection == | [] | assert | collection | tests/context/test_collection.py | test_empty_collection | 23 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import TreeMolecule
from aizynthfinder.chem.serialization import MoleculeDeserializer, MoleculeSerializer
from aizynthfinder.search.mcts import MctsNode, MctsSearchTree, MctsState
def test_serialize_deserialize_state(default_config):
mol = TreeMolecule(parent=None, smiles="CCC", transform=1... | id(mol) | assert | func_call | tests/mcts/test_serialization.py | test_serialize_deserialize_state | 16 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.analysis import TreeAnalysis
from aizynthfinder.context.scoring import (
NumberOfReactionsScorer,
StateScorer,
)
from aizynthfinder.search.mcts import MctsSearchTree
def test_custom_reward(setup_aizynthfinder):
"""Test using different custom reward functions for MCTS and route building."... | [post_process_reward_scorer] | assert | collection | tests/mcts/test_reward.py | test_custom_reward | 84 | null | |
MolecularAI/aizynthfinder | 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 | assert | numeric_literal | tests/retrostar/test_retrostar.py | test_one_expansion_with_finder | 65 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.search.mcts.node import ParetoMctsNode
from aizynthfinder.search.mcts import MctsSearchTree
def generate_root(default_config):
def wrapper(smiles, config=None):
return ParetoMctsNode.create_root(
smiles, tree=None, config=config or default_config
)
... | [None, None, None] | assert | collection | tests/mcts/test_multiobjective.py | test_expand_root_node | 44 | null | |
MolecularAI/aizynthfinder | 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 | assert | numeric_literal | tests/mcts/test_tree.py | test_route_to_node | 37 | null | |
MolecularAI/aizynthfinder | import os
from unittest import mock
import pytest
from aizynthfinder.aizynthfinder import AiZynthFinder
from aizynthfinder.context.config import Configuration
from aizynthfinder.context.stock import StockException
def test_load_from_file(write_yaml):
filename = write_yaml(
{
"search": {
... | "mcts" | assert | string_literal | tests/context/test_mcts_config.py | test_load_from_file | 45 | null | |
MolecularAI/aizynthfinder | 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 | variable | tests/mcts/test_node.py | test_promising_child_of_root | 78 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.search.mcts.node import ParetoMctsNode
from aizynthfinder.search.mcts import MctsSearchTree
def generate_root(default_config):
def wrapper(smiles, config=None):
return ParetoMctsNode.create_root(
smiles, tree=None, config=config or default_config
)
... | 3 | assert | numeric_literal | tests/mcts/test_multiobjective.py | test_expand_root_node | 40 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.context.collection import ContextCollection
def test_empty_single_collection():
collection = SingleStringCollection()
assert len(collection) == 0
assert collection.selection is | None | assert | none_literal | tests/context/test_collection.py | test_empty_single_collection | 166 | null | |
MolecularAI/aizynthfinder | 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 | assert | numeric_literal | tests/breadth_first/test_search.py | test_search_incomplete | 70 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import TreeMolecule
from aizynthfinder.chem.serialization import MoleculeDeserializer, MoleculeSerializer
from aizynthfinder.search.mcts import MctsNode, MctsSearchTree, MctsState
def test_deserialize_node(setup_mcts_search, default_config):
serializer = MoleculeSerializer()
root, _, _ ... | str(child.state) | assert | func_call | tests/mcts/test_serialization.py | test_deserialize_node | 110 | null | |
MolecularAI/aizynthfinder | 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 | assert | numeric_literal | tests/context/test_collection.py | test_deselect_all | 140 | null | |
MolecularAI/aizynthfinder | import os
from tarfile import TarFile
import pytest
from aizynthfinder.utils import image
from aizynthfinder.chem import TreeMolecule, TemplatedRetroReaction
def setup_graph():
mol1 = TreeMolecule(smiles="CCCO", parent=None)
reaction = TemplatedRetroReaction(mol=mol1, smarts="")
return [mol1], [reaction]... | tarobj.getnames() | assert | func_call | tests/utils/test_image.py | test_visjs_page | 46 | null | |
MolecularAI/aizynthfinder | import numpy as np
import pytest
import aizynthfinder.utils.models as models
from aizynthfinder.utils.models import (
SUPPORT_EXTERNAL_APIS,
ExternalModelViaGRPC,
ExternalModelViaREST,
)
def setup_rest_mock(mocker):
models.TF_SERVING_HOST = "localhost"
models.TF_SERVING_REST_PORT = "255"
mocke... | [0.0, 1.0] | assert | collection | tests/utils/test_external_tf_models.py | test_predict_tf_rest_model | 125 | null | |
MolecularAI/aizynthfinder | 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... | len(root.children) | assert | func_call | tests/breadth_first/test_nodes.py | test_serialization_deserialization | 68 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import (
FixedRetroReaction,
SmilesBasedRetroReaction,
TemplatedRetroReaction,
TreeMolecule,
UniqueMolecule,
hash_reactions,
)
def test_retro_reaction(get_action):
reaction = get_action(applicable=True)
products1 = reaction.reactants
assert products1[0][0].s... | "CNO" | assert | string_literal | tests/chem/test_reaction.py | test_retro_reaction | 16 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import TreeMolecule
from aizynthfinder.chem.serialization import MoleculeDeserializer, MoleculeSerializer
from aizynthfinder.search.mcts import MctsNode, MctsSearchTree, MctsState
def test_serialize_deserialize_state(default_config):
mol = TreeMolecule(parent=None, smiles="CCC", transform=1... | 1 | assert | numeric_literal | tests/mcts/test_serialization.py | test_serialize_deserialize_state | 15 | null | |
MolecularAI/aizynthfinder | 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
assert nodes[0] == route_nodes[0]
assert nodes[1] == | route_nodes[1] | assert | complex_expr | tests/mcts/test_tree.py | test_route_to_node | 39 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.context.collection import ContextCollection
def test_add_single_item():
collection = StringCollection()
collection.load("key1", "value1")
assert len(collection) == 1
assert collection.items == | ["key1"] | assert | collection | tests/context/test_collection.py | test_add_single_item | 32 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.reactiontree import ReactionTree
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[2]) == 2
asser... | 4 | assert | numeric_literal | tests/test_reactiontree.py | test_route_node_depth_from_mcts | 65 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.chem import TreeMolecule
from aizynthfinder.context.policy import (
MultiExpansionStrategy,
TemplateBasedExpansionStrategy,
)
from aizynthfinder.utils.exceptions import PolicyException
def test_load_templated_expansion_strategy(
default_config, setup_template_expansion_pol... | 3 | assert | numeric_literal | tests/context/test_expansion_strategies.py | test_load_templated_expansion_strategy | 163 | null | |
MolecularAI/aizynthfinder | import glob
import json
import os
import sys
from typing import Dict, List
import pandas as pd
import pytest
import yaml
from aizynthfinder.analysis import RouteCollection
from aizynthfinder.chem import MoleculeException
from aizynthfinder.interfaces import AiZynthApp
from aizynthfinder.interfaces.aizynthapp import m... | output.out | assert | complex_expr | tests/test_cli.py | test_cli_single_smiles | 164 | null | |
MolecularAI/aizynthfinder | from networkx import get_node_attributes, set_node_attributes
import numpy as np
import pytest
from aizynthfinder.chem import Molecule, UniqueMolecule
from aizynthfinder.context.config import Configuration
from aizynthfinder.context.scoring import (
AverageTemplateOccurrenceScorer,
BrokenBondsScorer,
Combi... | 5 | assert | numeric_literal | tests/context/test_score.py | test_template_occurrence_scorer | 99 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.chem import TreeMolecule
from aizynthfinder.context.policy import (
MultiExpansionStrategy,
TemplateBasedExpansionStrategy,
)
from aizynthfinder.utils.exceptions import PolicyException
def test_multi_expansion_strategy(default_config, setup_template_expansion_policy):
expa... | [0.7, 0.2, 0.7, 0.2] | assert | collection | tests/context/test_expansion_strategies.py | test_multi_expansion_strategy | 47 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.context.collection import ContextCollection
def test_select_single_collection():
collection = SingleStringCollection()
collection.load("key1", "value1")
collection.load("key2", "value2")
collection.selection = "key1"
assert collection.selection == "key1"
col... | "key2" | assert | string_literal | tests/context/test_collection.py | test_select_single_collection | 180 | null | |
MolecularAI/aizynthfinder | import numpy as np
import pytest
from aizynthfinder.chem import (
SmilesBasedRetroReaction,
TemplatedRetroReaction,
TreeMolecule,
)
from aizynthfinder.context.policy import (
BondFilter,
FrozenSubstructureFilter,
QuickKerasFilter,
ReactantsCountFilter,
TemplateBasedDirectExpansionStrate... | [0.7] | assert | collection | tests/context/test_policy.py | test_get_actions | 118 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.reactiontree import ReactionTree
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 | numeric_literal | tests/test_reactiontree.py | test_route_node_depth_from_mcts | 62 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import TreeMolecule
from aizynthfinder.chem.serialization import MoleculeDeserializer, MoleculeSerializer
from aizynthfinder.search.mcts import MctsNode, MctsSearchTree, MctsState
def test_serialize_deserialize_state(default_config):
mol = TreeMolecule(parent=None, smiles="CCC", transform=1... | state0.mols[0] | assert | complex_expr | tests/mcts/test_serialization.py | test_serialize_deserialize_state | 26 | null | |
MolecularAI/aizynthfinder | 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.smarts | assert | complex_expr | tests/breadth_first/test_nodes.py | test_serialization_deserialization | 71 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.analysis import TreeAnalysis
from aizynthfinder.context.scoring import (
NumberOfReactionsScorer,
StateScorer,
)
from aizynthfinder.search.mcts import MctsSearchTree
def test_reward_node_backward_compatibility(default_config):
reward_scorer = repr(NumberOfReactionsScorer())
default_c... | reward_scorer | assert | variable | tests/mcts/test_reward.py | test_reward_node_backward_compatibility | 116 | null | |
MolecularAI/aizynthfinder | import os
from unittest import mock
import pytest
from aizynthfinder.aizynthfinder import AiZynthFinder
from aizynthfinder.context.config import Configuration
from aizynthfinder.context.stock import StockException
def test_load_stock(write_yaml, create_dummy_stock1):
stock_filename = create_dummy_stock1("hdf5")
... | ["test"] | assert | collection | tests/context/test_mcts_config.py | test_load_stock | 132 | null | |
MolecularAI/aizynthfinder | 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 | assert | numeric_literal | tests/breadth_first/test_search.py | test_one_iteration | 26 | null | |
MolecularAI/aizynthfinder | from networkx import get_node_attributes, set_node_attributes
import numpy as np
import pytest
from aizynthfinder.chem import Molecule, UniqueMolecule
from aizynthfinder.context.config import Configuration
from aizynthfinder.context.scoring import (
AverageTemplateOccurrenceScorer,
BrokenBondsScorer,
Combi... | 1 | assert | numeric_literal | tests/context/test_score.py | test_scorers_one_mcts_node | 154 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.search.mcts.node import ParetoMctsNode
from aizynthfinder.search.mcts import MctsSearchTree
def generate_root(default_config):
def wrapper(smiles, config=None):
return ParetoMctsNode.create_root(
smiles, tree=None, config=config or default_config
)
... | 2 | assert | numeric_literal | tests/mcts/test_multiobjective.py | test_setup_weighted_sum_tree | 88 | null | |
MolecularAI/aizynthfinder | def test_backpropagation(setup_complete_mcts_tree, mocker):
tree, nodes = setup_complete_mcts_tree
for node in nodes:
node.backpropagate = mocker.MagicMock()
score = tree.reward_scorer[tree.reward_scorer_name](nodes[2])
tree.backpropagate(nodes[2])
nodes[0].backpropagate.assert_called_onc... | score) | assert_* | variable | tests/mcts/test_tree.py | test_backpropagation | 26 | null | |
MolecularAI/aizynthfinder | 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... | root.mol | assert | complex_expr | tests/breadth_first/test_nodes.py | test_serialization_deserialization | 67 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import (
FixedRetroReaction,
SmilesBasedRetroReaction,
TemplatedRetroReaction,
TreeMolecule,
UniqueMolecule,
hash_reactions,
)
def test_smiles_based_retroreaction():
mol = TreeMolecule(smiles="CNC(C)=O", parent=None)
reaction = SmilesBasedRetroReaction(mol, react... | "CN" | assert | string_literal | tests/chem/test_reaction.py | test_smiles_based_retroreaction | 92 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.chem import TreeMolecule
from aizynthfinder.context.policy import (
MultiExpansionStrategy,
TemplateBasedExpansionStrategy,
)
from aizynthfinder.utils.exceptions import PolicyException
def test_multi_expansion_strategy_wo_additive_expansion(
default_config, setup_template_... | [0.7, 0.2] | assert | collection | tests/context/test_expansion_strategies.py | test_multi_expansion_strategy_wo_additive_expansion | 68 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.context.collection import ContextCollection
def test_empty_collection():
collection = StringCollection()
assert len(collection) == | 0 | assert | numeric_literal | tests/context/test_collection.py | test_empty_collection | 22 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import TreeMolecule
from aizynthfinder.chem.serialization import MoleculeDeserializer, MoleculeSerializer
from aizynthfinder.search.mcts import MctsNode, MctsSearchTree, MctsState
def test_serialize_deserialize_tree(
setup_complete_mcts_tree,
default_config,
mocker,
tmpdir,
):
... | mocker.ANY) | assert_* | complex_expr | tests/mcts/test_serialization.py | test_serialize_deserialize_tree | 130 | null | |
MolecularAI/aizynthfinder | 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... | data2.b.to_list() | assert | func_call | tests/utils/test_file_utils.py | test_save_load_datafile_roundtrip | 146 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import (
FixedRetroReaction,
SmilesBasedRetroReaction,
TemplatedRetroReaction,
TreeMolecule,
UniqueMolecule,
hash_reactions,
)
def test_retro_reaction_copy(get_action):
reaction = get_action()
_ = reaction.reactants
copy_ = reaction.copy()
assert isinst... | reaction.index | assert | complex_expr | tests/chem/test_reaction.py | test_retro_reaction_copy | 77 | null | |
MolecularAI/aizynthfinder | 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
assert nodes[0] == | route_nodes[0] | assert | complex_expr | tests/mcts/test_tree.py | test_route_to_node | 38 | null | |
MolecularAI/aizynthfinder | 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 | assert | numeric_literal | tests/test_expander.py | test_expander_defaults | 12 | null | |
MolecularAI/aizynthfinder | 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 | collection | tests/mcts/test_node.py | test_promising_child_of_root | 79 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import TreeMolecule, SmilesBasedRetroReaction
from aizynthfinder.utils.bonds import BrokenBonds
def test_focussed_bonds_broken():
mol = TreeMolecule(smiles="[CH3:1][NH:2][C:3](C)=[O:4]", parent=None)
reaction = SmilesBasedRetroReaction(
mol,
mapped_prod_smiles="[CH3:1][N... | [(2, 3)] | assert | collection | tests/utils/test_bonds.py | test_focussed_bonds_broken | 19 | null | |
MolecularAI/aizynthfinder | 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(mol1) | assert | func_call | tests/chem/test_serialization.py | test_chaining | 86 | null | |
MolecularAI/aizynthfinder | import pytest
from rdkit import Chem
from aizynthfinder.chem import MoleculeException, Molecule
def test_sanitize():
mol = Molecule(smiles="O", sanitize=True)
assert Chem.MolToSmiles(mol.rd_mol) == "O"
mol = Molecule(smiles="c1ccccc1(C)(C)")
with pytest.raises(MoleculeException):
mol.saniti... | "CC1(C)CCCCC1" | assert | string_literal | tests/chem/test_mol.py | test_sanitize | 57 | null | |
MolecularAI/aizynthfinder | from networkx import get_node_attributes, set_node_attributes
import numpy as np
import pytest
from aizynthfinder.chem import Molecule, UniqueMolecule
from aizynthfinder.context.config import Configuration
from aizynthfinder.context.scoring import (
AverageTemplateOccurrenceScorer,
BrokenBondsScorer,
Combi... | 4 | assert | numeric_literal | tests/context/test_score.py | test_scoring_branched_mcts_tree | 188 | null | |
MolecularAI/aizynthfinder | import logging
import pandas as pd
import pytest
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
... | 0 | assert | numeric_literal | tests/test_finder.py | test_dead_end_expansion | 40 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import TreeMolecule, SmilesBasedRetroReaction
from aizynthfinder.utils.bonds import BrokenBonds
def test_focussed_bonds_not_broken():
mol = TreeMolecule(smiles="[CH3:1][NH:2][C:3](C)=[O:4]", parent=None)
reaction = SmilesBasedRetroReaction(
mol,
mapped_prod_smiles="[CH3:... | True | assert | bool_literal | tests/utils/test_bonds.py | test_focussed_bonds_not_broken | 34 | null | |
MolecularAI/aizynthfinder | import numpy as np
import pytest
from aizynthfinder.chem import (
SmilesBasedRetroReaction,
TemplatedRetroReaction,
TreeMolecule,
)
from aizynthfinder.context.policy import (
BondFilter,
FrozenSubstructureFilter,
QuickKerasFilter,
ReactantsCountFilter,
TemplateBasedDirectExpansionStrate... | None | assert | none_literal | tests/context/test_policy.py | test_get_actions_using_rdkit | 177 | null | |
MolecularAI/aizynthfinder | from typing import Dict, List
import numpy as np
import pytest
import pytest_mock
from aizynthfinder.utils import models
def test_local_onnx_model_length(mock_onnx_model: pytest_mock.MockerFixture) -> None:
onnx_model = models.LocalOnnxModel("test_model.onnx")
output = len(onnx_model)
expected_output = 3
... | expected_output | assert | variable | tests/utils/test_local_onnx_model.py | test_local_onnx_model_length | 22 | null | |
MolecularAI/aizynthfinder | import glob
import json
import os
import sys
from typing import Dict, List
import pandas as pd
import pytest
import yaml
from aizynthfinder.analysis import RouteCollection
from aizynthfinder.chem import MoleculeException
from aizynthfinder.interfaces import AiZynthApp
from aizynthfinder.interfaces.aizynthapp import m... | 0 | assert | numeric_literal | tests/test_cli.py | test_cli_multiple_smiles_unsanitizable | 316 | null | |
MolecularAI/aizynthfinder | import numpy as np
import pytest
from aizynthfinder.chem import (
SmilesBasedRetroReaction,
TemplatedRetroReaction,
TreeMolecule,
)
from aizynthfinder.context.policy import (
BondFilter,
FrozenSubstructureFilter,
QuickKerasFilter,
ReactantsCountFilter,
TemplateBasedDirectExpansionStrate... | 2 | assert | numeric_literal | tests/context/test_policy.py | test_reactants_count_rejection | 389 | null | |
MolecularAI/aizynthfinder | def test_select_leaf_root(setup_complete_mcts_tree):
tree, nodes = setup_complete_mcts_tree
nodes[0].is_expanded = False
leaf = tree.select_leaf()
assert leaf is | nodes[0] | assert | complex_expr | tests/mcts/test_tree.py | test_select_leaf_root | 7 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.reactiontree import ReactionTree
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", []):
r... | 3 | assert | numeric_literal | tests/test_reactiontree.py | test_mcts_route_to_reactiontree | 26 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.aizynthfinder import AiZynthExpander
def test_expander_top1(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, return_n=1)
... | ["CCCCOc1ccc(CC(=O)Cl)cc1", "CNO"] | assert | collection | tests/test_expander.py | test_expander_top1 | 33 | null | |
MolecularAI/aizynthfinder | 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... | "c\nd" | assert | string_literal | tests/utils/test_file_utils.py | test_split_file_even | 47 | null | |
MolecularAI/aizynthfinder | import os
from unittest import mock
import pytest
from aizynthfinder.aizynthfinder import AiZynthFinder
from aizynthfinder.context.config import Configuration
from aizynthfinder.context.stock import StockException
def test_init_search_yaml(write_yaml, create_dummy_templates, mock_onnx_model):
templates_filename ... | [[1, 2]] | assert | collection | tests/context/test_mcts_config.py | test_init_search_yaml | 388 | null | |
MolecularAI/aizynthfinder | import logging
import pandas as pd
import pytest
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
/ ... | 5 | assert | numeric_literal | tests/test_finder.py | test_two_expansions_two_children | 239 | null | |
MolecularAI/aizynthfinder | import pytest
import sys
import pandas as pd
from aizynthfinder.chem import Molecule
from aizynthfinder.context.stock import (
StockException,
)
from aizynthfinder.context.stock.queries import HAS_MOLBLOOM
from aizynthfinder.tools.make_stock import (
extract_plain_smiles,
extract_smiles_from_module,
m... | 8 | assert | numeric_literal | tests/context/test_stock.py | test_extract_smiles_from_plain_file | 474 | null | |
MolecularAI/aizynthfinder | import os
from unittest import mock
import pytest
from aizynthfinder.aizynthfinder import AiZynthFinder
from aizynthfinder.context.config import Configuration
from aizynthfinder.context.stock import StockException
def test_update_search(default_config):
config = default_config
assert config.search.algorithm... | 6 | assert | numeric_literal | tests/context/test_mcts_config.py | test_update_search | 75 | null | |
MolecularAI/aizynthfinder | 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... | "e\nf" | assert | string_literal | tests/utils/test_file_utils.py | test_split_file_even | 48 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.search.mcts.node import ParetoMctsNode
from aizynthfinder.search.mcts import MctsSearchTree
def generate_root(default_config):
def wrapper(smiles, config=None):
return ParetoMctsNode.create_root(
smiles, tree=None, config=config or default_config
)
... | [1, 1, 1] | assert | collection | tests/mcts/test_multiobjective.py | test_expand_root_node | 43 | null | |
MolecularAI/aizynthfinder | 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_conversion_to_reaction_tree(
setup_star_root... | root.mol.inchi_key | assert | complex_expr | tests/retrostar/test_retrostar_nodes.py | test_conversion_to_reaction_tree | 139 | null | |
MolecularAI/aizynthfinder | import logging
import pandas as pd
import pytest
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
|
... | 4 | assert | numeric_literal | tests/test_finder.py | test_three_expansions | 300 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem.serialization import MoleculeSerializer, MoleculeDeserializer
from aizynthfinder.chem import Molecule, TreeMolecule
def test_add_single_mol():
serializer = MoleculeSerializer()
mol = Molecule(smiles="CCC")
id_ = serializer[mol]
assert id_ == | id(mol) | assert | func_call | tests/chem/test_serialization.py | test_add_single_mol | 17 | null | |
MolecularAI/aizynthfinder | import os
from tarfile import TarFile
import numpy as np
import pytest
from aizynthfinder.analysis import TreeAnalysis, RouteCollection
from aizynthfinder.analysis.routes import SUPPORT_CLUSTERING
from aizynthfinder.analysis.utils import RouteSelectionArguments
from aizynthfinder.reactiontree import ReactionTree
from... | 5 | assert | numeric_literal | tests/test_analysis.py | test_sort_nodes | 20 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.reactiontree import ReactionTree
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 = list(rt.molecules... | 6 | assert | numeric_literal | tests/test_reactiontree.py | test_route_node_depth_from_json | 93 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import TreeMolecule
from aizynthfinder.chem.serialization import MoleculeDeserializer, MoleculeSerializer
from aizynthfinder.search.mcts import MctsNode, MctsSearchTree, MctsState
def test_serialize_deserialize_state(default_config):
mol = TreeMolecule(parent=None, smiles="CCC", transform=1... | scorer(node0) | assert | func_call | tests/mcts/test_serialization.py | test_serialize_deserialize_state | 28 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import TreeMolecule, SmilesBasedRetroReaction
from aizynthfinder.utils.bonds import BrokenBonds
def test_focussed_bonds_not_broken():
mol = TreeMolecule(smiles="[CH3:1][NH:2][C:3](C)=[O:4]", parent=None)
reaction = SmilesBasedRetroReaction(
mol,
mapped_prod_smiles="[CH3:... | [] | assert | collection | tests/utils/test_bonds.py | test_focussed_bonds_not_broken | 33 | null | |
MolecularAI/aizynthfinder | 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 | assert | numeric_literal | tests/retrostar/test_retrostar.py | test_one_iteration_filter_unfeasible | 22 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem.serialization import MoleculeSerializer, MoleculeDeserializer
from aizynthfinder.chem import Molecule, TreeMolecule
def test_add_tree_mol():
serializer = MoleculeSerializer()
mol1 = TreeMolecule(parent=None, smiles="CCC", transform=1)
mol2 = TreeMolecule(smiles="CCO", parent=mol1)
... | id(mol2) | assert | func_call | tests/chem/test_serialization.py | test_add_tree_mol | 28 | null | |
MolecularAI/aizynthfinder | import numpy as np
import pytest
from aizynthfinder.chem import (
SmilesBasedRetroReaction,
TemplatedRetroReaction,
TreeMolecule,
)
from aizynthfinder.context.policy import (
BondFilter,
FrozenSubstructureFilter,
QuickKerasFilter,
ReactantsCountFilter,
TemplateBasedDirectExpansionStrate... | 3 | assert | numeric_literal | tests/context/test_policy.py | test_load_expansion_policy_from_config_files | 49 | null | |
MolecularAI/aizynthfinder | import pytest
from aizynthfinder.chem import TreeMolecule
from aizynthfinder.context.policy import (
MultiExpansionStrategy,
TemplateBasedExpansionStrategy,
)
from aizynthfinder.utils.exceptions import PolicyException
def test_multi_expansion_strategy_cutoff(
default_config, setup_template_expansion_polic... | 4 | assert | numeric_literal | tests/context/test_expansion_strategies.py | test_multi_expansion_strategy_cutoff | 136 | null | |
MolecularAI/aizynthfinder | 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_ | assert | variable | tests/chem/test_serialization.py | test_chaining | 85 | null | |
MolecularAI/aizynthfinder | import glob
import json
import os
import sys
from typing import Dict, List
import pandas as pd
import pytest
import yaml
from aizynthfinder.analysis import RouteCollection
from aizynthfinder.chem import MoleculeException
from aizynthfinder.interfaces import AiZynthApp
from aizynthfinder.interfaces.aizynthapp import m... | 4 | assert | numeric_literal | tests/test_cli.py | test_cli_multiple_smiles | 211 | null | |
MolecularAI/aizynthfinder | from aizynthfinder.chem import (
FixedRetroReaction,
SmilesBasedRetroReaction,
TemplatedRetroReaction,
TreeMolecule,
UniqueMolecule,
hash_reactions,
)
def test_mapped_atom_bonds_rdchiral():
smi = "CC(C)C[C:1](=O)[N:2](C)O"
mol = TreeMolecule(smiles=smi, parent=None)
smarts = (
... | [(2, 8), (2, 9)] | assert | collection | tests/chem/test_reaction.py | test_mapped_atom_bonds_rdchiral | 219 | null | |
MolecularAI/aizynthfinder | import os
from tarfile import TarFile
import numpy as np
import pytest
from aizynthfinder.analysis import TreeAnalysis, RouteCollection
from aizynthfinder.analysis.routes import SUPPORT_CLUSTERING
from aizynthfinder.analysis.utils import RouteSelectionArguments
from aizynthfinder.reactiontree import ReactionTree
from... | 0 | assert | numeric_literal | tests/test_analysis.py | test_sort_nodes | 25 | null | |
MolecularAI/aizynthfinder | 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_conversion_to_reaction_tree(
setup_star_root... | reaction.reaction_smiles() | assert | func_call | tests/retrostar/test_retrostar_nodes.py | test_conversion_to_reaction_tree | 142 | null | |
MolecularAI/aizynthfinder | import numpy as np
from aizynthfinder.search.retrostar.search_tree import SearchTree
from aizynthfinder.chem.serialization import MoleculeSerializer
def test_serialization_deserialization(
mocker, setup_search_tree, tmpdir, default_config
):
tree = setup_search_tree
tree.one_iteration()
mocked_json_d... | mocker.ANY) | assert_* | complex_expr | tests/retrostar/test_retrostar.py | test_serialization_deserialization | 90 | null |
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