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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_http_method.py | test_when_request_has_no_method | assert | string_literal | 16 | from pytest import mark, raises
from scanapi.errors import HTTPMethodNotAllowedError
from scanapi.tree import EndpointNode, RequestNode
class TestHTTPMethod:
@mark.context("when request spec has no http method defined")
@mark.it("should set the http_method attribute as get")
def test_when_request_has_no_... | "GET" | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_http_method.py | test_when_method_is_invalid | assert | variable | 23 | from pytest import mark, raises
from scanapi.errors import HTTPMethodNotAllowedError
from scanapi.tree import EndpointNode, RequestNode
class TestHTTPMethod:
@mark.context("when request spec has and invalid http method defined")
@mark.it("should raise http method not allowed error")
def test_when_method_... | expected | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_init.py | test_init_spec_and_endpoint | assert | variable | 14 | from pytest import mark, raises
from scanapi.errors import MissingMandatoryKeyError
from scanapi.tree import EndpointNode, RequestNode
class TestInit:
@mark.context("when there are no mandatory keys missing")
@mark.it("should set endpoint and spec attributes accordingly")
def test_init_spec_and_endpoint(s... | endpoint | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_init.py | test_init_spec_and_endpoint | assert | collection | 15 | from pytest import mark, raises
from scanapi.errors import MissingMandatoryKeyError
from scanapi.tree import EndpointNode, RequestNode
class TestInit:
@mark.context("when there are no mandatory keys missing")
@mark.it("should set endpoint and spec attributes accordingly")
def test_init_spec_and_endpoint(s... | {"name": "bar"} | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_init.py | test_missing_required_keys | assert | string_literal | 18 | from pytest import mark, raises
from scanapi.errors import MissingMandatoryKeyError
from scanapi.tree import EndpointNode, RequestNode
class TestInit:
@mark.context("when required keys are missing")
@mark.it("should raise missing mandatory key error")
def test_missing_required_keys(self):
with ra... | "Missing 'name' key(s) at 'request' scope" | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_name.py | test_when_request_has_name | assert | string_literal | 24 | from pytest import fixture, mark, raises
from scanapi.errors import MissingMandatoryKeyError
from scanapi.tree import EndpointNode, RequestNode
class TestName:
def mock_evaluate(self, mocker):
mock_func = mocker.patch(
"scanapi.tree.request_node.SpecEvaluator.evaluate"
)
mock_... | "list-users" | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_name.py | test_when_request_has_no_name | assert | string_literal | 24 | from pytest import fixture, mark, raises
from scanapi.errors import MissingMandatoryKeyError
from scanapi.tree import EndpointNode, RequestNode
class TestName:
def mock_evaluate(self, mocker):
mock_func = mocker.patch(
"scanapi.tree.request_node.SpecEvaluator.evaluate"
)
mock_... | "Missing name, path at 'request'" | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_params.py | test_when_endpoint_has_no_params | assert | variable | 24 | from pytest import fixture, mark
from scanapi.tree import EndpointNode, RequestNode
class TestParams:
def mock_evaluate(self, mocker):
mock_func = mocker.patch(
"scanapi.tree.request_node.SpecEvaluator.evaluate"
)
mock_func.return_value = ""
return mock_func
@mar... | params | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_params.py | test_calls_evaluate | assert_* | variable | 34 | from pytest import fixture, mark
from scanapi.tree import EndpointNode, RequestNode
class TestParams:
def mock_evaluate(self, mocker):
mock_func = mocker.patch(
"scanapi.tree.request_node.SpecEvaluator.evaluate"
)
mock_func.return_value = ""
return mock_func
@mar... | calls) | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_params.py | test_when_endpoint_has_params | assert | collection | 32 | from pytest import fixture, mark
from scanapi.tree import EndpointNode, RequestNode
class TestParams:
def mock_evaluate(self, mocker):
mock_func = mocker.patch(
"scanapi.tree.request_node.SpecEvaluator.evaluate"
)
mock_func.return_value = ""
return mock_func
@mar... | {"abc": "def", "xxx": "www"} | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_repr.py | test_when_path_is_not_defined | assert | string_literal | 12 | from pytest import mark
from scanapi.tree import EndpointNode, RequestNode
class TestRepr:
@mark.context("when path is not defined")
@mark.it("should return <RequestNode >")
def test_when_path_is_not_defined(self):
endpoint = EndpointNode({"name": "foo", "requests": [{}]})
request = Reques... | "<RequestNode >" | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_repr.py | test_when_request_node_path_is_defined | assert | string_literal | 15 | from pytest import mark
from scanapi.tree import EndpointNode, RequestNode
class TestRepr:
@mark.context("when request node path is defined")
@mark.it("should return <RequestNode request_path>")
def test_when_request_node_path_is_defined(self):
endpoint = EndpointNode({"name": "foo", "requests": ... | "<RequestNode /bar/>" | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_repr.py | test_when_endpoint_path_is_defined | assert | string_literal | 20 | from pytest import mark
from scanapi.tree import EndpointNode, RequestNode
class TestRepr:
@mark.context("when endpoint node path is defined")
@mark.it("should return <RequestNode endpoint_path>")
def test_when_endpoint_path_is_defined(self):
base_path = "http://foo.com/api"
parent = Endp... | "<RequestNode http://foo.com/api/foo>" | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_repr.py | test_when_request_and_endpoint_paths_are_defined | assert | string_literal | 22 | from pytest import mark
from scanapi.tree import EndpointNode, RequestNode
class TestRepr:
@mark.context("when both request and endpoint paths are defined")
@mark.it("should return <RequestNode endpoint_path/request_path>")
def test_when_request_and_endpoint_paths_are_defined(self):
base_path = "... | "<RequestNode http://foo.com/api/foo/bar/>" | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_run.py | test_calls_request | assert_* | numeric_literal | 31 | from pytest import fixture, mark
from scanapi.tree import EndpointNode, RequestNode
class TestRun:
def mock_session(self, mocker):
return mocker.patch("scanapi.tree.request_node.session_with_retry")
def mock_run_tests(self, mocker):
return mocker.patch("scanapi.tree.request_node.RequestNode.... | 0.001) | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_run.py | test_calls_request | assert_* | complex_expr | 33 | from pytest import fixture, mark
from scanapi.tree import EndpointNode, RequestNode
class TestRun:
def mock_session(self, mocker):
return mocker.patch("scanapi.tree.request_node.session_with_retry")
def mock_run_tests(self, mocker):
return mocker.patch("scanapi.tree.request_node.RequestNode.... | request.full_url_path) | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_run.py | test_calls_request | assert | collection | 42 | from pytest import fixture, mark
from scanapi.tree import EndpointNode, RequestNode
class TestRun:
def mock_session(self, mocker):
return mocker.patch("scanapi.tree.request_node.session_with_retry")
def mock_run_tests(self, mocker):
return mocker.patch("scanapi.tree.request_node.RequestNode.... | { "response": mock_session().request(), "tests_results": [], "no_failure": True, "request_node_name": "request_name", } | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_run.py | test_build_result | assert | collection | 35 | from pytest import fixture, mark
from scanapi.tree import EndpointNode, RequestNode
class TestRun:
def mock_session(self, mocker):
return mocker.patch("scanapi.tree.request_node.session_with_retry")
def mock_run_tests(self, mocker):
return mocker.patch("scanapi.tree.request_node.RequestNode.... | { "response": mock_session().request(), "tests_results": test_results, "no_failure": expected_no_failure, "request_node_name": "request_name", } | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_validate.py | test_should_call_validate_keys | assert | numeric_literal | 41 | from pytest import fixture, mark
from scanapi.tree import EndpointNode, RequestNode, tree_keys
class TestValidate:
def mock_validate_keys(self, mocker):
return mocker.patch("scanapi.tree.request_node.validate_keys")
@mark.it("should call the validate_keys method")
def test_should_call_validate_k... | 3 | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_validate.py | test_should_call_validate_keys | assert | variable | 42 | from pytest import fixture, mark
from scanapi.tree import EndpointNode, RequestNode, tree_keys
class TestValidate:
def mock_validate_keys(self, mocker):
return mocker.patch("scanapi.tree.request_node.validate_keys")
@mark.it("should call the validate_keys method")
def test_should_call_validate_k... | keys | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/request_node/test_validate.py | test_should_call_validate_keys | assert_* | string_literal | 24 | from pytest import fixture, mark
from scanapi.tree import EndpointNode, RequestNode, tree_keys
class TestValidate:
def mock_validate_keys(self, mocker):
return mocker.patch("scanapi.tree.request_node.validate_keys")
@mark.it("should call the validate_keys method")
def test_should_call_validate_k... | "request") | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/testing_node/test_full_name.py | test_full_name | assert | string_literal | 17 | from pytest import mark
from scanapi.tree import EndpointNode, RequestNode, TestingNode
class TestFullName:
@mark.it(
"should set the full_name attribute as the concatanation of the parents' names separated by ::"
)
def test_full_name(self):
endpoint_node = EndpointNode({"name": "foo"})
... | "foo::bar::lol" | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/testing_node/test_init.py | test_missing_required_keys | assert | string_literal | 18 | from pytest import mark, raises
from scanapi.errors import MissingMandatoryKeyError
from scanapi.tree import EndpointNode, RequestNode, TestingNode
class TestInit:
@mark.context("when required keys are missing")
@mark.it("should raise missing mandatory key error")
def test_missing_required_keys(self):
... | "Missing 'assert', 'name' key(s) at 'test' scope" | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/testing_node/test_run.py | test_increment_successes | assert | numeric_literal | 48 | import logging
from pytest import fixture, mark
from scanapi.tree import EndpointNode, RequestNode, TestingNode
log = logging.getLogger(__name__)
class TestRun:
def testing_node(self):
endpoint_node = EndpointNode(spec={"name": "foo"})
request_node = RequestNode(spec={"name": "bar"}, endpoint=e... | 1 | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/testing_node/test_run.py | test_logs_test_results | assert | complex_expr | 43 | import logging
from pytest import fixture, mark
from scanapi.tree import EndpointNode, RequestNode, TestingNode
log = logging.getLogger(__name__)
class TestRun:
def testing_node(self):
endpoint_node = EndpointNode(spec={"name": "foo"})
request_node = RequestNode(spec={"name": "bar"}, endpoint=e... | caplog.text | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/testing_node/test_run.py | test_build_result | assert | collection | 44 | import logging
from pytest import fixture, mark
from scanapi.tree import EndpointNode, RequestNode, TestingNode
log = logging.getLogger(__name__)
class TestRun:
def testing_node(self):
endpoint_node = EndpointNode(spec={"name": "foo"})
request_node = RequestNode(spec={"name": "bar"}, endpoint=e... | { "name": "foo::bar::status_is_200", "status": "passed", "failure": None, "error": None, } | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scanapi/scanapi | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | train | train | tests/unit/tree/testing_node/test_run.py | test_build_result_2 | assert | collection | 47 | import logging
from pytest import fixture, mark
from scanapi.tree import EndpointNode, RequestNode, TestingNode
log = logging.getLogger(__name__)
class TestRun:
def testing_node(self):
endpoint_node = EndpointNode(spec={"name": "foo"})
request_node = RequestNode(spec={"name": "bar"}, endpoint=e... | { "name": "foo::bar::status_is_200", "status": "failed", "failure": "response.status_code == 200", "error": None, } | e84c677595d0111d23c8da8db0b3d5c9d19ebdc1 | 71 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/datasets/test_utils.py | run_basic_dataset_checks | assert_* | variable | 22 | from typing import Literal
import numpy as np
import pandas as pd
from rdkit.Chem import Mol
from skfp.preprocessing import MolFromSmilesTransformer
def run_basic_dataset_checks(
smiles_list: list[str],
y: np.ndarray,
df: pd.DataFrame,
expected_length: int,
num_tasks: int,
task_type: Literal[... | y) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/datasets/lrgb.py | test_load_lrgb_splits_as_dict | assert | variable | 23 | import pytest
from skfp.datasets.lrgb import (
load_lrgb_mol_benchmark,
load_lrgb_mol_splits,
load_peptides_func,
load_peptides_struct,
)
from tests.datasets.test_utils import run_basic_dataset_checks
def get_dataset_names() -> list[str]:
return ["Peptides-func", "Peptides-struct"]
@pytest.mark.p... | test | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/datasets/moleculenet.py | test_load_ogb_splits_as_dict | assert | variable | 47 | import pytest
from sklearn.utils._param_validation import InvalidParameterError
from skfp.datasets.moleculenet import (
load_bace,
load_bbbp,
load_clintox,
load_esol,
load_freesolv,
load_hiv,
load_lipophilicity,
load_moleculenet_benchmark,
load_muv,
load_ogb_splits,
load_pcb... | test | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/datasets/lrgb.py | test_load_lrgb_splits_as_dict | assert | variable | 21 | import pytest
from skfp.datasets.lrgb import (
load_lrgb_mol_benchmark,
load_lrgb_mol_splits,
load_peptides_func,
load_peptides_struct,
)
from tests.datasets.test_utils import run_basic_dataset_checks
def get_dataset_names() -> list[str]:
return ["Peptides-func", "Peptides-struct"]
@pytest.mark.p... | train | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/datasets/lrgb.py | test_load_lrgb_splits_as_dict | assert | variable | 22 | import pytest
from skfp.datasets.lrgb import (
load_lrgb_mol_benchmark,
load_lrgb_mol_splits,
load_peptides_func,
load_peptides_struct,
)
from tests.datasets.test_utils import run_basic_dataset_checks
def get_dataset_names() -> list[str]:
return ["Peptides-func", "Peptides-struct"]
@pytest.mark.p... | valid | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/datasets/moleculenet.py | test_load_ogb_splits_as_dict | assert | variable | 45 | import pytest
from sklearn.utils._param_validation import InvalidParameterError
from skfp.datasets.moleculenet import (
load_bace,
load_bbbp,
load_clintox,
load_esol,
load_freesolv,
load_hiv,
load_lipophilicity,
load_moleculenet_benchmark,
load_muv,
load_ogb_splits,
load_pcb... | train | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/datasets/moleculenet.py | test_load_ogb_splits_as_dict | assert | variable | 46 | import pytest
from sklearn.utils._param_validation import InvalidParameterError
from skfp.datasets.moleculenet import (
load_bace,
load_bbbp,
load_clintox,
load_esol,
load_freesolv,
load_hiv,
load_lipophilicity,
load_moleculenet_benchmark,
load_muv,
load_ogb_splits,
load_pcb... | valid | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/utils.py | assert_similarity_values | assert | variable | 6 | import numpy as np
def assert_similarity_values(similarity: float, comparison: str, value: float) -> None:
if comparison == ">":
assert similarity > | value | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/model_selection/hyperparam_search/grid_search.py | test_fp_estimator_grid_search_verbose | assert | variable | 26 | import numpy as np
from sklearn.dummy import DummyClassifier
from sklearn.model_selection import GridSearchCV
from skfp.fingerprints import AtomPairFingerprint
from skfp.model_selection import FingerprintEstimatorGridSearch
def test_fp_estimator_grid_search_verbose(smallest_mols_list, capsys):
num_mols = len(smal... | output | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/model_selection/hyperparam_search/randomized_selection.py | test_fp_estimator_randomized_search_verbose | assert | variable | 29 | import numpy as np
from sklearn.dummy import DummyClassifier
from sklearn.model_selection import GridSearchCV
from skfp.fingerprints import AtomPairFingerprint
from skfp.model_selection import FingerprintEstimatorRandomizedSearch
def test_fp_estimator_randomized_search_verbose(smallest_mols_list, capsys):
num_mol... | output | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/fingerprints/lingo.py | test_lingo_fingerprint_smiles_to_dict | assert | variable | 44 | import os
from typing import Union
import numpy as np
from scipy.sparse import csr_array, load_npz
from skfp.fingerprints import LingoFingerprint
def test_lingo_fingerprint_smiles_to_dict():
smiles = ["CC(=O)NCCC1=CNC2=C1C=C(C=C2)OC"]
lingo_fp = LingoFingerprint()
X_skfp = lingo_fp.smiles_to_dicts(smiles... | expected | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/braun_blanquet.py | test_braun_blanquet | assert_* | variable | 48 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
braun_blanquet_binary_distance,
braun_blanquet_binary_similarity,
)
from skfp.distances.braun_blanquet import (
bulk_braun_blanquet_binary_distance,
bulk_braun_blanquet_binary_similarity,
)
from skfp.finger... | distance) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/ct4.py | test_ct4_binary | assert_* | variable | 66 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
ct4_binary_distance,
ct4_binary_similarity,
ct4_count_distance,
ct4_count_similarity,
)
from skfp.distances.ct4 import (
bulk_ct4_binary_distance,
bulk_ct4_binary_similarity,
bulk_ct4_count_dist... | distance) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/dice.py | test_dice_binary | assert_* | variable | 66 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
dice_binary_distance,
dice_binary_similarity,
dice_count_distance,
dice_count_similarity,
)
from skfp.distances.dice import (
bulk_dice_binary_distance,
bulk_dice_binary_similarity,
bulk_dice_co... | distance) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/fraggle.py | test_fraggle | assert_* | variable | 35 | import pytest
from rdkit.Chem import Mol, MolFromSmiles
from skfp.distances import fraggle_distance, fraggle_similarity
from tests.distances.utils import assert_distance_values, assert_similarity_values
def _get_values() -> list[tuple[Mol, Mol, str, float, float]]:
# mol_query, mol_ref, comparison, similarity, di... | distance) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/harris_lahey.py | test_harris_lahey_unnormalized | assert_* | variable | 58 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
harris_lahey_binary_distance,
harris_lahey_binary_similarity,
)
from skfp.distances.harris_lahey import (
bulk_harris_lahey_binary_distance,
bulk_harris_lahey_binary_similarity,
)
from skfp.fingerprints.ecf... | distance) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/kulczynski.py | test_kulczynski | assert_* | variable | 42 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
kulczynski_binary_distance,
kulczynski_binary_similarity,
)
from tests.distances.utils import assert_distance_values, assert_similarity_values
def _get_values() -> list[tuple[list[int], list[int], str, float, floa... | distance) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/mcconnaughey.py | test_mcconnaughey | assert_* | variable | 46 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import mcconnaughey_binary_distance, mcconnaughey_binary_similarity
from tests.distances.utils import (
assert_distance_values,
assert_similarity_values,
)
def _get_values() -> list[tuple[list[int], list[int], str, float, ... | distance) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/rand.py | test_rand | assert_* | variable | 42 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import rand_binary_distance, rand_binary_similarity
from skfp.distances.rand import bulk_rand_binary_distance, bulk_rand_binary_similarity
from skfp.fingerprints.ecfp import ECFPFingerprint
from tests.distances.utils import assert_... | distance) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/rogot_goldberg.py | test_rogot_goldberg | assert_* | variable | 45 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
rogot_goldberg_binary_distance,
rogot_goldberg_binary_similarity,
)
from tests.distances.utils import (
assert_distance_values,
assert_similarity_values,
)
def _get_values() -> list[tuple[list[int], list[i... | distance) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/russell.py | test_russell | assert_* | variable | 43 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import russell_binary_distance, russell_binary_similarity
from tests.distances.utils import (
assert_distance_values,
assert_similarity_values,
)
def _get_values() -> list[tuple[list[int], list[int], str, float, float]]:
... | distance) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/simpson.py | test_simpson | assert_* | variable | 45 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import simpson_binary_distance, simpson_binary_similarity
from skfp.distances.simpson import (
bulk_simpson_binary_distance,
bulk_simpson_binary_similarity,
)
from skfp.fingerprints.ecfp import ECFPFingerprint
from tests.di... | distance) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/sokal_sneath.py | test_russell | assert_* | variable | 46 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
sokal_sneath_2_binary_distance,
sokal_sneath_2_binary_similarity,
)
from tests.distances.utils import (
assert_distance_values,
assert_similarity_values,
)
def _get_values() -> list[tuple[list[int], list[i... | distance) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/tanimoto.py | test_tanimoto_binary | assert_* | variable | 69 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
bulk_tanimoto_binary_similarity,
bulk_tanimoto_count_similarity,
tanimoto_binary_distance,
tanimoto_binary_similarity,
tanimoto_count_distance,
tanimoto_count_similarity,
)
from skfp.distances.tanim... | distance) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/common.py | test_different_types_raise_error | pytest.raises | variable | 29 | import inspect
from typing import Callable
import numpy as np
import pytest
from scipy.sparse import csr_array
from sklearn.metrics import pairwise_distances
from sklearn.neighbors import NearestNeighbors
import skfp.distances
def _get_distance_functions() -> list[Callable]:
return [
obj
for name... | TypeError) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/model_selection/splitters/maxmin_split.py | test_seed_consistency_train_valid_test_split | assert | variable | 36 | import pytest
from rdkit import Chem
from rdkit.Chem import Mol
from skfp.model_selection.splitters.maxmin_split import (
maxmin_train_test_split,
maxmin_train_valid_test_split,
)
def all_molecules() -> list[str]:
return [
"OCC3OC(OCC2OC(OC(C#N)c1ccccc1)C(O)C(O)C2O)C(O)C(O)C3O",
"Cc1occc1C... | test_set_2 | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/preprocessing/input_output/inchi.py | test_mol_to_and_from_inchi | assert | variable | 17 | import pytest
from rdkit.Chem import Mol, MolFromSmiles, MolToInchi
from skfp.preprocessing import MolFromInchiTransformer, MolToInchiTransformer
def inchi_list(smiles_list):
return [MolToInchi(MolFromSmiles(smi)) for smi in smiles_list]
def test_mol_to_and_from_inchi(inchi_list):
mol_from_inchi = MolFromInc... | inchi_list | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/utils/validators.py | test_require_mols_with_conf_ids | pytest.raises | variable | 9 | import pytest
from skfp.fingerprints import AtomPairFingerprint
from skfp.utils.validators import ensure_mols, ensure_smiles, require_mols_with_conf_ids
def test_require_mols_with_conf_ids(mols_conformers_list, mols_list):
require_mols_with_conf_ids(mols_conformers_list)
with pytest.raises( | TypeError) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/bases/base_fp_transformer.py | test_base_hash_fingerprint_bits_wrong_type | pytest.raises | variable | 18 | import numpy as np
import pytest
from rdkit.DataStructs import (
IntSparseIntVect,
LongSparseIntVect,
SparseBitVect,
UIntSparseIntVect,
ULongSparseIntVect,
)
from sklearn.utils._param_validation import InvalidParameterError
from skfp.bases.base_fp_transformer import BaseFingerprintTransformer
from ... | ValueError) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/datasets/moleculenet.py | test_load_moleculenet_benchmark_wrong_subset | pytest.raises | variable | 41 | import pytest
from sklearn.utils._param_validation import InvalidParameterError
from skfp.datasets.moleculenet import (
load_bace,
load_bbbp,
load_clintox,
load_esol,
load_freesolv,
load_hiv,
load_lipophilicity,
load_moleculenet_benchmark,
load_muv,
load_ogb_splits,
load_pcb... | ValueError) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/datasets/test_utils.py | assert_valid_dataframe | assert | variable | 112 | from typing import Literal
import numpy as np
import pandas as pd
from rdkit.Chem import Mol
from skfp.preprocessing import MolFromSmilesTransformer
def run_basic_dataset_checks(
smiles_list: list[str],
y: np.ndarray,
df: pd.DataFrame,
expected_length: int,
num_tasks: int,
task_type: Literal[... | smiles_list | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/braun_blanquet.py | test_braun_blanquet | assert_* | variable | 45 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
braun_blanquet_binary_distance,
braun_blanquet_binary_similarity,
)
from skfp.distances.braun_blanquet import (
bulk_braun_blanquet_binary_distance,
bulk_braun_blanquet_binary_similarity,
)
from skfp.finger... | similarity) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/ct4.py | test_ct4_binary | assert_* | variable | 63 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
ct4_binary_distance,
ct4_binary_similarity,
ct4_count_distance,
ct4_count_similarity,
)
from skfp.distances.ct4 import (
bulk_ct4_binary_distance,
bulk_ct4_binary_similarity,
bulk_ct4_count_dist... | similarity) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/dice.py | test_dice_binary | assert_* | variable | 63 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
dice_binary_distance,
dice_binary_similarity,
dice_count_distance,
dice_count_similarity,
)
from skfp.distances.dice import (
bulk_dice_binary_distance,
bulk_dice_binary_similarity,
bulk_dice_co... | similarity) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/fraggle.py | test_fraggle | assert_* | variable | 34 | import pytest
from rdkit.Chem import Mol, MolFromSmiles
from skfp.distances import fraggle_distance, fraggle_similarity
from tests.distances.utils import assert_distance_values, assert_similarity_values
def _get_values() -> list[tuple[Mol, Mol, str, float, float]]:
# mol_query, mol_ref, comparison, similarity, di... | similarity) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/harris_lahey.py | test_harris_lahey_unnormalized | assert_* | variable | 55 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
harris_lahey_binary_distance,
harris_lahey_binary_similarity,
)
from skfp.distances.harris_lahey import (
bulk_harris_lahey_binary_distance,
bulk_harris_lahey_binary_similarity,
)
from skfp.fingerprints.ecf... | similarity) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/kulczynski.py | test_kulczynski | assert_* | variable | 39 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
kulczynski_binary_distance,
kulczynski_binary_similarity,
)
from tests.distances.utils import assert_distance_values, assert_similarity_values
def _get_values() -> list[tuple[list[int], list[int], str, float, floa... | similarity) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/mcconnaughey.py | test_mcconnaughey | assert_* | variable | 43 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import mcconnaughey_binary_distance, mcconnaughey_binary_similarity
from tests.distances.utils import (
assert_distance_values,
assert_similarity_values,
)
def _get_values() -> list[tuple[list[int], list[int], str, float, ... | similarity) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/rand.py | test_rand | assert_* | variable | 39 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import rand_binary_distance, rand_binary_similarity
from skfp.distances.rand import bulk_rand_binary_distance, bulk_rand_binary_similarity
from skfp.fingerprints.ecfp import ECFPFingerprint
from tests.distances.utils import assert_... | similarity) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/rogot_goldberg.py | test_rogot_goldberg | assert_* | variable | 42 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
rogot_goldberg_binary_distance,
rogot_goldberg_binary_similarity,
)
from tests.distances.utils import (
assert_distance_values,
assert_similarity_values,
)
def _get_values() -> list[tuple[list[int], list[i... | similarity) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/russell.py | test_russell | assert_* | variable | 40 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import russell_binary_distance, russell_binary_similarity
from tests.distances.utils import (
assert_distance_values,
assert_similarity_values,
)
def _get_values() -> list[tuple[list[int], list[int], str, float, float]]:
... | similarity) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/simpson.py | test_simpson | assert_* | variable | 42 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import simpson_binary_distance, simpson_binary_similarity
from skfp.distances.simpson import (
bulk_simpson_binary_distance,
bulk_simpson_binary_similarity,
)
from skfp.fingerprints.ecfp import ECFPFingerprint
from tests.di... | similarity) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/sokal_sneath.py | test_russell | assert_* | variable | 43 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
sokal_sneath_2_binary_distance,
sokal_sneath_2_binary_similarity,
)
from tests.distances.utils import (
assert_distance_values,
assert_similarity_values,
)
def _get_values() -> list[tuple[list[int], list[i... | similarity) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/tanimoto.py | test_tanimoto_binary | assert_* | variable | 66 | import numpy as np
import pytest
from scipy.sparse import csr_array
from skfp.distances import (
bulk_tanimoto_binary_similarity,
bulk_tanimoto_count_similarity,
tanimoto_binary_distance,
tanimoto_binary_similarity,
tanimoto_count_distance,
tanimoto_count_similarity,
)
from skfp.distances.tanim... | similarity) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/filters/pains.py | test_pains_wrong_variant | pytest.raises | variable | 8 | import pytest
from rdkit.Chem import Mol
from skfp.filters import PAINSFilter
def test_pains_wrong_variant():
with pytest.raises( | ValueError) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/fingerprints/electroshape.py | test_mmff94_error | pytest.raises | variable | 16 | import numpy as np
import pytest
from skfp.fingerprints import ElectroShapeFingerprint
from skfp.preprocessing import ConformerGenerator, MolFromSmilesTransformer
def mols_conformers_3_plus_atoms(mols_conformers_list):
# electroshape descriptor requires at least 3 atoms to work
return [mol for mol in mols_con... | ValueError) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/sklearn_compatibility/basic_checks.py | check_transformers_unfitted_stateless | assert | func_call | 144 | import inspect
import pickle
from functools import partial
import numpy as np
import pytest
from sklearn import clone
from sklearn.utils._testing import create_memmap_backed_data, set_random_state
from sklearn.utils.estimator_checks import (
check_dont_overwrite_parameters,
check_estimators_fit_returns_self,
... | len(X) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/preprocessing/input_output/aminoseq.py | test_from_invalid_smiles_with_y | assert | func_call | 35 | import numpy as np
import pytest
from rdkit.Chem import Mol, MolFromFASTA, MolToSmiles
from skfp.preprocessing import MolFromAminoseqTransformer
def sequence_list(fasta_list):
return [fst.split("\n")[1] for fst in fasta_list]
def peptide_list(fasta_list):
return [MolFromFASTA(fst) for fst in fasta_list]
def... | len(y_2) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/preprocessing/input_output/smiles.py | test_from_invalid_smiles_with_y | assert | func_call | 25 | import numpy as np
from rdkit.Chem import Mol
from skfp.preprocessing import MolFromSmilesTransformer, MolToSmilesTransformer
def test_from_invalid_smiles_with_y(smiles_list):
invalid_smiles_list = ["[H]=[H]", "invalid"]
all_smiles_list = smiles_list + invalid_smiles_list
labels = np.ones(len(all_smiles_l... | len(y_2) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/datasets/lrgb.py | test_load_lrgb_splits | assert | func_call | 31 | import pytest
from skfp.datasets.lrgb import (
load_lrgb_mol_benchmark,
load_lrgb_mol_splits,
load_peptides_func,
load_peptides_struct,
)
from tests.datasets.test_utils import run_basic_dataset_checks
def get_dataset_names() -> list[str]:
return ["Peptides-func", "Peptides-struct"]
@pytest.mark.p... | len(test) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/datasets/moleculenet.py | test_load_ogb_splits | assert | func_call | 55 | import pytest
from sklearn.utils._param_validation import InvalidParameterError
from skfp.datasets.moleculenet import (
load_bace,
load_bbbp,
load_clintox,
load_esol,
load_freesolv,
load_hiv,
load_lipophilicity,
load_moleculenet_benchmark,
load_muv,
load_ogb_splits,
load_pcb... | len(test) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/preprocessing/conformer_generator.py | test_conformer_generator_error_handling | assert | func_call | 31 | import numpy as np
import pytest
from rdkit.Chem import AddHs
from skfp.preprocessing import ConformerGenerator, MolFromSmilesTransformer
def test_conformer_generator_error_handling(smallest_mols_list):
y = np.zeros(len(smallest_mols_list))
# last molecule has hard conformers, requiring many tries
mol_fr... | len(mols) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/datasets/lrgb.py | test_load_lrgb_splits | assert | func_call | 30 | import pytest
from skfp.datasets.lrgb import (
load_lrgb_mol_benchmark,
load_lrgb_mol_splits,
load_peptides_func,
load_peptides_struct,
)
from tests.datasets.test_utils import run_basic_dataset_checks
def get_dataset_names() -> list[str]:
return ["Peptides-func", "Peptides-struct"]
@pytest.mark.p... | len(valid) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/datasets/moleculenet.py | test_load_ogb_splits | assert | func_call | 54 | import pytest
from sklearn.utils._param_validation import InvalidParameterError
from skfp.datasets.moleculenet import (
load_bace,
load_bbbp,
load_clintox,
load_esol,
load_freesolv,
load_hiv,
load_lipophilicity,
load_moleculenet_benchmark,
load_muv,
load_ogb_splits,
load_pcb... | len(valid) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/fingerprints/electroshape.py | test_electroshape_bit_fingerprint_transform_x_y | assert | func_call | 21 | import numpy as np
import pytest
from skfp.fingerprints import ElectroShapeFingerprint
from skfp.preprocessing import ConformerGenerator, MolFromSmilesTransformer
def mols_conformers_3_plus_atoms(mols_conformers_list):
# electroshape descriptor requires at least 3 atoms to work
return [mol for mol in mols_con... | len(y_skfp) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/preprocessing/conformer_generator.py | test_conformer_generator_error_handling | assert | func_call | 23 | import numpy as np
import pytest
from rdkit.Chem import AddHs
from skfp.preprocessing import ConformerGenerator, MolFromSmilesTransformer
def test_conformer_generator_error_handling(smallest_mols_list):
y = np.zeros(len(smallest_mols_list))
# last molecule has hard conformers, requiring many tries
mol_fr... | len(y_conf) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/sklearn_compatibility/basic_checks.py | check_transformers_unfitted_stateless | assert | func_call | 146 | import inspect
import pickle
from functools import partial
import numpy as np
import pytest
from sklearn import clone
from sklearn.utils._testing import create_memmap_backed_data, set_random_state
from sklearn.utils.estimator_checks import (
check_dont_overwrite_parameters,
check_estimators_fit_returns_self,
... | len(X_trans) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/bases/base_fp_transformer.py | test_base_hash_fingerprint_bits_wrong_type | assert | func_call | 23 | import numpy as np
import pytest
from rdkit.DataStructs import (
IntSparseIntVect,
LongSparseIntVect,
SparseBitVect,
UIntSparseIntVect,
ULongSparseIntVect,
)
from sklearn.utils._param_validation import InvalidParameterError
from skfp.bases.base_fp_transformer import BaseFingerprintTransformer
from ... | str(exc_info) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/datasets/moleculenet.py | test_load_moleculenet_benchmark_wrong_subset | assert | func_call | 44 | import pytest
from sklearn.utils._param_validation import InvalidParameterError
from skfp.datasets.moleculenet import (
load_bace,
load_bbbp,
load_clintox,
load_esol,
load_freesolv,
load_hiv,
load_lipophilicity,
load_moleculenet_benchmark,
load_muv,
load_ogb_splits,
load_pcb... | str(exc_info) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/distances/common.py | test_different_types_raise_error | assert | func_call | 32 | import inspect
from typing import Callable
import numpy as np
import pytest
from scipy.sparse import csr_array
from sklearn.metrics import pairwise_distances
from sklearn.neighbors import NearestNeighbors
import skfp.distances
def _get_distance_functions() -> list[Callable]:
return [
obj
for name... | str(exc_info) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/filters/mol_weight.py | test_mol_weight_wrong_min_max_thresholds | assert | func_call | 62 | import numpy as np
import pytest
from rdkit.Chem import Mol
from sklearn.utils._param_validation import InvalidParameterError
from skfp.filters import MolecularWeightFilter
from skfp.preprocessing import MolFromSmilesTransformer
def smiles_light_mols() -> list[str]:
# less than 200 daltons
return [
# ... | str(exc_info) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/filters/pains.py | test_pains_wrong_variant | assert | func_call | 11 | import pytest
from rdkit.Chem import Mol
from skfp.filters import PAINSFilter
def test_pains_wrong_variant():
with pytest.raises(ValueError) as exc_info:
PAINSFilter(variant="D")
assert 'PAINS variant must be "A", "B" or "C", got' in | str(exc_info) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/fingerprints/electroshape.py | test_mmff94_error | assert | func_call | 19 | import numpy as np
import pytest
from skfp.fingerprints import ElectroShapeFingerprint
from skfp.preprocessing import ConformerGenerator, MolFromSmilesTransformer
def mols_conformers_3_plus_atoms(mols_conformers_list):
# electroshape descriptor requires at least 3 atoms to work
return [mol for mol in mols_con... | str(exc_info) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/fingerprints/electroshape.py | test_electroshape_ignore_errors | assert | func_call | 40 | import numpy as np
import pytest
from skfp.fingerprints import ElectroShapeFingerprint
from skfp.preprocessing import ConformerGenerator, MolFromSmilesTransformer
def mols_conformers_3_plus_atoms(mols_conformers_list):
# electroshape descriptor requires at least 3 atoms to work
return [mol for mol in mols_con... | len(all_mols) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/fingerprints/pharmacophore.py | test_pharmacophore_wrong_n_points | assert | func_call | 16 | import numpy as np
import pytest
from rdkit.Chem import Get3DDistanceMatrix, Mol
from rdkit.Chem.ChemicalFeatures import BuildFeatureFactoryFromString
from rdkit.Chem.Pharm2D import Gobbi_Pharm2D
from rdkit.Chem.Pharm2D.Generate import Gen2DFingerprint
from rdkit.Chem.Pharm2D.SigFactory import SigFactory
from scipy.spa... | str(exc_info) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/metrics/auroc.py | test_auroc_score_can_raise_error | assert | func_call | 13 | import numpy as np
import pytest
from sklearn.metrics import roc_auc_score
from skfp.metrics import auroc_score
def test_auroc_score_can_raise_error():
y_true = np.array([0, 0, 0])
y_score = np.array([0.7, 0.1, 0.05])
with pytest.raises(ValueError) as exc_info:
auroc_score(y_true, y_score, constan... | str(exc_info) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/preprocessing/conformer_generator.py | test_conformer_generator_too_few_tries | assert | func_call | 17 | import numpy as np
import pytest
from rdkit.Chem import AddHs
from skfp.preprocessing import ConformerGenerator, MolFromSmilesTransformer
def test_conformer_generator_too_few_tries():
# this molecule has hard conformers, requiring many tries
mol_from_smiles = MolFromSmilesTransformer()
mols = mol_from_smi... | str(exc_info) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/utils/parallel.py | test_run_in_parallel_invalid_batch_size | assert | func_call | 15 | import re
import pytest
from sklearn.utils.parallel import delayed
from skfp.utils.parallel import ProgressParallel, run_in_parallel
def test_run_in_parallel_invalid_batch_size():
func = lambda X: [x + 1 for x in X]
data = list(range(100))
with pytest.raises(ValueError) as exc_info:
run_in_parall... | str(exc_info) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/utils/validators.py | test_ensure_mols | assert | func_call | 12 | import pytest
from skfp.fingerprints import AtomPairFingerprint
from skfp.utils.validators import ensure_mols, ensure_smiles, require_mols_with_conf_ids
def test_ensure_mols(mols_list):
ensure_mols(mols_list)
with pytest.raises(ValueError) as exc_info:
ensure_mols(mols_list + [1])
assert "Passed... | str(exc_info) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/filters/bms.py | test_bms | assert | func_call | 10 | from rdkit.Chem import Mol
from skfp.filters import BMSFilter
def test_bms(mols_list):
pains = BMSFilter()
mols_filtered = pains.transform(mols_list)
assert all(isinstance(x, Mol) for x in mols_filtered)
assert len(mols_filtered) <= | len(mols_list) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/filters/brenk.py | test_brenk | assert | func_call | 10 | from rdkit.Chem import Mol
from skfp.filters import BrenkFilter
def test_brenk(mols_list):
pains = BrenkFilter()
mols_filtered = pains.transform(mols_list)
assert all(isinstance(x, Mol) for x in mols_filtered)
assert len(mols_filtered) <= | len(mols_list) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/filters/glaxo.py | test_glaxo | assert | func_call | 10 | from rdkit.Chem import Mol
from skfp.filters import GlaxoFilter
def test_glaxo(mols_list):
pains = GlaxoFilter()
mols_filtered = pains.transform(mols_list)
assert all(isinstance(x, Mol) for x in mols_filtered)
assert len(mols_filtered) <= | len(mols_list) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
scikit-fingerprints/scikit-fingerprints | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | train | train | tests/filters/inpharmatica.py | test_inpharmatica | assert | func_call | 10 | from rdkit.Chem import Mol
from skfp.filters import InpharmaticaFilter
def test_inpharmatica(mols_list):
pains = InpharmaticaFilter()
mols_filtered = pains.transform(mols_list)
assert all(isinstance(x, Mol) for x in mols_filtered)
assert len(mols_filtered) <= | len(mols_list) | ba59309f45598918c7bd11b0bbd393fb9695ec9f | 150 | v2_extractor_at_anchor |
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