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How to use _is_inferred method in pandera

Best Python code snippet using pandera_python

thing.py

Source:thing.py

1#2# Copyright (C) 2021 Vaticle3#4# Licensed to the Apache Software Foundation (ASF) under one5# or more contributor license agreements.  See the NOTICE file6# distributed with this work for additional information7# regarding copyright ownership.  The ASF licenses this file8# to you under the Apache License, Version 2.0 (the9# "License"); you may not use this file except in compliance10# with the License.  You may obtain a copy of the License at11#12#   http://www.apache.org/licenses/LICENSE-2.013#14# Unless required by applicable law or agreed to in writing,15# software distributed under the License is distributed on an16# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY17# KIND, either express or implied.  See the License for the18# specific language governing permissions and limitations19# under the License.20#21from abc import ABC22from typing import List, Union, TYPE_CHECKING23import typedb_protocol.common.transaction_pb2 as transaction_proto24from typedb.api.concept.thing.attribute import Attribute25from typedb.api.concept.thing.thing import Thing, RemoteThing26from typedb.common.exception import TypeDBClientException, MISSING_IID, MISSING_TRANSACTION, GET_HAS_WITH_MULTIPLE_FILTERS27from typedb.common.rpc.request_builder import thing_get_has_req, thing_get_relations_req, \28    thing_get_playing_req, thing_set_has_req, thing_unset_has_req, thing_delete_req29from typedb.concept.concept import _Concept, _RemoteConcept30from typedb.concept.proto import concept_proto_reader, concept_proto_builder31from typedb.concept.type.role_type import _RoleType32if TYPE_CHECKING:33    from typedb.api.connection.transaction import _TypeDBTransactionExtended, TypeDBTransaction34class _Thing(Thing, _Concept, ABC):35    def __init__(self, iid: str, is_inferred: bool):36        if not iid:37            raise TypeDBClientException.of(MISSING_IID)38        self._iid = iid39        self._is_inferred = is_inferred40    def get_iid(self):41        return self._iid42    def is_inferred(self) -> bool:43        return self._is_inferred44    def as_thing(self) -> "Thing":45        return self46    def __str__(self):47        return "%s[%s:%s]" % (type(self).__name__, self.get_type().get_label(), self.get_iid())48    def __eq__(self, other):49        if other is self:50            return True51        if not other or type(self) != type(other):52            return False53        return self.get_iid() == other.get_iid()54    def __hash__(self):55        return hash(self._iid)56class _RemoteThing(_RemoteConcept, RemoteThing, ABC):57    def __init__(self, transaction: Union["_TypeDBTransactionExtended", "TypeDBTransaction"], iid: str, is_inferred: bool):58        if not transaction:59            raise TypeDBClientException.of(MISSING_TRANSACTION)60        if not iid:61            raise TypeDBClientException.of(MISSING_IID)62        self._transaction_ext = transaction63        self._iid = iid64        self._is_inferred = is_inferred65        self._hash = hash((self._transaction_ext, iid))66    def get_iid(self):67        return self._iid68    def is_inferred(self) -> bool:69        return self._is_inferred70    def as_thing(self) -> "RemoteThing":71        return self72    def get_has(self, attribute_type=None, attribute_types: List = None, only_key=False):73        if [bool(attribute_type), bool(attribute_types), only_key].count(True) > 1:74            raise TypeDBClientException.of(GET_HAS_WITH_MULTIPLE_FILTERS)75        if attribute_type:76            attribute_types = [attribute_type]77        return (concept_proto_reader.attribute(a) for rp in self.stream(thing_get_has_req(self.get_iid(), concept_proto_builder.types(attribute_types), only_key))78                for a in rp.thing_get_has_res_part.attributes)79    def get_relations(self, role_types: list = None):80        if not role_types:81            role_types = []82        return (concept_proto_reader.thing(r) for rp in self.stream(thing_get_relations_req(self.get_iid(), concept_proto_builder.types(role_types)))83                for r in rp.thing_get_relations_res_part.relations)84    def get_playing(self):85        return (_RoleType.of(rt) for rp in self.stream(thing_get_playing_req(self.get_iid()))86                for rt in rp.thing_get_playing_res_part.role_types)87    def set_has(self, attribute: Attribute):88        self.execute(thing_set_has_req(self.get_iid(), concept_proto_builder.thing(attribute)))89    def unset_has(self, attribute: Attribute):90        self.execute(thing_unset_has_req(self.get_iid(), concept_proto_builder.thing(attribute)))91    def delete(self):92        self.execute(thing_delete_req(self.get_iid()))93    def is_deleted(self):94        return not self._transaction_ext.concepts().get_thing(self.get_iid())95    def execute(self, request: transaction_proto.Transaction.Req):96        return self._transaction_ext.execute(request).thing_res97    def stream(self, request: transaction_proto.Transaction.Req):98        return (rp.thing_res_part for rp in self._transaction_ext.stream(request))99    def __str__(self):100        return type(self).__name__ + "[iid:" + str(self._iid) + "]"101    def __eq__(self, other):102        if other is self:103            return True104        if not other or type(self) != type(other):105            return False106        return self._transaction_ext is other._transaction_ext and self._iid == other._iid107    def __hash__(self):...

test_schema_inference.py

Source:test_schema_inference.py

1# pylint: disable=W02122"""Unit tests for schema inference module."""3from typing import Type, Union4import pandas as pd5import pytest6import pandera as pa7from pandera import schema_inference8def _create_dataframe(9    multi_index: bool = False, nullable: bool = False10) -> pd.DataFrame:11    if multi_index:12        index = pd.MultiIndex.from_arrays(13            [[1, 1, 2], ["a", "b", "c"]],14            names=["int_index", "str_index"],15        )16    else:17        index = pd.Index([10, 11, 12], name="int_index")18    df = pd.DataFrame(19        data={20            "int": [1, 2, 3],21            "float": [1.0, 2.0, 3.0],22            "boolean": [True, False, True],23            "string": ["a", "b", "c"],24            "datetime": pd.to_datetime(["20180101", "20180102", "20180103"]),25        },26        index=index,27    )28    if nullable:29        df.iloc[0, :] = None30    return df31@pytest.mark.parametrize(32    "pandas_obj, expectation",33    [34        [pd.DataFrame({"col": [1, 2, 3]}), pa.DataFrameSchema],35        [pd.Series([1, 2, 3]), pa.SeriesSchema],36        # error cases37        [int, TypeError],38        [pd.Index([1, 2, 3]), TypeError],39        ["foobar", TypeError],40        [1, TypeError],41        [[1, 2, 3], TypeError],42        [{"key": "value"}, TypeError],43    ],44)45def test_infer_schema(46    pandas_obj,47    expectation: Type[Union[pa.DataFrameSchema, pa.SeriesSchema, TypeError]],48) -> None:49    """Test that convenience function correctly infers dataframe or series."""50    if expectation is TypeError:51        with pytest.raises(TypeError, match="^pandas_obj type not recognized"):52            schema_inference.infer_schema(pandas_obj)53    else:54        assert isinstance(55            schema_inference.infer_schema(pandas_obj), expectation56        )57@pytest.mark.parametrize(58    "multi_index",59    [False, True],60)61def test_infer_dataframe_schema(multi_index: bool) -> None:62    """Test dataframe schema is correctly inferred."""63    dataframe = _create_dataframe(multi_index=multi_index)64    schema = schema_inference.infer_dataframe_schema(dataframe)65    assert isinstance(schema, pa.DataFrameSchema)66    if multi_index:67        assert isinstance(schema.index, pa.MultiIndex)68    else:69        assert isinstance(schema.index, pa.Index)70    with pytest.warns(71        UserWarning,72        match="^This .+ is an inferred schema that hasn't been modified",73    ):74        schema.validate(dataframe)75    # modifying an inferred schema should set _is_inferred to False76    schema_with_added_cols = schema.add_columns({"foo": pa.Column(pa.String)})77    assert schema._is_inferred78    assert not schema_with_added_cols._is_inferred79    assert isinstance(80        schema_with_added_cols.validate(dataframe.assign(foo="a")),81        pd.DataFrame,82    )83    schema_with_removed_cols = schema.remove_columns(["int"])84    assert schema._is_inferred85    assert not schema_with_removed_cols._is_inferred86    assert isinstance(87        schema_with_removed_cols.validate(dataframe.drop("int", axis=1)),88        pd.DataFrame,89    )90@pytest.mark.parametrize(91    "series",92    [93        pd.Series([1, 2, 3]),94        pd.Series([1.0, 2.0, 3.0]),95        pd.Series([True, False, True]),96        pd.Series(list("abcdefg")),97        pd.Series(list("abcdefg"), dtype="category"),98        pd.Series(pd.to_datetime(["20180101", "20180102", "20180103"])),99    ],100)101def test_infer_series_schema(series: pd.Series) -> None:102    """Test series schema is correctly inferred."""103    schema = schema_inference.infer_series_schema(series)104    assert isinstance(schema, pa.SeriesSchema)105    with pytest.warns(106        UserWarning,107        match="^This .+ is an inferred schema that hasn't been modified",108    ):109        schema.validate(series)110    # modifying an inferred schema should set _is_inferred to False111    schema_with_new_checks = schema.set_checks(112        [pa.Check(lambda x: x is not None)]113    )114    assert schema._is_inferred115    assert not schema_with_new_checks._is_inferred...

ped_utils.py

Source:ped_utils.py

...32        if mom is None and dad is None:33            continue34        35        # ignore people whose parents are based on their own ped line36        # if mom._is_inferred() or dad._is_inferred():37        #     continue38        39        trio = Trio(x, dad, mom)40        # trio.add_person(x)41        # trio.add_person(mom)42        # trio.add_person(dad)43        # trio.set_mom(mom, x)44        # trio.set_dad(dad, x)45        46        trios.append(trio)47    48    return trios49def get_top_level_trios(all_trios):50    r_trios = []51    for t in all_trios:52        flag = 153        for i in t.get_parent():54            if i is not None and (i.mom != '0' or i.dad != '0'):55                flag = 056                break57        if flag == 1:58            r_trios.append(t)59    return r_trios60def get_as_parent_trios(person: Person, all_trios: List[Trio]):61    r_trios = []62    for t in all_trios:63        for i in t.get_parent():64            if i.id == person.id:65                if t not in r_trios:66                    r_trios.append(t)67    return r_trios68def get_as_child_trio(person: Person, trios: List[Trio]):69    for t in trios:70        if t.get_child().id == person.id:71            return t72def get_next_level_trios(all_trios: List[Trio], current_level_trios: List[Trio]) -> List[Trio]:73    r_trios = []74    for t in current_level_trios:75        n_l_t = get_as_parent_trios(t.child, all_trios)76        for item in n_l_t:77            if item not in r_trios:78                r_trios.append(item)79    return r_trios80def get_bottom_level_trios(all_trios):81    r_trios = []82    for t in all_trios:83        if len(get_as_parent_trios(t.child, all_trios)) == 0:84            r_trios.append(t)85    return r_trios86def get_prev_level_trios(all_trios: List[Trio], current_level_trios: List[Trio]) -> List[Trio]:87    r_trios = []88    for t in current_level_trios:89        for i in t.get_parent():90            p_t = get_as_child_trio(i, all_trios)91            if p_t is not None:92                r_trios.append(p_t)93    return r_trios94def get_probands(family):95    """ find probands within a Family96    97    Returns:98        list of probands (as peds.Person objects)99    """100    probands = []101    for x in family:102        # arbitrarily define probands as individuals who are affected, and do103        # not have any children in the family. This could be a bit looser,104        # to cope with multigenerational familes, but will do for now.105        if x.is_affected():106            if len(list(family.get_children(x))) == 0:107                probands.append(x)108            else:109                mom = family.get_mom(x)110                dad = family.get_dad(x)111                112                if mom is None and dad is None:113                    continue114                115                # ignore people whose parents are based on their own ped line116                if mom._is_inferred() or dad._is_inferred():117                    continue118                119                probands.append(x)120    ...

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