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How to use predecessor method in avocado

Best Python code snippet using avocado_python

fareysequences.py

Source:fareysequences.py

...62    if successor == Fraction(1, 1):63        return __predecessor_of_one_first_in_Fm(m)64    ref_point = ceil((successor.numerator * m) /65                     successor.denominator)66    return __get_numerator_and_return_predecessor(67        __find_numerator_of_predecessor((ref_point - successor.numerator, ref_point - 1),68                                        successor), successor)697071def successor_in_Fm(m: int, predecessor: Fraction) -> Fraction:72    # See Lemma 2.9(ii) and Table 2.3 of the monograph. Call for instance:73    #    >>> successor_in_Fm(6, Fraction(1, 3))74    # to get the result:75    #    Fraction(2, 5)76    if m < 1:77        # "N/A: Order m of the sequence should be > 0"78        return Fraction(1, -1)79    if (predecessor < Fraction(0, 1)) or (predecessor >= Fraction(1, 1)):80        # "N/A: predecessor should be between (0/1) (included) and (1/1) (excluded)"81        return Fraction(1, -2)82    if predecessor.denominator > m:83        # "N/A: Denominator of the predecessor should not exceed the order m of the sequence"84        return Fraction(1, -3)85    if predecessor == Fraction(0, 1):86        return __successor_of_zero_first_in_Fm(m)87    ref_point = ceil((predecessor.numerator * m + 2) /88                     predecessor.denominator)89    return __get_numerator_and_return_successor(90        __find_numerator_of_successor(91            (ref_point - predecessor.numerator, ref_point - 1), predecessor),92        predecessor)939495def predecessor_in_Fml(m: int, l: int, successor: Fraction) -> Fraction:96    # See Lemma 2.13(i)(a)-(b) and Table 2.1 of the monograph. Call for instance:97    #    >>> predecessor_in_Fml(6, 4, Fraction(1, 1))98    # to get the result:99    #    Fraction(4, 5)100    if m < 2:101        # "N/A: Parameter m of the sequence should be > 1"102        return Fraction(1, -1)103    if (l <= 0) or (l >= m):104        # "N/A: Parameter l should be between 0 (excluded) and m (excluded)"105        return Fraction(1, -2)106    if (successor <= Fraction(0, 1)) or (successor > Fraction(1, 1)):107        # "N/A: successor should be between (0/1) (excluded) and (1/1) (included)"108        return Fraction(1, -3)109    if successor.denominator > m:110        # "N/A: Denominator of the successor should not exceed the parameter m of the sequence"111        return Fraction(1, -4)112    if l < successor.numerator:113        # "N/A: Numerator of the successor should be between 1 (included) and l (included)"114        return Fraction(1, -5)115    if successor == Fraction(1, 1):116        return __predecessor_of_one_first_in_Fml(l)117    if successor.numerator * m - successor.denominator * l >= 1:118        return __get_numerator_and_return_predecessor(119            __find_numerator_of_predecessor((l - successor.numerator + 1, l), successor), successor)120    else:121        ref_point = ceil((successor.numerator * m) / successor.denominator)122        return __get_numerator_and_return_predecessor(123            __find_numerator_of_predecessor((ref_point - successor.numerator, ref_point - 1),124                                            successor), successor)125126127def successor_in_Fml(m: int, l: int, predecessor: Fraction) -> Fraction:128    # See Lemma 2.13(ii)(a)-(b) and Table 2.3 of the monograph. Call for instance:129    #    >>> successor_in_Fml(6, 4, Fraction(4, 5))130    # to get the result:131    #    Fraction(1, 1)132    if m < 2:133        # "N/A: Parameter m of the sequence should be > 1"134        return Fraction(1, -1)135    if (l <= 0) or (l >= m):136        # "N/A: Parameter l should be between 0 (excluded) and m (excluded)"137        return Fraction(1, -2)138    if (predecessor < Fraction(0, 1)) or (predecessor >= Fraction(1, 1)):139        # "N/A: predecessor should be between (0/1) (included) and (1/1) (excluded)"140        return Fraction(1, -3)141    if predecessor.denominator > m:142        # "N/A: Denominator of the predecessor should not exceed the parameter m of the sequence"143        return Fraction(1, -4)144    if l < predecessor.numerator:145        # "N/A: "N/A: Numerator of the predecessor should be between 1 (included) and l (included)"146        return Fraction(1, -5)147    if predecessor == Fraction(0, 1):148        return __successor_of_zero_first_in_Fml(m)149    if predecessor.denominator * l - predecessor.numerator * m >= 1:150        ref_point = ceil((predecessor.numerator * m + 2) /151                         predecessor.denominator)152        return __get_numerator_and_return_successor(153            __find_numerator_of_successor(154                (ref_point - predecessor.numerator, ref_point - 1), predecessor),155            predecessor)156    else:157        return __get_numerator_and_return_successor(158            __find_numerator_of_successor((l - predecessor.numerator + 1, l),159                                          predecessor), predecessor)160161162def predecessor_in_Gml(m: int, l: int, successor: Fraction) -> Fraction:163    # See Lemma 2.15(i)(a)-(b) and Table 2.1 of the monograph. Call for instance:164    #    >>> predecessor_in_Gml(6, 4, Fraction(1, 3))165    # to get the result:166    #    Fraction(0, 1)167    if m < 2:168        # "N/A: Parameter m of the sequence should be > 1"169        return Fraction(1, -1)170    if (l <= 0) or (l >= m):171        # "N/A: Parameter l should be between 0 (excluded) and m (excluded)"172        return Fraction(1, -2)173    if (successor <= Fraction(0, 1)) or (successor > Fraction(1, 1)):174        # "N/A: successor should be between (0/1) (excluded) and (1/1) (included)"175        return Fraction(1, -3)176    if successor.denominator > m:177        # "N/A: Denominator of the successor should not exceed the parameter m of the sequence"178        return Fraction(1, -4)179    if l + successor.denominator - m > successor.numerator:180        # "N/A: The quantity (l + denominator - m) should not exceed the numerator of the successor"181        return Fraction(1, -5)182    if successor == Fraction(1, 1):183        return __predecessor_of_one_first_in_Gml(l)184    if successor.numerator * m - successor.denominator * l >= 1:185        ref_point = ceil((successor.numerator * m) /186                         successor.denominator)187        return __get_numerator_and_return_predecessor(188            __find_numerator_of_predecessor(189                (ref_point - successor.numerator, ref_point - 1), successor),190            successor)191    else:192        ref_point = ceil(193            (successor.numerator * (m - l)) / (successor.denominator - successor.numerator))194        return __get_numerator_and_return_predecessor(195            __find_numerator_of_predecessor(196                (ref_point - successor.numerator, ref_point - 1), successor),197            successor)198199200def successor_in_Gml(m: int, l: int, predecessor: Fraction) -> Fraction:201    # See Lemma 2.15(ii)(a)-(b) and Table 2.3 of the monograph. Call for instance:202    #    >>> successor_in_Gml(6, 4, Fraction(1, 3))203    # to get the result:204    #    Fraction(1, 2)205    if m < 2:206        # "N/A: Parameter m of the sequence should be > 1"207        return Fraction(1, -1)208    if (l <= 0) or (l >= m):209        # "N/A: Parameter l should be between 0 (excluded) and m (excluded)"210        return Fraction(1, -2)211    if (predecessor < Fraction(0, 1)) or (predecessor >= Fraction(1, 1)):212        # "N/A: predecessor should be between (0/1) (included) and (1/1) (excluded)"213        return Fraction(1, -3)214    if predecessor.denominator > m:215        # "N/A: Denominator of the predecessor should not exceed the parameter m of the sequence"216        return Fraction(1, -4)217    if l + predecessor.denominator - m > predecessor.numerator:218        # "N/A: Denominator of the predecessor minus its numerator should not exceed (m - l)"219        return Fraction(1, -5)220    if predecessor == Fraction(0, 1):221        return __successor_of_zero_first_in_Gml(m, l)222    if predecessor.denominator * l - predecessor.numerator * m >= 1:223        ref_point = ceil((predecessor.numerator * (m - l) + 2) /224                         (predecessor.denominator - predecessor.numerator))225        return __get_numerator_and_return_successor(226            __find_numerator_of_successor(227                (ref_point - predecessor.numerator, ref_point - 1), predecessor),228            predecessor)229    else:230        ref_point = ceil((predecessor.numerator * m + 2) /231                         predecessor.denominator)232        return __get_numerator_and_return_successor(233            __find_numerator_of_successor(234                (ref_point - predecessor.numerator, ref_point - 1), predecessor),235            predecessor)236237238def __predecessor_in_FB2mm(m: int, successor: Fraction) -> Fraction:239    # See Remark 1.17 and Table 1.5;240    # see Remark 2.25 and Table 2.8;241    # see Remark 2.11 and Table 2.5;242    # see Remark 2.24 and Table 2.7;243    # see Proposition 2.12 (i) (a) and Proposition 2.12 (ii) (a), and Table 2.1 of the monograph. Call for instance:244    #    >>> __predecessor_in_FB2mm(3, Fraction(2, 5))245    # to get the result:246    #    Fraction(1, 3)247    if m < 1:248        # "N/A: Parameter m of the sequence should be > 0"249        return Fraction(1, -1)250    if (successor <= Fraction(0, 1)) or (successor > Fraction(1, 1)):251        # "N/A: successor should be between (0/1) (excluded) and (1/1) (included)"252        return Fraction(1, -2)253    if successor.denominator > 2 * m:254        # "N/A: Denominator of the successor should not exceed (2 * m)"255        return Fraction(1, -3)256    if (successor.denominator - m > successor.numerator) or (successor.numerator > m):257        # "N/A: Numerator of the successor should be between (denominator - m) (included) and m (included)"258        return Fraction(1, -4)259    match successor:260        case Fraction(numerator=1, denominator=1):261            return __predecessor_of_one_first_in_FB2mm(m)262        case Fraction(numerator=2, denominator=3):263            return __predecessor_of_two_thirds_in_FB2mm(m)264        case Fraction(numerator=1, denominator=2):265            return __predecessor_of_one_second_in_FB2mm(m)266        case Fraction(numerator=1, denominator=3):267            return __predecessor_of_one_third_in_FB2mm(m)268        case _:269            if successor > Fraction(1, 2):270                return __get_numerator_and_return_predecessor(271                    __find_numerator_of_predecessor((m - successor.numerator + 1, m),272                                                    successor), successor)273            else:274                ref_point = ceil((successor.numerator * m) /275                                 (successor.denominator - successor.numerator))276                return __get_numerator_and_return_predecessor(277                    __find_numerator_of_predecessor(278                        (ref_point - successor.numerator, ref_point - 1), successor),279                    successor)280281282def __successor_in_FB2mm(m: int, predecessor: Fraction) -> Fraction:283    # See Remark 1.17 and Table 1.5;284    # see Remark 2.24 and Table 2.7;285    # see Remark 2.11 and Table 2.5;286    # see Remark 2.25 and Table 2.8;287    # see Proposition 2.12 (i) (b) and Proposition 2.12 (ii) (b), and Table 2.3 of the monograph. Call for instance:288    #    >>> __successor_in_FB2mm(3, Fraction(3, 5))289    # to get the result:290    #    Fraction(2, 3)291    if m < 1:292        # "N/A: Parameter m of the sequence should be > 0"293        return Fraction(1, -1)294    if (predecessor < Fraction(0, 1)) or (predecessor >= Fraction(1, 1)):295        # "N/A: predecessor should be between (0/1) (included) and (1/1) (excluded)"296        return Fraction(1, -2)297    if predecessor.denominator > 2 * m:298        # "N/A: Denominator of the predecessor should not exceed (2 * m)"299        return Fraction(1, -3)300    if (predecessor.denominator - m > predecessor.numerator) or (predecessor.numerator > m):301        # "N/A: Numerator of the predecessor should be between (denominator - m) (included) and m (included)"302        return Fraction(1, -4)303    match predecessor:304        case Fraction(numerator=0, denominator=1):305            return __successor_of_zero_first_in_FB2mm(m)306        case Fraction(numerator=1, denominator=3):307            return __successor_of_one_third_in_FB2mm(m)308        case Fraction(numerator=1, denominator=2):309            return __successor_of_one_second_in_FB2mm(m)310        case Fraction(numerator=2, denominator=3):311            return __successor_of_two_thirds_in_FB2mm(m)312        case _:313            if predecessor < Fraction(1, 2):314                ref_point = ceil((predecessor.numerator * m + 2) /315                                 (predecessor.denominator - predecessor.numerator))316                return __get_numerator_and_return_successor(317                    __find_numerator_of_successor(318                        (ref_point - predecessor.numerator, ref_point - 1), predecessor),319                    predecessor)320            else:321                return __get_numerator_and_return_successor(322                    __find_numerator_of_successor((m - predecessor.numerator + 1, m),323                                                  predecessor), predecessor)324325326def predecessor_in_FBnm(n: int, m: int, successor: Fraction) -> Fraction:327    # See Remark 1.17 and Table 1.5 of the monograph;328    # see CORRECTED Remark 2.43(i) and Remark 2.43(ii) and CORRECTED Table 2.8;329    # see Remark 2.17 and Table 2.5;330    # See CORRECTED Remark 2.42 and Table 2.7;331    # see Propositions 2.18(i)(a) and 2.18(ii)(a), and Table 2.1;332    # see Propositions 2.19(i)(a) and 2.19(ii)(a), and Table 2.1.  Call for instance:333    #    >>> predecessor_in_FBnm(6, 4, Fraction(3, 4))334    # to get the result:335    #    Fraction(2, 3)336    if n == 2 * m:337        return __predecessor_in_FB2mm(m, successor)338    if n < 2:339        # "N/A: Parameter n of the sequence should be > 1"340        return Fraction(1, -1)341    if (m < 1) or (m >= n):342        # "N/A: Parameter m of the sequence should be between 0 (excluded) and n (excluded)"343        return Fraction(1, -2)344    if (successor <= Fraction(0, 1)) or (successor > Fraction(1, 1)):345        # "N/A: successor should be between (0/1) (excluded) and (1/1) (included)"346        return Fraction(1, -3)347    if successor.denominator > n:348        # "N/A: Denominator of the successor should not exceed the parameter n of the sequence"349        return Fraction(1, -4)350    if (m + successor.denominator - n > successor.numerator) or (successor.numerator > m):351        # "N/A: Numerator of the successor should be between (m + denominator - n) (included) and m (included)"352        return Fraction(1, -5)353    match successor:354        case Fraction(numerator=1, denominator=1):355            return __predecessor_of_one_first_in_FBnm(m)356        case Fraction(numerator=2, denominator=3):357            return __predecessor_of_two_thirds_in_FBnm(n, m)358        case Fraction(numerator=1, denominator=2):359            return __predecessor_of_one_second_in_FBnm(n, m)360        case Fraction(numerator=1, denominator=3):361            return __predecessor_of_one_third_in_FBnm(n, m)362        case _:363            if n < 2 * m:364                if (successor > Fraction(1, 2)) and (successor.numerator * n - successor.denominator * m >= 1):365                    return __get_numerator_and_return_predecessor(366                        __find_numerator_of_predecessor((m - successor.numerator + 1, m), successor), successor)367                else:368                    ref_point = ceil(369                        successor.numerator * (n - m) / (successor.denominator - successor.numerator))370                    return __get_numerator_and_return_predecessor(371                        __find_numerator_of_predecessor((ref_point - successor.numerator, ref_point - 1),372                                                        successor), successor)373            else:374                if (successor > Fraction(1, 2)) or (successor.numerator * n - successor.denominator * m >= 1):375                    return __get_numerator_and_return_predecessor(376                        __find_numerator_of_predecessor((m - successor.numerator + 1, m), successor), successor)377                else:378                    ref_point = ceil(379                        successor.numerator * (n - m) / (successor.denominator - successor.numerator))380                    return __get_numerator_and_return_predecessor(381                        __find_numerator_of_predecessor((ref_point - successor.numerator, ref_point - 1),382                                                        successor), successor)383384385def successor_in_FBnm(n: int, m: int, predecessor: Fraction) -> Fraction:386    # See Remark 1.17 and Table 1.5 of the monograph;387    # see CORRECTED Remark 2.42 and Table 2.7;388    # see Remark 2.17 and Table 2.5;389    # see Remark 2.43(i)-(ii) and Table 2.8;390    # see Propositions 2.18(i)(b) and 2.18(ii)(b), and Table 2.3;391    # see Propositions 2.19(i)(b) and 2.19(ii)(b), and Table 2.3.  Call for instance:392    #    >>> successor_in_FBnm(6, 4, Fraction(4, 5))393    # to get the result:394    #    Fraction(1, 1)395    if n == 2 * m:396        return __successor_in_FB2mm(m, predecessor)397    if n < 2:398        # "N/A: Parameter n of the sequence should be > 1"399        return Fraction(1, -1)400    if (m < 1) or (m >= n):401        # "N/A: Parameter m of the sequence should be between 0 (excluded) and n (excluded)"402        return Fraction(1, -2)403    if (predecessor < Fraction(0, 1)) or (predecessor >= Fraction(1, 1)):404        # "N/A: predecessor should be between (0 % 1) (included) and (1 % 1) (excluded)"405        return Fraction(1, -3)406    if predecessor.denominator > n:407        # "N/A: Denominator of the predecessor should not exceed the parameter n of the sequence"408        return Fraction(1, -4)409    if (m + predecessor.denominator - n > predecessor.numerator) or (predecessor.numerator > m):410        # "N/A: Numerator of the predecessor should be between (m + denominator - n) (included) and m (included)"411        return Fraction(1, -5)412    match predecessor:413        case Fraction(numerator=0, denominator=1):414            return __successor_of_zero_first_in_FBnm(n, m)415        case Fraction(numerator=1, denominator=3):416            return __successor_of_one_third_in_FBnm(n, m)417        case Fraction(numerator=1, denominator=2):418            return __successor_of_one_second_in_FBnm(n, m)419        case Fraction(numerator=2, denominator=3):420            return __successor_of_two_thirds_in_FBnm(n, m)421        case _:422            if n < 2 * m:423                if (predecessor > Fraction(1, 2)) and (424                        predecessor.denominator * m - predecessor.numerator * n <= 1):425                    return __get_numerator_and_return_successor(426                        __find_numerator_of_successor((m - predecessor.numerator + 1, m), predecessor), predecessor)427                else:428                    ref_point = ceil((predecessor.numerator * (n - m) + 2) /429                                     (predecessor.denominator - predecessor.numerator))430                    return __get_numerator_and_return_successor(431                        __find_numerator_of_successor((ref_point - predecessor.numerator, ref_point - 1),432                                                      predecessor), predecessor)433            else:434                if (predecessor > Fraction(1, 2)) or (predecessor.denominator * m - predecessor.numerator * n <= 1):435                    return __get_numerator_and_return_successor(436                        __find_numerator_of_successor((m - predecessor.numerator + 1, m), predecessor), predecessor)437                else:438                    ref_point = ceil((predecessor.numerator * (n - m) + 2) /439                                     (predecessor.denominator - predecessor.numerator))440                    return __get_numerator_and_return_successor(441                        __find_numerator_of_successor((ref_point - predecessor.numerator, ref_point - 1),442                                                      predecessor), predecessor)443444445def __get_numerator_and_return_predecessor(a: int, successor: Fraction) -> Fraction:446    return Fraction(a, (successor.denominator * a + 1) // successor.numerator)447448449def __get_numerator_and_return_successor(a: int, predecessor: Fraction) -> Fraction:450    return Fraction(a, (predecessor.denominator * a - 1) // predecessor.numerator)451452453def __find_numerator_of_predecessor(search_interval: Tuple(int, int), successor: Fraction) -> int:454    # Here we follow a suggestion found at https://code-maven.com/python-find-first-element-in-list-matching-condition455    return next(filter(lambda x: (successor.denominator * x + 1) % successor.numerator == 0,456                       range(search_interval[0], search_interval[1] + 1)))457458459def __find_numerator_of_successor(search_interval: Tuple(int, int), predecessor: Fraction) -> int:460    # Here we follow a suggestion found at https://code-maven.com/python-find-first-element-in-list-matching-condition461    return next(filter(lambda x: (predecessor.denominator * x - 1) % predecessor.numerator == 0,462                       range(search_interval[0], search_interval[1] + 1)))463464465def __predecessor_of_one_first_in_Fm(m: int) -> Fraction:466    return Fraction(m - 1, m)467
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method.py

Source:method.py

1"""Functionality related to using a PEtab Select model selection method."""2import logging3from dataclasses import dataclass4from enum import Enum5from typing import Callable, Dict, List, Optional, Tuple, Union6import numpy as np7import petab_select8from petab_select import (9    VIRTUAL_INITIAL_MODEL,10    CandidateSpace,11    Criterion,12    Method,13    Model,14)15from ..C import TYPE_POSTPROCESSOR16from .model_problem import ModelProblem17class MethodSignalProceed(str, Enum):18    """Indicators for how a model selection method should proceed."""19    # TODO move to PEtab Select?20    STOP = 'stop'21    CONTINUE = 'continue'22@dataclass23class MethodSignal:24    """The state of a model selection method after a single model calibration.25    Attributes26    ----------27    accept:28        Whether to accept the model.29    proceed:30        How the method should proceed.31    """32    accept: bool33    # TODO change to bool?34    proceed: MethodSignalProceed35class MethodLogger:36    """Log results from a model selection method.37    Attributes38    ----------39    column_width:40        The width of columns when logging.41    column_sep:42        The substring used to separate column values when logging.43    level:44        The logging level.45    logger:46        A logger from the `logging` module.47    """48    column_width: int = 1249    column_sep: str = " | "50    def __init__(self, level: str = 'info'):51        self.logger = logging.getLogger(__name__)52        self.level = level53    def log(self, message, level: str = None) -> None:54        """Log a message.55        Parameters56        ----------57        message:58            The message.59        level:60            The logging level. Defaults to the value defined in the61            constructor.62        """63        if level is None:64            level = self.level65        getattr(self.logger, level)(message)66    def new_selection(self) -> None:67        """Start logging a new model selection."""68        padding = 2069        self.log('-' * padding + 'New Selection' + '-' * padding)70        columns = {71            "Predecessor model subspace:ID": "model0",72            "Model subspace:ID": "model",73            "Criterion ID": "crit",74            "Predecessor model criterion": "model0_crit",75            "Model criterion": "model_crit",76            "Criterion difference": "crit_diff",77            "Accept": "accept",78        }79        columns = {80            k: v.ljust(self.column_width)[: self.column_width]81            for k, v in columns.items()82        }83        self.log(self.column_sep.join(columns.values()))84    def new_result(85        self,86        accept,87        criterion,88        model,89        predecessor_model,90        max_id_length: str = 12,91        precision: int = 3,92    ) -> None:93        """Log a model calibration result.94        Parameters95        ----------96        accept:97            Whether the model is accepted.98        criterion:99            The criterion type.100        max_id_length:101            Model and predecessor model IDs are truncated to this length in the102            logged message.103        model:104            The calibrated model.105        predecessor_model:106            The predecessor model.107        precision:108            The number of decimal places to log.109        """110        model_criterion = model.get_criterion(criterion)111        def get_model_id(model: Model) -> str:112            """Get a model ID for logging.113            Parameters114            ----------115            model:116                The model.117            Returns118            -------119            str120                The ID.121            """122            model_subspace_id = model.model_subspace_id or ''123            original_model_id = model.model_id or model.get_hash()124            model_id = model_subspace_id + ':' + original_model_id125            return model_id126        def float_to_str(value: float, precision: int = 3) -> str:127            return f"{value:.{precision}e}"128        if isinstance(predecessor_model, Model):129            predecessor_model_id = get_model_id(predecessor_model)130            predecessor_model_criterion = predecessor_model.get_criterion(131                criterion132            )133            criterion_difference = float_to_str(134                model_criterion - predecessor_model_criterion135            )136            predecessor_model_criterion = float_to_str(137                predecessor_model_criterion138            )139        else:140            criterion_difference = None141            predecessor_model_criterion = None142            predecessor_model_id = predecessor_model143        model_criterion = float_to_str(model_criterion)144        message_parts = [145            predecessor_model_id,146            get_model_id(model),147            criterion.value,148            predecessor_model_criterion,149            model_criterion,150            criterion_difference,151            accept,152        ]153        message = self.column_sep.join(154            [155                str(v).ljust(self.column_width)[: self.column_width]156                for v in message_parts157            ]158        )159        self.log(message)160class MethodCaller:161    """Handle calls to PEtab Select model selection methods.162    Attributes163    ----------164    petab_select_problem:165        The PEtab Select problem.166    candidate_space:167        A `petab_select.CandidateSpace`, used to generate candidate models.168    criterion:169        The criterion by which models will be compared.170    criterion_threshold:171        The minimum improvement in criterion that a test model must have to172        be selected. The comparison is made according to the method. For173        example, in `ForwardSelector`, test models are compared to the174        previously selected model.175    history:176        The history of the model selection, as a `dict` with model hashes177        as keys and models as values.178    limit:179        Limit the number of calibrated models. NB: the number of accepted180        models may (likely) be fewer.181    logger:182        A `MethodLogger`, used to log results.183    minimize_options:184        A dictionary that will be passed to `pypesto.minimize` as keyword185        arguments for model optimization.186    model_postprocessor:187        A method that is applied to each model after calibration.188    objective_customizer:189        A method that is applied to the pyPESTO objective after the190        objective is initialized, before calibration.191    predecessor_model:192        Specify the predecessor (initial) model for the model selection193        algorithm. If `None`, then the algorithm will generate an194        predecessor model if required.195    select_first_improvement:196        If `True`, model selection will terminate as soon as a better model197        is found. If `False`, all candidate models will be tested.198    startpoint_latest_mle:199        If `True`, one of the startpoints in the multistart optimization200        will be the MLE of the latest model.201    """202    def __init__(203        self,204        petab_select_problem: petab_select.Problem,205        history: Dict[str, Model],206        # Arguments/attributes that can simply take the default value here.207        criterion_threshold: float = 0.0,208        limit: int = np.inf,209        minimize_options: Dict = None,210        model_postprocessor: TYPE_POSTPROCESSOR = None,211        objective_customizer: Callable = None,212        select_first_improvement: bool = False,213        startpoint_latest_mle: bool = True,214        # Arguments/attributes that should be handled more carefully.215        candidate_space: CandidateSpace = None,216        criterion: Criterion = None,217        # TODO misleading, `Method` here is simply an Enum, not a callable...218        method: Method = None,219        predecessor_model: Model = None,220    ):221        """Arguments are used in every `__call__`, unless overridden."""222        self.petab_select_problem = petab_select_problem223        self.history = history224        self.criterion_threshold = criterion_threshold225        self.limit = limit226        self.minimize_options = minimize_options227        self.model_postprocessor = model_postprocessor228        self.objective_customizer = objective_customizer229        self.predecessor_model = predecessor_model230        self.select_first_improvement = select_first_improvement231        self.startpoint_latest_mle = startpoint_latest_mle232        self.criterion = criterion233        if self.criterion is None:234            self.criterion = self.petab_select_problem.criterion235        # Forbid specification of both a candidate space and a method.236        if candidate_space is not None and method is not None:237            self.logger.log(238                (239                    'Both `candidate_space` and `method` were provided. '240                    'Please only provide one. The method will be ignored here.'241                ),242                level='warning',243            )244        # Get method.245        self.method = (246            method247            if method is not None248            else candidate_space.method249            if candidate_space is not None250            else self.petab_select_problem.method251        )252        # Require either a candidate space or a method.253        if candidate_space is None and self.method is None:254            raise ValueError(255                'Please provide one of either `candidate_space` or `method`, '256                'or specify the `method` in the PEtab Select problem.'257            )258        # Use candidate space if provided.259        if candidate_space is not None:260            self.candidate_space = candidate_space261            if predecessor_model is not None:262                candidate_space.set_predecessor_model(predecessor_model)263        # Else generate one based on the PEtab Select problem.264        else:265            self.candidate_space = (266                self.petab_select_problem.new_candidate_space(267                    method=self.method,268                    predecessor_model=self.predecessor_model,269                )270            )271        # May have changed from `None` to `petab_select.VIRTUAL_INITIAL_MODEL`272        self.predecessor_model = self.candidate_space.get_predecessor_model()273        self.logger = MethodLogger()274    def __call__(275        self,276        predecessor_model: Optional[Union[Model, None]] = None,277    ) -> Tuple[List[Model], Dict[str, Model]]:278        """Run a single iteration of the model selection method.279        A single iteration here refers to calibration of all candidate models.280        For example, given a predecessor model with 3 estimated parameters,281        with the forward method, a single iteration would involve calibration282        of all models that have both: the same 3 estimated parameters; and 1283        additional estimated paramenter.284        Parameters285        ----------286        predecessor_model:287            The model that will be used for comparison. Example 1: the288            initial model of a forward method. Example 2: all models found289            with a brute force method should be better than this model.290        Returns291        -------292        tuple293            A 2-tuple, with the following values:294               1. the best model; and295               2. all candidate models in this iteration, as a `dict` with296                     model hashes as keys and models as values.297        """298        # Calibrated models in this iteration that improve on the predecessor299        # model.300        better_models = []301        # All calibrated models in this iteration (see second return value).302        local_history = {}303        self.logger.new_selection()304        if predecessor_model is None:305            # May still be `None` (e.g. brute force method)306            predecessor_model = self.predecessor_model307        candidate_models = petab_select.ui.candidates(308            problem=self.petab_select_problem,309            candidate_space=self.candidate_space,310            limit=self.limit,311            excluded_model_hashes=list(self.history),312            predecessor_model=predecessor_model,313        ).models314        if not candidate_models:315            raise StopIteration("No valid models found.")316        # TODO parallelize calibration (maybe not sensible if317        #      `self.select_first_improvement`)318        for candidate_model in candidate_models:319            # autoruns calibration320            self.new_model_problem(model=candidate_model)321            local_history[candidate_model.model_id] = candidate_model322            method_signal = self.handle_calibrated_model(323                model=candidate_model,324                predecessor_model=predecessor_model,325            )326            if method_signal.accept:327                better_models.append(candidate_model)328            if method_signal.proceed == MethodSignalProceed.STOP:329                break330        self.history.update(local_history)331        best_model = None332        if better_models:333            best_model = petab_select.ui.best(334                problem=self.petab_select_problem,335                models=better_models,336                criterion=self.criterion,337            )338        return best_model, local_history339    def handle_calibrated_model(340        self,341        model: Model,342        predecessor_model: Optional[Model],343    ) -> MethodSignal:344        """Handle the model selection method, given a new calibrated model.345        Parameters346        ----------347        model:348            The calibrated model.349        predecessor_model:350            The predecessor model.351        Returns352        -------353        MethodSignal354            A `MethodSignal` that describes the result.355        """356        # Use the predecessor model from `__init__` if an iteration-specific357        # predecessor model was not supplied to `__call__`.358        if predecessor_model is None:359            # May still be `None` after this assignment.360            predecessor_model = self.predecessor_model361        # Default to accepting the model and continuing the method.362        method_signal = MethodSignal(363            accept=True,364            proceed=MethodSignalProceed.CONTINUE,365        )366        # Reject the model if it doesn't improve on the predecessor model.367        if (368            predecessor_model is not None369            and predecessor_model != VIRTUAL_INITIAL_MODEL370            and not self.model1_gt_model0(371                model1=model, model0=predecessor_model372            )373        ):374            method_signal.accept = False375        # Stop the model selection method if it a first improvement is found.376        if self.select_first_improvement and method_signal.accept:377            method_signal.proceed = MethodSignalProceed.STOP378        # TODO allow users to supply an arbitrary constraint function to e.g.:379        #      - quit after 10 accepted models380        #      - reject models that are worse than the current 10 best models381        # Log result382        self.logger.new_result(383            accept=method_signal.accept,384            criterion=self.criterion,385            model=model,386            predecessor_model=predecessor_model,387        )388        return method_signal389    def model1_gt_model0(390        self,391        model1: Model,392        model0: Model,393    ) -> bool:394        """Compare models by criterion.395        Parameters396        ----------397        model1:398            The new model.399        model0:400            The original model.401        Returns402        -------403        bool404            `True`, if `model1` is superior to `model0` by the criterion,405            else `False`.406        """407        if self.criterion in [408            Criterion.AIC,409            Criterion.AICC,410            Criterion.BIC,411            Criterion.LH,412            Criterion.LLH,413            Criterion.NLLH,414        ]:415            result = petab_select.model.default_compare(416                model0=model0,417                model1=model1,418                criterion=self.criterion,419                criterion_threshold=self.criterion_threshold,420            )421        else:422            raise NotImplementedError(423                f"Model selection criterion: {self.criterion}."424            )425        return result426    def new_model_problem(427        self,428        model: Model,429        valid: bool = True,430        autorun: bool = True,431    ) -> ModelProblem:432        """Create a model problem, usually to calibrate a model.433        Parameters434        ----------435        model:436            The model.437        valid:438            Whether the model should be considered a valid model. If it is439            not valid, it will not be calibrated.440        autorun:441            Whether the model should be calibrated upon creation.442        Returns443        -------444        ModelProblem445            The model selection problem.446        """447        x_guess = None448        if (449            self.startpoint_latest_mle450            and model.predecessor_model_hash in self.history451        ):452            predecessor_model = self.history[model.predecessor_model_hash]453            if str(model.petab_yaml) != str(predecessor_model.petab_yaml):454                raise NotImplementedError(455                    'The PEtab YAML files differ between the model and its '456                    'predecessor model. This may imply different (fixed union '457                    'estimated) parameter sets. Support for this is not yet '458                    'implemented.'459                )460            x_guess = {461                **predecessor_model.parameters,462                **predecessor_model.estimated_parameters,463            }464        return ModelProblem(465            model=model,466            criterion=self.criterion,467            valid=valid,468            autorun=autorun,469            x_guess=x_guess,470            minimize_options=self.minimize_options,471            objective_customizer=self.objective_customizer,472            postprocessor=self.model_postprocessor,...

ForkTree.py

Source:ForkTree.py

2    def __init__(self, predecessor, data):3        self.predecessor = predecessor4        self.data = data5        self.sucessor = []6    def getpredecessor(self):7        return self.predecessor8    def setpredecessor(self, predecessor):9        self.predecessor = predecessor10        return predecessor11    def addsuccessor(self, sucessor):12        if isinstance(sucessor, Node):13            self.sucessor.append(sucessor)14            return 115        return 016    def getsuccessors(self):17        return self.sucessor18    def testsuccessor(self):19        if self.sucessor:20            return 121        return 022    def removesucessor(self, successor):23        if self.sucessor:24            return self.sucessor.remove(successor)25        else:26            return 027    def getdata(self):28        return self.data29class ForkTree:30    def __init__(self):31        self.Tree = []32        self.curNode = 033    def gettreenodecontent(self):34        ret = []35        for node in self.Tree:36            ret.append(node.getdata())37        return ret38    def getcurnode(self):39        return self.curNode40    def getcurnodepre(self):41        return self.curNode.getpredecessor()42    def getbasenode(self):43        for indsel in range(0, len(self.Tree)):44            found = 045            predecessor = self.Tree[indsel].getpredecessor()46            for indent in range(0, len(self.Tree)):47                if indsel != indent and predecessor == self.Tree[indent]:48                    found = 149                    break50            if not found:51                return predecessor52        return 053    def popcurnode(self):54        self.curNode = self.getcurnodepre()55        return self.curNode56    def popdelcurnode(self, curnode):57        prenode = self.popcurnode()58        self.Tree.remove(curnode)59        if prenode:60            prenode.removesucessor(curnode)61        return prenode62    def insertnode(self, data, prenode=0):63        if not prenode:64            node = self.curNode65        else:66            node = prenode67        newnode = Node(node, data)68        self.Tree.append(newnode)69        if node and self.curNode:70            self.curNode.addsuccessor(newnode)71        self.curNode = newnode72        return newnode73    def appendnodes(self, nodes, predecessor):74        if predecessor and predecessor not in self.Tree:75            return 076        for entry in nodes:77            entry.setpredecessor(predecessor)78            self.Tree.append(entry)79            if predecessor:80                predecessor.addsuccessor(entry)81            self.curNode = entry82        return self.curNode83    def appenddata(self, data, predecessor):84        nodes = []85        if predecessor and predecessor not in self.Tree:86            return 087        for entry in data:88            node = Node(predecessor, entry)89            nodes.append(node)90            self.Tree.append(node)91            if predecessor:92                predecessor.addsuccessor(node)93        return nodes94    def getpredecessor(self):95        self.curNode = self.curNode.getpredecessor()96        return self.curNode97    def getnodeandchilds(self):98        childs = self.curNode.getsuccessors()99        nodes = [self.curNode]100        while childs:101            newchilds = []102            for entry in childs:103                nodes.append(entry)104                newchilds += entry.getsuccessors()105            childs = newchilds106        return nodes107    def getchildnodes(self, curnode):108        children = [curnode]109        successors = curnode.getsuccessors()110        while successors:111            nextsuc = []112            for entry in successors:113                children.append(entry)114                nextsuc += entry.getsuccessors()115            if not nextsuc:116                return children117            successors = nextsuc118        return children119    def getendnodes(self):120        endnodes = []121        for entry in self.Tree:122            if not entry.testsuccessor():123                endnodes.append(entry)124        return endnodes125    def gettraces(self):126        traces = []127        endnodes = self.getendnodes()128        for endnode in endnodes:129            node = endnode130            trace = [node.getdata()]131            while node.getpredecessor():132                node = node.getpredecessor()133                trace.append(node.getdata())134            traces.append(trace)135        return traces136    def treetoarray(self):137        # Get end nodes138        endnodes = []139        for entry in self.Tree:140            if entry.testsuccessor():141                endnodes.append(entry)142        ret = []143        for entry in endnodes:144            curcond = []145            curcond += entry.getdata()146            predecessor = entry.getpredecessor()147            # Search backwards for predecessor148            while predecessor:149                curcond += predecessor.getdata()150                predecessor = predecessor.getpredecessor()151            ret.append(curcond)152    # Print all generated transactions153    def treetolist(self):154        ret = []155        for entry in self.Tree:156            ret.append(entry.getdata())...

Automation Testing Tutorials

Learn to execute automation testing from scratch with LambdaTest Learning Hub. Right from setting up the prerequisites to run your first automation test, to following best practices and diving deeper into advanced test scenarios. LambdaTest Learning Hubs compile a list of step-by-step guides to help you be proficient with different test automation frameworks i.e. Selenium, Cypress, TestNG etc.