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How to use sorted_data method in pytest-benchmark

Best Python code snippet using pytest-benchmark

train.py

Source:train.py

1import logging2import sys34import numpy as np5import numpy as np6import pandas as pd78import symfit as sf9from symfit.core.minimizers import BFGS, DifferentialEvolution101112logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)13logger = logging.getLogger(__name__)141516# Load data17logger.info("Loading data")18df = pd.read_csv(19    "https://opendata.ecdc.europa.eu/covid19/casedistribution/csv/",20    parse_dates=["dateRep"],21    infer_datetime_format=True,22    dayfirst=True,23)2425logger.info("Cleaning data")26df = df.rename(27    columns={"dateRep": "date", "countriesAndTerritories": "country"}28)  # Sane column names29df = df.drop(["day", "month", "year", "geoId"], axis=1)  # Not required3031# Create DF with sorted index32sorted_data = df.set_index(df["date"]).sort_index()3334# Remove all rows with zero deaths in it35sorted_data = sorted_data[sorted_data["deaths"] != 0]3637sorted_data["cumulative_cases"] = sorted_data.groupby(by="country")["cases"].cumsum()38sorted_data["cumulative_deaths"] = sorted_data.groupby(by="country")["deaths"].cumsum()3940# Filter out data with less than 100 deaths, we probably can't get very good estimates from these.41sorted_data = sorted_data[sorted_data["cumulative_deaths"] >= 100]4243# Remove "Czechia" it has a population of NaN44sorted_data = sorted_data[sorted_data["country"] != "Czechia"]4546# Get final list of countries47countries = sorted_data["country"].unique()48n_countries = len(countries)4950# Pull out population size per country51populations = {52    country: df[df["country"] == country].iloc[0]["popData2019"]53    for country in countries54}5556# A map from country to integer index (for the model)57idx_country = pd.Index(countries).get_indexer(sorted_data.country)5859# Create a new column with the number of days since first infection (the x-axis)60country_first_dates = {61    c: sorted_data[sorted_data["country"] == c].index.min() for c in countries62}63sorted_data["100_cases"] = sorted_data.apply(64    lambda x: country_first_dates[x.country], axis=165)66sorted_data["days_since_100_cases"] = (67    sorted_data.index - sorted_data["100_cases"]68).apply(lambda x: x.days)6970logger.info("Training...")71fit_result = {}72ode_model = {}73for country in countries:74    t, S, I, R, D = sf.variables("t, S, I, R, D")75    p_susceptible = 0.0008576    N_mu = populations[country] * p_susceptible77    Î²_0, Î³_0, Î¼_0 = 0.35, 0.1, 0.0378    N_0 = N_mu79    Î² = sf.Parameter("Î²", value=Î²_0, min=0.1, max=0.5)80    Î³ = sf.Parameter("Î³", value=Î³_0, min=0.01, max=0.2)81    N = sf.Parameter("N", value=N_0, min=1e4, max=1e7)82    Î¼ = sf.Parameter("Î¼", value=Î¼_0, min=0.0001, max=0.1)8384    print(country, N_0)8586    model_dict = {87        sf.D(S, t): -Î² * I * S / N,88        sf.D(I, t): Î² * I * S / N - Î³ * I - Î¼ * I,89        sf.D(R, t): Î³ * I,90        sf.D(D, t): Î¼ * I,91    }9293    p_infected = 0.0194    I_0, R_0, D_0 = N_mu * p_infected, N_mu * p_infected - 100.0, 100.095    S_0 = N_mu - I_0 - R_0 - D_096    ode_model[country] = sf.ODEModel(97        model_dict, initial={t: 0.0, S: S_0, I: I_0, R: R_0, D: D_0}98    )99100    idx = sorted_data["country"] == country101    x = sorted_data[idx]["days_since_100_cases"].values102    y = sorted_data[idx]["cumulative_deaths"].values103104    fit = sf.Fit(105        ode_model[country],106        t=x,107        S=None,108        I=None,109        R=None,110        D=y,111        minimizer=[DifferentialEvolution, BFGS],112    )113    fit_result[country] = fit.execute(114        DifferentialEvolution={"seed": 0, "tol": 1e-2, "maxiter": 5}, BFGS={"tol": 1e-6}115    )116    print(fit_result[country])117118logger.info("Inferencing...")119n_days = 365  # Daily predictions120121cumulative_prediction = {}122daily_prediction = {}123residuals_high = {}124residuals_low = {}125for country in countries:126    idx = sorted_data["country"] == country127    x = sorted_data[idx]["days_since_100_cases"].values128    y = sorted_data[idx]["cumulative_deaths"].values129    tvec = np.arange(x.max() + n_days)130    d, i, r, s = ode_model[country](t=tvec, **fit_result[country].params)131    cumulative_prediction[country] = d132    y = sorted_data[idx]["deaths"].values133    daily_prediction[country] = np.diff(d)134    residual_std = np.std(y - daily_prediction[country][: len(y)])135    residuals_high[country] = daily_prediction[country] + residual_std136    residuals_low[country] = daily_prediction[country] - residual_std137138# Remember this is one big vector that contains all countries at all times.139# To do inference we need to construct a new vector with new times140# Create the time index141time_index = np.arange(0, n_days, 1)142time_index = np.repeat(time_index, n_countries)143144# Create the country index145country_index = np.arange(n_countries)146country_index = np.tile(country_index, n_days)147dummy_y = np.zeros(len(time_index))148149logger.info("Saving model")150151# Calculate dates (must be in python datetime to work with pydantic)152country_start = [country_first_dates[x] for x in countries[country_index].tolist()]153country_offset = [pd.DateOffset(x) for x in time_index]154dates = list(155    map(lambda x: (x[0] + x[1]).to_pydatetime(), zip(country_start, country_offset))156)157158# Create a big dataframe with all this info159predictions = pd.DataFrame(160    {161        "timestamp": dates,162        "country": countries[country_index],163        "deaths_prediction": [164            daily_prediction[c][t]165            for t, c in zip(time_index, countries[country_index].tolist())166        ],167        "cumulative_deaths_prediction": [168            cumulative_prediction[c][t]169            for t, c in zip(time_index, countries[country_index].tolist())170        ],171        "residuals_low": [172            residuals_low[c][t]173            for t, c in zip(time_index, countries[country_index].tolist())174        ],175        "residuals_high": [176            residuals_high[c][t]177            for t, c in zip(time_index, countries[country_index].tolist())178        ],179        "days_since_100_cases": time_index,180    },181    index=dates,182)183184# Merge in the ground truth185predictions = pd.merge(186    predictions.rename_axis("index").reset_index(),187    sorted_data[["country", "deaths", "cumulative_deaths"]]188    .rename_axis("index")189    .reset_index(),190    on=["index", "country"],191    how="outer",192).set_index("index")193194# Save to file195predictions.to_pickle("predictions.pkl")
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finder.py

Source:finder.py

1import csv2from collections import Counter34def get_mean(total_weight, total_entries):5    #Calculating Mean6    mean = total_weight / total_entries7    print(f"Mean(Average) is: {mean:2f}")89def get_median(total_entries, sorted_data):10    #Calculating Median11    if total_entries % 2 == 0:12        median1 = float(sorted_data[total_entries//2])13        median2 = float(sorted_data[total_entries//2 - 1])14        median = (median1 + median2) / 215    else:16        median = float(sorted_data[total_entries//2])17    print(f"Median is: {median:2f}")1819def get_mode(sorted_data):20    #Calculating Mode21    data = Counter(sorted_data)22    mode_data_for_range = {23                            "75-85": 0,24                            "85-95": 0,25                            "95-105": 0,26                            "105-115": 0,27                            "115-125": 0,28                            "125-135": 0,29                            "135-145": 0,30                            "145-155": 0,31                            "155-165": 0,32                            "165-175": 033                        }34    for weight, occurence in data.items():35        if 75 < weight < 85:36            mode_data_for_range["75-85"] += occurence37        elif 85 < weight < 95:38            mode_data_for_range["85-95"] += occurence39        elif 95 < weight < 105:40            mode_data_for_range["95-105"] += occurence41        elif 105 < weight < 115:42            mode_data_for_range["105-115"] += occurence43        elif 115 < weight < 125:44            mode_data_for_range["115-125"] += occurence45        elif 125 < weight < 135:46            mode_data_for_range["125-135"] += occurence47        elif 135 < weight < 145:48            mode_data_for_range["135-145"] += occurence49        elif 145 < weight < 155:50            mode_data_for_range["145-155"] += occurence51        elif 155 < weight < 165:52            mode_data_for_range["155-165"] += occurence53        elif 165 < weight < 175:54            mode_data_for_range["165-175"] += occurence55    mode_range, mode_occurence = 0, 056    for range, occurence in mode_data_for_range.items():57        if occurence > mode_occurence:58            mode_range, mode_occurence = [int(range.split("-")[0]), int(range.split("-")[1])], occurence59    mode = float((mode_range[0] + mode_range[1]) / 2)60    print(f"Mode is: {mode:2f}")6162with open('SOCR-HeightWeight.csv', newline='') as f:63    reader = csv.reader(f)64    file_data = list(reader)6566file_data.pop(0)6768total_weight = 069total_entries = len(file_data)70sorted_data = []7172for person_data in file_data:73    total_weight += float(person_data[2])74    sorted_data.append(float(person_data[2]))7576sorted_data.sort()7778get_mean(total_weight, total_entries)79get_median(total_entries, sorted_data)
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task1.py

Source:task1.py

1import numpy as np2import matplotlib.pyplot as plt3from matplotlib.ticker import AutoMinorLocator4from lab2.kernel_functions import box_kernel5def interquartile_range(down_quartile_val, up_quartile_val):6    return up_quartile_val - down_quartile_val7def down_quartile(sorted_data):8    l = len(sorted_data)9    down = sorted_data[int((2 + l) / 4)]10    up = sorted_data[np.math.ceil((2 + l) / 4)]11    return (down + up) / 212def up_quartile(sorted_data):13    l = len(sorted_data)14    down = sorted_data[int((2 + 3 * l) / 4)]15    up = sorted_data[np.math.ceil((2 + 3 * l) / 4)]16    return (down + up) / 217def silverman_bandwidth(data):18    sorted_data = sorted(data)19    return 0.9 * min(np.std(data), interquartile_range(down_quartile(sorted_data), up_quartile(sorted_data)) / 1.34) * np.math.pow(len(data), -0.2)20def general_naive_density_estimator(x, data, bandwidth, kernel_function):21    n = len(data)22    kernel_sum = 023    for i in range(n):24        kernel_sum += kernel_function((x - data[i]) / bandwidth)25    return 1 / (n * bandwidth) * kernel_sum26def task1(data):27    sorted_data = sorted(data)28    silverman_band = silverman_bandwidth(data)29    print(silverman_band)30    small_band = 0.131    large_band = 332    val = 0.33    ins = []34    silverman_outs = []35    small_outs = []36    large_outs = []37    for x in sorted_data:38        ins.append(x)39        silverman_outs.append(general_naive_density_estimator(x, data, silverman_band, box_kernel))40        small_outs.append(general_naive_density_estimator(x, data, small_band, box_kernel))41        large_outs.append(general_naive_density_estimator(x, data, large_band, box_kernel))42    plt.figure(2)43    ax = plt.axes()44    ax.yaxis.set_minor_locator(AutoMinorLocator(2))45    ax.xaxis.set_minor_locator(AutoMinorLocator(2))46    ax.spines['top'].set_visible(False)47    ax.spines['right'].set_visible(False)48    plt.plot(ins, small_outs)49    plt.plot(sorted_data, np.zeros_like(sorted_data) + val, 'x', color='orange')50    plt.xlabel('x')51    plt.ylabel('f(x)')52    plt.show()53    plt.figure(3)54    ax = plt.axes()55    ax.yaxis.set_minor_locator(AutoMinorLocator(2))56    ax.xaxis.set_minor_locator(AutoMinorLocator(2))57    ax.spines['top'].set_visible(False)58    ax.spines['right'].set_visible(False)59    plt.plot(ins, silverman_outs)60    plt.plot(sorted_data, np.zeros_like(sorted_data) + val, 'x', color='orange')61    plt.xlabel('x')62    plt.ylabel('f(x)')63    plt.show()64    plt.figure(4)65    ax = plt.axes()66    ax.yaxis.set_minor_locator(AutoMinorLocator(2))67    ax.xaxis.set_minor_locator(AutoMinorLocator(2))68    ax.spines['top'].set_visible(False)69    ax.spines['right'].set_visible(False)70    plt.plot(ins, large_outs)71    plt.plot(sorted_data, np.zeros_like(sorted_data) + val, 'x', color='orange')72    plt.xlabel('x')73    plt.ylabel('f(x)')...

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