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How to use is_not_inf method in assertpy

Best Python code snippet using assertpy_python

deciles_charts.py

Source:deciles_charts.py

1import argparse2import glob3import json4import logging5import pathlib6import re7import jsonschema8import numpy9import pandas10from ebmdatalab import charts11# replicate cohort-extractor's logging12logger = logging.getLogger(__name__)13logger.setLevel(logging.INFO)14handler = logging.StreamHandler()15handler.setFormatter(16    logging.Formatter(17        fmt="%(asctime)s [%(levelname)-9s] %(message)s [%(module)s]",18        datefmt="%Y-%m-%d %H:%M:%S",19    )20)21logger.addHandler(handler)22DEFAULT_CONFIG = {23    "show_outer_percentiles": False,24    "tables": {25        "output": True,26    },27    "charts": {28        "output": True,29    },30}31CONFIG_SCHEMA = {32    "type": "object",33    "additionalProperties": False,34    "properties": {35        "show_outer_percentiles": {"type": "boolean"},36        "tables": {37            "type": "object",38            "additionalProperties": False,39            "properties": {40                "output": {"type": "boolean"},41            },42        },43        "charts": {44            "type": "object",45            "additionalProperties": False,46            "properties": {47                "output": {"type": "boolean"},48            },49        },50    },51}52MEASURE_FNAME_REGEX = re.compile(r"measure_(?P<id>\w+)\.csv")53def get_measure_tables(input_files):54    for input_file in input_files:55        measure_fname_match = re.match(MEASURE_FNAME_REGEX, input_file.name)56        if measure_fname_match is not None:57            measure_table = pandas.read_csv(input_file, parse_dates=["date"])58            measure_table.attrs["id"] = measure_fname_match.group("id")59            yield measure_table60def drop_zero_denominator_rows(measure_table):61    """62    Zero-denominator rows could cause the deciles to be computed incorrectly, so should63    be dropped beforehand. For example, a practice can have zero registered patients. If64    the measure is computed from the number of registered patients by practice, then65    this practice will have a denominator of zero and, consequently, a value of inf.66    Depending on the implementation, this practice's value may be sorted as greater than67    other practices' values, which may increase the deciles.68    """69    # It's non-trivial to identify the denominator column without the associated Measure70    # instance. It's much easier to test the value column for inf, which is returned by71    # Pandas when the second argument of a division operation is zero.72    is_not_inf = measure_table["value"] != numpy.inf73    num_is_inf = len(is_not_inf) - is_not_inf.sum()74    logger.info(f"Dropping {num_is_inf} zero-denominator rows")75    return measure_table[is_not_inf].reset_index(drop=True)76def get_deciles_table(measure_table, config):77    return charts.add_percentiles(78        measure_table,79        period_column="date",80        column="value",81        show_outer_percentiles=config["show_outer_percentiles"],82    )83def write_deciles_table(deciles_table, path, filename):84    create_dir(path)85    deciles_table.to_csv(path / filename, index=False)86def get_deciles_chart(measure_table, config):87    return charts.deciles_chart(88        measure_table,89        period_column="date",90        column="value",91        show_outer_percentiles=config["show_outer_percentiles"],92    )93def write_deciles_chart(deciles_chart, path, filename):94    create_dir(path)95    deciles_chart.savefig(path / filename, bbox_inches="tight")96def create_dir(path):97    pathlib.Path(path).mkdir(parents=True, exist_ok=True)98def get_path(*args):99    return pathlib.Path(*args).resolve()100def match_paths(pattern):101    return [get_path(x) for x in glob.glob(pattern)]102def parse_config(config_json):103    user_config = json.loads(config_json)104    config = DEFAULT_CONFIG.copy()105    config.update(user_config)106    try:107        jsonschema.validate(config, CONFIG_SCHEMA)108    except jsonschema.ValidationError as e:109        raise argparse.ArgumentTypeError(e.message) from e110    return config111def parse_args():112    parser = argparse.ArgumentParser()113    parser.add_argument(114        "--input-files",115        required=True,116        type=match_paths,117        help="Glob pattern for matching one or more input files",118    )119    parser.add_argument(120        "--output-dir",121        required=True,122        type=get_path,123        help="Path to the output directory",124    )125    parser.add_argument(126        "--config",127        default=DEFAULT_CONFIG.copy(),128        type=parse_config,129        help="JSON-encoded configuration",130    )131    return parser.parse_args()132def main():133    args = parse_args()134    input_files = args.input_files135    output_dir = args.output_dir136    config = args.config137    for measure_table in get_measure_tables(input_files):138        measure_table = drop_zero_denominator_rows(measure_table)139        id_ = measure_table.attrs["id"]140        if config["tables"]["output"]:141            deciles_table = get_deciles_table(measure_table, config)142            fname = f"deciles_table_{id_}.csv"143            write_deciles_table(deciles_table, output_dir, fname)144        if config["charts"]["output"]:145            chart = get_deciles_chart(measure_table, config)146            fname = f"deciles_chart_{id_}.png"147            write_deciles_chart(chart, output_dir, fname)148if __name__ == "__main__":...

numeric.pyi

Source:numeric.pyi

...5    def is_not_zero(self) -> AssertionBuilder: ...6    def is_nan(self) -> AssertionBuilder: ...7    def is_not_nan(self) -> AssertionBuilder: ...8    def is_inf(self) -> AssertionBuilder: ...9    def is_not_inf(self) -> AssertionBuilder: ...10    def is_greater_than(self, other: Any) -> AssertionBuilder: ...11    def is_greater_than_or_equal_to(self, other: Any) -> AssertionBuilder: ...12    def is_less_than(self, other: Any) -> AssertionBuilder: ...13    def is_less_than_or_equal_to(self, other: Any) -> AssertionBuilder: ...14    def is_positive(self) -> AssertionBuilder: ...15    def is_negative(self) -> AssertionBuilder: ...16    def is_between(self, low: Any, high: Any) -> AssertionBuilder: ...17    def is_not_between(self, low: Any, high: Any) -> AssertionBuilder: ...18    def is_close_to(self, other: Any, tolerance: Any) -> AssertionBuilder: ......

assertpy_floats.py

Source:assertpy_floats.py

...13assert_that(123.4).is_close_to(123, 0.5)14assert_that(float('NaN')).is_nan()15assert_that(123.4).is_not_nan()16assert_that(float('Inf')).is_inf()...

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