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How to use reports_folder method in Selene

Best Python code snippet using selene_python

acv_xml_parser.py

Source:acv_xml_parser.py

1import xml.etree.ElementTree as ET2import csv3import os4reports_folder = "/path/to/reports/"5csv_fields = ["package_name", "instruction_coverage_percent", "method_coverage_percent", "class_coverage_percent", "total_instr", "total_method", "total_class"]6csv_rows = []7coverage_dict = {8    "covered" : 0,9    "missed" : 0,10    "covered_total" : 0,11    "missed_total" : 0,12}13def increment_cov_dict(cov_dict):14    cov_dict["covered_total"] += cov_dict["covered"]15    cov_dict["missed_total"] += cov_dict["missed"]16    cov_dict["covered"] = 017    cov_dict["missed"] = 018def get_coverage(package_name, dir_name):19    instr = coverage_dict.copy()20    method = coverage_dict.copy()21    tree = ET.parse(f"{reports_folder}{dir_name}/{package_name}")22    root = tree.getroot()23    class_missed = 024    class_miss = 025    class_total = 026    for package in root.findall("package"):27        for cl4ss in package.findall("class"):28            class_total += 129            for counter in cl4ss.findall("counter"):30                if counter.get("type") == "INSTRUCTION":31                    instr["covered"] += int(counter.get("covered"))32                    instr["missed"] += int(counter.get("missed"))33                if counter.get("type") == "METHOD":34                    method["covered"] += int(counter.get("covered"))35                    method["missed"] += int(counter.get("missed"))36                    class_miss += int(counter.get("covered"))37            if class_miss == 0:38                class_missed += 139            class_miss = 040        increment_cov_dict(instr)41        increment_cov_dict(method)42    total_instr = instr["covered_total"] + instr["missed_total"]43    total_method = method["covered_total"] + method["missed_total"]44    csv_rows.append([package_name,45                     round((instr["covered_total"] / total_instr) * 100, 3),46                     round((method["covered_total"] / total_method) * 100, 3),47                     round(((class_total - class_missed) / class_total) * 100, 3),48                     total_instr,49                     total_method,50                     class_total])51if __name__ == "__main__":52    for dirname in os.listdir(reports_folder):53        if os.path.isdir(reports_folder + dirname):54            for filename in os.listdir(reports_folder + dirname):55                get_coverage(filename, dirname)56            with open(dirname, 'w') as f:57                write = csv.writer(f)58                write.writerow(csv_fields)59                write.writerows(csv_rows)...

load_analyse_data_module.py

Source:load_analyse_data_module.py

1"""2------------------------------------------------------------------------3This module is responsible for loading, analysing and splitting the data4------------------------------------------------------------------------5"""67import os8import matplotlib.pyplot as plt9from utils_classes import FoldersUtils, DataUtils, TimeSeriesPlots10from reports_class import StatsReports11import config12import warnings13warnings.filterwarnings("ignore")1415# Extract the generated paths by the create_dirs_module.py16sub_dirs = FoldersUtils.unpickle_file('sub_dirs_list')17data_folder = sub_dirs.get('Data')18models_folder = sub_dirs.get('Models')19graphics_folder = sub_dirs.get('Graphics')20reports_folder = sub_dirs.get('Reports')2122def main():23    """24    Functionalities to be executed by the module.25    """26    # Loads dataset inside the "Data" folder27    DATASET = DataUtils.get_data_file(folder = data_folder)2829    # Checks any missing dates or values and if finds any, fills30    # the dates and then the missing values through linear interpolation31    print("\n> Checking any missing dates or values...")32    DATASET = DataUtils.check_missing_dates_and_values(DATASET)3334    print(35        f'\n> Generating a report with descriptive statistics of the time series in {reports_folder}')36    StatsReports.general_stats(DATASET, report_name='0. TS descriptive stats', out_folder=reports_folder)3738    print(f'\n> Saving the time plot to {graphics_folder}')39    TimeSeriesPlots.time_plot(DATASET, out_folder=graphics_folder)4041    print(f'> Saving the ACF and PACF plots to {graphics_folder}')42    TimeSeriesPlots.acf_plot(DATASET, 35, out_folder=graphics_folder)43    TimeSeriesPlots.pacf_plot(DATASET, 35, out_folder=graphics_folder)4445    print(f'\n> Creating a KPSS test report in {reports_folder}')46    StatsReports.kpss_(DATASET, significance=0.05, report_name='1. KPSS report', out_folder=reports_folder)4748    print('\n> Spliting the time series dataset in a training and a test set based on the split point provided in the config.py file')49    train, test = DataUtils.train_test_split(DATASET, split_point=config.SPLIT_POINT)5051    DataUtils.train_test_to_csv(train, test, out_folder=data_folder) 52    print(f'> Train and test sets saved to {data_folder}')535455if __name__ == '__main__':5657    main()5859
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biomodel_reports.py

Source:biomodel_reports.py

1"""2Creates SBML reports with sbmlutils for all curated3models in the latest biomodel release.4Models are 31th Biomodels Release5https://www.ebi.ac.uk/biomodels/content/news/biomodels-release-26th-june-20176"""7import os8from pprint import pprint9from sbmlutils.report import sbmlreport10def model_reports(biomodels_folder, reports_folder):11    """ Create sbmlreports for all biomodels.12    :return:13    """14    #if not os.path.exists(reports_folder):15    #    os.mkdir(reports_folder)16    # get all SBML files17    sbml_paths = []18    for f in os.listdir(biomodels_folder):19        if f.endswith('.xml'):20            f_path = os.path.join(biomodels_folder, f)21            if os.path.isfile(f_path):22                sbml_paths.append(f_path)23    pprint(sbml_paths)24    sbmlreport.create_reports(sorted(sbml_paths)[:10], output_dir=reports_folder,25                              validate=False)26if __name__ == "__main__":27    biomodels_folder = "/home/mkoenig/biomodels/releases/R31_2017-06-26/curated"28    reports_folder = "/home/mkoenig/biomodels/reports"29    model_reports(biomodels_folder=biomodels_folder,...

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