How to use reports_folder method in Selene

Best Python code snippet using selene_python

acv_xml_parser.py

Source: acv_xml_parser.py Github

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1import xml.etree.ElementTree as ET2import csv3import os4reports_folder = "/โ€‹path/โ€‹to/โ€‹reports/โ€‹"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}/โ€‹{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"] /โ€‹ total_instr) * 100, 3),46 round((method["covered_total"] /โ€‹ total_method) * 100, 3),47 round(((class_total - class_missed) /โ€‹ 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)...

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load_analyse_data_module.py

Source: load_analyse_data_module.py Github

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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 Github

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1"""2Creates SBML reports with sbmlutils for all curated3models in the latest biomodel release.4Models are 31th Biomodels Release5https:/โ€‹/โ€‹www.ebi.ac.uk/โ€‹biomodels/โ€‹content/โ€‹news/โ€‹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 = "/โ€‹home/โ€‹mkoenig/โ€‹biomodels/โ€‹releases/โ€‹R31_2017-06-26/โ€‹curated"28 reports_folder = "/โ€‹home/โ€‹mkoenig/โ€‹biomodels/โ€‹reports"29 model_reports(biomodels_folder=biomodels_folder,...

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