comparison package_output.py @ 19:cefa7625d6cb draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 2840545abeeca2dc0a6e6df138633e561d379e52

18:a5769923297c

import argparse
import configparser
import json
import os
import sys
import tarfile
import typing

import bashlex


class PackageFile:
    def __init__(
        self,

def main() -> None:
    parser = argparse.ArgumentParser()
    parser.add_argument("--tool_directory", type=str, required=True, help="tool directory")
    parser.add_argument("--format_selector", type=str, required=True, help="format selector")
    args = parser.parse_args()

    lastz_command_config_file: str = os.path.join(args.tool_directory, "lastz-cmd.ini")

    config: configparser.ConfigParser = configparser.ConfigParser()
    config.read(lastz_command_config_file)

    package_file = PackageFile()
    lastz_command_file = "lastz-commands.txt"
    bashCommandLineFile(lastz_command_file, config, args, package_file)
    package_file.close()


if __name__ == "__main__":
    main()

19:cefa7625d6cb

import argparse
import configparser
import json
import os
import resource
import sys
import tarfile
import time
import typing

import bashlex

RUSAGE_ATTRS: typing.Final = ["ru_utime", "ru_stime", "ru_maxrss", "ru_minflt", "ru_majflt", "ru_inblock", "ru_oublock", "ru_nvcsw", "ru_nivcsw"]


class PackageFile:
    def __init__(
        self,

def main() -> None:
    parser = argparse.ArgumentParser()
    parser.add_argument("--tool_directory", type=str, required=True, help="tool directory")
    parser.add_argument("--format_selector", type=str, required=True, help="format selector")
    parser.add_argument("--debug", action="store_true", help="enable debug messages")
    args = parser.parse_args()

    if args.debug:
        r_beg = resource.getrusage(resource.RUSAGE_SELF)
        beg: int = time.monotonic_ns()

    lastz_command_config_file: str = os.path.join(args.tool_directory, "lastz-cmd.ini")

    config: configparser.ConfigParser = configparser.ConfigParser()
    config.read(lastz_command_config_file)

    package_file = PackageFile()
    lastz_command_file = "lastz-commands.txt"
    bashCommandLineFile(lastz_command_file, config, args, package_file)
    package_file.close()

    if args.debug:
        ns: int = time.monotonic_ns() - beg
        r_end = resource.getrusage(resource.RUSAGE_SELF)
        print(f"package output clock time: {ns} ns", file=sys.stderr, flush=True)
        for rusage_attr in RUSAGE_ATTRS:
            value = getattr(r_end, rusage_attr) - getattr(r_beg, rusage_attr)
            print(f"  package output {rusage_attr}: {value}", file=sys.stderr, flush=True)


if __name__ == "__main__":
    main()