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How to use make_listfile method in stestr

Best Python code snippet using stestr_python

test_processor.py

Source:test_processor.py

...137                self.test_ids, exclude_list=self.exclude_list,138                include_list=self.include_list,139                regexes=self.test_filters,140                exclude_regex=self.exclude_regex)141            name = self.make_listfile()142            variables['IDFILE'] = name143            idlist = ' '.join(self.test_ids)144        variables['IDLIST'] = idlist145        def subst(match):146            return variables.get(match.groups(1)[0], '')147        if self.test_ids is None:148            # No test ids, no id option.149            idoption = ''150        else:151            idoption = re.sub(variable_regex, subst, self.idoption)152            variables['IDOPTION'] = idoption153        self.cmd = re.sub(variable_regex, subst, cmd)154    def make_listfile(self):155        name = None156        try:157            if self._listpath:158                name = self._listpath159                stream = open(name, 'wb')160            else:161                fd, name = tempfile.mkstemp()162                stream = os.fdopen(fd, 'wb')163            with stream:164                self.list_file_name = name165                testlist.write_list(stream, self.test_ids)166        except Exception:167            if name:168                os.unlink(name)...

zrank.py

Source:zrank.py

...13    LOCAL = ["zrank"]14    def rank(self, complex_path, refinement=False, retry_with_protonatation=True):15        if not isinstance(complex_path, (list, tuple)):16            complex_path = [complex_path]17        listfile = self.make_listfile(complex_path)18        try:19            self(list_file=list_file, refinement=refinement)20        except (SystemExit, KeyboardInterrupt):21            raise22        except Exception as e:23            pdb2pqr = Pdb2pqr(work_dir=self.work_dir, job=self.job)24            if retry_with_protonatation:25                protonated_complex_file = pdb2pqr.debump_add_h(complex_path)26                listfile = self.make_listfile(protonated_complex_file)27                self(list_file=list_file, refinement=refinement)28        assert os.path.isfile(listfile+".zr.out"), "No output for zrank"29        with open(listfile+".zr.out") as f:30            scores = dict(line.rstrip().split() for line in f)31        if len(complex_path) == 1:32            scores = list(scores.values())[0]33        safe_remove((listfile, listfile.name+".zr.out"))34        return scores35    def make_listfile(self, complex_path):36        listfile = tempfile.NamedTemporaryFile(dir=work_dir, prefix="listfile", suffix=".txt", delete=False)37        for pdb in complex_path:38            print(os.path.basename(pdb), file=listfile)39        listfile.close()40        return listfile.name41# def run_zrank(complex_path, refinement=False, retry_with_protonatation=True,42#   work_dir=None, docker=True, job=None):43#     if work_dir is None:44#         work_dir = os.getcwd()45#46#     _parameters = ["-R"] if refinement else []47#48#     if not isinstance(complex_path, (list, tuple)):49#         complex_path = [complex_path]...

makelist.py

Source:makelist.py

...13import datetime14import numpy as np15import logging16logger = logging.getLogger(__name__)17def make_listfile(appdir, outname, outthread):18    outf = open(outname,'w')19    namepat = '([^_]*)_.*_(\d+)x(\d+)_.*'20    for dirpath, dnames, fnames in os.walk(appdir):21        for f in fnames:22            if f.endswith('.likelihood'):23                basename = f[:f.rfind('.')]24                #extract the <trainer, node, thread> from f25                m = re.search(namepat, f)26                if m:27                    trainer = m.group(1)28                    node = m.group(2)29                    thread = m.group(3)30                    if outthread:31                        outf.write('%s %s %s\n'%(basename, trainer, thread)) 32                    else:33                        outf.write('%s %s %s\n'%(basename, trainer, node)) 34if __name__ == "__main__":35    program = os.path.basename(sys.argv[0])36    logger = logging.getLogger(program)37    # logging configure38    import logging.config39    logging.basicConfig(format='%(asctime)s : %(levelname)s : %(message)s')40    logging.root.setLevel(level=logging.DEBUG)41    logger.info("running %s" % ' '.join(sys.argv))42    # check and process input arguments43    if len(sys.argv) < 3:44        logger.error(globals()['__doc__'] % locals())45        sys.exit(1)46    # check the path47    logdir = sys.argv[1]48    outname = sys.argv[2]49    outthread = True if sys.argv[3]=='thread' else False...

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