String with the list of files and prefixes needed to execute ABINIT.
763273
def filesfile_string(self):
        """"""
        lines = []
        app = lines.append

        app(self.input_file.path)          # 1) Path of the input file
        app(self.output_file.path)         # 2) Path of the output file
        app(self.ddb_filepath)             # 3) Input derivative database e.g. t13.ddb.in
        app(self.md_filepath)              # 4) Output molecular dynamics e.g. t13.md
        app(self.gkk_filepath)             # 5) Input elphon matrix elements  (GKK file)
        app(self.outdir.path_join("out"))  # 6) Base name for elphon output files e.g. t13
        app(self.ddk_filepath)             # 7) File containing ddk filenames for elphon/transport.

        return "\n".join(lines)
1062124
def _assembled_out_file_name(self):
        """"""
        if self.Parameters['-s'].isOn():
            assembled_reads = self._absolute(str(self.Parameters['-s'].Value))
        else:
            raise ValueError(
                "No assembled-reads (flag -s) output path specified")
        return assembled_reads
60302
def _mkstemp_inner(dir, pre, suf, flags):
    """"""

    names = _get_candidate_names()

    for seq in range(TMP_MAX):
        name = next(names)
        file = _os.path.join(dir, pre + name + suf)
        try:
            fd = _os.open(file, flags, 0o600)
            return (fd, _os.path.abspath(file))
        except FileExistsError:
            continue    # try again
        except PermissionError:
            # This exception is thrown when a directory with the chosen name
            # already exists on windows.
            if _os.name == 'nt':
                continue
            else:
                raise

    raise FileExistsError(_errno.EEXIST,
                          "No usable temporary file name found")
492554
def list_blobs(self, prefix=''):
    """"""
    return [b.name for b in self.bucket.list_blobs(prefix=prefix)]
118885
def listing(self):
        ""
        return ['.'.join([f,ext]) if ext else f for (f,ext) in self._files.keys()]
334068
def get_filesystem(filename):
    """"""
    filename = compat.as_str_any(filename)
    prefix = ""
    index = filename.find("://")
    if index >= 0:
        prefix = filename[:index]
    fs = _REGISTERED_FILESYSTEMS.get(prefix, None)
    if fs is None:
        raise ValueError("No recognized filesystem for prefix %s" % prefix)
    return fs
148166
public static List<String> listByPrefix(String directory, String prefix, String suffix) {
		List<String> ret = new ArrayList<>();

		File d = new File(directory);

		if( !d.isDirectory() ) {
			try {
				URL url = new URL(directory);
				if( url.getProtocol().equals("file")) {
					d = new File(url.getFile());
				} else if( url.getProtocol().equals("jar")){
					return listJarPrefix(url,prefix,suffix);
				}
			} catch( MalformedURLException ignore){}
		}
		if( !d.isDirectory() )
			throw new IllegalArgumentException("Must specify an directory. "+directory);

		File files[] = d.listFiles();

		for( File f : files ) {
			if( f.isDirectory() || f.isHidden() )
				continue;

			if( prefix == null || f.getName().startsWith(prefix )) {
				if( suffix ==null || f.getName().endsWith(suffix)) {
					ret.add(f.getAbsolutePath());
				}
			}
		}

		return ret;
	}
930486
def filename(self, prefix='', suffix='', extension='.py'):
        """"""
        return BASE_NAME.format(prefix, self.num, suffix, extension)
624551
def _all_files_matching_ext(start, ext):
    """"""
    md_files = []
    for root, _, files in os.walk(start):
        md_files += fnfilter([os.path.join(root, f) for f in files],
                             "*." + ext)

    return md_files
186088
def files_with_exts(root='.', suffix=''):
    
    return (os.path.join(rootdir, filename)
            for rootdir, dirnames, filenames in os.walk(root)
            for filename in filenames
            if filename.endswith(suffix))
737043
def _list_files(self, args):
        '''
        
        '''
        if len(args) < 2:
            raise SPMInvocationError('A package name must be specified')

        package = args[-1]

        files = self._pkgdb_fun('list_files', package, self.db_conn)
        if files is None:
            raise SPMPackageError('package {0} not installed'.format(package))
        else:
            for file_ in files:
                if self.opts['verbose']:
                    status_msg = ','.join(file_)
                else:
                    status_msg = file_[0]
                self.ui.status(status_msg)
1280924
def list_files(path, extension=".cpp", exclude="S.cpp"):
    """"""
    return ["%s/%s" % (path, f) for f in listdir(path) if f.endswith(extension) and (not f.endswith(exclude))]
901787
def _add_path_traversal_strings(self, lib):
        '''
        
        '''
        entries = [
            (('/etc/passwd', 'absolute - /etc/passwd')),
            (('./../../../../../../../../../../../../../../etc/passwd', 'relative - /etc/passwd')),
            (('../../../../../../../../../../../../../../etc/passwd', 'relative - /etc/passwd')),
            (('/proc/cpuinfo', 'absolute path - /proc/cpuinfo')),
            (('./../../../../../../../../../../../../../../proc/cpuinfo', 'relative - /proc/cpuinfo')),
            (('../../../../../../../../../../../../../../proc/cpuinfo', 'relative - /proc/cpuinfo')),
            (('~/.profile', 'absolute - home')),
            (('$HOME/.profile', 'environment - home')),
            (('/../../../../../../../../../../../../boot.ini', 'relative - boot.ini')),
        ]
        for (s, desc) in entries:
            lib.append((s, 'path traversal - %s' % desc))
1151343
def create_prefix_dir(self, path, fmt):
        """"""
        create_prefix_dir(self._get_os_path(path.strip('/')), fmt)
239774
def listCLIExecutables(baseDir):
    """"""
    return [path for path in glob.glob(os.path.join(os.path.normpath(baseDir), '*'))
            if isCLIExecutable(path)]
1012938
def symlink_list(self, load):
        '''
        
        '''
        if 'env' in load:
            # "env" is not supported; Use "saltenv".
            load.pop('env')

        ret = {}
        if 'saltenv' not in load:
            return {}
        if not isinstance(load['saltenv'], six.string_types):
            load['saltenv'] = six.text_type(load['saltenv'])

        for fsb in self.backends(load.pop('fsbackend', None)):
            symlstr = '{0}.symlink_list'.format(fsb)
            if symlstr in self.servers:
                ret = self.servers[symlstr](load)
        # some *fs do not handle prefix. Ensure it is filtered
        prefix = load.get('prefix', '').strip('/')
        if prefix != '':
            ret = dict([
                (x, y) for x, y in six.iteritems(ret) if x.startswith(prefix)
            ])
        return ret
357717
public static File [] getFilesWithPrefix(File dir, final String prefix) {
        FileFilter prefixFilter = new FileFilter() {
                public boolean accept(File pathname)
                {
                    return pathname.getName().toLowerCase().
                        startsWith(prefix.toLowerCase());
                }
            };
        return dir.listFiles(prefixFilter);
    }