Python tempfile.mktemp方法代码示例

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def pooled_gold_standard_by_dir(self, list_of_directory_bam, dict_id_to_file_path_fasta, file_path_output=None):
        """
            Make a gold standard assembly merging bam files of several samples

            @attention: bam files must have same name to be merged

            @param list_of_directory_bam: list of directories containing bam files
            @type list_of_directory_bam: list[str|unicode]
            @param dict_id_to_file_path_fasta: path to reference files by key
            @type dict_id_to_file_path_fasta: dict[str|unicode, str|unicode]

            @return: output file path
            @rtype: str | unicode
        """
        if file_path_output is None:
            file_path_output = tempfile.mktemp(dir=self._tmp_dir)
        self._logger.info("Creating pooled gold standard")
        self.merge_bam_files_by_list_of_dir(list_of_directory_bam, output_dir=self._temp_merges_bam_directory)
        dict_id_to_file_path_bam = self.get_dict_id_to_file_path_bam_from_dir(self._temp_merges_bam_directory)
        return self.gold_standard_assembly(dict_id_to_file_path_bam, dict_id_to_file_path_fasta, file_path_output) 

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def test_recordio():
    frec = tempfile.mktemp()
    N = 255

    writer = mx.recordio.MXRecordIO(frec, 'w')
    for i in range(N):
        if sys.version_info[0] < 3:
            writer.write(str(chr(i)))
        else:
            writer.write(bytes(str(chr(i)), 'utf-8'))
    del writer

    reader = mx.recordio.MXRecordIO(frec, 'r')
    for i in range(N):
        res = reader.read()
        if sys.version_info[0] < 3:
            assert res == str(chr(i))
        else:
            assert res == bytes(str(chr(i)), 'utf-8') 

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def test_indexed_recordio():
    fidx = tempfile.mktemp()
    frec = tempfile.mktemp()
    N = 255

    writer = mx.recordio.MXIndexedRecordIO(fidx, frec, 'w')
    for i in range(N):
        if sys.version_info[0] < 3:
            writer.write_idx(i, str(chr(i)))
        else:
            writer.write_idx(i, bytes(str(chr(i)), 'utf-8'))
    del writer

    reader = mx.recordio.MXIndexedRecordIO(fidx, frec, 'r')
    keys = reader.keys
    assert sorted(keys) == [i for i in range(N)]
    random.shuffle(keys)
    for i in keys:
        res = reader.read_idx(i)
        if sys.version_info[0] < 3:
            assert res == str(chr(i))
        else:
            assert res == bytes(str(chr(i)), 'utf-8') 

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def SHCISCF(mf, norb, nelec, maxM=1000, tol=1.0e-8, *args, **kwargs):
    """Shortcut function to setup CASSCF using the SHCI solver.  The SHCI
    solver is properly initialized in this function so that the 1-step
    algorithm can applied with SHCI-CASSCF.

    Examples:

    >>> mol = gto.M(atom='C 0 0 0; C 0 0 1')
    >>> mf = scf.RHF(mol).run()
    >>> mc = SHCISCF(mf, 4, 4)
    >>> mc.kernel()
    -74.414908818611522
    """

    mc = mcscf.CASSCF(mf, norb, nelec, *args, **kwargs)
    mc.fcisolver = SHCI(mf.mol, maxM, tol=tol)
    # mc.callback = mc.fcisolver.restart_scheduler_() #TODO
    if mc.chkfile == mc._scf._chkfile.name:
        # Do not delete chkfile after mcscf
        mc.chkfile = tempfile.mktemp(dir=settings.SHCISCRATCHDIR)
        if not os.path.exists(settings.SHCISCRATCHDIR):
            os.makedirs(settings.SHCISCRATCHDIR)
    return mc 

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def DMRGSCF(mf, norb, nelec, maxM=1000, tol=1.e-8, *args, **kwargs):
    '''Shortcut function to setup CASSCF using the DMRG solver.  The DMRG
    solver is properly initialized in this function so that the 1-step
    algorithm can be applied with DMRG-CASSCF.

    Examples:

    >>> mol = gto.M(atom='C 0 0 0; C 0 0 1')
    >>> mf = scf.RHF(mol).run()
    >>> mc = DMRGSCF(mf, 4, 4)
    >>> mc.kernel()
    -74.414908818611522
    '''
    if getattr(mf, 'with_df', None):
        mc = mcscf.DFCASSCF(mf, norb, nelec, *args, **kwargs)
    else:
        mc = mcscf.CASSCF(mf, norb, nelec, *args, **kwargs)
    mc.fcisolver = DMRGCI(mf.mol, maxM, tol=tol)
    mc.callback = mc.fcisolver.restart_scheduler_()
    if mc.chkfile == mc._scf._chkfile.name:
        # Do not delete chkfile after mcscf
        mc.chkfile = tempfile.mktemp(dir=settings.BLOCKSCRATCHDIR)
        if not os.path.exists(settings.BLOCKSCRATCHDIR):
            os.makedirs(settings.BLOCKSCRATCHDIR)
    return mc 

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def test_Node_save():
    test_list = [1,2,3]
    generic_node = mdp.Node()
    generic_node.dummy_attr = test_list
    # test string save
    copy_node_pic = generic_node.save(None)
    copy_node = cPickle.loads(copy_node_pic)
    assert generic_node.dummy_attr == copy_node.dummy_attr,\
           'Node save (string) method did not work'
    copy_node.dummy_attr[0] = 10
    assert generic_node.dummy_attr != copy_node.dummy_attr,\
           'Node save (string) method did not work'
    # test file save
    dummy_file = tempfile.mktemp(prefix='MDP_', suffix=".pic",
                                 dir=py.test.mdp_tempdirname)
    generic_node.save(dummy_file, protocol=1)
    dummy_file = open(dummy_file, 'rb')
    copy_node = cPickle.load(dummy_file)
    assert generic_node.dummy_attr == copy_node.dummy_attr,\
           'Node save (file) method did not work'
    copy_node.dummy_attr[0] = 10
    assert generic_node.dummy_attr != copy_node.dummy_attr,\
           'Node save (file) method did not work' 

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def testFlow_save():
    dummy_list = [1,2,3]
    flow = _get_default_flow()
    flow[0].dummy_attr = dummy_list
    # test string save
    copy_flow_pic = flow.save(None)
    copy_flow = cPickle.loads(copy_flow_pic)
    assert flow[0].dummy_attr == copy_flow[0].dummy_attr, \
           'Flow save (string) method did not work'
    copy_flow[0].dummy_attr[0] = 10
    assert flow[0].dummy_attr != copy_flow[0].dummy_attr, \
           'Flow save (string) method did not work'
    # test file save
    dummy_file = tempfile.mktemp(prefix='MDP_', suffix=".pic",
                                 dir=py.test.mdp_tempdirname)
    flow.save(dummy_file, protocol=1)
    dummy_file = open(dummy_file, 'rb')
    copy_flow = cPickle.load(dummy_file)
    assert flow[0].dummy_attr == copy_flow[0].dummy_attr, \
           'Flow save (file) method did not work'
    copy_flow[0].dummy_attr[0] = 10
    assert flow[0].dummy_attr != copy_flow[0].dummy_attr, \
           'Flow save (file) method did not work' 

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def test_setmtime(self):
        import tempfile
        import time
        try:
            fd, name = tempfile.mkstemp()
            os.close(fd)
        except AttributeError:
            name = tempfile.mktemp()
            open(name, 'w').close()
        try:
            mtime = int(time.time())-100
            path = local(name)
            assert path.mtime() != mtime
            path.setmtime(mtime)
            assert path.mtime() == mtime
            path.setmtime()
            assert path.mtime() != mtime
        finally:
            os.remove(name) 

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def test_binary(self, enable_randomness=True, times=1, timeout=15):
        """
        Test the binary generated
        """

        # dump the binary code
        pov_binary_filename = tempfile.mktemp(dir='/tmp', prefix='rex-pov-')
        self.dump_binary(filename=pov_binary_filename)
        os.chmod(pov_binary_filename, 0o755)

        pov_tester = CGCPovSimulator()
        result = pov_tester.test_binary_pov(
                pov_binary_filename,
                self.crash.binary,
                enable_randomness=enable_randomness,
                timeout=timeout,
                times=times)

        # remove the generated pov
        os.remove(pov_binary_filename)

        return result 

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def generate_report(self, register_setters, leakers):

        stat_name = tempfile.mktemp(dir=".", prefix='rex-results-')

        l.info("exploitation report being written to '%s'", stat_name)

        f = open(stat_name, 'w')
        f.write("Binary %s:\n" % os.path.basename(self.crash.project.filename))
        f.write("Register setting exploits:\n")
        for register_setter in register_setters:
            f.write("\t%s\n" % str(register_setter))
        f.write("\n")
        f.write("Leaker exploits:\n")
        for leaker in leakers:
            f.write("\t%s\n" % str(leaker))

        f.close() 

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def prepare_run(self, *args, **kwargs):
        self._args = args
        self._kwargs = kwargs

        try:
            # tempfile.mktemp is deprecated and discouraged, but we use it here
            # to create a FIFO since the only other alternative would be to
            # create a directory and place the FIFO there, which sucks. Since
            # os.mkfifo will raise an exception anyways when the path doesn't
            # exist, it shouldn't be a big issue.
            self._filepath = tempfile.mktemp(prefix='qutebrowser-userscript-',
                                             dir=standarddir.runtime())
            # pylint: disable=no-member,useless-suppression
            os.mkfifo(self._filepath, mode=0o600)
            # pylint: enable=no-member,useless-suppression
        except OSError as e:
            self._filepath = None  # Make sure it's not used
            message.error("Error while creating FIFO: {}".format(e))
            return

        self._reader = _QtFIFOReader(self._filepath)
        self._reader.got_line.connect(self.got_cmd)  # type: ignore[arg-type] 

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def test_custom_build(clean_dir):
    """Test building with specific parameters."""
    dunst_temp_path = shared.rel_to_cwd('templates', 'dunst')
    base_output_dir = tempfile.mktemp()
    builder.build(templates=[dunst_temp_path], schemes=['atelier-heath-light'],
                  base_output_dir=base_output_dir)

    dunst_temps = builder.TemplateGroup(dunst_temp_path).get_templates()
    # out_dirs = [dunst_temps[temp]['output'] for temp in dunst_temps.keys()]
    for temp, sub in dunst_temps.items():
        out_path = os.path.join(base_output_dir, 'dunst',
                                sub['output'])
        theme_file = 'base16-atelier-heath-light{}'.format(sub['extension'])
        out_file = os.path.join(out_path, theme_file)

        assert os.path.exists(out_file)
        assert len(os.listdir(out_path)) == 1 

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def test_version_2_0_memmap():
    # requires more than 2 byte for header
    dt = [(("%d" % i) * 100, float) for i in range(500)]
    d = np.ones(1000, dtype=dt)
    tf = tempfile.mktemp('', 'mmap', dir=tempdir)

    # 1.0 requested but data cannot be saved this way
    assert_raises(ValueError, format.open_memmap, tf, mode='w+', dtype=d.dtype,
                            shape=d.shape, version=(1, 0))

    ma = format.open_memmap(tf, mode='w+', dtype=d.dtype,
                            shape=d.shape, version=(2, 0))
    ma[...] = d
    del ma

    with warnings.catch_warnings(record=True) as w:
        warnings.filterwarnings('always', '', UserWarning)
        ma = format.open_memmap(tf, mode='w+', dtype=d.dtype,
                                shape=d.shape, version=None)
        assert_(w[0].category is UserWarning)
        ma[...] = d
        del ma

    ma = format.open_memmap(tf, mode='r')
    assert_array_equal(ma, d) 

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def test_exit_crash():
    # For each Widget subclass, run a simple python script that creates an
    # instance and then shuts down. The intent is to check for segmentation
    # faults when each script exits.
    tmp = tempfile.mktemp(".py")
    path = os.path.dirname(pg.__file__)

    initArgs = {
        'CheckTable': "[]",
        'ProgressDialog': '"msg"',
        'VerticalLabel': '"msg"',
    }

    for name in dir(pg):
        obj = getattr(pg, name)
        if not isinstance(obj, type) or not issubclass(obj, pg.QtGui.QWidget):
            continue

        print(name)
        argstr = initArgs.get(name, "")
        open(tmp, 'w').write(code.format(path=path, classname=name, args=argstr))
        proc = subprocess.Popen([sys.executable, tmp])
        assert proc.wait() == 0

    os.remove(tmp) 

# 需要导入模块: import tempfile [as 别名]
# 或者: from tempfile import mktemp [as 别名]
def test_cli_writecoverage_source(runner, devnull):
    from covimerage.coveragepy import CoverageWrapper

    fname = tempfile.mktemp()
    result = runner.invoke(cli.main, [
        'write_coverage', '--data-file', fname, '--source', '.',
        'tests/fixtures/conditional_function.profile'])
    assert result.output == '\n'.join([
        'Writing coverage file %s.' % fname,
        ''])
    assert result.exit_code == 0

    cov = CoverageWrapper(data_file=fname)
    assert cov.lines[
        os.path.abspath('tests/test_plugin/conditional_function.vim')] == [
            3, 8, 9, 11, 13, 14, 15, 17, 23]
    assert cov.lines[
        os.path.abspath('tests/test_plugin/autoload/test_plugin.vim')] == []