gonglinyuan/CoSQA huggingface dataset:
Query: examble of static methods in python

def get_all_attributes(klass_or_instance):
    """Get all attribute members (attribute, property style method).
    """
    pairs = list()
    for attr, value in inspect.getmembers(
            klass_or_instance, lambda x: not inspect.isroutine(x)):
        if not (attr.startswith("__") or attr.endswith("__")):
            pairs.append((attr, value))
    return pairs
Query: python good way to load a yaml file

def load_yaml(filepath):
    """Convenience function for loading yaml-encoded data from disk."""
    with open(filepath) as f:
        txt = f.read()
    return yaml.load(txt)
Query: execute a stored procedure in python

def query_proc_row(procname, args=(), factory=None):
    """
    Execute a stored procedure. Returns the first row of the result set,
    or `None`.
    """
    for row in query_proc(procname, args, factory):
        return row
    return None
Query: python graphviz not found

def _check_graphviz_available(output_format):
    """check if we need graphviz for different output format"""
    try:
        subprocess.call(["dot", "-V"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    except OSError:
        print(
            "The output format '%s' is currently not available.\n"
            "Please install 'Graphviz' to have other output formats "
            "than 'dot' or 'vcg'." % output_format
        )
        sys.exit(32)
Query: execute python files simultaneously from a single python file

def load_files(files):
    """Load and execute a python file."""

    for py_file in files:
        LOG.debug("exec %s", py_file)
        execfile(py_file, globals(), locals())
Query: python gridtablebase column width

def table_width(self):
        """Return the width of the table including padding and borders."""
        outer_widths = max_dimensions(self.table_data, self.padding_left, self.padding_right)[2]
        outer_border = 2 if self.outer_border else 0
        inner_border = 1 if self.inner_column_border else 0
        return table_width(outer_widths, outer_border, inner_border)
Query: export a graph python to a file

def to_dotfile(G: nx.DiGraph, filename: str):
    """ Output a networkx graph to a DOT file. """
    A = to_agraph(G)
    A.write(filename)
Query: python gtk get parent window of a widget

def get_window(self): 
        """
        Returns the object's parent window. Returns None if no window found.
        """
        x = self
        while not x._parent == None and \
              not isinstance(x._parent, Window): 
                  x = x._parent
        return x._parent
Query: python gui move window location

def OnMove(self, event):
        """Main window move event"""

        # Store window position in config
        position = self.main_window.GetScreenPositionTuple()

        config["window_position"] = repr(position)
Query: extract even fourier components from an image python

def correlation_2D(image):
    """

    :param image: 2d image
    :return: psd1D, psd2D
    """
    # Take the fourier transform of the image.
    F1 = fftpack.fft2(image)

    # Now shift the quadrants around so that low spatial frequencies are in
    # the center of the 2D fourier transformed image.
    F2 = fftpack.fftshift(F1)

    # Calculate a 2D power spectrum
    psd2D = np.abs(F2)

    # Calculate the azimuthally averaged 1D power spectrum
    psd1D = analysis_util.azimuthalAverage(psd2D)
    return psd1D, psd2D
Query: python gzip test if a gzip file is valid

def is_gzipped_fastq(file_name):
    """
    Determine whether indicated file appears to be a gzipped FASTQ.

    :param str file_name: Name/path of file to check as gzipped FASTQ.
    :return bool: Whether indicated file appears to be in gzipped FASTQ format.
    """
    _, ext = os.path.splitext(file_name)
    return file_name.endswith(".fastq.gz") or file_name.endswith(".fq.gz")
Query: extract only words from topics without probability in topic modeling in python

def get_least_distinct_words(vocab, topic_word_distrib, doc_topic_distrib, doc_lengths, n=None):
    """
    Order the words from `vocab` by "distinctiveness score" (Chuang et al. 2012) from least to most distinctive.
    Optionally only return the `n` least distinctive words.

    J. Chuang, C. Manning, J. Heer 2012: "Termite: Visualization Techniques for Assessing Textual Topic Models"
    """
    return _words_by_distinctiveness_score(vocab, topic_word_distrib, doc_topic_distrib, doc_lengths, n,
                                           least_to_most=True)
Query: fasta file parsing biopython to get sequence only

def load_fasta_file(filename):
    """Load a FASTA file and return the sequences as a list of SeqRecords

    Args:
        filename (str): Path to the FASTA file to load

    Returns:
        list: list of all sequences in the FASTA file as Biopython SeqRecord objects

    """

    with open(filename, "r") as handle:
        records = list(SeqIO.parse(handle, "fasta"))
    return records
Query: fastest way to render dynamic bitmap graphics python

def draw_image(self, ax, image):
        """Process a matplotlib image object and call renderer.draw_image"""
        self.renderer.draw_image(imdata=utils.image_to_base64(image),
                                 extent=image.get_extent(),
                                 coordinates="data",
                                 style={"alpha": image.get_alpha(),
                                        "zorder": image.get_zorder()},
                                 mplobj=image)
Query: python hamming distance between columns of strings

def hamming(s, t):
    """
    Calculate the Hamming distance between two strings. From Wikipedia article: Iterative with two matrix rows.

    :param s: string 1
    :type s: str
    :param t: string 2
    :type s: str
    :return: Hamming distance
    :rtype: float
    """
    if len(s) != len(t):
        raise ValueError('Hamming distance needs strings of equal length.')
    return sum(s_ != t_ for s_, t_ in zip(s, t))
Query: ffmpeg not working with python

def ffmpeg_version():
    """Returns the available ffmpeg version

    Returns
    ----------
    version : str
        version number as string
    """

    cmd = [
        'ffmpeg',
        '-version'
    ]

    output = sp.check_output(cmd)
    aac_codecs = [
        x for x in
        output.splitlines() if "ffmpeg version " in str(x)
    ][0]
    hay = aac_codecs.decode('ascii')
    match = re.findall(r'ffmpeg version (\d+\.)?(\d+\.)?(\*|\d+)', hay)
    if match:
        return "".join(match[0])
    else:
        return None
Query: python hamming distance string

def hamming(s, t):
    """
    Calculate the Hamming distance between two strings. From Wikipedia article: Iterative with two matrix rows.

    :param s: string 1
    :type s: str
    :param t: string 2
    :type s: str
    :return: Hamming distance
    :rtype: float
    """
    if len(s) != len(t):
        raise ValueError('Hamming distance needs strings of equal length.')
    return sum(s_ != t_ for s_, t_ in zip(s, t))
Query: python hashlib calc sha1 of file

def _get_file_sha1(file):
    """Return the SHA1 hash of the given a file-like object as ``file``.
    This will seek the file back to 0 when it's finished.

    """
    bits = file.read()
    file.seek(0)
    h = hashlib.new('sha1', bits).hexdigest()
    return h
Query: field default with python

def normalize_field(self, value):
        """
        Method that must transform the value from string
        Ex: if the expected type is int, it should return int(self._attr)

        """
        if self.default is not None:
            if value is None or value == '':
                value = self.default
        return value
Query: python hdfs detect file exist

def exists(self, path):
        """
        Returns true if the path exists and false otherwise.
        """
        import hdfs
        try:
            self.client.status(path)
            return True
        except hdfs.util.HdfsError as e:
            if str(e).startswith('File does not exist: '):
                return False
            else:
                raise e
Query: figure out data type of an object python

def is_integer(obj):
    """Is this an integer.

    :param object obj:
    :return:
    """
    if PYTHON3:
        return isinstance(obj, int)
    return isinstance(obj, (int, long))
Query: python histogram get data with in bin

def get_bin_indices(self, values):
        """Returns index tuple in histogram of bin which contains value"""
        return tuple([self.get_axis_bin_index(values[ax_i], ax_i)
                      for ax_i in range(self.dimensions)])
Query: file path username case sensitivity python

def normalize_path(path):
    """
    Convert a path to its canonical, case-normalized, absolute version.

    """
    return os.path.normcase(os.path.realpath(os.path.expanduser(path)))
Query: python how do i get a stacked widget height

def getSize(self):
        """
        Returns the size of the layer, with the border size already subtracted.
        """
        return self.widget.size[0]-self.border[0]*2,self.widget.size[1]-self.border[1]*2
Query: file permissions python write

def make_writeable(filename):
    """
    Make sure that the file is writeable.
    Useful if our source is read-only.
    """
    if not os.access(filename, os.W_OK):
        st = os.stat(filename)
        new_permissions = stat.S_IMODE(st.st_mode) | stat.S_IWUSR
        os.chmod(filename, new_permissions)
Query: python how do i get the image size

def get_image_dimension(self, url):
        """
        Return a tuple that contains (width, height)
        Pass in a url to an image and find out its size without loading the whole file
        If the image wxh could not be found, the tuple will contain `None` values
        """
        w_h = (None, None)
        try:
            if url.startswith('//'):
                url = 'http:' + url
            data = requests.get(url).content
            im = Image.open(BytesIO(data))

            w_h = im.size
        except Exception:
            logger.warning("Error getting image size {}".format(url), exc_info=True)

        return w_h
Query: filer the values of a table in python based upon variable

def filter_bolts(table, header):
  """ filter to keep bolts """
  bolts_info = []
  for row in table:
    if row[0] == 'bolt':
      bolts_info.append(row)
  return bolts_info, header
Query: python how do you check the array attribute

def is_array(self, key):
        """Return True if variable is a numpy array"""
        data = self.model.get_data()
        return isinstance(data[key], (ndarray, MaskedArray))
Query: fill is null with other columns python

def clean_dataframe(df):
    """Fill NaNs with the previous value, the next value or if all are NaN then 1.0"""
    df = df.fillna(method='ffill')
    df = df.fillna(0.0)
    return df
Query: python how do you split a dictionary into evenly sized chunks

def chunks(dictionary, chunk_size):
    """
    Yield successive n-sized chunks from dictionary.
    """
    iterable = iter(dictionary)
    for __ in range(0, len(dictionary), chunk_size):
        yield {key: dictionary[key] for key in islice(iterable, chunk_size)}
Query: filling around an image with white python

def inpaint(self):
        """ Replace masked-out elements in an array using an iterative image inpainting algorithm. """

        import inpaint
        filled = inpaint.replace_nans(np.ma.filled(self.raster_data, np.NAN).astype(np.float32), 3, 0.01, 2)
        self.raster_data = np.ma.masked_invalid(filled)
Query: python how not to close the window after running

def quit(self):
        """ Quits the application (called when the last window is closed)
        """
        logger.debug("ArgosApplication.quit called")
        assert len(self.mainWindows) == 0, \
            "Bug: still {} windows present at application quit!".format(len(self.mainWindows))
        self.qApplication.quit()
Query: fillna with string for specific columnin python

def stringify_col(df, col_name):
    """
    Take a dataframe and string-i-fy a column of values.
    Turn nan/None into "" and all other values into strings.

    Parameters
    ----------
    df : dataframe
    col_name : string
    """
    df = df.copy()
    df[col_name] = df[col_name].fillna("")
    df[col_name] = df[col_name].astype(str)
    return df
Query: filter dictionary python with certain keys

def filter_dict(d, keys):
    """
    Creates a new dict from an existing dict that only has the given keys
    """
    return {k: v for k, v in d.items() if k in keys}
Query: python how to apply label encoder all all columns

def _transform_col(self, x, i):
        """Encode one categorical column into labels.

        Args:
            x (pandas.Series): a categorical column to encode
            i (int): column index

        Returns:
            x (pandas.Series): a column with labels.
        """
        return x.fillna(NAN_INT).map(self.label_encoders[i]).fillna(0)
Query: filter twitter user tweepy python

def twitter_timeline(screen_name, since_id=None):
    """ Return relevant twitter timeline """
    consumer_key = twitter_credential('consumer_key')
    consumer_secret = twitter_credential('consumer_secret')
    access_token = twitter_credential('access_token')
    access_token_secret = twitter_credential('access_secret')
    auth = tweepy.OAuthHandler(consumer_key, consumer_secret)
    auth.set_access_token(access_token, access_token_secret)
    api = tweepy.API(auth)
    return get_all_tweets(screen_name, api, since_id)
Query: finding index of a specific element in a list python

def binSearch(arr, val):
  """ 
  Function for running binary search on a sorted list.

  :param arr: (list) a sorted list of integers to search
  :param val: (int)  a integer to search for in the sorted array
  :returns: (int) the index of the element if it is found and -1 otherwise.
  """
  i = bisect_left(arr, val)
  if i != len(arr) and arr[i] == val:
    return i
  return -1
Query: python how to bind paramters to function

def _bind_parameter(self, parameter, value):
        """Assigns a parameter value to matching instructions in-place."""
        for (instr, param_index) in self._parameter_table[parameter]:
            instr.params[param_index] = value
Query: finding nearest numbers in python

def index_nearest(value, array):
    """
    expects a _n.array
    returns the global minimum of (value-array)^2
    """

    a = (array-value)**2
    return index(a.min(), a)
Query: python how to change file extension

def lower_ext(abspath):
    """Convert file extension to lowercase.
    """
    fname, ext = os.path.splitext(abspath)
    return fname + ext.lower()
Query: finding patterns in python string

def iter_finds(regex_obj, s):
    """Generate all matches found within a string for a regex and yield each match as a string"""
    if isinstance(regex_obj, str):
        for m in re.finditer(regex_obj, s):
            yield m.group()
    else:
        for m in regex_obj.finditer(s):
            yield m.group()
Query: python how to check if environment defined

def _pip_exists(self):
        """Returns True if pip exists inside the virtual environment. Can be
        used as a naive way to verify that the environment is installed."""
        return os.path.isfile(os.path.join(self.path, 'bin', 'pip'))
Query: finding sets of consecutive numbers in a list python

def check_if_numbers_are_consecutive(list_):
    """
    Returns True if numbers in the list are consecutive

    :param list_: list of integers
    :return: Boolean
    """
    return all((True if second - first == 1 else False
                for first, second in zip(list_[:-1], list_[1:])))
Query: python how to check list or array

def class_check(vector):
    """
    Check different items in matrix classes.

    :param vector: input vector
    :type vector : list
    :return: bool
    """
    for i in vector:
        if not isinstance(i, type(vector[0])):
            return False
    return True
Query: python how to check whether the process with pid exist

def pid_exists(pid):
    """ Determines if a system process identifer exists in process table.
        """
    try:
        os.kill(pid, 0)
    except OSError as exc:
        return exc.errno == errno.EPERM
    else:
        return True
Query: python how to clear memory

def Flush(self):
    """Flush all items from cache."""
    while self._age:
      node = self._age.PopLeft()
      self.KillObject(node.data)

    self._hash = dict()
Query: fins max in array python

def findMax(arr):
    """
    in comparison to argrelmax() more simple and  reliable peak finder
    """
    out = np.zeros(shape=arr.shape, dtype=bool)
    _calcMax(arr, out)
    return out
Query: fitting a gaussian in python direct method

def fit_gaussian(x, y, yerr, p0):
    """ Fit a Gaussian to the data """
    try:
        popt, pcov = curve_fit(gaussian, x, y, sigma=yerr, p0=p0, absolute_sigma=True)
    except RuntimeError:
        return [0],[0]
    return popt, pcov
Query: python how to compute chi square

def chi_square_calc(classes, table, TOP, P, POP):
    """
    Calculate chi-squared.

    :param classes: confusion matrix classes
    :type classes : list
    :param table: confusion matrix table
    :type table : dict
    :param TOP: test outcome positive
    :type TOP : dict
    :param P: condition positive
    :type P : dict
    :param POP: population
    :type POP : dict
    :return: chi-squared as float
    """
    try:
        result = 0
        for i in classes:
            for index, j in enumerate(classes):
                expected = (TOP[j] * P[i]) / (POP[i])
                result += ((table[i][j] - expected)**2) / expected
        return result
    except Exception:
        return "None"
Query: flask jinja if get python

def sbatch_template(self):
        """:return Jinja sbatch template for the current tag"""
        template = self.sbatch_template_str
        if template.startswith('#!'):
            # script is embedded in YAML
            return jinja_environment.from_string(template)
        return jinja_environment.get_template(template)
Query: python how to covert binary to byte arry

def be_array_from_bytes(fmt, data):
    """
    Reads an array from bytestring with big-endian data.
    """
    arr = array.array(str(fmt), data)
    return fix_byteorder(arr)
Query: flexibility for barwidth in python matplotlib barplot

def _change_height(self, ax, new_value):
        """Make bars in horizontal bar chart thinner"""
        for patch in ax.patches:
            current_height = patch.get_height()
            diff = current_height - new_value

            # we change the bar height
            patch.set_height(new_value)

            # we recenter the bar
            patch.set_y(patch.get_y() + diff * .5)
Query: python how to decorate for both instance methods

def auto_update(cls, function):
        """
        This class method could be used as decorator on subclasses, it ensures
        update method is called after function execution.
        """

        def wrapper(self, *args, **kwargs):
            f = function(self, *args, **kwargs)
            self.update()
            return f
        return wrapper
Query: flip image using python

def hflip(img):
    """Horizontally flip the given PIL Image.

    Args:
        img (PIL Image): Image to be flipped.

    Returns:
        PIL Image:  Horizontall flipped image.
    """
    if not _is_pil_image(img):
        raise TypeError('img should be PIL Image. Got {}'.format(type(img)))

    return img.transpose(Image.FLIP_LEFT_RIGHT)
Query: python how to delete files on local disk

def _delete_local(self, filename):
        """Deletes the specified file from the local filesystem."""

        if os.path.exists(filename):
            os.remove(filename)
Query: flush standard output python

def safe_exit(output):
    """exit without breaking pipes."""
    try:
        sys.stdout.write(output)
        sys.stdout.flush()
    except IOError:
        pass
Query: follow redirection to get actual link in python

def get_page_and_url(session, url):
    """
    Download an HTML page using the requests session and return
    the final URL after following redirects.
    """
    reply = get_reply(session, url)
    return reply.text, reply.url
Query: python how to do a boxplot

def compute_boxplot(self, series):
        """
        Compute boxplot for given pandas Series.
        """
        from matplotlib.cbook import boxplot_stats
        series = series[series.notnull()]
        if len(series.values) == 0:
            return {}
        elif not is_numeric_dtype(series):
            return self.non_numeric_stats(series)
        stats = boxplot_stats(list(series.values))[0]
        stats['count'] = len(series.values)
        stats['fliers'] = "|".join(map(str, stats['fliers']))
        return stats
Query: for in python unhashable type list

def serialize(self, value, **kwargs):
        """Serialize every item of the list."""
        return [self.item_type.serialize(val, **kwargs) for val in value]
Query: fourier transform audio file python

def find_frequencies(data, freq=44100, bits=16):
    """Convert audio data into a frequency-amplitude table using fast fourier
    transformation.

    Return a list of tuples (frequency, amplitude).

    Data should only contain one channel of audio.
    """
    # Fast fourier transform
    n = len(data)
    p = _fft(data)
    uniquePts = numpy.ceil((n + 1) / 2.0)

    # Scale by the length (n) and square the value to get the amplitude
    p = [(abs(x) / float(n)) ** 2 * 2 for x in p[0:uniquePts]]
    p[0] = p[0] / 2
    if n % 2 == 0:
        p[-1] = p[-1] / 2

    # Generate the frequencies and zip with the amplitudes
    s = freq / float(n)
    freqArray = numpy.arange(0, uniquePts * s, s)
    return zip(freqArray, p)
Query: python how to enumerate serial ports in linux usb hub

def autoscan():
    """autoscan will check all of the serial ports to see if they have
       a matching VID:PID for a MicroPython board.
    """
    for port in serial.tools.list_ports.comports():
        if is_micropython_usb_device(port):
            connect_serial(port[0])
Query: fraction and whole number string to float python

def parse_float(float_str):
    """Parse a string of the form 305.48b into a Python float.
       The terminal letter, if present, indicates e.g. billions."""
    factor = __get_factor(float_str)
    if factor != 1:
        float_str = float_str[:-1]

    try:
        return float(float_str.replace(',', '')) * factor
    except ValueError:
        return None
Query: python how to exit a project

def cli(ctx, project_dir):
    """Clean the previous generated files."""
    exit_code = SCons(project_dir).clean()
    ctx.exit(exit_code)
Query: free servers for testing ftp in python

def connect():
    """Connect to FTP server, login and return an ftplib.FTP instance."""
    ftp_class = ftplib.FTP if not SSL else ftplib.FTP_TLS
    ftp = ftp_class(timeout=TIMEOUT)
    ftp.connect(HOST, PORT)
    ftp.login(USER, PASSWORD)
    if SSL:
        ftp.prot_p()  # secure data connection
    return ftp
Query: python how to format a duration in seconds

def fmt_duration(secs):
    """Format a duration in seconds."""
    return ' '.join(fmt.human_duration(secs, 0, precision=2, short=True).strip().split())
Query: python how to get a decimal range

def _digits(minval, maxval):
    """Digits needed to comforatbly display values in [minval, maxval]"""
    if minval == maxval:
        return 3
    else:
        return min(10, max(2, int(1 + abs(np.log10(maxval - minval)))))
Query: from python json to bytes

def _bytes_to_json(value):
    """Coerce 'value' to an JSON-compatible representation."""
    if isinstance(value, bytes):
        value = base64.standard_b64encode(value).decode("ascii")
    return value
Query: python how to get number of cores on computer

def _num_cpus_darwin():
    """Return the number of active CPUs on a Darwin system."""
    p = subprocess.Popen(['sysctl','-n','hw.ncpu'],stdout=subprocess.PIPE)
    return p.stdout.read()