Test failures in seaborn project

[kgilpin]

Running tests with appmap enabled:

============================================================== FAILURES ==============================================================
________________________________________________ TestHeatmap.test_mask_input[object] _________________________________________________

fill_value = array('?', dtype='<U1'), ndtype = dtype('float64')

    def _check_fill_value(fill_value, ndtype):
        """
        Private function validating the given `fill_value` for the given dtype.
    
        If fill_value is None, it is set to the default corresponding to the dtype.
    
        If fill_value is not None, its value is forced to the given dtype.
    
        The result is always a 0d array.
    
        """
        ndtype = np.dtype(ndtype)
        if fill_value is None:
            fill_value = default_fill_value(ndtype)
        elif ndtype.names is not None:
            if isinstance(fill_value, (ndarray, np.void)):
                try:
                    fill_value = np.array(fill_value, copy=False, dtype=ndtype)
                except ValueError as e:
                    err_msg = "Unable to transform %s to dtype %s"
                    raise ValueError(err_msg % (fill_value, ndtype)) from e
            else:
                fill_value = np.asarray(fill_value, dtype=object)
                fill_value = np.array(_recursive_set_fill_value(fill_value, ndtype),
                                      dtype=ndtype)
        else:
            if isinstance(fill_value, str) and (ndtype.char not in 'OSVU'):
                # Note this check doesn't work if fill_value is not a scalar
                err_msg = "Cannot set fill value of string with array of dtype %s"
                raise TypeError(err_msg % ndtype)
            else:
                # In case we want to convert 1e20 to int.
                # Also in case of converting string arrays.
                try:
>                   fill_value = np.array(fill_value, copy=False, dtype=ndtype)
E                   ValueError: could not convert string to float: '?'

venv/lib/python3.12/site-packages/numpy/ma/core.py:467: ValueError

The above exception was the direct cause of the following exception:

self = <tests.test_matrix.TestHeatmap object at 0x1552b99a0>, dtype = <class 'object'>

    @pytest.mark.parametrize("dtype", [float, np.int64, object])
    def test_mask_input(self, dtype):
        kws = self.default_kws.copy()
    
        mask = self.x_norm > 0
        kws['mask'] = mask
        data = self.x_norm.astype(dtype)
>       p = mat._HeatMapper(data, **kws)

tests/test_matrix.py:98: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
seaborn/matrix.py:163: in __init__
    self._determine_cmap_params(plot_data, vmin, vmax,
venv/lib/python3.12/site-packages/_appmap/wrapt/wrappers.py:712: in __call__
    return self._self_wrapper(self.__wrapped__, self._self_instance,
venv/lib/python3.12/site-packages/_appmap/instrument.py:129: in instrumented_fn
    return call_instrumented(f, instance, args, kwargs)
venv/lib/python3.12/site-packages/_appmap/instrument.py:92: in call_instrumented
    ret = f.fn(*args, **kwargs)
seaborn/matrix.py:197: in _determine_cmap_params
    calc_data = plot_data.astype(float).filled(np.nan)
venv/lib/python3.12/site-packages/numpy/ma/core.py:3066: in __array_finalize__
    self._fill_value = _check_fill_value(self._fill_value, self.dtype)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

fill_value = array('?', dtype='<U1'), ndtype = dtype('float64')

    def _check_fill_value(fill_value, ndtype):
        """
        Private function validating the given `fill_value` for the given dtype.
    
        If fill_value is None, it is set to the default corresponding to the dtype.
    
        If fill_value is not None, its value is forced to the given dtype.
    
        The result is always a 0d array.
    
        """
        ndtype = np.dtype(ndtype)
        if fill_value is None:
            fill_value = default_fill_value(ndtype)
        elif ndtype.names is not None:
            if isinstance(fill_value, (ndarray, np.void)):
                try:
                    fill_value = np.array(fill_value, copy=False, dtype=ndtype)
                except ValueError as e:
                    err_msg = "Unable to transform %s to dtype %s"
                    raise ValueError(err_msg % (fill_value, ndtype)) from e
            else:
                fill_value = np.asarray(fill_value, dtype=object)
                fill_value = np.array(_recursive_set_fill_value(fill_value, ndtype),
                                      dtype=ndtype)
        else:
            if isinstance(fill_value, str) and (ndtype.char not in 'OSVU'):
                # Note this check doesn't work if fill_value is not a scalar
                err_msg = "Cannot set fill value of string with array of dtype %s"
                raise TypeError(err_msg % ndtype)
            else:
                # In case we want to convert 1e20 to int.
                # Also in case of converting string arrays.
                try:
                    fill_value = np.array(fill_value, copy=False, dtype=ndtype)
                except (OverflowError, ValueError) as e:
                    # Raise TypeError instead of OverflowError or ValueError.
                    # OverflowError is seldom used, and the real problem here is
                    # that the passed fill_value is not compatible with the ndtype.
                    err_msg = "Cannot convert fill_value %s to dtype %s"
>                   raise TypeError(err_msg % (fill_value, ndtype)) from e
E                   TypeError: Cannot convert fill_value ? to dtype float64

venv/lib/python3.12/site-packages/numpy/ma/core.py:473: TypeError
--------------------------------------------------------- Captured log call ----------------------------------------------------------
INFO     _appmap.recording:recording.py:77 writing /Users/kgilpin/source/land-of-apps/seaborn/tmp/appmap/pytest/tests_test_matrix_TestHeatmap_test_mask_input_object.appmap.json
_________________________________________________________ test_load_datasets _________________________________________________________

self = <urllib.request.HTTPSHandler object at 0x44d8bac00>, http_class = <class 'http.client.HTTPSConnection'>
req = <urllib.request.Request object at 0x49bc70ec0>, http_conn_args = {'context': <ssl.SSLContext object at 0x44d805d50>}
host = 'raw.githubusercontent.com', h = <http.client.HTTPSConnection object at 0x49bc9d5b0>
headers = {'Connection': 'close', 'Host': 'raw.githubusercontent.com', 'User-Agent': 'Python-urllib/3.12'}

    def do_open(self, http_class, req, **http_conn_args):
        """Return an HTTPResponse object for the request, using http_class.
    
        http_class must implement the HTTPConnection API from http.client.
        """
        host = req.host
        if not host:
            raise URLError('no host given')
    
        # will parse host:port
        h = http_class(host, timeout=req.timeout, **http_conn_args)
        h.set_debuglevel(self._debuglevel)
    
        headers = dict(req.unredirected_hdrs)
        headers.update({k: v for k, v in req.headers.items()
                        if k not in headers})
    
        # TODO(jhylton): Should this be redesigned to handle
        # persistent connections?
    
        # We want to make an HTTP/1.1 request, but the addinfourl
        # class isn't prepared to deal with a persistent connection.
        # It will try to read all remaining data from the socket,
        # which will block while the server waits for the next request.
        # So make sure the connection gets closed after the (only)
        # request.
        headers["Connection"] = "close"
        headers = {name.title(): val for name, val in headers.items()}
    
        if req._tunnel_host:
            tunnel_headers = {}
            proxy_auth_hdr = "Proxy-Authorization"
            if proxy_auth_hdr in headers:
                tunnel_headers[proxy_auth_hdr] = headers[proxy_auth_hdr]
                # Proxy-Authorization should not be sent to origin
                # server.
                del headers[proxy_auth_hdr]
            h.set_tunnel(req._tunnel_host, headers=tunnel_headers)
    
        try:
            try:
>               h.request(req.get_method(), req.selector, req.data, headers,
                          encode_chunked=req.has_header('Transfer-encoding'))

/opt/miniconda3/lib/python3.12/urllib/request.py:1344: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
venv/lib/python3.12/site-packages/_appmap/wrapt/wrappers.py:712: in __call__
    return self._self_wrapper(self.__wrapped__, self._self_instance,
venv/lib/python3.12/site-packages/_appmap/instrument.py:129: in instrumented_fn
    return call_instrumented(f, instance, args, kwargs)
venv/lib/python3.12/site-packages/_appmap/instrument.py:92: in call_instrumented
    ret = f.fn(*args, **kwargs)
/opt/miniconda3/lib/python3.12/http/client.py:1327: in request
    self._send_request(method, url, body, headers, encode_chunked)
/opt/miniconda3/lib/python3.12/http/client.py:1373: in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
/opt/miniconda3/lib/python3.12/http/client.py:1322: in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
/opt/miniconda3/lib/python3.12/http/client.py:1081: in _send_output
    self.send(msg)
/opt/miniconda3/lib/python3.12/http/client.py:1025: in send
    self.connect()
/opt/miniconda3/lib/python3.12/http/client.py:1468: in connect
    self.sock = self._context.wrap_socket(self.sock,
/opt/miniconda3/lib/python3.12/ssl.py:455: in wrap_socket
    return self.sslsocket_class._create(
/opt/miniconda3/lib/python3.12/ssl.py:1046: in _create
    self.do_handshake()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <ssl.SSLSocket [closed] fd=-1, family=2, type=1, proto=0>, block = False

    @_sslcopydoc
    def do_handshake(self, block=False):
        self._check_connected()
        timeout = self.gettimeout()
        try:
            if timeout == 0.0 and block:
                self.settimeout(None)
>           self._sslobj.do_handshake()
E           ConnectionResetError: [Errno 54] Connection reset by peer

/opt/miniconda3/lib/python3.12/ssl.py:1321: ConnectionResetError

During handling of the above exception, another exception occurred:

args = (), kwargs = {}, f = <http.client.HTTPResponse object at 0x49ba0cd60>

    def wrapper(*args, **kwargs):
        # attempt to connect
        try:
            f = urlopen(url)
        except (OSError, HTTPException):
            pytest.skip("No internet connection")
        else:
            f.close()
>           return t(*args, **kwargs)

tests/test_utils.py:62: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/test_utils.py:486: in test_load_datasets
    check_load_dataset(name)
tests/test_utils.py:456: in check_load_dataset
    ds = load_dataset(name, cache=False)
venv/lib/python3.12/site-packages/_appmap/wrapt/wrappers.py:622: in __call__
    return self._self_wrapper(self.__wrapped__, self._self_instance,
venv/lib/python3.12/site-packages/_appmap/instrument.py:129: in instrumented_fn
    return call_instrumented(f, instance, args, kwargs)
venv/lib/python3.12/site-packages/_appmap/instrument.py:92: in call_instrumented
    ret = f.fn(*args, **kwargs)
seaborn/utils.py:579: in load_dataset
    df = pd.read_csv(full_path, **kws)
venv/lib/python3.12/site-packages/pandas/io/parsers/readers.py:1026: in read_csv
    return _read(filepath_or_buffer, kwds)
venv/lib/python3.12/site-packages/pandas/io/parsers/readers.py:620: in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
venv/lib/python3.12/site-packages/pandas/io/parsers/readers.py:1620: in __init__
    self._engine = self._make_engine(f, self.engine)
venv/lib/python3.12/site-packages/pandas/io/parsers/readers.py:1880: in _make_engine
    self.handles = get_handle(
venv/lib/python3.12/site-packages/pandas/io/common.py:728: in get_handle
    ioargs = _get_filepath_or_buffer(
venv/lib/python3.12/site-packages/pandas/io/common.py:384: in _get_filepath_or_buffer
    with urlopen(req_info) as req:
venv/lib/python3.12/site-packages/pandas/io/common.py:289: in urlopen
    return urllib.request.urlopen(*args, **kwargs)
/opt/miniconda3/lib/python3.12/urllib/request.py:215: in urlopen
    return opener.open(url, data, timeout)
/opt/miniconda3/lib/python3.12/urllib/request.py:515: in open
    response = self._open(req, data)
/opt/miniconda3/lib/python3.12/urllib/request.py:532: in _open
    result = self._call_chain(self.handle_open, protocol, protocol +
/opt/miniconda3/lib/python3.12/urllib/request.py:492: in _call_chain
    result = func(*args)
/opt/miniconda3/lib/python3.12/urllib/request.py:1392: in https_open
    return self.do_open(http.client.HTTPSConnection, req,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <urllib.request.HTTPSHandler object at 0x44d8bac00>, http_class = <class 'http.client.HTTPSConnection'>
req = <urllib.request.Request object at 0x49bc70ec0>, http_conn_args = {'context': <ssl.SSLContext object at 0x44d805d50>}
host = 'raw.githubusercontent.com', h = <http.client.HTTPSConnection object at 0x49bc9d5b0>
headers = {'Connection': 'close', 'Host': 'raw.githubusercontent.com', 'User-Agent': 'Python-urllib/3.12'}

    def do_open(self, http_class, req, **http_conn_args):
        """Return an HTTPResponse object for the request, using http_class.
    
        http_class must implement the HTTPConnection API from http.client.
        """
        host = req.host
        if not host:
            raise URLError('no host given')
    
        # will parse host:port
        h = http_class(host, timeout=req.timeout, **http_conn_args)
        h.set_debuglevel(self._debuglevel)
    
        headers = dict(req.unredirected_hdrs)
        headers.update({k: v for k, v in req.headers.items()
                        if k not in headers})
    
        # TODO(jhylton): Should this be redesigned to handle
        # persistent connections?
    
        # We want to make an HTTP/1.1 request, but the addinfourl
        # class isn't prepared to deal with a persistent connection.
        # It will try to read all remaining data from the socket,
        # which will block while the server waits for the next request.
        # So make sure the connection gets closed after the (only)
        # request.
        headers["Connection"] = "close"
        headers = {name.title(): val for name, val in headers.items()}
    
        if req._tunnel_host:
            tunnel_headers = {}
            proxy_auth_hdr = "Proxy-Authorization"
            if proxy_auth_hdr in headers:
                tunnel_headers[proxy_auth_hdr] = headers[proxy_auth_hdr]
                # Proxy-Authorization should not be sent to origin
                # server.
                del headers[proxy_auth_hdr]
            h.set_tunnel(req._tunnel_host, headers=tunnel_headers)
    
        try:
            try:
                h.request(req.get_method(), req.selector, req.data, headers,
                          encode_chunked=req.has_header('Transfer-encoding'))
            except OSError as err: # timeout error
>               raise URLError(err)
E               urllib.error.URLError: <urlopen error [Errno 54] Connection reset by peer>

/opt/miniconda3/lib/python3.12/urllib/request.py:1347: URLError
--------------------------------------------------------- Captured log call ----------------------------------------------------------
INFO     _appmap.recording:recording.py:77 writing /Users/kgilpin/source/land-of-apps/seaborn/tmp/appmap/pytest/test_load_datasets.appmap.json
========================================================== warnings summary ==========================================================
venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1285
  /Users/kgilpin/source/land-of-apps/seaborn/venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1285: PytestAssertRewriteWarning: Module already imported so cannot be rewritten: _appmap
    self._mark_plugins_for_rewrite(hook)

venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1285
  /Users/kgilpin/source/land-of-apps/seaborn/venv/lib/python3.12/site-packages/_pytest/config/__init__.py:1285: PytestAssertRewriteWarning: Module already imported so cannot be rewritten: appmap
    self._mark_plugins_for_rewrite(hook)

tests/test_base.py:1337
  /Users/kgilpin/source/land-of-apps/seaborn/tests/test_base.py:1337: PytestRemovedIn9Warning: Marks applied to fixtures have no effect
  See docs: https://docs.pytest.org/en/stable/deprecations.html#applying-a-mark-to-a-fixture-function
    @pytest.fixture(

tests/test_base.py::TestSizeMapping::test_array_palette_deprecation
  /Users/kgilpin/source/land-of-apps/seaborn/venv/lib/python3.12/site-packages/_appmap/instrument.py:92: UserWarning: 
  The palette list has fewer values (2) than needed (3) and will cycle, which may produce an uninterpretable plot.
    ret = f.fn(*args, **kwargs)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
====================================================== short test summary info =======================================================
FAILED tests/test_matrix.py::TestHeatmap::test_mask_input[object] - TypeError: Cannot convert fill_value ? to dtype float64
FAILED tests/test_utils.py::test_load_datasets - urllib.error.URLError: <urlopen error [Errno 54] Connection reset by peer>
=========================== 2 failed, 2304 passed, 69 skipped, 6 xfailed, 4 warnings in 543.84s (0:09:03) ============================