Feat/gaff bespoke example

[mikemhenry]

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[codecov]

❌ 4 Tests Failed:

Tests completed	Failed	Passed	Skipped
47	4	43	17

View the top 3 failed test(s) by shortest run time

examples/pipeline/Small_Molecule_Pipeline_GAFF.ipynb::ipynb::Cell 9

Stack Traces | 0.029s run time

#x1B[91mNotebook cell execution failed#x1B[0m
#x1B[94mCell 9: Cell execution caused an exception

Input:
#x1B[0msmp.interchange.visualize("nglview")

#x1B[94mTraceback:#x1B[0m

#x1B[31m---------------------------------------------------------------------------#x1B[39m
#x1B[31mAttributeError#x1B[39m                            Traceback (most recent call last)
#x1B[36mCell#x1B[39m#x1B[36m #x1B[39m#x1B[32mIn[2]#x1B[39m#x1B[32m, line 1#x1B[39m
#x1B[32m----> #x1B[39m#x1B[32m1#x1B[39m #x1B[43msmp#x1B[49m#x1B[43m.#x1B[49m#x1B[43minterchange#x1B[49m.visualize(#x1B[33m"#x1B[39m#x1B[33mnglview#x1B[39m#x1B[33m"#x1B[39m)

#x1B[31mAttributeError#x1B[39m: 'SmallMoleculePipeline' object has no attribute 'interchange'

examples/pipeline/Small_Molecule_Pipeline_GAFF.ipynb::ipynb::Cell 10

Stack Traces | 0.031s run time

#x1B[91mNotebook cell execution failed#x1B[0m
#x1B[94mCell 10: Cell execution caused an exception

Input:
#x1B[0msmp.simulate()

#x1B[94mTraceback:#x1B[0m

#x1B[31m---------------------------------------------------------------------------#x1B[39m
#x1B[31mAttributeError#x1B[39m                            Traceback (most recent call last)
#x1B[36mCell#x1B[39m#x1B[36m #x1B[39m#x1B[32mIn[2]#x1B[39m#x1B[32m, line 1#x1B[39m
#x1B[32m----> #x1B[39m#x1B[32m1#x1B[39m #x1B[43msmp#x1B[49m#x1B[43m.#x1B[49m#x1B[43msimulate#x1B[49m#x1B[43m(#x1B[49m#x1B[43m)#x1B[49m

#x1B[36mFile #x1B[39m#x1B[32m~.../pipeline/sm/pipeline.py:238#x1B[39m, in #x1B[36mSmallMoleculePipeline.simulate#x1B[39m#x1B[34m(self)#x1B[39m
#x1B[32m    237#x1B[39m #x1B[38;5;28;01mdef#x1B[39;00m#x1B[38;5;250m #x1B[39m#x1B[34msimulate#x1B[39m(#x1B[38;5;28mself#x1B[39m):
#x1B[32m--> #x1B[39m#x1B[32m238#x1B[39m     #x1B[38;5;28mself#x1B[39m.simulation = create_simulation(#x1B[38;5;28mself#x1B[39m.simulate_config, #x1B[38;5;28;43mself#x1B[39;49m#x1B[43m.#x1B[49m#x1B[43minterchange#x1B[49m)
#x1B[32m    239#x1B[39m     run_simulation(#x1B[38;5;28mself#x1B[39m.simulate_config, #x1B[38;5;28mself#x1B[39m.simulation)

#x1B[31mAttributeError#x1B[39m: 'SmallMoleculePipeline' object has no attribute 'interchange'

examples/pipeline/Small_Molecule_Pipeline_GAFF.ipynb::ipynb::Cell 8

Stack Traces | 0.247s run time

#x1B[91mNotebook cell execution failed#x1B[0m
#x1B[94mCell 8: Cell execution caused an exception

Input:
#x1B[0msmp.parameterize()

#x1B[94mTraceback:#x1B[0m

#x1B[31m---------------------------------------------------------------------------#x1B[39m
#x1B[31mModuleNotFoundError#x1B[39m                       Traceback (most recent call last)
#x1B[36mCell#x1B[39m#x1B[36m #x1B[39m#x1B[32mIn[2]#x1B[39m#x1B[32m, line 1#x1B[39m
#x1B[32m----> #x1B[39m#x1B[32m1#x1B[39m #x1B[43msmp#x1B[49m#x1B[43m.#x1B[49m#x1B[43mparameterize#x1B[49m#x1B[43m(#x1B[49m#x1B[43m)#x1B[49m

#x1B[36mFile #x1B[39m#x1B[32m~.../pipeline/sm/pipeline.py:148#x1B[39m, in #x1B[36mSmallMoleculePipeline.parameterize#x1B[39m#x1B[34m(self)#x1B[39m
#x1B[32m    146#x1B[39m #x1B[38;5;28;01mfrom#x1B[39;00m#x1B[38;5;250m #x1B[39m#x1B[34;01mopenmm#x1B[39;00m#x1B[34;01m.#x1B[39;00m#x1B[34;01munit#x1B[39;00m#x1B[38;5;250m #x1B[39m#x1B[38;5;28;01mimport#x1B[39;00m angstrom
#x1B[32m    147#x1B[39m #x1B[38;5;28;01mfrom#x1B[39;00m#x1B[38;5;250m #x1B[39m#x1B[34;01mopenmm#x1B[39;00m#x1B[34;01m.#x1B[39;00m#x1B[34;01munit#x1B[39;00m#x1B[38;5;250m #x1B[39m#x1B[38;5;28;01mimport#x1B[39;00m nanometer
#x1B[32m--> #x1B[39m#x1B[32m148#x1B[39m #x1B[38;5;28;01mfrom#x1B[39;00m#x1B[38;5;250m #x1B[39m#x1B[34;01mopenmmforcefields#x1B[39;00m#x1B[34;01m.#x1B[39;00m#x1B[34;01mgenerators#x1B[39;00m#x1B[38;5;250m #x1B[39m#x1B[38;5;28;01mimport#x1B[39;00m GAFFTemplateGenerator
#x1B[32m    150#x1B[39m gaff = GAFFTemplateGenerator(
#x1B[32m    151#x1B[39m     molecules=#x1B[38;5;28mlist#x1B[39m(#x1B[38;5;28mself#x1B[39m.loaded_mols.values()),
#x1B[32m    152#x1B[39m     forcefield=#x1B[38;5;28mself#x1B[39m.parameterize_config.force_field,
#x1B[32m    153#x1B[39m )
#x1B[32m    154#x1B[39m forcefield_gaff = openmm.app.ForceField()

#x1B[31mModuleNotFoundError#x1B[39m: No module named 'openmmforcefields'

examples/pipeline/Large_Molecule_Pipeline.ipynb::ipynb::Cell 4

Stack Traces | 3005s run time

#x1B[91mNotebook cell execution failed#x1B[0m
#x1B[94mCell 4: Timeout of 3000 seconds exceeded while executing cell. Failed to interrupt kernel in 5 seconds, so failing without traceback.

Input:
#x1B[0msmp.load()

View the full list of 1 ❄️ flaky test(s)

openpharmmdflow/tests/bespokefit/bespokefit_test.py::test_bespokefit

Flake rate in main: 44.34% (Passed 295 times, Failed 235 times)

Stack Traces | 363s run time

self = <urllib3.connection.HTTPConnection object at 0x7fd88dc4d350>

    def _new_conn(self) -> socket.socket:
        """Establish a socket connection and set nodelay settings on it.
    
        :return: New socket connection.
        """
        try:
>           sock = connection.create_connection(
                (self._dns_host, self.port),
                self.timeout,
                source_address=self.source_address,
                socket_options=self.socket_options,
            )

../../...../openpharmflow/lib/python3.11............/site-packages/urllib3/connection.py:198: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../../...../openpharmflow/lib/python3.11.../urllib3/util/connection.py:85: in create_connection
    raise err
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

address = ('127.0.0.1', 8000), timeout = None, source_address = None
socket_options = [(6, 1, 1)]

    def create_connection(
        address: tuple[str, int],
        timeout: _TYPE_TIMEOUT = _DEFAULT_TIMEOUT,
        source_address: tuple[str, int] | None = None,
        socket_options: _TYPE_SOCKET_OPTIONS | None = None,
    ) -> socket.socket:
        """Connect to *address* and return the socket object.
    
        Convenience function.  Connect to *address* (a 2-tuple ``(host,
        port)``) and return the socket object.  Passing the optional
        *timeout* parameter will set the timeout on the socket instance
        before attempting to connect.  If no *timeout* is supplied, the
        global default timeout setting returned by :func:`socket.getdefaulttimeout`
        is used.  If *source_address* is set it must be a tuple of (host, port)
        for the socket to bind as a source address before making the connection.
        An host of '' or port 0 tells the OS to use the default.
        """
    
        host, port = address
        if host.startswith("["):
            host = host.strip("[]")
        err = None
    
        # Using the value from allowed_gai_family() in the context of getaddrinfo lets
        # us select whether to work with IPv4 DNS records, IPv6 records, or both.
        # The original create_connection function always returns all records.
        family = allowed_gai_family()
    
        try:
            host.encode("idna")
        except UnicodeError:
            raise LocationParseError(f"'{host}', label empty or too long") from None
    
        for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
            af, socktype, proto, canonname, sa = res
            sock = None
            try:
                sock = socket.socket(af, socktype, proto)
    
                # If provided, set socket level options before connecting.
                _set_socket_options(sock, socket_options)
    
                if timeout is not _DEFAULT_TIMEOUT:
                    sock.settimeout(timeout)
                if source_address:
                    sock.bind(source_address)
>               sock.connect(sa)
E               ConnectionRefusedError: [Errno 111] Connection refused

../../...../openpharmflow/lib/python3.11.../urllib3/util/connection.py:73: ConnectionRefusedError

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

self = <urllib3.connectionpool.HTTPConnectionPool object at 0x7fd88db06dd0>
method = 'GET', url = '.../v1/tasks/1', body = None
headers = {'User-Agent': 'python-requests/2.32.5', 'Accept-Encoding': 'gzip, deflate, br, zstd', 'Accept': '*/*', 'Connection': 'keep-alive', 'bespokefit-token': ''}
retries = Retry(total=7, connect=0, read=None, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None, preload_content = False
decode_content = False, response_kw = {}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='.../v1/tasks/1', query=None, fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False

    def urlopen(  # type: ignore[override]
        self,
        method: str,
        url: str,
        body: _TYPE_BODY | None = None,
        headers: typing.Mapping[str, str] | None = None,
        retries: Retry | bool | int | None = None,
        redirect: bool = True,
        assert_same_host: bool = True,
        timeout: _TYPE_TIMEOUT = _DEFAULT_TIMEOUT,
        pool_timeout: int | None = None,
        release_conn: bool | None = None,
        chunked: bool = False,
        body_pos: _TYPE_BODY_POSITION | None = None,
        preload_content: bool = True,
        decode_content: bool = True,
        **response_kw: typing.Any,
    ) -> BaseHTTPResponse:
        """
        Get a connection from the pool and perform an HTTP request. This is the
        lowest level call for making a request, so you'll need to specify all
        the raw details.
    
        .. note::
    
           More commonly, it's appropriate to use a convenience method
           such as :meth:`request`.
    
        .. note::
    
           `release_conn` will only behave as expected if
           `preload_content=False` because we want to make
           `preload_content=False` the default behaviour someday soon without
           breaking backwards compatibility.
    
        :param method:
            HTTP request method (such as GET, POST, PUT, etc.)
    
        :param url:
            The URL to perform the request on.
    
        :param body:
            Data to send in the request body, either :class:`str`, :class:`bytes`,
            an iterable of :class:`str`/:class:`bytes`, or a file-like object.
    
        :param headers:
            Dictionary of custom headers to send, such as User-Agent,
            If-None-Match, etc. If None, pool headers are used. If provided,
            these headers completely replace any pool-specific headers.
    
        :param retries:
            Configure the number of retries to allow before raising a
            :class:`~urllib3.exceptions.MaxRetryError` exception.
    
            If ``None`` (default) will retry 3 times, see ``Retry.DEFAULT``. Pass a
            :class:`~urllib3.util.retry.Retry` object for fine-grained control
            over different types of retries.
            Pass an integer number to retry connection errors that many times,
            but no other types of errors. Pass zero to never retry.
    
            If ``False``, then retries are disabled and any exception is raised
            immediately. Also, instead of raising a MaxRetryError on redirects,
            the redirect response will be returned.
    
        :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
    
        :param redirect:
            If True, automatically handle redirects (status codes 301, 302,
            303, 307, 308). Each redirect counts as a retry. Disabling retries
            will disable redirect, too.
    
        :param assert_same_host:
            If ``True``, will make sure that the host of the pool requests is
            consistent else will raise HostChangedError. When ``False``, you can
            use the pool on an HTTP proxy and request foreign hosts.
    
        :param timeout:
            If specified, overrides the default timeout for this one
            request. It may be a float (in seconds) or an instance of
            :class:`urllib3.util.Timeout`.
    
        :param pool_timeout:
            If set and the pool is set to block=True, then this method will
            block for ``pool_timeout`` seconds and raise EmptyPoolError if no
            connection is available within the time period.
    
        :param bool preload_content:
            If True, the response's body will be preloaded into memory.
    
        :param bool decode_content:
            If True, will attempt to decode the body based on the
            'content-encoding' header.
    
        :param release_conn:
            If False, then the urlopen call will not release the connection
            back into the pool once a response is received (but will release if
            you read the entire contents of the response such as when
            `preload_content=True`). This is useful if you're not preloading
            the response's content immediately. You will need to call
            ``r.release_conn()`` on the response ``r`` to return the connection
            back into the pool. If None, it takes the value of ``preload_content``
            which defaults to ``True``.
    
        :param bool chunked:
            If True, urllib3 will send the body using chunked transfer
            encoding. Otherwise, urllib3 will send the body using the standard
            content-length form. Defaults to False.
    
        :param int body_pos:
            Position to seek to in file-like body in the event of a retry or
            redirect. Typically this won't need to be set because urllib3 will
            auto-populate the value when needed.
        """
        parsed_url = parse_url(url)
        destination_scheme = parsed_url.scheme
    
        if headers is None:
            headers = self.headers
    
        if not isinstance(retries, Retry):
            retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
    
        if release_conn is None:
            release_conn = preload_content
    
        # Check host
        if assert_same_host and not self.is_same_host(url):
            raise HostChangedError(self, url, retries)
    
        # Ensure that the URL we're connecting to is properly encoded
        if url.startswith("/"):
            url = to_str(_encode_target(url))
        else:
            url = to_str(parsed_url.url)
    
        conn = None
    
        # Track whether `conn` needs to be released before
        # returning/raising/recursing. Update this variable if necessary, and
        # leave `release_conn` constant throughout the function. That way, if
        # the function recurses, the original value of `release_conn` will be
        # passed down into the recursive call, and its value will be respected.
        #
        # See issue #651 [1] for details.
        #
        # [1] <https://github..../urllib3/issues/651>
        release_this_conn = release_conn
    
        http_tunnel_required = connection_requires_http_tunnel(
            self.proxy, self.proxy_config, destination_scheme
        )
    
        # Merge the proxy headers. Only done when not using HTTP CONNECT. We
        # have to copy the headers dict so we can safely change it without those
        # changes being reflected in anyone else's copy.
        if not http_tunnel_required:
            headers = headers.copy()  # type: ignore[attr-defined]
            headers.update(self.proxy_headers)  # type: ignore[union-attr]
    
        # Must keep the exception bound to a separate variable or else Python 3
        # complains about UnboundLocalError.
        err = None
    
        # Keep track of whether we cleanly exited the except block. This
        # ensures we do proper cleanup in finally.
        clean_exit = False
    
        # Rewind body position, if needed. Record current position
        # for future rewinds in the event of a redirect/retry.
        body_pos = set_file_position(body, body_pos)
    
        try:
            # Request a connection from the queue.
            timeout_obj = self._get_timeout(timeout)
            conn = self._get_conn(timeout=pool_timeout)
    
            conn.timeout = timeout_obj.connect_timeout  # type: ignore[assignment]
    
            # Is this a closed/new connection that requires CONNECT tunnelling?
            if self.proxy is not None and http_tunnel_required and conn.is_closed:
                try:
                    self._prepare_proxy(conn)
                except (BaseSSLError, OSError, SocketTimeout) as e:
                    self._raise_timeout(
                        err=e, url=self.proxy.url, timeout_value=conn.timeout
                    )
                    raise
    
            # If we're going to release the connection in ``finally:``, then
            # the response doesn't need to know about the connection. Otherwise
            # it will also try to release it and we'll have a double-release
            # mess.
            response_conn = conn if not release_conn else None
    
            # Make the request on the HTTPConnection object
>           response = self._make_request(
                conn,
                method,
                url,
                timeout=timeout_obj,
                body=body,
                headers=headers,
                chunked=chunked,
                retries=retries,
                response_conn=response_conn,
                preload_content=preload_content,
                decode_content=decode_content,
                **response_kw,
            )

../../...../openpharmflow/lib/python3.11................../site-packages/urllib3/connectionpool.py:787: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../../...../openpharmflow/lib/python3.11................../site-packages/urllib3/connectionpool.py:493: in _make_request
    conn.request(
../../...../openpharmflow/lib/python3.11............/site-packages/urllib3/connection.py:494: in request
    self.endheaders()
../../...../openpharmflow/lib/python3.11/http/client.py:1298: in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
../../...../openpharmflow/lib/python3.11/http/client.py:1058: in _send_output
    self.send(msg)
../../...../openpharmflow/lib/python3.11/http/client.py:996: in send
    self.connect()
../../...../openpharmflow/lib/python3.11............/site-packages/urllib3/connection.py:325: in connect
    self.sock = self._new_conn()
                ^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <urllib3.connection.HTTPConnection object at 0x7fd88dc4d350>

    def _new_conn(self) -> socket.socket:
        """Establish a socket connection and set nodelay settings on it.
    
        :return: New socket connection.
        """
        try:
            sock = connection.create_connection(
                (self._dns_host, self.port),
                self.timeout,
                source_address=self.source_address,
                socket_options=self.socket_options,
            )
        except socket.gaierror as e:
            raise NameResolutionError(self.host, self, e) from e
        except SocketTimeout as e:
            raise ConnectTimeoutError(
                self,
                f"Connection to {self.host} timed out. (connect timeout={self.timeout})",
            ) from e
    
        except OSError as e:
>           raise NewConnectionError(
                self, f"Failed to establish a new connection: {e}"
            ) from e
E           urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7fd88dc4d350>: Failed to establish a new connection: [Errno 111] Connection refused

../../...../openpharmflow/lib/python3.11............/site-packages/urllib3/connection.py:213: NewConnectionError

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

self = <requests.adapters.HTTPAdapter object at 0x7fd88dc4f590>
request = <PreparedRequest [GET]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()

    def send(
        self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
    ):
        """Sends PreparedRequest object. Returns Response object.
    
        :param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
        :param stream: (optional) Whether to stream the request content.
        :param timeout: (optional) How long to wait for the server to send
            data before giving up, as a float, or a :ref:`(connect timeout,
            read timeout) <timeouts>` tuple.
        :type timeout: float or tuple or urllib3 Timeout object
        :param verify: (optional) Either a boolean, in which case it controls whether
            we verify the server's TLS certificate, or a string, in which case it
            must be a path to a CA bundle to use
        :param cert: (optional) Any user-provided SSL certificate to be trusted.
        :param proxies: (optional) The proxies dictionary to apply to the request.
        :rtype: requests.Response
        """
    
        try:
            conn = self.get_connection_with_tls_context(
                request, verify, proxies=proxies, cert=cert
            )
        except LocationValueError as e:
            raise InvalidURL(e, request=request)
    
        self.cert_verify(conn, request.url, verify, cert)
        url = self.request_url(request, proxies)
        self.add_headers(
            request,
            stream=stream,
            timeout=timeout,
            verify=verify,
            cert=cert,
            proxies=proxies,
        )
    
        chunked = not (request.body is None or "Content-Length" in request.headers)
    
        if isinstance(timeout, tuple):
            try:
                connect, read = timeout
                timeout = TimeoutSauce(connect=connect, read=read)
            except ValueError:
                raise ValueError(
                    f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
                    f"or a single float to set both timeouts to the same value."
                )
        elif isinstance(timeout, TimeoutSauce):
            pass
        else:
            timeout = TimeoutSauce(connect=timeout, read=timeout)
    
        try:
>           resp = conn.urlopen(
                method=request.method,
                url=url,
                body=request.body,
                headers=request.headers,
                redirect=False,
                assert_same_host=False,
                preload_content=False,
                decode_content=False,
                retries=self.max_retries,
                timeout=timeout,
                chunked=chunked,
            )

../../...../openpharmflow/lib/python3.11....../site-packages/requests/adapters.py:644: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../../...../openpharmflow/lib/python3.11................../site-packages/urllib3/connectionpool.py:871: in urlopen
    return self.urlopen(
../../...../openpharmflow/lib/python3.11................../site-packages/urllib3/connectionpool.py:871: in urlopen
    return self.urlopen(
../../...../openpharmflow/lib/python3.11................../site-packages/urllib3/connectionpool.py:871: in urlopen
    return self.urlopen(
../../...../openpharmflow/lib/python3.11................../site-packages/urllib3/connectionpool.py:841: in urlopen
    retries = retries.increment(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = Retry(total=7, connect=0, read=None, redirect=None, status=None)
method = 'GET', url = '.../v1/tasks/1', response = None
error = NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fd88dc4d350>: Failed to establish a new connection: [Errno 111] Connection refused')
_pool = <urllib3.connectionpool.HTTPConnectionPool object at 0x7fd88db06dd0>
_stacktrace = <traceback object at 0x7fd88dc4d380>

    def increment(
        self,
        method: str | None = None,
        url: str | None = None,
        response: BaseHTTPResponse | None = None,
        error: Exception | None = None,
        _pool: ConnectionPool | None = None,
        _stacktrace: TracebackType | None = None,
    ) -> Self:
        """Return a new Retry object with incremented retry counters.
    
        :param response: A response object, or None, if the server did not
            return a response.
        :type response: :class:`~urllib3.response.BaseHTTPResponse`
        :param Exception error: An error encountered during the request, or
            None if the response was received successfully.
    
        :return: A new ``Retry`` object.
        """
        if self.total is False and error:
            # Disabled, indicate to re-raise the error.
            raise reraise(type(error), error, _stacktrace)
    
        total = self.total
        if total is not None:
            total -= 1
    
        connect = self.connect
        read = self.read
        redirect = self.redirect
        status_count = self.status
        other = self.other
        cause = "unknown"
        status = None
        redirect_location = None
    
        if error and self._is_connection_error(error):
            # Connect retry?
            if connect is False:
                raise reraise(type(error), error, _stacktrace)
            elif connect is not None:
                connect -= 1
    
        elif error and self._is_read_error(error):
            # Read retry?
            if read is False or method is None or not self._is_method_retryable(method):
                raise reraise(type(error), error, _stacktrace)
            elif read is not None:
                read -= 1
    
        elif error:
            # Other retry?
            if other is not None:
                other -= 1
    
        elif response and response.get_redirect_location():
            # Redirect retry?
            if redirect is not None:
                redirect -= 1
            cause = "too many redirects"
            response_redirect_location = response.get_redirect_location()
            if response_redirect_location:
                redirect_location = response_redirect_location
            status = response.status
    
        else:
            # Incrementing because of a server error like a 500 in
            # status_forcelist and the given method is in the allowed_methods
            cause = ResponseError.GENERIC_ERROR
            if response and response.status:
                if status_count is not None:
                    status_count -= 1
                cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status)
                status = response.status
    
        history = self.history + (
            RequestHistory(method, url, error, status, redirect_location),
        )
    
        new_retry = self.new(
            total=total,
            connect=connect,
            read=read,
            redirect=redirect,
            status=status_count,
            other=other,
            history=history,
        )
    
        if new_retry.is_exhausted():
            reason = error or ResponseError(cause)
>           raise MaxRetryError(_pool, url, reason) from reason  # type: ignore[arg-type]
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
E           urllib3.exceptions.MaxRetryError: HTTPConnectionPool(host='127.0.0.1', port=8000): Max retries exceeded with url: .../v1/tasks/1 (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fd88dc4d350>: Failed to establish a new connection: [Errno 111] Connection refused'))

../../...../openpharmflow/lib/python3.11.../urllib3/util/retry.py:519: MaxRetryError

During handling of the above exception, another exception occurred:

    @skip_if_missing("openff.bespokefit")
    @pytest.mark.flaky(retries=3, delay=1, only_on=[ConnectionError, RuntimeError])
    def test_bespokefit():
        from openff.bespokefit.executor import BespokeExecutor
        from openff.bespokefit.executor import BespokeWorkerConfig
        from openff.bespokefit.executor.client import BespokeFitClient
        from openff.bespokefit.executor.client import Settings
        from openff.bespokefit.workflows import BespokeWorkflowFactory
        from openff.qcsubmit.common_structures import QCSpec
        from openff.toolkit.topology import Molecule
    
        factory = BespokeWorkflowFactory(
            # Define the starting force field that will be augmented with bespoke
            # parameters.
            initial_force_field="openff-2.2.1.offxml",
            # Change the level of theory that the reference QC data is generated at
            default_qc_specs=[
                QCSpec(
                    method="gfn2xtb",
                    basis=None,
                    program="xtb",
                    spec_name="xtb",
                    spec_description="gfn2xtb",
                )
            ],
        )
    
        input_molecule = Molecule.from_smiles("C(C(=O)O)N")  # Glycine
    
        workflow_schema = factory.optimization_schema_from_molecule(molecule=input_molecule)
    
        # create a client to interface with the executor
        settings = Settings()
        client = BespokeFitClient(settings=settings)
    
        with BespokeExecutor(
            n_fragmenter_workers=1,
            n_optimizer_workers=1,
            n_qc_compute_workers=2,
            qc_compute_worker_config=BespokeWorkerConfig(n_cores=1),
        ) as executor:
            # Submit our workflow to the executor
            task_id = client.submit_optimization(input_schema=workflow_schema)
            # Wait until the executor is done
>           output = client.wait_until_complete(task_id)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.../tests/bespokefit/bespokefit_test.py:49: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../../...../openpharmflow/lib/python3.11.../bespokefit/executor/client.py:269: in wait_until_complete
    stage = self._wait_for_stage(
../../...../openpharmflow/lib/python3.11.../bespokefit/executor/client.py:292: in _wait_for_stage
    response = self._query_coordinator(optimization_href=query)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
../../...../openpharmflow/lib/python3.11.../bespokefit/executor/client.py:185: in _query_coordinator
    coordinator_request = self._session.get(optimization_href)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
../../...../openpharmflow/lib/python3.11........./site-packages/requests/sessions.py:602: in get
    return self.request("GET", url, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
../../...../openpharmflow/lib/python3.11........./site-packages/requests/sessions.py:589: in request
    resp = self.send(prep, **send_kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
../../...../openpharmflow/lib/python3.11........./site-packages/requests/sessions.py:703: in send
    r = adapter.send(request, **kwargs)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <requests.adapters.HTTPAdapter object at 0x7fd88dc4f590>
request = <PreparedRequest [GET]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()

    def send(
        self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
    ):
        """Sends PreparedRequest object. Returns Response object.
    
        :param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
        :param stream: (optional) Whether to stream the request content.
        :param timeout: (optional) How long to wait for the server to send
            data before giving up, as a float, or a :ref:`(connect timeout,
            read timeout) <timeouts>` tuple.
        :type timeout: float or tuple or urllib3 Timeout object
        :param verify: (optional) Either a boolean, in which case it controls whether
            we verify the server's TLS certificate, or a string, in which case it
            must be a path to a CA bundle to use
        :param cert: (optional) Any user-provided SSL certificate to be trusted.
        :param proxies: (optional) The proxies dictionary to apply to the request.
        :rtype: requests.Response
        """
    
        try:
            conn = self.get_connection_with_tls_context(
                request, verify, proxies=proxies, cert=cert
            )
        except LocationValueError as e:
            raise InvalidURL(e, request=request)
    
        self.cert_verify(conn, request.url, verify, cert)
        url = self.request_url(request, proxies)
        self.add_headers(
            request,
            stream=stream,
            timeout=timeout,
            verify=verify,
            cert=cert,
            proxies=proxies,
        )
    
        chunked = not (request.body is None or "Content-Length" in request.headers)
    
        if isinstance(timeout, tuple):
            try:
                connect, read = timeout
                timeout = TimeoutSauce(connect=connect, read=read)
            except ValueError:
                raise ValueError(
                    f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
                    f"or a single float to set both timeouts to the same value."
                )
        elif isinstance(timeout, TimeoutSauce):
            pass
        else:
            timeout = TimeoutSauce(connect=timeout, read=timeout)
    
        try:
            resp = conn.urlopen(
                method=request.method,
                url=url,
                body=request.body,
                headers=request.headers,
                redirect=False,
                assert_same_host=False,
                preload_content=False,
                decode_content=False,
                retries=self.max_retries,
                timeout=timeout,
                chunked=chunked,
            )
    
        except (ProtocolError, OSError) as err:
            raise ConnectionError(err, request=request)
    
        except MaxRetryError as e:
            if isinstance(e.reason, ConnectTimeoutError):
                # TODO: Remove this in 3.0.0: see #2811
                if not isinstance(e.reason, NewConnectionError):
                    raise ConnectTimeout(e, request=request)
    
            if isinstance(e.reason, ResponseError):
                raise RetryError(e, request=request)
    
            if isinstance(e.reason, _ProxyError):
                raise ProxyError(e, request=request)
    
            if isinstance(e.reason, _SSLError):
                # This branch is for urllib3 v1.22 and later.
                raise SSLError(e, request=request)
    
>           raise ConnectionError(e, request=request)
E           requests.exceptions.ConnectionError: HTTPConnectionPool(host='127.0.0.1', port=8000): Max retries exceeded with url: .../v1/tasks/1 (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fd88dc4d350>: Failed to establish a new connection: [Errno 111] Connection refused'))

../../...../openpharmflow/lib/python3.11....../site-packages/requests/adapters.py:677: ConnectionError

To view more test analytics, go to the Test Analytics Dashboard
_{📋 Got 3 mins? Take this short survey to help us improve Test Analytics.}