style: Fix variable names #3785

flying-sheep · 2025-09-04T09:28:16Z

codecov · 2025-09-04T09:38:00Z

❌ 32 Tests Failed:

Tests completed	Failed	Passed	Skipped
2404	32	2372	137

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

tests/test_highly_variable_genes.py::test_pearson_residuals_batch[csr_matrix-int64-200n-subset]

Stack Traces | 0s run time

self = <urllib.request.HTTPSHandler object at 0x7f400af10440>
http_class = <class 'http.client.HTTPSConnection'>
req = <urllib.request.Request object at 0x7f400e95b620>
http_conn_args = {'context': <ssl.SSLContext object at 0x7f400f60c0e0>}
host = 'falexwolf.de'
h = <http.client.HTTPSConnection object at 0x7f400af10590>
headers = {'Connection': 'close', 'Host': 'falexwolf.de', 'User-Agent': 'scanpy-user'}

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mdo_open#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, http_class, req, **http_conn_args):#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Return an HTTPResponse object for the request, using http_class.#x1B[39;49;00m
    #x1B[33m#x1B[39;49;00m
    #x1B[33m    http_class must implement the HTTPConnection API from http.client.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        host = req.host#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m host:#x1B[90m#x1B[39;49;00m
            #x1B[94mraise#x1B[39;49;00m URLError(#x1B[33m'#x1B[39;49;00m#x1B[33mno host given#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# will parse host:port#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        h = http_class(host, timeout=req.timeout, **http_conn_args)#x1B[90m#x1B[39;49;00m
        h.set_debuglevel(#x1B[96mself#x1B[39;49;00m._debuglevel)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        headers = #x1B[96mdict#x1B[39;49;00m(req.unredirected_hdrs)#x1B[90m#x1B[39;49;00m
        headers.update({k: v #x1B[94mfor#x1B[39;49;00m k, v #x1B[95min#x1B[39;49;00m req.headers.items()#x1B[90m#x1B[39;49;00m
                        #x1B[94mif#x1B[39;49;00m k #x1B[95mnot#x1B[39;49;00m #x1B[95min#x1B[39;49;00m headers})#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# TODO(jhylton): Should this be redesigned to handle#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# persistent connections?#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# We want to make an HTTP/1.1 request, but the addinfourl#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# class isn't prepared to deal with a persistent connection.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# It will try to read all remaining data from the socket,#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# which will block while the server waits for the next request.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# So make sure the connection gets closed after the (only)#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# request.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        headers[#x1B[33m"#x1B[39;49;00m#x1B[33mConnection#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] = #x1B[33m"#x1B[39;49;00m#x1B[33mclose#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        headers = {name.title(): val #x1B[94mfor#x1B[39;49;00m name, val #x1B[95min#x1B[39;49;00m headers.items()}#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m req._tunnel_host:#x1B[90m#x1B[39;49;00m
            tunnel_headers = {}#x1B[90m#x1B[39;49;00m
            proxy_auth_hdr = #x1B[33m"#x1B[39;49;00m#x1B[33mProxy-Authorization#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m proxy_auth_hdr #x1B[95min#x1B[39;49;00m headers:#x1B[90m#x1B[39;49;00m
                tunnel_headers[proxy_auth_hdr] = headers[proxy_auth_hdr]#x1B[90m#x1B[39;49;00m
                #x1B[90m# Proxy-Authorization should not be sent to origin#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[90m# server.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[94mdel#x1B[39;49;00m headers[proxy_auth_hdr]#x1B[90m#x1B[39;49;00m
            h.set_tunnel(req._tunnel_host, headers=tunnel_headers)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>               h.request(req.get_method(), req.selector, req.data, headers,#x1B[90m#x1B[39;49;00m
                          encode_chunked=req.has_header(#x1B[33m'#x1B[39;49;00m#x1B[33mTransfer-encoding#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m))#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:1319: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1338: in request
    #x1B[0m#x1B[96mself#x1B[39;49;00m._send_request(method, url, body, headers, encode_chunked)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1384: in _send_request
    #x1B[0m#x1B[96mself#x1B[39;49;00m.endheaders(body, encode_chunked=encode_chunked)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1333: in endheaders
    #x1B[0m#x1B[96mself#x1B[39;49;00m._send_output(message_body, encode_chunked=encode_chunked)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1093: in _send_output
    #x1B[0m#x1B[96mself#x1B[39;49;00m.send(msg)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1037: in send
    #x1B[0m#x1B[96mself#x1B[39;49;00m.connect()#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1472: in connect
    #x1B[0m#x1B[96msuper#x1B[39;49;00m().connect()#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1003: in connect
    #x1B[0m#x1B[96mself#x1B[39;49;00m.sock = #x1B[96mself#x1B[39;49;00m._create_connection(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/socket.py#x1B[0m:864: in create_connection
    #x1B[0m#x1B[94mraise#x1B[39;49;00m exceptions[#x1B[94m0#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

address = ('falexwolf.de', 443), timeout = <object object at 0x7f404d180900>
source_address = None

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mcreate_connection#x1B[39;49;00m(address, timeout=_GLOBAL_DEFAULT_TIMEOUT,#x1B[90m#x1B[39;49;00m
                          source_address=#x1B[94mNone#x1B[39;49;00m, *, all_errors=#x1B[94mFalse#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Connect to *address* and return the socket object.#x1B[39;49;00m
    #x1B[33m#x1B[39;49;00m
    #x1B[33m    Convenience function.  Connect to *address* (a 2-tuple ``(host,#x1B[39;49;00m
    #x1B[33m    port)``) and return the socket object.  Passing the optional#x1B[39;49;00m
    #x1B[33m    *timeout* parameter will set the timeout on the socket instance#x1B[39;49;00m
    #x1B[33m    before attempting to connect.  If no *timeout* is supplied, the#x1B[39;49;00m
    #x1B[33m    global default timeout setting returned by :func:`getdefaulttimeout`#x1B[39;49;00m
    #x1B[33m    is used.  If *source_address* is set it must be a tuple of (host, port)#x1B[39;49;00m
    #x1B[33m    for the socket to bind as a source address before making the connection.#x1B[39;49;00m
    #x1B[33m    A host of '' or port 0 tells the OS to use the default. When a connection#x1B[39;49;00m
    #x1B[33m    cannot be created, raises the last error if *all_errors* is False,#x1B[39;49;00m
    #x1B[33m    and an ExceptionGroup of all errors if *all_errors* is True.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        host, port = address#x1B[90m#x1B[39;49;00m
        exceptions = []#x1B[90m#x1B[39;49;00m
        #x1B[94mfor#x1B[39;49;00m res #x1B[95min#x1B[39;49;00m getaddrinfo(host, port, #x1B[94m0#x1B[39;49;00m, SOCK_STREAM):#x1B[90m#x1B[39;49;00m
            af, socktype, proto, canonname, sa = res#x1B[90m#x1B[39;49;00m
            sock = #x1B[94mNone#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                sock = socket(af, socktype, proto)#x1B[90m#x1B[39;49;00m
                #x1B[94mif#x1B[39;49;00m timeout #x1B[95mis#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m _GLOBAL_DEFAULT_TIMEOUT:#x1B[90m#x1B[39;49;00m
                    sock.settimeout(timeout)#x1B[90m#x1B[39;49;00m
                #x1B[94mif#x1B[39;49;00m source_address:#x1B[90m#x1B[39;49;00m
                    sock.bind(source_address)#x1B[90m#x1B[39;49;00m
>               sock.connect(sa)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE               TimeoutError: [Errno 110] Connection timed out#x1B[0m

#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/socket.py#x1B[0m:849: TimeoutError

#x1B[33mDuring handling of the above exception, another exception occurred:#x1B[0m

url = 'https://falexwolf.de/data/pbmc3k_raw.h5ad'
path = PosixPath('data/pbmc3k_raw.h5ad')

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92m_download#x1B[39;49;00m(url: #x1B[96mstr#x1B[39;49;00m, path: Path):#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96murllib#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96merror#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m URLError#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96murllib#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mrequest#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m Request, urlopen#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mtqdm#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mauto#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m tqdm#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        blocksize = #x1B[94m1024#x1B[39;49;00m * #x1B[94m8#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        blocknum = #x1B[94m0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            req = Request(url, headers={#x1B[33m"#x1B[39;49;00m#x1B[33mUser-agent#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m: #x1B[33m"#x1B[39;49;00m#x1B[33mscanpy-user#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m})#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>               open_url = urlopen(req)#x1B[90m#x1B[39;49;00m
                           ^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:1080: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:189: in urlopen
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m opener.open(url, data, timeout)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:489: in open
    #x1B[0mresponse = #x1B[96mself#x1B[39;49;00m._open(req, data)#x1B[90m#x1B[39;49;00m
               ^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:506: in _open
    #x1B[0mresult = #x1B[96mself#x1B[39;49;00m._call_chain(#x1B[96mself#x1B[39;49;00m.handle_open, protocol, protocol +#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:466: in _call_chain
    #x1B[0mresult = func(*args)#x1B[90m#x1B[39;49;00m
             ^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:1367: in https_open
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m.do_open(http.client.HTTPSConnection, req,#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <urllib.request.HTTPSHandler object at 0x7f400af10440>
http_class = <class 'http.client.HTTPSConnection'>
req = <urllib.request.Request object at 0x7f400e95b620>
http_conn_args = {'context': <ssl.SSLContext object at 0x7f400f60c0e0>}
host = 'falexwolf.de'
h = <http.client.HTTPSConnection object at 0x7f400af10590>
headers = {'Connection': 'close', 'Host': 'falexwolf.de', 'User-Agent': 'scanpy-user'}

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mdo_open#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, http_class, req, **http_conn_args):#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Return an HTTPResponse object for the request, using http_class.#x1B[39;49;00m
    #x1B[33m#x1B[39;49;00m
    #x1B[33m    http_class must implement the HTTPConnection API from http.client.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        host = req.host#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m host:#x1B[90m#x1B[39;49;00m
            #x1B[94mraise#x1B[39;49;00m URLError(#x1B[33m'#x1B[39;49;00m#x1B[33mno host given#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# will parse host:port#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        h = http_class(host, timeout=req.timeout, **http_conn_args)#x1B[90m#x1B[39;49;00m
        h.set_debuglevel(#x1B[96mself#x1B[39;49;00m._debuglevel)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        headers = #x1B[96mdict#x1B[39;49;00m(req.unredirected_hdrs)#x1B[90m#x1B[39;49;00m
        headers.update({k: v #x1B[94mfor#x1B[39;49;00m k, v #x1B[95min#x1B[39;49;00m req.headers.items()#x1B[90m#x1B[39;49;00m
                        #x1B[94mif#x1B[39;49;00m k #x1B[95mnot#x1B[39;49;00m #x1B[95min#x1B[39;49;00m headers})#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# TODO(jhylton): Should this be redesigned to handle#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# persistent connections?#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# We want to make an HTTP/1.1 request, but the addinfourl#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# class isn't prepared to deal with a persistent connection.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# It will try to read all remaining data from the socket,#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# which will block while the server waits for the next request.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# So make sure the connection gets closed after the (only)#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# request.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        headers[#x1B[33m"#x1B[39;49;00m#x1B[33mConnection#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] = #x1B[33m"#x1B[39;49;00m#x1B[33mclose#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        headers = {name.title(): val #x1B[94mfor#x1B[39;49;00m name, val #x1B[95min#x1B[39;49;00m headers.items()}#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m req._tunnel_host:#x1B[90m#x1B[39;49;00m
            tunnel_headers = {}#x1B[90m#x1B[39;49;00m
            proxy_auth_hdr = #x1B[33m"#x1B[39;49;00m#x1B[33mProxy-Authorization#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m proxy_auth_hdr #x1B[95min#x1B[39;49;00m headers:#x1B[90m#x1B[39;49;00m
                tunnel_headers[proxy_auth_hdr] = headers[proxy_auth_hdr]#x1B[90m#x1B[39;49;00m
                #x1B[90m# Proxy-Authorization should not be sent to origin#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[90m# server.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[94mdel#x1B[39;49;00m headers[proxy_auth_hdr]#x1B[90m#x1B[39;49;00m
            h.set_tunnel(req._tunnel_host, headers=tunnel_headers)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                h.request(req.get_method(), req.selector, req.data, headers,#x1B[90m#x1B[39;49;00m
                          encode_chunked=req.has_header(#x1B[33m'#x1B[39;49;00m#x1B[33mTransfer-encoding#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m))#x1B[90m#x1B[39;49;00m
            #x1B[94mexcept#x1B[39;49;00m #x1B[96mOSError#x1B[39;49;00m #x1B[94mas#x1B[39;49;00m err: #x1B[90m# timeout error#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
>               #x1B[94mraise#x1B[39;49;00m URLError(err)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE               urllib.error.URLError: <urlopen error [Errno 110] Connection timed out>#x1B[0m

#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:1322: URLError

#x1B[33mDuring handling of the above exception, another exception occurred:#x1B[0m

request = <SubRequest 'pbmc3ks_parametrized_session' for <Function test_pearson_residuals_general[csr_matrix-int64-200n-inftheta-noclip-full]>>

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.fixture(#x1B[90m#x1B[39;49;00m
        scope=#x1B[33m"#x1B[39;49;00m#x1B[33msession#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
        params=#x1B[96mlist#x1B[39;49;00m(#x1B[90m#x1B[39;49;00m
            product([sparse.csr_matrix.toarray, sparse.csr_matrix], [#x1B[33m"#x1B[39;49;00m#x1B[33mfloat32#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mint64#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])  #x1B[90m# noqa: TID251#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        ),#x1B[90m#x1B[39;49;00m
        ids=#x1B[94mlambda#x1B[39;49;00m x: #x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mx[#x1B[94m0#x1B[39;49;00m].#x1B[91m__name__#x1B[39;49;00m#x1B[33m}#x1B[39;49;00m#x1B[33m-#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mx[#x1B[94m1#x1B[39;49;00m]#x1B[33m}#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
    )#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mpbmc3ks_parametrized_session#x1B[39;49;00m(request) -> #x1B[96mdict#x1B[39;49;00m[#x1B[96mbool#x1B[39;49;00m, AnnData]:#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96m_helpers#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mdata#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m pbmc3k#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        sparsity_func, dtype = request.param#x1B[90m#x1B[39;49;00m
        #x1B[94mreturn#x1B[39;49;00m {#x1B[90m#x1B[39;49;00m
>           small: _prepare_pbmc_testdata(pbmc3k(), sparsity_func, dtype, small=small)#x1B[90m#x1B[39;49;00m
                                          ^^^^^^^^#x1B[90m#x1B[39;49;00m
            #x1B[94mfor#x1B[39;49;00m small #x1B[95min#x1B[39;49;00m [#x1B[94mTrue#x1B[39;49;00m, #x1B[94mFalse#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
        }#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[.../_pytest/fixtures/data.py#x1B[0m:55: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[.../scanpy/_helpers/data.py#x1B[0m:31: in pbmc3k
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m _pbmc3k().copy()#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/datasets/_utils.py#x1B[0m:20: in wrapper
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m f(*args, **kwargs)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/datasets/_datasets.py#x1B[0m:414: in pbmc3k
    #x1B[0madata = read(settings.datasetdir / #x1B[33m"#x1B[39;49;00m#x1B[33mpbmc3k_raw.h5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, backup_url=url)#x1B[90m#x1B[39;49;00m
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.../site-packages/legacy_api_wrap/__init__.py#x1B[0m:82: in fn_compatible
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m fn(*args_all, **kw)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:152: in read
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m _read(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:836: in _read
    #x1B[0mis_present = _check_datafile_present_and_download(filename, backup_url=backup_url)#x1B[90m#x1B[39;49;00m
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:1139: in _check_datafile_present_and_download
    #x1B[0m_download(backup_url, path)#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

url = 'https://falexwolf.de/data/pbmc3k_raw.h5ad'
path = PosixPath('data/pbmc3k_raw.h5ad')

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92m_download#x1B[39;49;00m(url: #x1B[96mstr#x1B[39;49;00m, path: Path):#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96murllib#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96merror#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m URLError#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96murllib#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mrequest#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m Request, urlopen#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mtqdm#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mauto#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m tqdm#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        blocksize = #x1B[94m1024#x1B[39;49;00m * #x1B[94m8#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        blocknum = #x1B[94m0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            req = Request(url, headers={#x1B[33m"#x1B[39;49;00m#x1B[33mUser-agent#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m: #x1B[33m"#x1B[39;49;00m#x1B[33mscanpy-user#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m})#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                open_url = urlopen(req)#x1B[90m#x1B[39;49;00m
            #x1B[94mexcept#x1B[39;49;00m URLError:#x1B[90m#x1B[39;49;00m
                #x1B[94mif#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m url.startswith(#x1B[33m"#x1B[39;49;00m#x1B[33mhttps://#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
                    #x1B[94mraise#x1B[39;49;00m  #x1B[90m# No need to try using certifi#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
                msg = #x1B[33m"#x1B[39;49;00m#x1B[33mFailed to open the url with default certificates.#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>                   #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mcertifi#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m where#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE                   ModuleNotFoundError: No module named 'certifi'#x1B[0m
#x1B[1m#x1B[31mE                   Failed to open the url with default certificates. Please install `certifi` and try again.#x1B[0m

#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:1087: ModuleNotFoundError

tests/test_highly_variable_genes.py::test_pearson_residuals_general[csr_matrix-int64-100n-100theta-30clip-subset]

Stack Traces | 0s run time

self = <urllib.request.HTTPSHandler object at 0x7f400af10440>
http_class = <class 'http.client.HTTPSConnection'>
req = <urllib.request.Request object at 0x7f400e95b620>
http_conn_args = {'context': <ssl.SSLContext object at 0x7f400f60c0e0>}
host = 'falexwolf.de'
h = <http.client.HTTPSConnection object at 0x7f400af10590>
headers = {'Connection': 'close', 'Host': 'falexwolf.de', 'User-Agent': 'scanpy-user'}

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mdo_open#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, http_class, req, **http_conn_args):#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Return an HTTPResponse object for the request, using http_class.#x1B[39;49;00m
    #x1B[33m#x1B[39;49;00m
    #x1B[33m    http_class must implement the HTTPConnection API from http.client.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        host = req.host#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m host:#x1B[90m#x1B[39;49;00m
            #x1B[94mraise#x1B[39;49;00m URLError(#x1B[33m'#x1B[39;49;00m#x1B[33mno host given#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# will parse host:port#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        h = http_class(host, timeout=req.timeout, **http_conn_args)#x1B[90m#x1B[39;49;00m
        h.set_debuglevel(#x1B[96mself#x1B[39;49;00m._debuglevel)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        headers = #x1B[96mdict#x1B[39;49;00m(req.unredirected_hdrs)#x1B[90m#x1B[39;49;00m
        headers.update({k: v #x1B[94mfor#x1B[39;49;00m k, v #x1B[95min#x1B[39;49;00m req.headers.items()#x1B[90m#x1B[39;49;00m
                        #x1B[94mif#x1B[39;49;00m k #x1B[95mnot#x1B[39;49;00m #x1B[95min#x1B[39;49;00m headers})#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# TODO(jhylton): Should this be redesigned to handle#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# persistent connections?#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# We want to make an HTTP/1.1 request, but the addinfourl#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# class isn't prepared to deal with a persistent connection.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# It will try to read all remaining data from the socket,#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# which will block while the server waits for the next request.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# So make sure the connection gets closed after the (only)#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# request.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        headers[#x1B[33m"#x1B[39;49;00m#x1B[33mConnection#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] = #x1B[33m"#x1B[39;49;00m#x1B[33mclose#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        headers = {name.title(): val #x1B[94mfor#x1B[39;49;00m name, val #x1B[95min#x1B[39;49;00m headers.items()}#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m req._tunnel_host:#x1B[90m#x1B[39;49;00m
            tunnel_headers = {}#x1B[90m#x1B[39;49;00m
            proxy_auth_hdr = #x1B[33m"#x1B[39;49;00m#x1B[33mProxy-Authorization#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m proxy_auth_hdr #x1B[95min#x1B[39;49;00m headers:#x1B[90m#x1B[39;49;00m
                tunnel_headers[proxy_auth_hdr] = headers[proxy_auth_hdr]#x1B[90m#x1B[39;49;00m
                #x1B[90m# Proxy-Authorization should not be sent to origin#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[90m# server.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[94mdel#x1B[39;49;00m headers[proxy_auth_hdr]#x1B[90m#x1B[39;49;00m
            h.set_tunnel(req._tunnel_host, headers=tunnel_headers)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>               h.request(req.get_method(), req.selector, req.data, headers,#x1B[90m#x1B[39;49;00m
                          encode_chunked=req.has_header(#x1B[33m'#x1B[39;49;00m#x1B[33mTransfer-encoding#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m))#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:1319: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1338: in request
    #x1B[0m#x1B[96mself#x1B[39;49;00m._send_request(method, url, body, headers, encode_chunked)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1384: in _send_request
    #x1B[0m#x1B[96mself#x1B[39;49;00m.endheaders(body, encode_chunked=encode_chunked)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1333: in endheaders
    #x1B[0m#x1B[96mself#x1B[39;49;00m._send_output(message_body, encode_chunked=encode_chunked)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1093: in _send_output
    #x1B[0m#x1B[96mself#x1B[39;49;00m.send(msg)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1037: in send
    #x1B[0m#x1B[96mself#x1B[39;49;00m.connect()#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1472: in connect
    #x1B[0m#x1B[96msuper#x1B[39;49;00m().connect()#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1003: in connect
    #x1B[0m#x1B[96mself#x1B[39;49;00m.sock = #x1B[96mself#x1B[39;49;00m._create_connection(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/socket.py#x1B[0m:864: in create_connection
    #x1B[0m#x1B[94mraise#x1B[39;49;00m exceptions[#x1B[94m0#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

address = ('falexwolf.de', 443), timeout = <object object at 0x7f404d180900>
source_address = None

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mcreate_connection#x1B[39;49;00m(address, timeout=_GLOBAL_DEFAULT_TIMEOUT,#x1B[90m#x1B[39;49;00m
                          source_address=#x1B[94mNone#x1B[39;49;00m, *, all_errors=#x1B[94mFalse#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Connect to *address* and return the socket object.#x1B[39;49;00m
    #x1B[33m#x1B[39;49;00m
    #x1B[33m    Convenience function.  Connect to *address* (a 2-tuple ``(host,#x1B[39;49;00m
    #x1B[33m    port)``) and return the socket object.  Passing the optional#x1B[39;49;00m
    #x1B[33m    *timeout* parameter will set the timeout on the socket instance#x1B[39;49;00m
    #x1B[33m    before attempting to connect.  If no *timeout* is supplied, the#x1B[39;49;00m
    #x1B[33m    global default timeout setting returned by :func:`getdefaulttimeout`#x1B[39;49;00m
    #x1B[33m    is used.  If *source_address* is set it must be a tuple of (host, port)#x1B[39;49;00m
    #x1B[33m    for the socket to bind as a source address before making the connection.#x1B[39;49;00m
    #x1B[33m    A host of '' or port 0 tells the OS to use the default. When a connection#x1B[39;49;00m
    #x1B[33m    cannot be created, raises the last error if *all_errors* is False,#x1B[39;49;00m
    #x1B[33m    and an ExceptionGroup of all errors if *all_errors* is True.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        host, port = address#x1B[90m#x1B[39;49;00m
        exceptions = []#x1B[90m#x1B[39;49;00m
        #x1B[94mfor#x1B[39;49;00m res #x1B[95min#x1B[39;49;00m getaddrinfo(host, port, #x1B[94m0#x1B[39;49;00m, SOCK_STREAM):#x1B[90m#x1B[39;49;00m
            af, socktype, proto, canonname, sa = res#x1B[90m#x1B[39;49;00m
            sock = #x1B[94mNone#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                sock = socket(af, socktype, proto)#x1B[90m#x1B[39;49;00m
                #x1B[94mif#x1B[39;49;00m timeout #x1B[95mis#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m _GLOBAL_DEFAULT_TIMEOUT:#x1B[90m#x1B[39;49;00m
                    sock.settimeout(timeout)#x1B[90m#x1B[39;49;00m
                #x1B[94mif#x1B[39;49;00m source_address:#x1B[90m#x1B[39;49;00m
                    sock.bind(source_address)#x1B[90m#x1B[39;49;00m
>               sock.connect(sa)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE               TimeoutError: [Errno 110] Connection timed out#x1B[0m

#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/socket.py#x1B[0m:849: TimeoutError

#x1B[33mDuring handling of the above exception, another exception occurred:#x1B[0m

url = 'https://falexwolf.de/data/pbmc3k_raw.h5ad'
path = PosixPath('data/pbmc3k_raw.h5ad')

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92m_download#x1B[39;49;00m(url: #x1B[96mstr#x1B[39;49;00m, path: Path):#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96murllib#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96merror#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m URLError#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96murllib#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mrequest#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m Request, urlopen#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mtqdm#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mauto#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m tqdm#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        blocksize = #x1B[94m1024#x1B[39;49;00m * #x1B[94m8#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        blocknum = #x1B[94m0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            req = Request(url, headers={#x1B[33m"#x1B[39;49;00m#x1B[33mUser-agent#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m: #x1B[33m"#x1B[39;49;00m#x1B[33mscanpy-user#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m})#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>               open_url = urlopen(req)#x1B[90m#x1B[39;49;00m
                           ^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:1080: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:189: in urlopen
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m opener.open(url, data, timeout)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:489: in open
    #x1B[0mresponse = #x1B[96mself#x1B[39;49;00m._open(req, data)#x1B[90m#x1B[39;49;00m
               ^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:506: in _open
    #x1B[0mresult = #x1B[96mself#x1B[39;49;00m._call_chain(#x1B[96mself#x1B[39;49;00m.handle_open, protocol, protocol +#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:466: in _call_chain
    #x1B[0mresult = func(*args)#x1B[90m#x1B[39;49;00m
             ^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:1367: in https_open
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m.do_open(http.client.HTTPSConnection, req,#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <urllib.request.HTTPSHandler object at 0x7f400af10440>
http_class = <class 'http.client.HTTPSConnection'>
req = <urllib.request.Request object at 0x7f400e95b620>
http_conn_args = {'context': <ssl.SSLContext object at 0x7f400f60c0e0>}
host = 'falexwolf.de'
h = <http.client.HTTPSConnection object at 0x7f400af10590>
headers = {'Connection': 'close', 'Host': 'falexwolf.de', 'User-Agent': 'scanpy-user'}

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mdo_open#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, http_class, req, **http_conn_args):#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Return an HTTPResponse object for the request, using http_class.#x1B[39;49;00m
    #x1B[33m#x1B[39;49;00m
    #x1B[33m    http_class must implement the HTTPConnection API from http.client.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        host = req.host#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m host:#x1B[90m#x1B[39;49;00m
            #x1B[94mraise#x1B[39;49;00m URLError(#x1B[33m'#x1B[39;49;00m#x1B[33mno host given#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# will parse host:port#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        h = http_class(host, timeout=req.timeout, **http_conn_args)#x1B[90m#x1B[39;49;00m
        h.set_debuglevel(#x1B[96mself#x1B[39;49;00m._debuglevel)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        headers = #x1B[96mdict#x1B[39;49;00m(req.unredirected_hdrs)#x1B[90m#x1B[39;49;00m
        headers.update({k: v #x1B[94mfor#x1B[39;49;00m k, v #x1B[95min#x1B[39;49;00m req.headers.items()#x1B[90m#x1B[39;49;00m
                        #x1B[94mif#x1B[39;49;00m k #x1B[95mnot#x1B[39;49;00m #x1B[95min#x1B[39;49;00m headers})#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# TODO(jhylton): Should this be redesigned to handle#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# persistent connections?#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# We want to make an HTTP/1.1 request, but the addinfourl#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# class isn't prepared to deal with a persistent connection.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# It will try to read all remaining data from the socket,#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# which will block while the server waits for the next request.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# So make sure the connection gets closed after the (only)#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# request.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        headers[#x1B[33m"#x1B[39;49;00m#x1B[33mConnection#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] = #x1B[33m"#x1B[39;49;00m#x1B[33mclose#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        headers = {name.title(): val #x1B[94mfor#x1B[39;49;00m name, val #x1B[95min#x1B[39;49;00m headers.items()}#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m req._tunnel_host:#x1B[90m#x1B[39;49;00m
            tunnel_headers = {}#x1B[90m#x1B[39;49;00m
            proxy_auth_hdr = #x1B[33m"#x1B[39;49;00m#x1B[33mProxy-Authorization#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m proxy_auth_hdr #x1B[95min#x1B[39;49;00m headers:#x1B[90m#x1B[39;49;00m
                tunnel_headers[proxy_auth_hdr] = headers[proxy_auth_hdr]#x1B[90m#x1B[39;49;00m
                #x1B[90m# Proxy-Authorization should not be sent to origin#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[90m# server.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[94mdel#x1B[39;49;00m headers[proxy_auth_hdr]#x1B[90m#x1B[39;49;00m
            h.set_tunnel(req._tunnel_host, headers=tunnel_headers)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                h.request(req.get_method(), req.selector, req.data, headers,#x1B[90m#x1B[39;49;00m
                          encode_chunked=req.has_header(#x1B[33m'#x1B[39;49;00m#x1B[33mTransfer-encoding#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m))#x1B[90m#x1B[39;49;00m
            #x1B[94mexcept#x1B[39;49;00m #x1B[96mOSError#x1B[39;49;00m #x1B[94mas#x1B[39;49;00m err: #x1B[90m# timeout error#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
>               #x1B[94mraise#x1B[39;49;00m URLError(err)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE               urllib.error.URLError: <urlopen error [Errno 110] Connection timed out>#x1B[0m

#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:1322: URLError

#x1B[33mDuring handling of the above exception, another exception occurred:#x1B[0m

request = <SubRequest 'pbmc3ks_parametrized_session' for <Function test_pearson_residuals_general[csr_matrix-int64-200n-inftheta-noclip-full]>>

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.fixture(#x1B[90m#x1B[39;49;00m
        scope=#x1B[33m"#x1B[39;49;00m#x1B[33msession#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
        params=#x1B[96mlist#x1B[39;49;00m(#x1B[90m#x1B[39;49;00m
            product([sparse.csr_matrix.toarray, sparse.csr_matrix], [#x1B[33m"#x1B[39;49;00m#x1B[33mfloat32#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mint64#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])  #x1B[90m# noqa: TID251#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        ),#x1B[90m#x1B[39;49;00m
        ids=#x1B[94mlambda#x1B[39;49;00m x: #x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mx[#x1B[94m0#x1B[39;49;00m].#x1B[91m__name__#x1B[39;49;00m#x1B[33m}#x1B[39;49;00m#x1B[33m-#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mx[#x1B[94m1#x1B[39;49;00m]#x1B[33m}#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
    )#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mpbmc3ks_parametrized_session#x1B[39;49;00m(request) -> #x1B[96mdict#x1B[39;49;00m[#x1B[96mbool#x1B[39;49;00m, AnnData]:#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96m_helpers#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mdata#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m pbmc3k#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        sparsity_func, dtype = request.param#x1B[90m#x1B[39;49;00m
        #x1B[94mreturn#x1B[39;49;00m {#x1B[90m#x1B[39;49;00m
>           small: _prepare_pbmc_testdata(pbmc3k(), sparsity_func, dtype, small=small)#x1B[90m#x1B[39;49;00m
                                          ^^^^^^^^#x1B[90m#x1B[39;49;00m
            #x1B[94mfor#x1B[39;49;00m small #x1B[95min#x1B[39;49;00m [#x1B[94mTrue#x1B[39;49;00m, #x1B[94mFalse#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
        }#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[.../_pytest/fixtures/data.py#x1B[0m:55: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[.../scanpy/_helpers/data.py#x1B[0m:31: in pbmc3k
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m _pbmc3k().copy()#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/datasets/_utils.py#x1B[0m:20: in wrapper
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m f(*args, **kwargs)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/datasets/_datasets.py#x1B[0m:414: in pbmc3k
    #x1B[0madata = read(settings.datasetdir / #x1B[33m"#x1B[39;49;00m#x1B[33mpbmc3k_raw.h5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, backup_url=url)#x1B[90m#x1B[39;49;00m
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.../site-packages/legacy_api_wrap/__init__.py#x1B[0m:82: in fn_compatible
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m fn(*args_all, **kw)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:152: in read
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m _read(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:836: in _read
    #x1B[0mis_present = _check_datafile_present_and_download(filename, backup_url=backup_url)#x1B[90m#x1B[39;49;00m
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:1139: in _check_datafile_present_and_download
    #x1B[0m_download(backup_url, path)#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

url = 'https://falexwolf.de/data/pbmc3k_raw.h5ad'
path = PosixPath('data/pbmc3k_raw.h5ad')

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92m_download#x1B[39;49;00m(url: #x1B[96mstr#x1B[39;49;00m, path: Path):#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96murllib#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96merror#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m URLError#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96murllib#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mrequest#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m Request, urlopen#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mtqdm#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mauto#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m tqdm#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        blocksize = #x1B[94m1024#x1B[39;49;00m * #x1B[94m8#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        blocknum = #x1B[94m0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            req = Request(url, headers={#x1B[33m"#x1B[39;49;00m#x1B[33mUser-agent#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m: #x1B[33m"#x1B[39;49;00m#x1B[33mscanpy-user#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m})#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                open_url = urlopen(req)#x1B[90m#x1B[39;49;00m
            #x1B[94mexcept#x1B[39;49;00m URLError:#x1B[90m#x1B[39;49;00m
                #x1B[94mif#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m url.startswith(#x1B[33m"#x1B[39;49;00m#x1B[33mhttps://#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
                    #x1B[94mraise#x1B[39;49;00m  #x1B[90m# No need to try using certifi#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
                msg = #x1B[33m"#x1B[39;49;00m#x1B[33mFailed to open the url with default certificates.#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>                   #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mcertifi#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m where#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE                   ModuleNotFoundError: No module named 'certifi'#x1B[0m
#x1B[1m#x1B[31mE                   Failed to open the url with default certificates. Please install `certifi` and try again.#x1B[0m

#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:1087: ModuleNotFoundError

tests/test_highly_variable_genes.py::test_pearson_residuals_general[csr_matrix-int64-200n-100theta-noclip-subset]

Stack Traces | 0s run time

self = <urllib.request.HTTPSHandler object at 0x7f400af10440>
http_class = <class 'http.client.HTTPSConnection'>
req = <urllib.request.Request object at 0x7f400e95b620>
http_conn_args = {'context': <ssl.SSLContext object at 0x7f400f60c0e0>}
host = 'falexwolf.de'
h = <http.client.HTTPSConnection object at 0x7f400af10590>
headers = {'Connection': 'close', 'Host': 'falexwolf.de', 'User-Agent': 'scanpy-user'}

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mdo_open#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, http_class, req, **http_conn_args):#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Return an HTTPResponse object for the request, using http_class.#x1B[39;49;00m
    #x1B[33m#x1B[39;49;00m
    #x1B[33m    http_class must implement the HTTPConnection API from http.client.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        host = req.host#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m host:#x1B[90m#x1B[39;49;00m
            #x1B[94mraise#x1B[39;49;00m URLError(#x1B[33m'#x1B[39;49;00m#x1B[33mno host given#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# will parse host:port#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        h = http_class(host, timeout=req.timeout, **http_conn_args)#x1B[90m#x1B[39;49;00m
        h.set_debuglevel(#x1B[96mself#x1B[39;49;00m._debuglevel)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        headers = #x1B[96mdict#x1B[39;49;00m(req.unredirected_hdrs)#x1B[90m#x1B[39;49;00m
        headers.update({k: v #x1B[94mfor#x1B[39;49;00m k, v #x1B[95min#x1B[39;49;00m req.headers.items()#x1B[90m#x1B[39;49;00m
                        #x1B[94mif#x1B[39;49;00m k #x1B[95mnot#x1B[39;49;00m #x1B[95min#x1B[39;49;00m headers})#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# TODO(jhylton): Should this be redesigned to handle#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# persistent connections?#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# We want to make an HTTP/1.1 request, but the addinfourl#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# class isn't prepared to deal with a persistent connection.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# It will try to read all remaining data from the socket,#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# which will block while the server waits for the next request.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# So make sure the connection gets closed after the (only)#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# request.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        headers[#x1B[33m"#x1B[39;49;00m#x1B[33mConnection#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] = #x1B[33m"#x1B[39;49;00m#x1B[33mclose#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        headers = {name.title(): val #x1B[94mfor#x1B[39;49;00m name, val #x1B[95min#x1B[39;49;00m headers.items()}#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m req._tunnel_host:#x1B[90m#x1B[39;49;00m
            tunnel_headers = {}#x1B[90m#x1B[39;49;00m
            proxy_auth_hdr = #x1B[33m"#x1B[39;49;00m#x1B[33mProxy-Authorization#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m proxy_auth_hdr #x1B[95min#x1B[39;49;00m headers:#x1B[90m#x1B[39;49;00m
                tunnel_headers[proxy_auth_hdr] = headers[proxy_auth_hdr]#x1B[90m#x1B[39;49;00m
                #x1B[90m# Proxy-Authorization should not be sent to origin#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[90m# server.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[94mdel#x1B[39;49;00m headers[proxy_auth_hdr]#x1B[90m#x1B[39;49;00m
            h.set_tunnel(req._tunnel_host, headers=tunnel_headers)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>               h.request(req.get_method(), req.selector, req.data, headers,#x1B[90m#x1B[39;49;00m
                          encode_chunked=req.has_header(#x1B[33m'#x1B[39;49;00m#x1B[33mTransfer-encoding#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m))#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:1319: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1338: in request
    #x1B[0m#x1B[96mself#x1B[39;49;00m._send_request(method, url, body, headers, encode_chunked)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1384: in _send_request
    #x1B[0m#x1B[96mself#x1B[39;49;00m.endheaders(body, encode_chunked=encode_chunked)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1333: in endheaders
    #x1B[0m#x1B[96mself#x1B[39;49;00m._send_output(message_body, encode_chunked=encode_chunked)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1093: in _send_output
    #x1B[0m#x1B[96mself#x1B[39;49;00m.send(msg)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1037: in send
    #x1B[0m#x1B[96mself#x1B[39;49;00m.connect()#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1472: in connect
    #x1B[0m#x1B[96msuper#x1B[39;49;00m().connect()#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/http/client.py#x1B[0m:1003: in connect
    #x1B[0m#x1B[96mself#x1B[39;49;00m.sock = #x1B[96mself#x1B[39;49;00m._create_connection(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/socket.py#x1B[0m:864: in create_connection
    #x1B[0m#x1B[94mraise#x1B[39;49;00m exceptions[#x1B[94m0#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

address = ('falexwolf.de', 443), timeout = <object object at 0x7f404d180900>
source_address = None

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mcreate_connection#x1B[39;49;00m(address, timeout=_GLOBAL_DEFAULT_TIMEOUT,#x1B[90m#x1B[39;49;00m
                          source_address=#x1B[94mNone#x1B[39;49;00m, *, all_errors=#x1B[94mFalse#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Connect to *address* and return the socket object.#x1B[39;49;00m
    #x1B[33m#x1B[39;49;00m
    #x1B[33m    Convenience function.  Connect to *address* (a 2-tuple ``(host,#x1B[39;49;00m
    #x1B[33m    port)``) and return the socket object.  Passing the optional#x1B[39;49;00m
    #x1B[33m    *timeout* parameter will set the timeout on the socket instance#x1B[39;49;00m
    #x1B[33m    before attempting to connect.  If no *timeout* is supplied, the#x1B[39;49;00m
    #x1B[33m    global default timeout setting returned by :func:`getdefaulttimeout`#x1B[39;49;00m
    #x1B[33m    is used.  If *source_address* is set it must be a tuple of (host, port)#x1B[39;49;00m
    #x1B[33m    for the socket to bind as a source address before making the connection.#x1B[39;49;00m
    #x1B[33m    A host of '' or port 0 tells the OS to use the default. When a connection#x1B[39;49;00m
    #x1B[33m    cannot be created, raises the last error if *all_errors* is False,#x1B[39;49;00m
    #x1B[33m    and an ExceptionGroup of all errors if *all_errors* is True.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        host, port = address#x1B[90m#x1B[39;49;00m
        exceptions = []#x1B[90m#x1B[39;49;00m
        #x1B[94mfor#x1B[39;49;00m res #x1B[95min#x1B[39;49;00m getaddrinfo(host, port, #x1B[94m0#x1B[39;49;00m, SOCK_STREAM):#x1B[90m#x1B[39;49;00m
            af, socktype, proto, canonname, sa = res#x1B[90m#x1B[39;49;00m
            sock = #x1B[94mNone#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                sock = socket(af, socktype, proto)#x1B[90m#x1B[39;49;00m
                #x1B[94mif#x1B[39;49;00m timeout #x1B[95mis#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m _GLOBAL_DEFAULT_TIMEOUT:#x1B[90m#x1B[39;49;00m
                    sock.settimeout(timeout)#x1B[90m#x1B[39;49;00m
                #x1B[94mif#x1B[39;49;00m source_address:#x1B[90m#x1B[39;49;00m
                    sock.bind(source_address)#x1B[90m#x1B[39;49;00m
>               sock.connect(sa)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE               TimeoutError: [Errno 110] Connection timed out#x1B[0m

#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/socket.py#x1B[0m:849: TimeoutError

#x1B[33mDuring handling of the above exception, another exception occurred:#x1B[0m

url = 'https://falexwolf.de/data/pbmc3k_raw.h5ad'
path = PosixPath('data/pbmc3k_raw.h5ad')

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92m_download#x1B[39;49;00m(url: #x1B[96mstr#x1B[39;49;00m, path: Path):#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96murllib#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96merror#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m URLError#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96murllib#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mrequest#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m Request, urlopen#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mtqdm#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mauto#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m tqdm#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        blocksize = #x1B[94m1024#x1B[39;49;00m * #x1B[94m8#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        blocknum = #x1B[94m0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            req = Request(url, headers={#x1B[33m"#x1B[39;49;00m#x1B[33mUser-agent#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m: #x1B[33m"#x1B[39;49;00m#x1B[33mscanpy-user#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m})#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>               open_url = urlopen(req)#x1B[90m#x1B[39;49;00m
                           ^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:1080: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:189: in urlopen
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m opener.open(url, data, timeout)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:489: in open
    #x1B[0mresponse = #x1B[96mself#x1B[39;49;00m._open(req, data)#x1B[90m#x1B[39;49;00m
               ^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:506: in _open
    #x1B[0mresult = #x1B[96mself#x1B[39;49;00m._call_chain(#x1B[96mself#x1B[39;49;00m.handle_open, protocol, protocol +#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:466: in _call_chain
    #x1B[0mresult = func(*args)#x1B[90m#x1B[39;49;00m
             ^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:1367: in https_open
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m.do_open(http.client.HTTPSConnection, req,#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <urllib.request.HTTPSHandler object at 0x7f400af10440>
http_class = <class 'http.client.HTTPSConnection'>
req = <urllib.request.Request object at 0x7f400e95b620>
http_conn_args = {'context': <ssl.SSLContext object at 0x7f400f60c0e0>}
host = 'falexwolf.de'
h = <http.client.HTTPSConnection object at 0x7f400af10590>
headers = {'Connection': 'close', 'Host': 'falexwolf.de', 'User-Agent': 'scanpy-user'}

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mdo_open#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, http_class, req, **http_conn_args):#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Return an HTTPResponse object for the request, using http_class.#x1B[39;49;00m
    #x1B[33m#x1B[39;49;00m
    #x1B[33m    http_class must implement the HTTPConnection API from http.client.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        host = req.host#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m host:#x1B[90m#x1B[39;49;00m
            #x1B[94mraise#x1B[39;49;00m URLError(#x1B[33m'#x1B[39;49;00m#x1B[33mno host given#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# will parse host:port#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        h = http_class(host, timeout=req.timeout, **http_conn_args)#x1B[90m#x1B[39;49;00m
        h.set_debuglevel(#x1B[96mself#x1B[39;49;00m._debuglevel)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        headers = #x1B[96mdict#x1B[39;49;00m(req.unredirected_hdrs)#x1B[90m#x1B[39;49;00m
        headers.update({k: v #x1B[94mfor#x1B[39;49;00m k, v #x1B[95min#x1B[39;49;00m req.headers.items()#x1B[90m#x1B[39;49;00m
                        #x1B[94mif#x1B[39;49;00m k #x1B[95mnot#x1B[39;49;00m #x1B[95min#x1B[39;49;00m headers})#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# TODO(jhylton): Should this be redesigned to handle#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# persistent connections?#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# We want to make an HTTP/1.1 request, but the addinfourl#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# class isn't prepared to deal with a persistent connection.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# It will try to read all remaining data from the socket,#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# which will block while the server waits for the next request.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# So make sure the connection gets closed after the (only)#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# request.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        headers[#x1B[33m"#x1B[39;49;00m#x1B[33mConnection#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] = #x1B[33m"#x1B[39;49;00m#x1B[33mclose#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        headers = {name.title(): val #x1B[94mfor#x1B[39;49;00m name, val #x1B[95min#x1B[39;49;00m headers.items()}#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m req._tunnel_host:#x1B[90m#x1B[39;49;00m
            tunnel_headers = {}#x1B[90m#x1B[39;49;00m
            proxy_auth_hdr = #x1B[33m"#x1B[39;49;00m#x1B[33mProxy-Authorization#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m proxy_auth_hdr #x1B[95min#x1B[39;49;00m headers:#x1B[90m#x1B[39;49;00m
                tunnel_headers[proxy_auth_hdr] = headers[proxy_auth_hdr]#x1B[90m#x1B[39;49;00m
                #x1B[90m# Proxy-Authorization should not be sent to origin#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[90m# server.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[94mdel#x1B[39;49;00m headers[proxy_auth_hdr]#x1B[90m#x1B[39;49;00m
            h.set_tunnel(req._tunnel_host, headers=tunnel_headers)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                h.request(req.get_method(), req.selector, req.data, headers,#x1B[90m#x1B[39;49;00m
                          encode_chunked=req.has_header(#x1B[33m'#x1B[39;49;00m#x1B[33mTransfer-encoding#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m))#x1B[90m#x1B[39;49;00m
            #x1B[94mexcept#x1B[39;49;00m #x1B[96mOSError#x1B[39;49;00m #x1B[94mas#x1B[39;49;00m err: #x1B[90m# timeout error#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
>               #x1B[94mraise#x1B[39;49;00m URLError(err)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE               urllib.error.URLError: <urlopen error [Errno 110] Connection timed out>#x1B[0m

#x1B[1m#x1B[31m../../../..../uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/urllib/request.py#x1B[0m:1322: URLError

#x1B[33mDuring handling of the above exception, another exception occurred:#x1B[0m

request = <SubRequest 'pbmc3ks_parametrized_session' for <Function test_pearson_residuals_general[csr_matrix-int64-200n-inftheta-noclip-full]>>

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.fixture(#x1B[90m#x1B[39;49;00m
        scope=#x1B[33m"#x1B[39;49;00m#x1B[33msession#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
        params=#x1B[96mlist#x1B[39;49;00m(#x1B[90m#x1B[39;49;00m
            product([sparse.csr_matrix.toarray, sparse.csr_matrix], [#x1B[33m"#x1B[39;49;00m#x1B[33mfloat32#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mint64#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])  #x1B[90m# noqa: TID251#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        ),#x1B[90m#x1B[39;49;00m
        ids=#x1B[94mlambda#x1B[39;49;00m x: #x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mx[#x1B[94m0#x1B[39;49;00m].#x1B[91m__name__#x1B[39;49;00m#x1B[33m}#x1B[39;49;00m#x1B[33m-#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mx[#x1B[94m1#x1B[39;49;00m]#x1B[33m}#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
    )#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mpbmc3ks_parametrized_session#x1B[39;49;00m(request) -> #x1B[96mdict#x1B[39;49;00m[#x1B[96mbool#x1B[39;49;00m, AnnData]:#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96m_helpers#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mdata#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m pbmc3k#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        sparsity_func, dtype = request.param#x1B[90m#x1B[39;49;00m
        #x1B[94mreturn#x1B[39;49;00m {#x1B[90m#x1B[39;49;00m
>           small: _prepare_pbmc_testdata(pbmc3k(), sparsity_func, dtype, small=small)#x1B[90m#x1B[39;49;00m
                                          ^^^^^^^^#x1B[90m#x1B[39;49;00m
            #x1B[94mfor#x1B[39;49;00m small #x1B[95min#x1B[39;49;00m [#x1B[94mTrue#x1B[39;49;00m, #x1B[94mFalse#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
        }#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[.../_pytest/fixtures/data.py#x1B[0m:55: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[.../scanpy/_helpers/data.py#x1B[0m:31: in pbmc3k
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m _pbmc3k().copy()#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/datasets/_utils.py#x1B[0m:20: in wrapper
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m f(*args, **kwargs)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/datasets/_datasets.py#x1B[0m:414: in pbmc3k
    #x1B[0madata = read(settings.datasetdir / #x1B[33m"#x1B[39;49;00m#x1B[33mpbmc3k_raw.h5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, backup_url=url)#x1B[90m#x1B[39;49;00m
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.../site-packages/legacy_api_wrap/__init__.py#x1B[0m:82: in fn_compatible
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m fn(*args_all, **kw)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:152: in read
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m _read(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:836: in _read
    #x1B[0mis_present = _check_datafile_present_and_download(filename, backup_url=backup_url)#x1B[90m#x1B[39;49;00m
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:1139: in _check_datafile_present_and_download
    #x1B[0m_download(backup_url, path)#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

url = 'https://falexwolf.de/data/pbmc3k_raw.h5ad'
path = PosixPath('data/pbmc3k_raw.h5ad')

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92m_download#x1B[39;49;00m(url: #x1B[96mstr#x1B[39;49;00m, path: Path):#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96murllib#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96merror#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m URLError#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96murllib#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mrequest#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m Request, urlopen#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mtqdm#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mauto#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m tqdm#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        blocksize = #x1B[94m1024#x1B[39;49;00m * #x1B[94m8#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        blocknum = #x1B[94m0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            req = Request(url, headers={#x1B[33m"#x1B[39;49;00m#x1B[33mUser-agent#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m: #x1B[33m"#x1B[39;49;00m#x1B[33mscanpy-user#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m})#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
            #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                open_url = urlopen(req)#x1B[90m#x1B[39;49;00m
            #x1B[94mexcept#x1B[39;49;00m URLError:#x1B[90m#x1B[39;49;00m
                #x1B[94mif#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m url.startswith(#x1B[33m"#x1B[39;49;00m#x1B[33mhttps://#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
                    #x1B[94mraise#x1B[39;49;00m  #x1B[90m# No need to try using certifi#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
                msg = #x1B[33m"#x1B[39;49;00m#x1B[33mFailed to open the url with default certificates.#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>                   #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mcertifi#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m where#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE                   ModuleNotFoundError: No module named 'certifi'#x1B[0m
#x1B[1m#x1B[31mE                   Failed to open the url with default certificates. Please install `certifi` and try again.#x1B[0m

#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:1087: ModuleNotFoundError

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Fix variable names

1e68c7a

flying-sheep changed the title ~~Fix variable names~~ style: Fix variable names Sep 4, 2025

flying-sheep added this to the 1.11.4 milestone Sep 4, 2025

flying-sheep added 3 commits September 4, 2025 11:44

fix paga

58e6253

fix metrics

855d3c2

fix _read_softgz

3eb2ebd

flying-sheep merged commit 9dceb9e into main Sep 4, 2025
10 of 11 checks passed

flying-sheep deleted the pa/fix-names branch September 4, 2025 10:46

lumberbot-app bot added the Still Needs Manual Backport label Sep 4, 2025

flying-sheep added a commit that referenced this pull request Sep 4, 2025

Backport PR #3785: style: Fix variable names

893d36f

flying-sheep mentioned this pull request Sep 4, 2025

Backport PR #3785 on branch 1.11.x (style: Fix variable names) #3786

Merged

flying-sheep removed the Still Needs Manual Backport label Sep 4, 2025

scverse deleted a comment from lumberbot-app bot Sep 4, 2025

flying-sheep added a commit that referenced this pull request Sep 4, 2025

Backport PR #3785 on branch 1.11.x (style: Fix variable names) (#3786)

d98d75b

flying-sheep mentioned this pull request Apr 11, 2025

Extend linter config scverse/anndata#1241

Open

18 tasks

Nismamjad1 pushed a commit to Nismamjad1/scanpy-yomix that referenced this pull request Oct 3, 2025

style: Fix variable names (scverse#3785)

0b48e9e

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style: Fix variable names #3785

style: Fix variable names #3785

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flying-sheep commented Sep 4, 2025 •

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style: Fix variable names #3785

style: Fix variable names #3785

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flying-sheep commented Sep 4, 2025 •

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