Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Backport PR #3225: [pre-commit.ci] pre-commit autoupdate #3229

Backport PR #3225: [pre-commit.ci] pre-commit autoupdate

f07b1b9
Select commit
Loading
Failed to load commit list.
Merged

Backport PR #3225: [pre-commit.ci] pre-commit autoupdate #3229

Backport PR #3225: [pre-commit.ci] pre-commit autoupdate
f07b1b9
Select commit
Loading
Failed to load commit list.
Azure Pipelines / scverse.scanpy failed Sep 13, 2024 in 29m 55s

Build #20240913.2 had test failures

Details

Tests

  • Failed: 1 (0.01%)
  • Passed: 8,099 (93.15%)
  • Other: 595 (6.84%)
  • Total: 8,695
Code coverage

  • 9610 of 12569 line covered (76.46%)

Annotations

Check failure on line 2322 in Build log

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

Build log #L2322

Bash exited with code '1'.

Check failure on line 1 in tests/test_datasets.py::test_burczynski06

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

tests/test_datasets.py::test_burczynski06

self = <urllib.request.FTPHandler object at 0x7fb56060c760>
req = <urllib.request.Request object at 0x7fb568320100>

    def ftp_open(self, req):
        import ftplib
        import mimetypes
        host = req.host
        if not host:
            raise URLError('ftp error: no host given')
        host, port = _splitport(host)
        if port is None:
            port = ftplib.FTP_PORT
        else:
            port = int(port)
    
        # username/password handling
        user, host = _splituser(host)
        if user:
            user, passwd = _splitpasswd(user)
        else:
            passwd = None
        host = unquote(host)
        user = user or ''
        passwd = passwd or ''
    
        try:
            host = socket.gethostbyname(host)
        except OSError as msg:
            raise URLError(msg)
        path, attrs = _splitattr(req.selector)
        dirs = path.split('/')
        dirs = list(map(unquote, dirs))
        dirs, file = dirs[:-1], dirs[-1]
        if dirs and not dirs[0]:
            dirs = dirs[1:]
        try:
            fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)
            type = file and 'I' or 'D'
            for attr in attrs:
                attr, value = _splitvalue(attr)
                if attr.lower() == 'type' and \
                   value in ('a', 'A', 'i', 'I', 'd', 'D'):
                    type = value.upper()
>           fp, retrlen = fw.retrfile(file, type)

/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/urllib/request.py:1570: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/urllib/request.py:2434: in retrfile
    conn, retrlen = self.ftp.ntransfercmd(cmd)
/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/ftplib.py:359: in ntransfercmd
    resp = self.sendcmd(cmd)
/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/ftplib.py:281: in sendcmd
    return self.getresp()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <ftplib.FTP object at 0x7fb568776100>

    def getresp(self):
        resp = self.getmultiline()
        if self.debugging:
            print('*resp*', self.sanitize(resp))
        self.lastresp = resp[:3]
        c = resp[:1]
        if c in {'1', '2', '3'}:
            return resp
        if c == '4':
>           raise error_temp(resp)
E           ftplib.error_temp: 421 No transfer timeout (60 seconds): closing control connection

/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/ftplib.py:252: error_temp

During handling of the above exception, another exception occurred:

url = 'ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS1nnn/GDS1615/soft/GDS1615_full.soft.gz'
path = PosixPath('/tmp/pytest-of-vsts/pytest-0/test_burczynski060/scanpy_data/burczynski06/GDS1615_full.soft.gz')

    def _download(url: str, path: Path):
        try:
            import ipywidgets  # noqa: F401
            from tqdm.auto import tqdm
        except ImportError:
            from tqdm import tqdm
    
        from urllib.error import URLError
        from urllib.request import Request, urlopen
    
        blocksize = 1024 * 8
        blocknum = 0
    
        try:
            req = Request(url, headers={"User-agent": "scanpy-user"})
    
            try:
>               open_url = urlopen(req)

/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/scanpy/readwrite.py:1001: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/urllib/request.py:214: in urlopen
    return opener.open(url, data, timeout)
/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/urllib/request.py:517: in open
    response = self._open(req, data)
/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/urllib/request.py:534: in _open
    result = self._call_chain(self.handle_open, protocol, protocol +
/opt/hostedtoolcache/Python/3.9.19/x6
Raw output
/home/vsts/work/1/s/tests/test_datasets.py:39: Failed: DID NOT WARN. No warnings of type (<class 'UserWarning'>,) were emitted.