Package: src:pymatgen
Version: 2025.2.18+dfsg1-4
Severity: serious
Tags: ftbfs trixie sid

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build:

--------------------------------------------------------------------------------
[...]
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fce1d0e9ba0> err = TimeoutError('The read operation timed out')
url = '/wiki/api.php?action=query&list=categorymembers&cmtitle=Category:INCAR_tag&cmlimit=500&format=json'
timeout_value = 60

def _raise_timeout(
self,
err: BaseSSLError | OSError | SocketTimeout,
url: str,
timeout_value: _TYPE_TIMEOUT | None,
) -> None:
"""Is the error actually a timeout? Will raise a ReadTimeout or pass"""

if isinstance(err, SocketTimeout):

raise ReadTimeoutError(

self, url, f"Read timed out. (read timeout={timeout_value})"
) from err
E urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='www.vasp.at', port=443): Read timed out. (read timeout=60)
--------------------------------------------------------------------------------

The reason is in tests/io/vasp/test_help.py which reads like this:


try:
website_down = requests.get("https://www.vasp.at", timeout=5).status_code != 200
except (requests.exceptions.ConnectionError, requests.exceptions.ReadTimeout):
website_down = True


I guess that for the package build as such, we could do this instead of the above four lines:

website_down = True

and the remaining code would not need to be touched.


But I see in #1103427 that some network tests are deliberately run in CI
so I'm not sure if the above simple fix would be compatible with running
the network tests in CI, so I leave it to you.

Thanks.

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

This is a multi-part message in MIME format.
Hi. I found a different mode of failure today:

=================================== FAILURES ===================================
______________________ TestVaspDoc.test_print_help[ISYM] _______________________

self = <vasp.test_help.TestVaspDoc object at 0x7f34bfc4cb90>, tag = 'ISYM'

@pytest.mark.parametrize("tag", ["ISYM"])
def test_print_help(self, tag):
vasp_doc = VaspDoc()
with patch("sys.stdout", new=io.StringIO()) as fake_stdout:

vasp_doc.print_help(tag)

.pybuild/test_python3.13/tests/io/vasp/test_help.py:26:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ .pybuild/test_python3.13/pymatgen/io/vasp/help.py:32: in print_help
print(self.get_help(tag))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

cls = <class 'pymatgen.io.vasp.help.VaspDoc'>, tag = 'ISYM', fmt = 'text'

@classmethod
def get_help(cls, tag: str, fmt: str = "text") -> str:
"""Get help on a VASP tag.

Args:
tag (str): VASP tag, e.g. ISYM.

Returns:
Help text.
"""
tag = tag.upper()
response = requests.get(
f"https://www.vasp.at/wiki/index.php/{tag}",
timeout=60,
)
soup = BeautifulSoup(response.text, features="html.parser")
main_doc = soup.find(id="mw-content-text")
if fmt == "text":

output = main_doc.text

E AttributeError: 'NoneType' object has no attribute 'text' ---------------------------------------------------------------------

However, this also comes from tests/io/vasp/test_help.py, so
hardcoding website_down to True would also fix this one.

I'm attaching the trivial patch here, but someone should still
determine if it's good enough for the package as a whole
(i.e. considering also the CI tests).

Thanks. LS0tIGEvdGVzdHMvaW8vdmFzcC90ZXN0X2hlbHAucHkKKysrIGIvdGVzdHMvaW8vdmFzcC90 ZXN0X2hlbHAucHkKQEAgLTExLDEwICsxMSw3IEBAIGZyb20gcHltYXRnZW4uaW8udmFzcC5o ZWxwIGltcG9ydCBWYXNwRG9jCiBCZWF1dGlmdWxTb3VwID0gcHl0ZXN0LmltcG9ydG9yc2tp cCgiYnM0IikuQmVhdXRpZnVsU291cAogCiAKLXRyeToKLSAgICB3ZWJzaXRlX2Rvd24gPSBy ZXF1ZXN0cy5nZXQoImh0dHBzOi8vd3d3LnZhc3AuYXQiLCB0aW1lb3V0PTUpLnN0YXR1c19j b2RlICE9IDIwMAotZXhjZXB0IChyZXF1ZXN0cy5leGNlcHRpb25zLkNvbm5lY3Rpb25FcnJv ciwgcmVxdWVzdHMuZXhjZXB0aW9ucy5SZWFkVGltZW91dCk6Ci0gICAgd2Vic2l0ZV9kb3du ID0gVHJ1ZQord2Vic2l0ZV9kb3duID0gVHJ1ZQogCiAKIEBweXRlc3QubWFyay5za2lwaWYo d2Vic2l0ZV9kb3duLCByZWFzb249Ind3dy52YXNwLmF0IGlzIGRvd24iKQo=

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)