Unable to install 'bio' package

[LiSun92]

Hey guys;
So I'm pretty new to bioinformatics, just trying to install biostar handbook as instructed (windows system, ubuntu 22.04). The automatic installation consistently fails at step 6/10 (bio installation), so I tried the step-by-step method; the same error occurs at the bio stage. I'm in China if that helps, tends to do funny things to net connections. Already tried doing this with VPN on/off.

$ pip install bio --upgrade
Collecting bio
Using cached bio-1.5.9-py3-none-any.whl (276 kB)
Collecting biopython>=1.80 (from bio)
Downloading biopython-1.81-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0.2/3.1 MB 14.5 kB/s eta 0:03:22
ERROR: Exception:
Traceback (most recent call last):
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_vendor/urllib3/response.py", line 438, in _error_catcher
yield
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_vendor/urllib3/response.py", line 561, in read
data = self._fp_read(amt) if not fp_closed else b""
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_vendor/urllib3/response.py", line 527, in _fp_read
return self._fp.read(amt) if amt is not None else self._fp.read()
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_vendor/cachecontrol/filewrapper.py", line 90, in read
data = self.__fp.read(amt)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/http/client.py", line 459, in read
n = self.readinto(b)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/http/client.py", line 503, in readinto
n = self.fp.readinto(b)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/socket.py", line 669, in readinto
return self._sock.recv_into(b)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/ssl.py", line 1241, in recv_into
return self.read(nbytes, buffer)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/ssl.py", line 1099, in read
return self._sslobj.read(len, buffer)
socket.timeout: The read operation timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
status = run_func(*args)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 248, in wrapper
return func(self, options, args)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/commands/install.py", line 377, in run
requirement_set = resolver.resolve(
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 92, in resolve
result = self._result = resolver.resolve(
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_vendor/resolvelib/resolvers.py", line 546, in resolve
state = resolution.resolve(requirements, max_rounds=max_rounds)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_vendor/resolvelib/resolvers.py", line 427, in resolve
failure_causes = self._attempt_to_pin_criterion(name)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_vendor/resolvelib/resolvers.py", line 239, in _attempt_to_pin_criterion
criteria = self._get_updated_criteria(candidate)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_vendor/resolvelib/resolvers.py", line 230, in _get_updated_criteria
self._add_to_criteria(criteria, requirement, parent=candidate)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_vendor/resolvelib/resolvers.py", line 173, in _add_to_criteria
if not criterion.candidates:
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_vendor/resolvelib/structs.py", line 156, in bool
return bool(self._sequence)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in bool
return any(self)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 143, in
return (c for c in iterator if id(c) not in self._incompatible_ids)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 47, in _iter_built
candidate = func()
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 206, in _make_candidate_from_link
self._link_candidate_cache[link] = LinkCandidate(
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 293, in init
super().init(
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in init
self.dist = self._prepare()
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 225, in _prepare
dist = self._prepare_distribution()
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in _prepare_distribution
return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/operations/prepare.py", line 538, in prepare_linked_requirement
return self._prepare_linked_requirement(req, parallel_builds)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/operations/prepare.py", line 609, in _prepare_linked_requirement
local_file = unpack_url(
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/operations/prepare.py", line 166, in unpack_url
file = get_http_url(
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/operations/prepare.py", line 107, in get_http_url
from_path, content_type = download(link, temp_dir.path)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/network/download.py", line 147, in call
for chunk in chunks:
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/cli/progress_bars.py", line 53, in _rich_progress_bar
for chunk in iterable:
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_internal/network/utils.py", line 63, in response_chunks
for chunk in response.raw.stream(
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_vendor/urllib3/response.py", line 622, in stream
data = self.read(amt=amt, decode_content=decode_content)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_vendor/urllib3/response.py", line 587, in read
raise IncompleteRead(self._fp_bytes_read, self.length_remaining)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/contextlib.py", line 131, in exit
self.gen.throw(type, value, traceback)
File "/home/biouser/micromamba/envs/bioinfo/lib/python3.8/site-packages/pip/_vendor/urllib3/response.py", line 443, in _error_catcher
raise ReadTimeoutError(self._pool, None, "Read timed out.")
pip._vendor.urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out.

[LiSun92]

Nevermind! By setting pip to one of the domestic pypi mirrors, I've solved the issue!

[kw45382]

Nevermind! By setting pip to one of the domestic pypi mirrors, I've solved the issue!

Seemingly insignificant information is a real help, thank you, bro!