Unable to install 'bio' package

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.

biostars / biostar-handbook

Unable to install 'bio' package #286