Unable to install DIG in Colab environment

[chriswu99aaa]

Hi I am trying to use DIG on Colab. I have installed and checked the pytorch and pytorch geometric version, which are satisfied. I have encountered the following error message when running the command !pip install dive-into-graphs. I was trying to build from git installation, and I have git clone the code, and changed the directory to the DIG

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Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/
Processing /content/DIG
Preparing metadata (setup.py) ... done
Requirement already satisfied: scipy in /usr/local/lib/python3.8/dist-packages (from dive-into-graphs==1.0.0) (1.7.3)
Collecting cilog
Using cached cilog-1.2.3-py3-none-any.whl (14 kB)
Collecting typed-argument-parser==1.7.2
Using cached typed-argument-parser-1.7.2.tar.gz (27 kB)
Preparing metadata (setup.py) ... done
Collecting captum==0.2.0
Using cached captum-0.2.0-py3-none-any.whl (1.4 MB)
Collecting munch
Using cached munch-2.5.0-py2.py3-none-any.whl (10 kB)
Requirement already satisfied: gdown in /usr/local/lib/python3.8/dist-packages (from dive-into-graphs==1.0.0) (4.4.0)
Collecting shap
Using cached shap-0.41.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (575 kB)
Requirement already satisfied: IPython in /usr/local/lib/python3.8/dist-packages (from dive-into-graphs==1.0.0) (7.9.0)
Requirement already satisfied: tqdm in /usr/local/lib/python3.8/dist-packages (from dive-into-graphs==1.0.0) (4.64.1)
Collecting rdkit-pypi
Using cached rdkit_pypi-2022.9.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (29.3 MB)
Requirement already satisfied: pandas in /usr/local/lib/python3.8/dist-packages (from dive-into-graphs==1.0.0) (1.3.5)
Requirement already satisfied: sympy in /usr/local/lib/python3.8/dist-packages (from dive-into-graphs==1.0.0) (1.7.1)
Collecting pyscf==1.7.6
Downloading pyscf-1.7.6-cp38-cp38-manylinux1_x86_64.whl (29.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━ 17.8/29.7 MB 166.9 MB/s eta 0:00:01
ERROR: Exception:
Traceback (most recent call last):
File "/usr/local/lib/python3.8/dist-packages/pip/_vendor/urllib3/response.py", line 438, in _error_catcher
yield
File "/usr/local/lib/python3.8/dist-packages/pip/_vendor/urllib3/response.py", line 519, in read
data = self._fp.read(amt) if not fp_closed else b""
File "/usr/local/lib/python3.8/dist-packages/pip/_vendor/cachecontrol/filewrapper.py", line 90, in read
data = self.__fp.read(amt)
File "/usr/lib/python3.8/http/client.py", line 459, in read
n = self.readinto(b)
File "/usr/lib/python3.8/http/client.py", line 503, in readinto
n = self.fp.readinto(b)
File "/usr/lib/python3.8/socket.py", line 669, in readinto
return self._sock.recv_into(b)
File "/usr/lib/python3.8/ssl.py", line 1241, in recv_into
return self.read(nbytes, buffer)
File "/usr/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 "/usr/local/lib/python3.8/dist-packages/pip/_internal/cli/base_command.py", line 167, in exc_logging_wrapper
status = run_func(*args)
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/cli/req_command.py", line 199, in wrapper
return func(self, options, args)
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/commands/install.py", line 339, in run
requirement_set = resolver.resolve(
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 94, in resolve
result = self._result = resolver.resolve(
File "/usr/local/lib/python3.8/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 481, in resolve
state = resolution.resolve(requirements, max_rounds=max_rounds)
File "/usr/local/lib/python3.8/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 373, in resolve
failure_causes = self._attempt_to_pin_criterion(name)
File "/usr/local/lib/python3.8/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 213, in _attempt_to_pin_criterion
criteria = self._get_updated_criteria(candidate)
File "/usr/local/lib/python3.8/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 204, in _get_updated_criteria
self._add_to_criteria(criteria, requirement, parent=candidate)
File "/usr/local/lib/python3.8/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 172, in _add_to_criteria
if not criterion.candidates:
File "/usr/local/lib/python3.8/dist-packages/pip/_vendor/resolvelib/structs.py", line 151, in bool
return bool(self._sequence)
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in bool
return any(self)
File "/usr/local/lib/python3.8/dist-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 "/usr/local/lib/python3.8/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 47, in _iter_built
candidate = func()
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 215, in _make_candidate_from_link
self._link_candidate_cache[link] = LinkCandidate(
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 288, in init
super().init(
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 158, in init
self.dist = self._prepare()
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 227, in _prepare
dist = self._prepare_distribution()
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 299, in _prepare_distribution
return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/operations/prepare.py", line 487, in prepare_linked_requirement
return self._prepare_linked_requirement(req, parallel_builds)
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/operations/prepare.py", line 532, in _prepare_linked_requirement
local_file = unpack_url(
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/operations/prepare.py", line 214, in unpack_url
file = get_http_url(
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/operations/prepare.py", line 94, in get_http_url
from_path, content_type = download(link, temp_dir.path)
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/network/download.py", line 146, in call
for chunk in chunks:
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/cli/progress_bars.py", line 304, in _rich_progress_bar
for chunk in iterable:
File "/usr/local/lib/python3.8/dist-packages/pip/_internal/network/utils.py", line 63, in response_chunks
for chunk in response.raw.stream(
File "/usr/local/lib/python3.8/dist-packages/pip/_vendor/urllib3/response.py", line 576, in stream
data = self.read(amt=amt, decode_content=decode_content)
File "/usr/local/lib/python3.8/dist-packages/pip/_vendor/urllib3/response.py", line 541, in read
raise IncompleteRead(self._fp_bytes_read, self.length_remaining)
File "/usr/lib/python3.8/contextlib.py", line 131, in exit
self.gen.throw(type, value, traceback)
File "/usr/local/lib/python3.8/dist-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.

[mengliu1998]

Hi @chriswu99aaa, this looks like some network problem. Have you resolved this?