Unable to install DIG in Colab environment

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

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.

divelab / DIG

Unable to install DIG in Colab environment #181