Read the Docs build information Build id: 2265651 Project: icb-scanpy Version: 3101 Commit: 93a220c059e4796f0824ffdc1901fd5693973ef9 Date: 2024-06-06T12:29:53.513676Z State: finished Success: False [rtd-command-info] start-time: 2024-06-06T12:29:54.714032Z, end-time: 2024-06-06T12:29:55.777771Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2024-06-06T12:29:55.862582Z, end-time: 2024-06-06T12:29:56.487264Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/3101/head:external-3101 From https://github.com/scverse/scanpy * [new ref] refs/pull/3101/head -> external-3101 [rtd-command-info] start-time: 2024-06-06T12:29:56.621378Z, end-time: 2024-06-06T12:29:56.840303Z, duration: 0, exit-code: 0 git checkout --force 93a220c059e4796f0824ffdc1901fd5693973ef9 Note: switching to '93a220c059e4796f0824ffdc1901fd5693973ef9'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 93a220c Add test failing with pandas 1 [rtd-command-info] start-time: 2024-06-06T12:29:56.919540Z, end-time: 2024-06-06T12:29:56.989147Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-06-06T12:29:57.063166Z, end-time: 2024-06-06T12:29:57.127732Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 submodules: include: all build: os: ubuntu-20.04 tools: python: '3.12' sphinx: fail_on_warning: true # do not change or you will be fired configuration: docs/conf.py python: install: - method: pip path: . extra_requirements: - doc - leiden [rtd-command-info] start-time: 2024-06-06T12:29:57.247885Z, end-time: 2024-06-06T12:29:57.332939Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2024-06-06T12:29:57.400872Z, end-time: 2024-06-06T12:30:11.099009Z, duration: 13, exit-code: 0 git submodule update --init --force -- Submodule 'notebooks' (https://github.com/scverse/scanpy-tutorials/) registered for path 'notebooks' Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3101/notebooks'... Submodule path 'notebooks': checked out '02c4946e0be47e033355ef84b2a4909b302d2513' [rtd-command-info] start-time: 2024-06-06T12:30:17.643544Z, end-time: 2024-06-06T12:30:17.727182Z, duration: 0, exit-code: 0 asdf global python 3.12.0 [rtd-command-info] start-time: 2024-06-06T12:30:18.164931Z, end-time: 2024-06-06T12:30:19.341718Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.12.0.final.0-64 in 828ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2024-06-06T12:30:19.409488Z, end-time: 2024-06-06T12:30:26.138298Z, duration: 6, exit-code: 2 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages (23.1) Collecting pip Downloading pip-24.0-py3-none-any.whl (2.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 42.8 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages (67.6.1) ERROR: Exception: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 169, in exc_logging_wrapper status = run_func(*args) ^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 248, in wrapper return func(self, options, args) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 377, in run requirement_set = resolver.resolve( ^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 92, in resolve result = self._result = resolver.resolve( ^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_vendor/resolvelib/resolvers.py", line 546, in resolve state = resolution.resolve(requirements, max_rounds=max_rounds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_vendor/resolvelib/resolvers.py", line 397, in resolve self._add_to_criteria(self.state.criteria, r, parent=None) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_vendor/resolvelib/resolvers.py", line 173, in _add_to_criteria if not criterion.candidates: ^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_vendor/resolvelib/structs.py", line 156, in __bool__ return bool(self._sequence) ^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in __bool__ return any(self) ^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/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/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 90, in _iter_built_with_inserted for version, func in infos: File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 279, in iter_index_candidate_infos result = self._finder.find_best_candidate( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_internal/index/package_finder.py", line 890, in find_best_candidate candidates = self.find_all_candidates(project_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_internal/index/package_finder.py", line 831, in find_all_candidates page_candidates = list(page_candidates_it) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_internal/index/sources.py", line 134, in page_candidates yield from self._candidates_from_page(self._link) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_internal/index/package_finder.py", line 795, in process_project_url page_links = list(parse_links(index_response)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_internal/index/collector.py", line 223, in wrapper_wrapper return list(fn(page)) ^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3101/lib/python3.12/site-packages/pip/_internal/index/collector.py", line 236, in parse_links data = json.loads(page.content) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.asdf/installs/python/3.12.0/lib/python3.12/json/__init__.py", line 346, in loads return _default_decoder.decode(s) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.asdf/installs/python/3.12.0/lib/python3.12/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.asdf/installs/python/3.12.0/lib/python3.12/json/decoder.py", line 353, in raw_decode obj, end = self.scan_once(s, idx) ^^^^^^^^^^^^^^^^^^^^^^ json.decoder.JSONDecodeError: Unterminated string starting at: line 1 column 191499 (char 191498) [notice] A new release of pip is available: 23.1 -> 24.0 [notice] To update, run: pip install --upgrade pip