Read the Docs build information
Build id: 2147876
Project: icb-anndata
Version: 1469
Commit: ae5396cfc0fa6ce47463453320dc6cbe45a520e2
Date: 2024-04-12T08:35:27.799639Z
State: cancelled
Success: False


[rtd-command-info] start-time: 2024-04-12T08:35:28.995707Z, end-time: 2024-04-12T08:35:30.008779Z, duration: 1, exit-code: 0
git clone --depth 1 https://github.com/scverse/anndata.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-04-12T08:35:30.110282Z, end-time: 2024-04-12T08:35:30.933786Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/1469/head:external-1469
From https://github.com/scverse/anndata
 * [new ref]         refs/pull/1469/head -> external-1469

[rtd-command-info] start-time: 2024-04-12T08:35:31.071920Z, end-time: 2024-04-12T08:35:31.131915Z, duration: 0, exit-code: 0
git checkout --force ae5396cfc0fa6ce47463453320dc6cbe45a520e2
Note: switching to 'ae5396cfc0fa6ce47463453320dc6cbe45a520e2'.

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 <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at ae5396c (chore): remove string handling

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git clean -d -f -f


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cat .readthedocs.yml
version: 2
build:
  os: ubuntu-20.04
  tools:
    python: "3.12"
sphinx:
  configuration: docs/conf.py
  fail_on_warning: true # do not change or you will be fired
python:
  install:
    - method: pip
      path: .
      extra_requirements:
        - doc
submodules:
  include:
    - "docs/tutorials/notebooks"
  recursive: true

[rtd-command-info] start-time: 2024-04-12T08:35:31.535681Z, end-time: 2024-04-12T08:35:31.615607Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2024-04-12T08:35:31.685465Z, end-time: 2024-04-12T08:35:32.937979Z, duration: 1, exit-code: 0
git submodule update --init --force --recursive -- docs/tutorials/notebooks
Submodule 'docs/tutorials/notebooks' (https://github.com/scverse/anndata-tutorials) registered for path 'docs/tutorials/notebooks'
Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1469/docs/tutorials/notebooks'...
Submodule path 'docs/tutorials/notebooks': checked out '9e186c5c694793bb04ea1397721d154d6e0b7069'

[rtd-command-info] start-time: 2024-04-12T08:35:39.327125Z, end-time: 2024-04-12T08:35:39.403074Z, duration: 0, exit-code: 0
asdf global python 3.12.0


[rtd-command-info] start-time: 2024-04-12T08:35:39.811938Z, end-time: 2024-04-12T08:35:40.999797Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.12.0.final.0-64 in 871ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1469, 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: 2024-04-12T08:35:41.069347Z, end-time: 2024-04-12T08:35:51.498024Z, duration: 10, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1469/lib/python3.12/site-packages (23.1)
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1469/lib/python3.12/site-packages (67.6.1)
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Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 67.6.1
    Uninstalling setuptools-67.6.1:
      Successfully uninstalled setuptools-67.6.1
  Attempting uninstall: pip
    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-24.0 setuptools-69.2.0

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python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
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Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx, readthedocs-sphinx-ext
Successfully installed Jinja2-3.1.3 MarkupSafe-2.1.5 Pygments-2.17.2 alabaster-0.7.16 babel-2.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.7 imagesize-1.4.1 packaging-24.0 readthedocs-sphinx-ext-2.2.5 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.2.1

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python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1469
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Building wheels for collected packages: anndata, asciitree
  Building wheel for anndata (pyproject.toml): started
  Building wheel for anndata (pyproject.toml): finished with status 'done'
  Created wheel for anndata: filename=anndata-0.1.dev50+gae5396c-py3-none-any.whl size=126377 sha256=5b72e08fe8214f0075e5da99864f6454282815637e86b4d288c5a0926a2916c5
  Stored in directory: /tmp/pip-ephem-wheel-cache-fu3jhqnk/wheels/12/85/47/eeb02fc8d4660d21a006d2f492a5337eafbf7863fe55fd9b31
  Building wheel for asciitree (setup.py): started
  Building wheel for asciitree (setup.py): finished with status 'done'
  Created wheel for asciitree: filename=asciitree-0.3.3-py3-none-any.whl size=5034 sha256=1ac7ae5b67aae45548002c0a5a1606d606b9de976983d79e2f86c6a105f61c91
  Stored in directory: /tmp/pip-ephem-wheel-cache-fu3jhqnk/wheels/a5/d7/98/f56ae733748cd0fa577172bda0e73e0b1f1793c98e09b9e458
Successfully built anndata asciitree
Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, fastjsonschema, asciitree, array-api-compat, tzdata, typing-extensions, traitlets, tornado, tinycss2, soupsieve, six, rpds-py, readthedocs-sphinx-search, pyzmq, pyyaml, prompt-toolkit, platformdirs, pexpect, parso, pandocfilters, numpy, natsort, mistune, mdurl, jupyterlab-pygments, fsspec, fasteners, executing, defusedxml, decorator, attrs, accessible-pygments, scipy, referencing, python-dateutil, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jedi, h5py, bleach, beautifulsoup4, awkward-cpp, asttokens, zarr, stack-data, sphinxext-opengraph, sphinx-issues, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, scanpydoc, pydata-sphinx-theme, pandas, mdit-py-plugins, jupyter-client, jsonschema-specifications, awkward, sphinx-book-theme, myst-parser, jsonschema, ipython, anndata, nbformat, nbclient, nbconvert, nbsphinx
Successfully installed accessible-pygments-0.0.4 anndata-0.1.dev50+gae5396c array-api-compat-1.6 asciitree-0.3.3 asttokens-2.4.1 attrs-23.2.0 awkward-2.6.3 awkward-cpp-32 beautifulsoup4-4.12.3 bleach-6.1.0 decorator-5.1.1 defusedxml-0.7.1 executing-2.0.1 fasteners-0.19 fastjsonschema-2.19.1 fsspec-2024.3.1 h5py-3.11.0 ipython-8.23.0 jedi-0.19.1 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 jupyter-client-8.6.1 jupyter-core-5.7.2 jupyterlab-pygments-0.3.0 markdown-it-py-3.0.0 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 mistune-3.0.2 myst-parser-2.0.0 natsort-8.4.0 nbclient-0.10.0 nbconvert-7.16.3 nbformat-5.10.4 nbsphinx-0.9.3 numcodecs-0.12.1 numpy-1.26.4 pandas-2.2.2 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 platformdirs-4.2.0 prompt-toolkit-3.0.43 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.15.2 python-dateutil-2.9.0.post0 pytz-2024.1 pyyaml-6.0.1 pyzmq-25.1.2 readthedocs-sphinx-search-0.3.2 referencing-0.34.0 rpds-py-0.18.0 scanpydoc-0.13.4 scipy-1.13.0 six-1.16.0 soupsieve-2.5 sphinx-autodoc-typehints-2.0.1 sphinx-book-theme-1.1.2 sphinx-copybutton-0.5.2 sphinx-design-0.5.0 sphinx-issues-4.0.0 sphinxext-opengraph-0.9.1 stack-data-0.6.3 tinycss2-1.2.1 tornado-6.4 traitlets-5.14.2 typing-extensions-4.11.0 tzdata-2024.1 wcwidth-0.2.13 webencodings-0.5.1 zarr-2.17.2