Read the Docs build information Build id: 239518 Project: icb-scanpy Version: latest Commit: 02140a8bfe893c82cd9141ea65d0089fb7d51fa4 Date: 2019-09-06T17:40:50.890544Z State: finished Success: False [rtd-command-info] start-time: 2019-09-06T17:40:51.369503Z, end-time: 2019-09-06T17:40:51.377347Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/theislab/scanpy.git [rtd-command-info] start-time: 2019-09-06T17:40:51.758603Z, end-time: 2019-09-06T17:40:52.043096Z, duration: 0, exit-code: 0 git fetch origin --tags --prune --prune-tags --depth 50 From https://github.com/theislab/scanpy 1bcf492..02140a8 master -> origin/master [rtd-command-info] start-time: 2019-09-06T17:40:52.288639Z, end-time: 2019-09-06T17:40:52.298451Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 1bcf492 Link to stable AnnData HEAD is now at 02140a8 Fix weird discrepancy between travis and local [rtd-command-info] start-time: 2019-09-06T17:40:52.415258Z, end-time: 2019-09-06T17:40:52.424049Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-09-06T17:40:53.401281Z, end-time: 2019-09-06T17:40:57.960745Z, duration: 4, exit-code: 0 python3.6 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.6.8' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.6 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.6) Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-09-06T17:40:58.059517Z, end-time: 2019-09-06T17:40:59.261987Z, duration: 1, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (19.2.3) [rtd-command-info] start-time: 2019-09-06T17:40:59.340026Z, end-time: 2019-09-06T17:41:03.716471Z, duration: 4, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (2.3.1) Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (41.0.1) Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.14) Collecting mock==1.0.1 Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (5.4.1) Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.7.12) Requirement already up-to-date: commonmark==0.8.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.8.1) Requirement already up-to-date: recommonmark==0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.5.0) Collecting sphinx<2 Using cached https://files.pythonhosted.org/packages/7d/66/a4af242b4348b729b9d46ce5db23943ce9bca7da9bbe2ece60dc27f26420/Sphinx-1.8.5-py2.py3-none-any.whl Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.4.3) Requirement already up-to-date: readthedocs-sphinx-ext<1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (1.0.0) Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from commonmark==0.8.1) (0.17.1) Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.1.0) Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.12.0) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.7.0) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.9.1) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.10.1) Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.1.2) Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (19.1) Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.22.0) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.2) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from packaging->sphinx<2) (2.4.2) Requirement already satisfied, skipping upgrade: attrs in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from packaging->sphinx<2) (19.1.0) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (1.25.3) Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2.8) Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2019.6.16) ERROR: tables 3.5.2 has requirement mock>=2.0, but you'll have mock 1.0.1 which is incompatible. ERROR: sphinx-autodoc-typehints 1.7.0 has requirement Sphinx>=2.1, but you'll have sphinx 1.8.5 which is incompatible. Installing collected packages: mock, sphinx Found existing installation: mock 3.0.5 Uninstalling mock-3.0.5: Successfully uninstalled mock-3.0.5 Found existing installation: Sphinx 2.2.0 Uninstalling Sphinx-2.2.0: Successfully uninstalled Sphinx-2.2.0 Successfully installed mock-1.0.1 sphinx-1.8.5 [rtd-command-info] start-time: 2019-09-06T17:41:03.820384Z, end-time: 2019-09-06T17:41:06.603933Z, duration: 2, exit-code: 0 python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip -r docs/requirements.txt Requirement already satisfied: sphinx_rtd_theme>=0.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 2)) (0.4.3) Collecting sphinx>=2.0.1 (from -r docs/requirements.txt (line 5)) Using cached https://files.pythonhosted.org/packages/8e/4c/95a21788db2e1653e931420f561015a0bbc9bd4660c4520467ab9e733eb2/Sphinx-2.2.0-py3-none-any.whl Requirement already satisfied: sphinx-autodoc-typehints in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 6)) (1.7.0) Requirement already satisfied: scanpydoc>=0.4 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 7)) (0.4) Requirement already satisfied: anndata>=0.6.18 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 9)) (0.6.22.post1) Requirement already satisfied: matplotlib>=2.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 10)) (3.1.1) Requirement already satisfied: pandas>=0.21 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 11)) (0.25.1) Requirement already satisfied: scipy in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 12)) (1.3.1) Requirement already satisfied: seaborn in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 13)) (0.9.0) Requirement already satisfied: h5py in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 14)) (2.9.0) Requirement already satisfied: tables in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 15)) (3.5.2) Requirement already satisfied: scikit-learn>=0.19.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 16)) (0.21.3) Requirement already satisfied: networkx in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 18)) (2.3) Requirement already satisfied: natsort in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 19)) (6.0.0) Requirement already satisfied: joblib in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 20)) (0.13.2) Requirement already satisfied: numba in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 21)) (0.45.1) Requirement already satisfied: tqdm in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 22)) (4.35.0) Requirement already satisfied: importlib_metadata in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 23)) (0.20) Requirement already satisfied: setuptools_scm in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 24)) (3.3.3) Requirement already satisfied: umap-learn in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 25)) (0.3.10) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.1.3) Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.0.1) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (41.0.1) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (19.1) Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.0.2) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.10.1) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.9.1) Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.0.1) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.1.0) Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.0.1) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (0.7.12) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.22.0) Requirement already satisfied: sphinxcontrib-htmlhelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.0.2) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.7.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.3.1) Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (0.14) Requirement already satisfied: get_version in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from scanpydoc>=0.4->-r docs/requirements.txt (line 7)) (2.0.6) Requirement already satisfied: numpy~=1.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from anndata>=0.6.18->-r docs/requirements.txt (line 9)) (1.17.1) Requirement already satisfied: python-dateutil>=2.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from matplotlib>=2.2->-r docs/requirements.txt (line 10)) (2.8.0) Requirement already satisfied: kiwisolver>=1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from matplotlib>=2.2->-r docs/requirements.txt (line 10)) (1.1.0) Requirement already satisfied: cycler>=0.10 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from matplotlib>=2.2->-r docs/requirements.txt (line 10)) (0.10.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from matplotlib>=2.2->-r docs/requirements.txt (line 10)) (2.4.2) Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from pandas>=0.21->-r docs/requirements.txt (line 11)) (2019.2) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from h5py->-r docs/requirements.txt (line 14)) (1.12.0) Collecting mock>=2.0 (from tables->-r docs/requirements.txt (line 15)) Using cached https://files.pythonhosted.org/packages/05/d2/f94e68be6b17f46d2c353564da56e6fb89ef09faeeff3313a046cb810ca9/mock-3.0.5-py2.py3-none-any.whl Requirement already satisfied: numexpr>=2.6.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from tables->-r docs/requirements.txt (line 15)) (2.7.0) Requirement already satisfied: decorator>=4.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from networkx->-r docs/requirements.txt (line 18)) (4.4.0) Requirement already satisfied: llvmlite>=0.29.0dev0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from numba->-r docs/requirements.txt (line 21)) (0.29.0) Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from importlib_metadata->-r docs/requirements.txt (line 23)) (0.6.0) Requirement already satisfied: attrs in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from packaging->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (19.1.0) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.1.1) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.25.3) Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.8) Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (3.0.4) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2019.6.16) Requirement already satisfied: future-fstrings in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from get_version->scanpydoc>=0.4->-r docs/requirements.txt (line 7)) (1.2.0) Requirement already satisfied: more-itertools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from zipp>=0.5->importlib_metadata->-r docs/requirements.txt (line 23)) (7.2.0) Installing collected packages: sphinx, mock Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Found existing installation: mock 1.0.1 Uninstalling mock-1.0.1: Successfully uninstalled mock-1.0.1 Successfully installed mock-3.0.5 sphinx-2.2.0 [rtd-command-info] start-time: 2019-09-06T17:41:07.364188Z, end-time: 2019-09-06T17:41:07.664060Z, duration: 0, exit-code: 0 cat docs/conf.py import os import sys import warnings from pathlib import Path from datetime import datetime import matplotlib # noqa # Don’t use tkinter agg when importing scanpy → … → matplotlib matplotlib.use('agg') HERE = Path(__file__).parent sys.path.insert(0, str(HERE.parent)) import scanpy # noqa with warnings.catch_warnings(): warnings.filterwarnings('ignore', category=FutureWarning) import scanpy.api on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- General configuration ------------------------------------------------ nitpicky = True # Warn about broken links needs_sphinx = '1.7' # autosummary bugfix suppress_warnings = ['ref.citation'] # General information project = 'Scanpy' author = scanpy.__author__ copyright = f'{datetime.now():%Y}, {author}.' version = scanpy.__version__.replace('.dirty', '') release = version # default settings templates_path = ['_templates'] source_suffix = '.rst' master_doc = 'index' default_role = 'literal' exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] pygments_style = 'sphinx' extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary', # 'plot_generator', # 'plot_directive', 'sphinx_autodoc_typehints', # needs to be after napoleon # 'ipython_directive', # 'ipython_console_highlighting', 'scanpydoc', ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = 'bysource' # autodoc_default_flags = ['members'] napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [('Params', 'Parameters')] todo_include_todos = False intersphinx_mapping = dict( anndata=('https://anndata.readthedocs.io/en/stable/', None), bbknn=('https://bbknn.readthedocs.io/en/latest/', None), cycler=('https://matplotlib.org/cycler/', None), ipython=('https://ipython.readthedocs.io/en/stable/', None), leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None), louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None), matplotlib=('https://matplotlib.org/', None), networkx=('https://networkx.github.io/documentation/networkx-1.10/', None), numpy=('https://docs.scipy.org/doc/numpy/', None), pandas=('https://pandas.pydata.org/pandas-docs/stable/', None), python=('https://docs.python.org/3', None), scipy=('https://docs.scipy.org/doc/scipy/reference/', None), scvelo=('https://scvelo.readthedocs.io/en/stable/', None), seaborn=('https://seaborn.pydata.org/', None), sklearn=('https://scikit-learn.org/stable/', None), scanpy_tutorials=('https://scanpy-tutorials.readthedocs.io/en/latest', None), ) # -- Options for HTML output ---------------------------------------------- html_theme = 'sphinx_rtd_theme' html_theme_options = dict( navigation_depth=4, logo_only=True, # Only show the logo ) html_context = dict( display_github=True, # Integrate GitHub github_user='theislab', # Username github_repo='scanpy', # Repo name github_version='master', # Version conf_py_path='/docs/', # Path in the checkout to the docs root ) html_static_path = ['_static'] html_show_sphinx = False html_logo = '_static/img/Scanpy_Logo_RGB.png' gh_url = 'https://github.com/{github_user}/{github_repo}'.format_map(html_context) def setup(app): app.warningiserror = on_rtd app.add_stylesheet('css/custom.css') app.connect('autodoc-process-docstring', insert_function_images) app.connect('build-finished', show_param_warnings) app.add_role('pr', autolink(f'{gh_url}/pull/{{}}', 'PR {}')) # -- Options for other output formats ------------------------------------------ htmlhelp_basename = f'{project}doc' doc_title = f'{project} Documentation' latex_documents = [ (master_doc, f'{project}.tex', doc_title, author, 'manual'), ] man_pages = [ (master_doc, project, doc_title, [author], 1) ] texinfo_documents = [ (master_doc, project, doc_title, author, project, 'One line description of project.', 'Miscellaneous'), ] # -- Images for plot functions ------------------------------------------------- def insert_function_images(app, what, name, obj, options, lines): path = Path(__file__).parent / 'api' / f'{name}.png' if what != 'function' or not path.is_file(): return lines[0:0] = [f'.. image:: {path.name}', ' :width: 200', ' :align: right', ''] # -- GitHub links -------------------------------------------------------------- def autolink(url_template, title_template='{}'): from docutils import nodes def role(name, rawtext, text, lineno, inliner, options={}, content=[]): url = url_template.format(text) title = title_template.format(text) node = nodes.reference(rawtext, title, refuri=url, **options) return [node], [] return role # -- Test for new scanpydoc functionality -------------------------------------- import re from sphinx.ext.napoleon import NumpyDocstring def process_return(lines): for line in lines: m = re.fullmatch(r'(?P\w+)\s+:\s+(?P[\w.]+)', line) if m: # Once this is in scanpydoc, we can use the fancy hover stuff yield f'**{m["param"]}** : :class:`~{m["type"]}`' else: yield line def scanpy_parse_returns_section(self, section): lines_raw = list(process_return(self._dedent(self._consume_to_next_section()))) lines = self._format_block(':returns: ', lines_raw) if lines and lines[-1]: lines.append('') return lines NumpyDocstring._parse_returns_section = scanpy_parse_returns_section # -- Warn for non-annotated params --------------------------------------------- _format_docutils_params_orig = NumpyDocstring._format_docutils_params param_warnings = {} def scanpy_log_param_types(self, fields, field_role='param', type_role='type'): for _name, _type, _desc in fields: if not _type: continue set_item = r"`'[a-z0-9_.-]+'`" if re.fullmatch(rf"{{{set_item}(, {set_item})*}}", _type): continue param_warnings.setdefault((self._name, self._obj), []).append((_name, _type)) return _format_docutils_params_orig(self, fields, field_role, type_role) def show_param_warnings(app, exception): import inspect for (fname, fun), params in param_warnings.items(): _, line = inspect.getsourcelines(fun) file_name = inspect.getsourcefile(fun) params_str = '\n'.join(f'\t{n}: {t}' for n, t in params) warnings.warn_explicit( f'\nParameters in `{fname}` not set-like: {{`elm-1`, `s_el.2`}}.\n' 'Convert to this format or replace with type annotations:\n' + params_str, UserWarning, file_name, line, ) NumpyDocstring._format_docutils_params = scanpy_log_param_types # -- Debug code ---------------------------------------------------------------- # Just do the following to see the rst of a function: # rm -f _build/doctrees/api/scanpy..doctree; DEBUG=1 make html import os if os.environ.get('DEBUG') is not None: import sphinx.ext.napoleon pd = sphinx.ext.napoleon._process_docstring def pd_new(app, what, name, obj, options, lines): pd(app, what, name, obj, options, lines) print(*lines, sep='\n') sphinx.ext.napoleon._process_docstring = pd_new # -- Suppress link warnings ---------------------------------------------------- qualname_overrides = { "sklearn.neighbors.dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric", } nitpick_ignore = [ # Will probably be documented ('py:class', 'scanpy._settings.Verbosity'), # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810 ('py:class', 'seaborn.ClusterGrid'), # Bug: https://github.com/agronholm/sphinx-autodoc-typehints/issues/96 ('py:class', 'typing.Textio'), ] for mod_name in [ 'pp', 'tl', 'pl', 'queries', 'logging', 'datasets', 'export_to', None, ]: if mod_name is None: mod = scanpy.api mod_name = 'scanpy.api' else: mod = getattr(scanpy.api, mod_name) mod_name = f'scanpy.api.{mod_name}' for name, item in vars(mod).items(): if not callable(item): continue for kind in ['func', 'obj']: nitpick_ignore.append((f'py:{kind}', f'{mod_name}.{name}')) ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://media.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("contributors", "/en/contributors/"), ], 'downloads': [ ("html", "//readthedocs.com/projects/icb-scanpy/downloads/htmlzip/latest/"), ], 'subprojects': [ ], 'slug': 'icb-scanpy', 'name': u'scanpy', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://icb-scanpy.readthedocs-hosted.com/en/stable/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'github_repo': 'scanpy', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '02140a8b', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' [rtd-command-info] start-time: 2019-09-06T17:41:07.754893Z, end-time: 2019-09-06T17:42:45.763792Z, duration: 98, exit-code: 2 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v2.2.0 loading translations [en]... done making output directory... done loading intersphinx inventory from https://anndata.readthedocs.io/en/stable/objects.inv... loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://matplotlib.org/cycler/objects.inv... loading intersphinx inventory from https://ipython.readthedocs.io/en/stable/objects.inv... loading intersphinx inventory from https://leidenalg.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://louvain-igraph.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://matplotlib.org/objects.inv... loading intersphinx inventory from https://networkx.github.io/documentation/networkx-1.10/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/numpy/objects.inv... loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv... loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv... loading intersphinx inventory from https://scvelo.readthedocs.io/en/stable/objects.inv... loading intersphinx inventory from https://seaborn.pydata.org/objects.inv... loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv... loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv... [autosummary] generating autosummary for: api/index.rst, api/plotting.rst, api/scanpy.Neighbors.compute_eigen.rst, api/scanpy.Neighbors.compute_neighbors.rst, api/scanpy.Neighbors.compute_transitions.rst, api/scanpy.Neighbors.connectivities.rst, api/scanpy.Neighbors.distances.rst, api/scanpy.Neighbors.distances_dpt.rst, api/scanpy.Neighbors.eigen_basis.rst, api/scanpy.Neighbors.eigen_values.rst, ..., external/scanpy.external.tl.cyclone.rst, external/scanpy.external.tl.palantir.rst, external/scanpy.external.tl.phate.rst, external/scanpy.external.tl.phenograph.rst, external/scanpy.external.tl.sandbag.rst, index.rst, installation.rst, references.rst, release_notes.rst, tutorials.rst building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 153 source files that are out of date updating environment: [new config] 153 added, 0 changed, 0 removed reading sources... [ 0%] api/index reading sources... [ 1%] api/plotting reading sources... [ 1%] api/scanpy.Neighbors reading sources... [ 2%] api/scanpy.Neighbors.compute_eigen reading sources... [ 3%] api/scanpy.Neighbors.compute_neighbors reading sources... [ 3%] api/scanpy.Neighbors.compute_transitions reading sources... [ 4%] api/scanpy.Neighbors.connectivities reading sources... [ 5%] api/scanpy.Neighbors.distances reading sources... [ 5%] api/scanpy.Neighbors.distances_dpt reading sources... [ 6%] api/scanpy.Neighbors.eigen_basis reading sources... [ 7%] api/scanpy.Neighbors.eigen_values reading sources... [ 7%] api/scanpy.Neighbors.getdoc reading sources... [ 8%] api/scanpy.Neighbors.rp_forest reading sources... [ 9%] api/scanpy.Neighbors.to_igraph reading sources... [ 9%] api/scanpy.Neighbors.transitions reading sources... [ 10%] api/scanpy.Neighbors.transitions_sym reading sources... [ 11%] api/scanpy._settings.ScanpyConfig reading sources... [ 11%] api/scanpy._settings.ScanpyConfig.autosave reading sources... [ 12%] api/scanpy._settings.ScanpyConfig.autoshow reading sources... [ 13%] api/scanpy._settings.ScanpyConfig.cachedir reading sources... [ 13%] api/scanpy._settings.ScanpyConfig.categories_to_ignore reading sources... [ 14%] api/scanpy._settings.ScanpyConfig.datasetdir reading sources... [ 15%] api/scanpy._settings.ScanpyConfig.figdir reading sources... [ 15%] api/scanpy._settings.ScanpyConfig.file_format_data reading sources... [ 16%] api/scanpy._settings.ScanpyConfig.file_format_figs reading sources... [ 16%] api/scanpy._settings.ScanpyConfig.logfile reading sources... [ 17%] api/scanpy._settings.ScanpyConfig.logpath reading sources... [ 18%] api/scanpy._settings.ScanpyConfig.max_memory reading sources... [ 18%] api/scanpy._settings.ScanpyConfig.n_jobs reading sources... [ 19%] api/scanpy._settings.ScanpyConfig.plot_suffix reading sources... [ 20%] api/scanpy._settings.ScanpyConfig.set_figure_params reading sources... [ 20%] api/scanpy._settings.ScanpyConfig.verbosity reading sources... [ 21%] api/scanpy._settings.ScanpyConfig.writedir reading sources... [ 22%] api/scanpy.api reading sources... [ 22%] api/scanpy.datasets.blobs reading sources... [ 23%] api/scanpy.datasets.ebi_expression_atlas reading sources... [ 24%] api/scanpy.datasets.krumsiek11 reading sources... [ 24%] api/scanpy.datasets.moignard15 reading sources... [ 25%] api/scanpy.datasets.paul15 reading sources... [ 26%] api/scanpy.datasets.pbmc3k reading sources... [ 26%] api/scanpy.datasets.pbmc68k_reduced reading sources... [ 27%] api/scanpy.datasets.toggleswitch reading sources... [ 28%] api/scanpy.external reading sources... [ 28%] api/scanpy.get.obs_df reading sources... [ 29%] api/scanpy.get.rank_genes_groups_df reading sources... [ 30%] api/scanpy.get.var_df reading sources... [ 30%] api/scanpy.logging.print_versions reading sources... [ 31%] api/scanpy.pl.clustermap reading sources... [ 32%] api/scanpy.pl.diffmap reading sources... [ 32%] api/scanpy.pl.dotplot reading sources... [ 33%] api/scanpy.pl.dpt_groups_pseudotime reading sources... [ 33%] api/scanpy.pl.dpt_timeseries reading sources... [ 34%] api/scanpy.pl.draw_graph reading sources... [ 35%] api/scanpy.pl.embedding reading sources... [ 35%] api/scanpy.pl.embedding_density reading sources... [ 36%] api/scanpy.pl.filter_genes_dispersion reading sources... [ 37%] api/scanpy.pl.heatmap reading sources... [ 37%] api/scanpy.pl.highest_expr_genes reading sources... [ 38%] api/scanpy.pl.highly_variable_genes reading sources... [ 39%] api/scanpy.pl.matrixplot reading sources... [ 39%] api/scanpy.pl.paga reading sources... [ 40%] api/scanpy.pl.paga_compare reading sources... [ 41%] api/scanpy.pl.paga_path reading sources... [ 41%] api/scanpy.pl.pca reading sources... [ 42%] api/scanpy.pl.pca_loadings reading sources... [ 43%] api/scanpy.pl.pca_overview reading sources... [ 43%] api/scanpy.pl.pca_variance_ratio reading sources... [ 44%] api/scanpy.pl.rank_genes_groups reading sources... [ 45%] api/scanpy.pl.rank_genes_groups_dotplot reading sources... [ 45%] api/scanpy.pl.rank_genes_groups_heatmap reading sources... [ 46%] api/scanpy.pl.rank_genes_groups_matrixplot reading sources... [ 47%] api/scanpy.pl.rank_genes_groups_stacked_violin reading sources... [ 47%] api/scanpy.pl.rank_genes_groups_tracksplot reading sources... [ 48%] api/scanpy.pl.rank_genes_groups_violin reading sources... [ 49%] api/scanpy.pl.ranking reading sources... [ 49%] api/scanpy.pl.scatter reading sources... [ 50%] api/scanpy.pl.sim reading sources... [ 50%] api/scanpy.pl.stacked_violin reading sources... [ 51%] api/scanpy.pl.tracksplot reading sources... [ 52%] api/scanpy.pl.tsne reading sources... [ 52%] api/scanpy.pl.umap reading sources... [ 53%] api/scanpy.pl.violin reading sources... [ 54%] api/scanpy.plotting reading sources... [ 54%] api/scanpy.pp.calculate_qc_metrics reading sources... [ 55%] api/scanpy.pp.combat reading sources... [ 56%] api/scanpy.pp.downsample_counts reading sources... [ 56%] api/scanpy.pp.filter_cells reading sources... [ 57%] api/scanpy.pp.filter_genes reading sources... [ 58%] api/scanpy.pp.filter_genes_dispersion reading sources... [ 58%] api/scanpy.pp.highly_variable_genes reading sources... [ 59%] api/scanpy.pp.log1p reading sources... [ 60%] api/scanpy.pp.neighbors reading sources... [ 60%] api/scanpy.pp.normalize_per_cell reading sources... [ 61%] api/scanpy.pp.normalize_total reading sources... [ 62%] api/scanpy.pp.pca reading sources... [ 62%] api/scanpy.pp.recipe_seurat reading sources... [ 63%] api/scanpy.pp.recipe_weinreb17 reading sources... [ 64%] api/scanpy.pp.recipe_zheng17 reading sources... [ 64%] api/scanpy.pp.regress_out reading sources... [ 65%] api/scanpy.pp.scale reading sources... [ 66%] api/scanpy.pp.subsample reading sources... [ 66%] api/scanpy.queries.biomart_annotations reading sources... [ 67%] api/scanpy.queries.enrich reading sources... [ 67%] api/scanpy.queries.gene_coordinates reading sources... [ 68%] api/scanpy.queries.mitochondrial_genes reading sources... [ 69%] api/scanpy.read reading sources... [ 69%] api/scanpy.read_10x_h5 reading sources... [ 70%] api/scanpy.read_10x_mtx reading sources... [ 71%] api/scanpy.read_csv reading sources... [ 71%] api/scanpy.read_excel reading sources... [ 72%] api/scanpy.read_h5ad reading sources... [ 73%] api/scanpy.read_hdf reading sources... [ 73%] api/scanpy.read_loom reading sources... [ 74%] api/scanpy.read_mtx reading sources... [ 75%] api/scanpy.read_text reading sources... [ 75%] api/scanpy.read_umi_tools reading sources... [ 76%] api/scanpy.set_figure_params reading sources... [ 77%] api/scanpy.tl.dendrogram reading sources... [ 77%] api/scanpy.tl.diffmap reading sources... [ 78%] api/scanpy.tl.dpt reading sources... [ 79%] api/scanpy.tl.draw_graph reading sources... [ 79%] api/scanpy.tl.filter_rank_genes_groups reading sources... [ 80%] api/scanpy.tl.leiden reading sources... [ 81%] api/scanpy.tl.louvain reading sources... [ 81%] api/scanpy.tl.marker_gene_overlap reading sources... [ 82%] api/scanpy.tl.paga reading sources... [ 83%] api/scanpy.tl.pca reading sources... [ 83%] api/scanpy.tl.rank_genes_groups reading sources... [ 84%] api/scanpy.tl.score_genes reading sources... [ 84%] api/scanpy.tl.score_genes_cell_cycle reading sources... [ 85%] api/scanpy.tl.sim reading sources... [ 86%] api/scanpy.tl.tsne reading sources... [ 86%] api/scanpy.tl.umap reading sources... [ 87%] basic_usage reading sources... [ 88%] examples reading sources... [ 88%] external/index reading sources... [ 89%] external/scanpy.external.exporting.cellbrowser reading sources... [ 90%] external/scanpy.external.exporting.spring_project reading sources... [ 90%] external/scanpy.external.pl.phate reading sources... [ 91%] external/scanpy.external.pp.bbknn reading sources... [ 92%] external/scanpy.external.pp.dca reading sources... [ 92%] external/scanpy.external.pp.magic reading sources... [ 93%] external/scanpy.external.pp.mnn_correct reading sources... [ 94%] external/scanpy.external.tl.cyclone reading sources... [ 94%] external/scanpy.external.tl.palantir reading sources... [ 95%] external/scanpy.external.tl.phate reading sources... [ 96%] external/scanpy.external.tl.phenograph reading sources... [ 96%] external/scanpy.external.tl.sandbag reading sources... [ 97%] index reading sources... [ 98%] installation reading sources... [ 98%] references reading sources... [ 99%] release_notes reading sources... [100%] tutorials looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 0%] api/index writing output... [ 1%] api/plotting writing output... [ 1%] api/scanpy.Neighbors writing output... [ 2%] api/scanpy.Neighbors.compute_eigen writing output... [ 3%] api/scanpy.Neighbors.compute_neighbors writing output... [ 3%] api/scanpy.Neighbors.compute_transitions writing output... [ 4%] api/scanpy.Neighbors.connectivities writing output... [ 5%] api/scanpy.Neighbors.distances writing output... [ 5%] api/scanpy.Neighbors.distances_dpt writing output... [ 6%] api/scanpy.Neighbors.eigen_basis writing output... [ 7%] api/scanpy.Neighbors.eigen_values writing output... [ 7%] api/scanpy.Neighbors.getdoc writing output... [ 8%] api/scanpy.Neighbors.rp_forest writing output... [ 9%] api/scanpy.Neighbors.to_igraph writing output... [ 9%] api/scanpy.Neighbors.transitions writing output... [ 10%] api/scanpy.Neighbors.transitions_sym writing output... [ 11%] api/scanpy._settings.ScanpyConfig writing output... [ 11%] api/scanpy._settings.ScanpyConfig.autosave writing output... [ 12%] api/scanpy._settings.ScanpyConfig.autoshow writing output... [ 13%] api/scanpy._settings.ScanpyConfig.cachedir writing output... [ 13%] api/scanpy._settings.ScanpyConfig.categories_to_ignore writing output... [ 14%] api/scanpy._settings.ScanpyConfig.datasetdir writing output... [ 15%] api/scanpy._settings.ScanpyConfig.figdir writing output... [ 15%] api/scanpy._settings.ScanpyConfig.file_format_data writing output... [ 16%] api/scanpy._settings.ScanpyConfig.file_format_figs writing output... [ 16%] api/scanpy._settings.ScanpyConfig.logfile writing output... [ 17%] api/scanpy._settings.ScanpyConfig.logpath writing output... [ 18%] api/scanpy._settings.ScanpyConfig.max_memory writing output... [ 18%] api/scanpy._settings.ScanpyConfig.n_jobs writing output... [ 19%] api/scanpy._settings.ScanpyConfig.plot_suffix writing output... [ 20%] api/scanpy._settings.ScanpyConfig.set_figure_params writing output... [ 20%] api/scanpy._settings.ScanpyConfig.verbosity writing output... [ 21%] api/scanpy._settings.ScanpyConfig.writedir writing output... [ 22%] api/scanpy.api writing output... [ 22%] api/scanpy.datasets.blobs writing output... [ 23%] api/scanpy.datasets.ebi_expression_atlas writing output... [ 24%] api/scanpy.datasets.krumsiek11 writing output... [ 24%] api/scanpy.datasets.moignard15 writing output... [ 25%] api/scanpy.datasets.paul15 writing output... [ 26%] api/scanpy.datasets.pbmc3k writing output... [ 26%] api/scanpy.datasets.pbmc68k_reduced writing output... [ 27%] api/scanpy.datasets.toggleswitch writing output... [ 28%] api/scanpy.external writing output... [ 28%] api/scanpy.get.obs_df writing output... [ 29%] api/scanpy.get.rank_genes_groups_df writing output... [ 30%] api/scanpy.get.var_df writing output... [ 30%] api/scanpy.logging.print_versions writing output... [ 31%] api/scanpy.pl.clustermap writing output... [ 32%] api/scanpy.pl.diffmap writing output... [ 32%] api/scanpy.pl.dotplot writing output... [ 33%] api/scanpy.pl.dpt_groups_pseudotime writing output... [ 33%] api/scanpy.pl.dpt_timeseries writing output... [ 34%] api/scanpy.pl.draw_graph writing output... [ 35%] api/scanpy.pl.embedding writing output... [ 35%] api/scanpy.pl.embedding_density writing output... [ 36%] api/scanpy.pl.filter_genes_dispersion writing output... [ 37%] api/scanpy.pl.heatmap writing output... [ 37%] api/scanpy.pl.highest_expr_genes writing output... [ 38%] api/scanpy.pl.highly_variable_genes writing output... [ 39%] api/scanpy.pl.matrixplot writing output... [ 39%] api/scanpy.pl.paga writing output... [ 40%] api/scanpy.pl.paga_compare writing output... [ 41%] api/scanpy.pl.paga_path writing output... [ 41%] api/scanpy.pl.pca writing output... [ 42%] api/scanpy.pl.pca_loadings writing output... [ 43%] api/scanpy.pl.pca_overview writing output... [ 43%] api/scanpy.pl.pca_variance_ratio writing output... [ 44%] api/scanpy.pl.rank_genes_groups writing output... [ 45%] api/scanpy.pl.rank_genes_groups_dotplot writing output... [ 45%] api/scanpy.pl.rank_genes_groups_heatmap writing output... [ 46%] api/scanpy.pl.rank_genes_groups_matrixplot writing output... [ 47%] api/scanpy.pl.rank_genes_groups_stacked_violin writing output... [ 47%] api/scanpy.pl.rank_genes_groups_tracksplot writing output... [ 48%] api/scanpy.pl.rank_genes_groups_violin writing output... [ 49%] api/scanpy.pl.ranking writing output... [ 49%] api/scanpy.pl.scatter writing output... [ 50%] api/scanpy.pl.sim writing output... [ 50%] api/scanpy.pl.stacked_violin writing output... [ 51%] api/scanpy.pl.tracksplot writing output... [ 52%] api/scanpy.pl.tsne writing output... [ 52%] api/scanpy.pl.umap writing output... [ 53%] api/scanpy.pl.violin writing output... [ 54%] api/scanpy.plotting writing output... [ 54%] api/scanpy.pp.calculate_qc_metrics writing output... [ 55%] api/scanpy.pp.combat writing output... [ 56%] api/scanpy.pp.downsample_counts writing output... [ 56%] api/scanpy.pp.filter_cells writing output... [ 57%] api/scanpy.pp.filter_genes writing output... [ 58%] api/scanpy.pp.filter_genes_dispersion writing output... [ 58%] api/scanpy.pp.highly_variable_genes writing output... [ 59%] api/scanpy.pp.log1p writing output... [ 60%] api/scanpy.pp.neighbors writing output... [ 60%] api/scanpy.pp.normalize_per_cell writing output... [ 61%] api/scanpy.pp.normalize_total writing output... [ 62%] api/scanpy.pp.pca writing output... [ 62%] api/scanpy.pp.recipe_seurat writing output... [ 63%] api/scanpy.pp.recipe_weinreb17 writing output... [ 64%] api/scanpy.pp.recipe_zheng17 writing output... [ 64%] api/scanpy.pp.regress_out writing output... [ 65%] api/scanpy.pp.scale writing output... [ 66%] api/scanpy.pp.subsample writing output... [ 66%] api/scanpy.queries.biomart_annotations writing output... [ 67%] api/scanpy.queries.enrich writing output... [ 67%] api/scanpy.queries.gene_coordinates writing output... [ 68%] api/scanpy.queries.mitochondrial_genes writing output... [ 69%] api/scanpy.read writing output... [ 69%] api/scanpy.read_10x_h5 writing output... [ 70%] api/scanpy.read_10x_mtx writing output... [ 71%] api/scanpy.read_csv writing output... [ 71%] api/scanpy.read_excel writing output... [ 72%] api/scanpy.read_h5ad writing output... [ 73%] api/scanpy.read_hdf writing output... [ 73%] api/scanpy.read_loom writing output... [ 74%] api/scanpy.read_mtx writing output... [ 75%] api/scanpy.read_text writing output... [ 75%] api/scanpy.read_umi_tools writing output... [ 76%] api/scanpy.set_figure_params writing output... [ 77%] api/scanpy.tl.dendrogram writing output... [ 77%] api/scanpy.tl.diffmap writing output... [ 78%] api/scanpy.tl.dpt writing output... [ 79%] api/scanpy.tl.draw_graph writing output... [ 79%] api/scanpy.tl.filter_rank_genes_groups writing output... [ 80%] api/scanpy.tl.leiden writing output... [ 81%] api/scanpy.tl.louvain writing output... [ 81%] api/scanpy.tl.marker_gene_overlap writing output... [ 82%] api/scanpy.tl.paga writing output... [ 83%] api/scanpy.tl.pca writing output... [ 83%] api/scanpy.tl.rank_genes_groups writing output... [ 84%] api/scanpy.tl.score_genes writing output... [ 84%] api/scanpy.tl.score_genes_cell_cycle writing output... [ 85%] api/scanpy.tl.sim writing output... [ 86%] api/scanpy.tl.tsne writing output... [ 86%] api/scanpy.tl.umap writing output... [ 87%] basic_usage writing output... [ 88%] examples writing output... [ 88%] external/index writing output... [ 89%] external/scanpy.external.exporting.cellbrowser writing output... [ 90%] external/scanpy.external.exporting.spring_project writing output... [ 90%] external/scanpy.external.pl.phate writing output... [ 91%] external/scanpy.external.pp.bbknn writing output... [ 92%] external/scanpy.external.pp.dca writing output... [ 92%] external/scanpy.external.pp.magic writing output... [ 93%] external/scanpy.external.pp.mnn_correct writing output... [ 94%] external/scanpy.external.tl.cyclone writing output... [ 94%] external/scanpy.external.tl.palantir writing output... [ 95%] external/scanpy.external.tl.phate writing output... [ 96%] external/scanpy.external.tl.phenograph writing output... [ 96%] external/scanpy.external.tl.sandbag writing output... [ 97%] index writing output... [ 98%] installation writing output... [ 98%] references writing output... [ 99%] release_notes writing output... [100%] tutorials /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest" is shallow and may cause errors warnings.warn('"%s" is shallow and may cause errors' % (wd.path,)) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_highly_variable_genes.py:160: UserWarning: Parameters in `scanpy.pp.highly_variable_genes` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: min_mean: `float`, optional (default: 0.0125) max_mean: `float`, optional (default: 3) min_disp: `float`, optional (default: 0.5) max_disp: `float`, optional (default: `None`) n_top_genes: `int` or `None`, optional (default: `None`) n_bins: `int`, optional (default: 20) subset: `bool`, optional (default: `False`) inplace: `bool`, optional (default: `True`) batch_key: `str`, optional (default: `None`) min_mean: `float`, optional (default: 0.0125) max_mean: `float`, optional (default: 3) min_disp: `float`, optional (default: 0.5) max_disp: `float`, optional (default: `None`) n_top_genes: `int` or `None`, optional (default: `None`) n_bins: `int`, optional (default: 20) subset: `bool`, optional (default: `False`) inplace: `bool`, optional (default: `True`) batch_key: `str`, optional (default: `None`) def highly_variable_genes( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:714: UserWarning: Parameters in `scanpy.pp.regress_out` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` keys: `str` or list of `str` n_jobs: `int` or `None`, optional. If None is given, then the n_jobs seting is used (default: `None`) copy: `bool`, optional (default: `False`) adata: :class:`~anndata.AnnData` keys: `str` or list of `str` n_jobs: `int` or `None`, optional. If None is given, then the n_jobs seting is used (default: `None`) copy: `bool`, optional (default: `False`) def regress_out(adata, keys, n_jobs=None, copy=False) -> Optional[AnnData]: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:842: UserWarning: Parameters in `scanpy.pp.scale` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` zero_center: `bool`, optional (default: `True`) max_value: `float` or `None`, optional (default: `None`) copy: `bool`, optional (default: `False`) data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` zero_center: `bool`, optional (default: `True`) max_value: `float` or `None`, optional (default: `None`) copy: `bool`, optional (default: `False`) def scale(data, zero_center=True, max_value=None, copy=False) -> Optional[AnnData]: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:898: UserWarning: Parameters in `scanpy.pp.subsample` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` fraction: `float` in [0, 1] or `None`, optional (default: `None`) n_obs: `int` or `None`, optional (default: `None`) random_state: `int` or `None`, optional (default: 0) copy: `bool`, optional (default: `False`) data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` fraction: `float` in [0, 1] or `None`, optional (default: `None`) n_obs: `int` or `None`, optional (default: `None`) random_state: `int` or `None`, optional (default: 0) copy: `bool`, optional (default: `False`) def subsample(data, fraction=None, n_obs=None, random_state=0, copy=False) -> Optional[AnnData]: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_recipes.py:74: UserWarning: Parameters in `scanpy.pp.recipe_zheng17` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_top_genes: `int`, optional (default: 1000) log: `bool`, optional (default: `True`) plot: `bool`, optional (default: `True`) copy: `bool`, optional (default: `False`) adata: :class:`~anndata.AnnData` n_top_genes: `int`, optional (default: 1000) log: `bool`, optional (default: `True`) plot: `bool`, optional (default: `True`) copy: `bool`, optional (default: `False`) def recipe_zheng17(adata, n_top_genes=1000, log=True, plot=False, copy=False): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_combat.py:135: UserWarning: Parameters in `scanpy.pp.combat` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` key: `str`, optional (default: `"batch"`) inplace: bool, optional (default: `True`) adata: :class:`~anndata.AnnData` key: `str`, optional (default: `"batch"`) inplace: bool, optional (default: `True`) def combat(adata: AnnData, key: str = 'batch', covariates: Optional[Collection[str]] = None, inplace: bool = True): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:22: UserWarning: Parameters in `scanpy.pp.neighbors` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) method: {`'umap'`, `'gauss'`, `None`} (default: `'umap'`) n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) method: {`'umap'`, `'gauss'`, `None`} (default: `'umap'`) @_doc_params(n_pcs=doc_n_pcs, use_rep=doc_use_rep) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_tsne.py:7: UserWarning: Parameters in `scanpy.tl.tsne` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) perplexity: `float`, optional (default: 30) early_exaggeration: `float`, optional (default: 12.0) learning_rate: `float`, optional (default: 1000) random_state: `int` or `None`, optional (default: 0) use_fast_tsne: `bool`, optional (default: `True`) n_jobs: `int` or `None` (default: `sc.settings.n_jobs`) copy: `bool` (default: `False`) adata: :class:`~anndata.AnnData` n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) perplexity: `float`, optional (default: 30) early_exaggeration: `float`, optional (default: 12.0) learning_rate: `float`, optional (default: 1000) random_state: `int` or `None`, optional (default: 0) use_fast_tsne: `bool`, optional (default: `True`) n_jobs: `int` or `None` (default: `sc.settings.n_jobs`) copy: `bool` (default: `False`) @_doc_params(doc_n_pcs=doc_n_pcs, use_rep=doc_use_rep) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_umap.py:10: UserWarning: Parameters in `scanpy.tl.umap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` min_dist: `float`, optional (default: 0.5) spread: `float` (optional, default 1.0) n_components: `int`, optional (default: 2) maxiter: `int`, optional (default: `None`) alpha: `float`, optional (default: 1.0) gamma: `float` (optional, default 1.0) negative_sample_rate: `int` (optional, default 5) init_pos: `string` or `np.array`, optional (default: 'spectral') random_state: `int`, `RandomState` or `None`, optional (default: 0) a: `float` (optional, default `None`) b: `float` (optional, default `None`) copy: `bool` (default: `False`) adata: :class:`~anndata.AnnData` min_dist: `float`, optional (default: 0.5) spread: `float` (optional, default 1.0) n_components: `int`, optional (default: 2) maxiter: `int`, optional (default: `None`) alpha: `float`, optional (default: 1.0) gamma: `float` (optional, default 1.0) negative_sample_rate: `int` (optional, default 5) init_pos: `string` or `np.array`, optional (default: 'spectral') random_state: `int`, `RandomState` or `None`, optional (default: 0) a: `float` (optional, default `None`) b: `float` (optional, default `None`) copy: `bool` (default: `False`) def umap( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_diffmap.py:4: UserWarning: Parameters in `scanpy.tl.diffmap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_comps: `int`, optional (default: 15) copy: `bool` (default: `False`) adata: :class:`~anndata.AnnData` n_comps: `int`, optional (default: 15) copy: `bool` (default: `False`) def diffmap(adata, n_comps=15, copy=False): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_louvain.py:22: UserWarning: Parameters in `scanpy.tl.louvain` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: flavor: {``'vtraag'``, ``'igraph'``} flavor: {``'vtraag'``, ``'igraph'``} def louvain( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_dendrogram.py:16: UserWarning: Parameters in `scanpy.tl.dendrogram` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) @_doc_params(n_pcs=doc_n_pcs, use_rep=doc_use_rep) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_dpt.py:30: UserWarning: Parameters in `scanpy.tl.dpt` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_dcs: `int`, optional (default: 10) n_branchings: `int`, optional (default: 0) min_group_size: [0, 1] or `float`, optional (default: 0.01) allow_kendall_tau_shift: `bool`, optional (default: `True`) copy: `bool`, optional (default: `False`) adata: :class:`~anndata.AnnData` n_dcs: `int`, optional (default: 10) n_branchings: `int`, optional (default: 0) min_group_size: [0, 1] or `float`, optional (default: 0.01) allow_kendall_tau_shift: `bool`, optional (default: `True`) copy: `bool`, optional (default: `False`) def dpt(adata, n_dcs=10, n_branchings=0, min_group_size=0.01, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_rank_genes_groups.py:17: UserWarning: Parameters in `scanpy.tl.rank_genes_groups` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: method: {`'logreg'`, `'t-test'`, `'wilcoxon'`, `'t-test_overestim_var'`}` method: {`'logreg'`, `'t-test'`, `'wilcoxon'`, `'t-test_overestim_var'`}` def rank_genes_groups( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_marker_gene_overlap.py:70: UserWarning: Parameters in `scanpy.tl.marker_gene_overlap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: method: `{'overlap_count', 'overlap_coef', 'jaccard'}`, optional normalize: `{'reference', 'data', 'None'}`, optional (default: `None`) method: `{'overlap_count', 'overlap_coef', 'jaccard'}`, optional normalize: `{'reference', 'data', 'None'}`, optional (default: `None`) def marker_gene_overlap( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/readwrite.py:39: UserWarning: Parameters in `scanpy.read` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: backed: {``None``, ``'r'``, ``'r+'``} backed: {``None``, ``'r'``, ``'r+'``} def read( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/anndata/readwrite/read.py:416: UserWarning: Parameters in `scanpy.read_h5ad` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: backed: {``None``, ``'r'``, ``'r+'``} backed: {``None``, ``'r'``, ``'r+'``} def read_h5ad(filename, backed: Optional[str] = None, chunk_size: int = 6000): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_settings.py:349: UserWarning: Parameters in `scanpy.set_figure_params` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: format: {`'png'`, `'pdf'`, `'svg'`, etc.}, optional (default: `'pdf'`) format: {`'png'`, `'pdf'`, `'svg'`, etc.}, optional (default: `'pdf'`) def set_figure_params( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:544: UserWarning: Parameters in `scanpy.pp.normalize_per_cell` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` counts_per_cell_after: `float` or `None`, optional (default: `None`) counts_per_cell: `np.array`, optional (default: `None`) key_n_counts: `str`, optional (default: `'n_counts'`) copy: `bool`, optional (default: `False`) min_counts: `int`, optional (default: 1) data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` counts_per_cell_after: `float` or `None`, optional (default: `None`) counts_per_cell: `np.array`, optional (default: `None`) key_n_counts: `str`, optional (default: `'n_counts'`) copy: `bool`, optional (default: `False`) min_counts: `int`, optional (default: 1) def normalize_per_cell( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:768: UserWarning: Parameters in `scanpy.Neighbors.compute_eigen` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: n_comps: `int` sym: `bool` matrix: sparse matrix, np.ndarray, optional (default: `.connectivities`) n_comps: `int` sym: `bool` matrix: sparse matrix, np.ndarray, optional (default: `.connectivities`) def compute_eigen(self, n_comps=15, sym=None, sort='decrease'): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:576: UserWarning: Parameters in `scanpy.Neighbors.compute_neighbors` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) @_doc_params(n_pcs=doc_n_pcs, use_rep=doc_use_rep) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:730: UserWarning: Parameters in `scanpy.Neighbors.compute_transitions` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: density_normalize: `bool` density_normalize: `bool` def compute_transitions(self, density_normalize=True): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_settings.py:349: UserWarning: Parameters in `scanpy._settings.ScanpyConfig.set_figure_params` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: format: {`'png'`, `'pdf'`, `'svg'`, etc.}, optional (default: `'pdf'`) format: {`'png'`, `'pdf'`, `'svg'`, etc.}, optional (default: `'pdf'`) def set_figure_params( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_highly_variable_genes.py:160: UserWarning: Parameters in `scanpy.api.pp.highly_variable_genes` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: min_mean: `float`, optional (default: 0.0125) max_mean: `float`, optional (default: 3) min_disp: `float`, optional (default: 0.5) max_disp: `float`, optional (default: `None`) n_top_genes: `int` or `None`, optional (default: `None`) n_bins: `int`, optional (default: 20) subset: `bool`, optional (default: `False`) inplace: `bool`, optional (default: `True`) batch_key: `str`, optional (default: `None`) def highly_variable_genes( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:544: UserWarning: Parameters in `scanpy.api.pp.normalize_per_cell` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` counts_per_cell_after: `float` or `None`, optional (default: `None`) counts_per_cell: `np.array`, optional (default: `None`) key_n_counts: `str`, optional (default: `'n_counts'`) copy: `bool`, optional (default: `False`) min_counts: `int`, optional (default: 1) def normalize_per_cell( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:714: UserWarning: Parameters in `scanpy.api.pp.regress_out` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` keys: `str` or list of `str` n_jobs: `int` or `None`, optional. If None is given, then the n_jobs seting is used (default: `None`) copy: `bool`, optional (default: `False`) def regress_out(adata, keys, n_jobs=None, copy=False) -> Optional[AnnData]: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:842: UserWarning: Parameters in `scanpy.api.pp.scale` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` zero_center: `bool`, optional (default: `True`) max_value: `float` or `None`, optional (default: `None`) copy: `bool`, optional (default: `False`) def scale(data, zero_center=True, max_value=None, copy=False) -> Optional[AnnData]: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:898: UserWarning: Parameters in `scanpy.api.pp.subsample` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` fraction: `float` in [0, 1] or `None`, optional (default: `None`) n_obs: `int` or `None`, optional (default: `None`) random_state: `int` or `None`, optional (default: 0) copy: `bool`, optional (default: `False`) def subsample(data, fraction=None, n_obs=None, random_state=0, copy=False) -> Optional[AnnData]: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_recipes.py:74: UserWarning: Parameters in `scanpy.api.pp.recipe_zheng17` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_top_genes: `int`, optional (default: 1000) log: `bool`, optional (default: `True`) plot: `bool`, optional (default: `True`) copy: `bool`, optional (default: `False`) def recipe_zheng17(adata, n_top_genes=1000, log=True, plot=False, copy=False): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp/_dca.py:6: UserWarning: Parameters in `scanpy.api.pp.dca` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: mode: `str`, optional. `denoise`(default), or `latent`. ae_type: `str`, optional. `zinb-conddisp`(default), `zinb`, `nb-conddisp` or `nb`. normalize_per_cell: `bool`, optional. Default: `True`. scale: `bool`, optional. Default: `True`. log1p: `bool`, optional. Default: `True`. hidden_size: `tuple` or `list`, optional. Default: (64, 32, 64). hidden_dropout: `float`, `tuple` or `list`, optional. Default: 0.0. batchnorm: `bool`, optional. Default: `True`. activation: `str`, optional. Default: `relu`. init: `str`, optional. Default: `glorot_uniform`. network_kwds: `dict`, optional. epochs: `int`, optional. Default: 300. reduce_lr: `int`, optional. Default: 10. early_stop: `int`, optional. Default: 15. batch_size: `int`, optional. Default: 32. optimizer: `str`, optional. Default: "rmsprop". random_state: `int`, optional. Default: 0. threads: `int` or None, optional. Default: None learning_rate: `float`, optional. Default: None. verbose: `bool`, optional. Default: `False`. training_kwds: `dict`, optional. return_model: `bool`, optional. Default: `False`. return_info: `bool`, optional. Default: `False`. copy: `bool`, optional. Default: `False`. def dca( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:22: UserWarning: Parameters in `scanpy.api.pp.neighbors` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) method: {`'umap'`, `'gauss'`, `None`} (default: `'umap'`) @_doc_params(n_pcs=doc_n_pcs, use_rep=doc_use_rep) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_tsne.py:7: UserWarning: Parameters in `scanpy.api.tl.tsne` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) perplexity: `float`, optional (default: 30) early_exaggeration: `float`, optional (default: 12.0) learning_rate: `float`, optional (default: 1000) random_state: `int` or `None`, optional (default: 0) use_fast_tsne: `bool`, optional (default: `True`) n_jobs: `int` or `None` (default: `sc.settings.n_jobs`) copy: `bool` (default: `False`) @_doc_params(doc_n_pcs=doc_n_pcs, use_rep=doc_use_rep) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_umap.py:10: UserWarning: Parameters in `scanpy.api.tl.umap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` min_dist: `float`, optional (default: 0.5) spread: `float` (optional, default 1.0) n_components: `int`, optional (default: 2) maxiter: `int`, optional (default: `None`) alpha: `float`, optional (default: 1.0) gamma: `float` (optional, default 1.0) negative_sample_rate: `int` (optional, default 5) init_pos: `string` or `np.array`, optional (default: 'spectral') random_state: `int`, `RandomState` or `None`, optional (default: 0) a: `float` (optional, default `None`) b: `float` (optional, default `None`) copy: `bool` (default: `False`) def umap( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_diffmap.py:4: UserWarning: Parameters in `scanpy.api.tl.diffmap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_comps: `int`, optional (default: 15) copy: `bool` (default: `False`) def diffmap(adata, n_comps=15, copy=False): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_louvain.py:22: UserWarning: Parameters in `scanpy.api.tl.louvain` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: flavor: {``'vtraag'``, ``'igraph'``} def louvain( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_dpt.py:30: UserWarning: Parameters in `scanpy.api.tl.dpt` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_dcs: `int`, optional (default: 10) n_branchings: `int`, optional (default: 0) min_group_size: [0, 1] or `float`, optional (default: 0.01) allow_kendall_tau_shift: `bool`, optional (default: `True`) copy: `bool`, optional (default: `False`) def dpt(adata, n_dcs=10, n_branchings=0, min_group_size=0.01, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_rank_genes_groups.py:17: UserWarning: Parameters in `scanpy.api.tl.rank_genes_groups` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: method: {`'logreg'`, `'t-test'`, `'wilcoxon'`, `'t-test_overestim_var'`}` def rank_genes_groups( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/readwrite.py:39: UserWarning: Parameters in `scanpy.api.read` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: backed: {``None``, ``'r'``, ``'r+'``} def read( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/anndata/readwrite/read.py:416: UserWarning: Parameters in `scanpy.api.read_h5ad` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: backed: {``None``, ``'r'``, ``'r+'``} def read_h5ad(filename, backed: Optional[str] = None, chunk_size: int = 6000): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/_settings.py:349: UserWarning: Parameters in `scanpy.api.set_figure_params` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: format: {`'png'`, `'pdf'`, `'svg'`, etc.}, optional (default: `'pdf'`) def set_figure_params( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:24: UserWarning: Parameters in `scanpy.pl.diffmap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: legend_fontweight: {`'normal'`, `'bold'`, ...} legend_fontweight: {`'normal'`, `'bold'`, ...} @_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:1354: UserWarning: Parameters in `scanpy.pl.dotplot` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) expression_cutoff: `float` (default: `0.`) mean_only_expressed: `bool` (default: `False`) color_map: `str`, optional (default: `Reds`) dot_max: `float` optional (default: `None`) dot_min: `float` optional (default: `None`) standard_scale: {`'var'`, `'group'`}, optional (default: `None`) smallest_dot: `float` optional (default: 0.) adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) expression_cutoff: `float` (default: `0.`) mean_only_expressed: `bool` (default: `False`) color_map: `str`, optional (default: `Reds`) dot_max: `float` optional (default: `None`) dot_min: `float` optional (default: `None`) standard_scale: {`'var'`, `'group'`}, optional (default: `None`) smallest_dot: `float` optional (default: 0.) @_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:24: UserWarning: Parameters in `scanpy.pl.draw_graph` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: layout: {`'fa'`, `'fr'`, `'drl'`, ...}, optional (default: last computed) edges_color: matplotlib color(s), optional (default: `'grey'`) legend_fontweight: {`'normal'`, `'bold'`, ...} layout: {`'fa'`, `'fr'`, `'drl'`, ...}, optional (default: last computed) edges_color: matplotlib color(s), optional (default: `'grey'`) legend_fontweight: {`'normal'`, `'bold'`, ...} @_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:24: UserWarning: Parameters in `scanpy.pl.embedding` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: edges_color: matplotlib color(s), optional (default: `'grey'`) legend_fontweight: {`'normal'`, `'bold'`, ...} edges_color: matplotlib color(s), optional (default: `'grey'`) legend_fontweight: {`'normal'`, `'bold'`, ...} @_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_preprocessing.py:69: UserWarning: Parameters in `scanpy.pl.filter_genes_dispersion` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: show: bool, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) show: bool, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) def filter_genes_dispersion( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:1065: UserWarning: Parameters in `scanpy.pl.heatmap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) standard_scale: {`'var'`, `'obs'`}, optional (default: `None`) swap_axes: `bool`, optional (default: `False`) show_gene_labels: `bool`, optional (default: `None`). adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) standard_scale: {`'var'`, `'obs'`}, optional (default: `None`) swap_axes: `bool`, optional (default: `False`) show_gene_labels: `bool`, optional (default: `None`). @_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_preprocessing.py:14: UserWarning: Parameters in `scanpy.pl.highly_variable_genes` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData`, `np.recarray` log: `bool` show: bool, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) adata: :class:`~anndata.AnnData`, `np.recarray` log: `bool` show: bool, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) def highly_variable_genes(adata_or_result, log=False, show=None, save=None, highly_variable_genes=True): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:1686: UserWarning: Parameters in `scanpy.pl.matrixplot` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) standard_scale: {`'var'`, `'group'`}, optional (default: `None`) adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) standard_scale: {`'var'`, `'group'`}, optional (default: `None`) @_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/paga.py:242: UserWarning: Parameters in `scanpy.pl.paga` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: layout: {`'fa'`, `'fr'`, `'rt'`, `'rt_circular'`, `'eq_tree'`, ...}, optional (default: `'fr'`) normalize_to_color: `bool`, optional (default: `False`) layout: {`'fa'`, `'fr'`, `'rt'`, `'rt_circular'`, `'eq_tree'`, ...}, optional (default: `'fr'`) normalize_to_color: `bool`, optional (default: `False`) def paga( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/paga.py:22: UserWarning: Parameters in `scanpy.pl.paga_compare` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` kwds_scatter: `dict` kwds_paga: `dict` adata: :class:`~anndata.AnnData` kwds_scatter: `dict` kwds_paga: `dict` def paga_compare( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:24: UserWarning: Parameters in `scanpy.pl.pca` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: legend_fontweight: {`'normal'`, `'bold'`, ...} legend_fontweight: {`'normal'`, `'bold'`, ...} @_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:26: UserWarning: Parameters in `scanpy.pl.pca_overview` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: color: string or list of strings, optional (default: `None`) use_raw: `bool`, optional (default: `True`) legend_fontweight: {`'normal'`, `'bold'`, ...} show: bool, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) color: string or list of strings, optional (default: `None`) use_raw: `bool`, optional (default: `True`) legend_fontweight: {`'normal'`, `'bold'`, ...} show: bool, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) @_doc_params(scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:104: UserWarning: Parameters in `scanpy.pl.pca_variance_ratio` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: n_pcs: `int`, optional (default: `30`) log: `bool`, optional (default: `False`) show: `bool`, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) n_pcs: `int`, optional (default: `30`) log: `bool`, optional (default: `False`) show: `bool`, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) def pca_variance_ratio(adata, n_pcs=30, log=False, show=None, save=None): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:395: UserWarning: Parameters in `scanpy.pl.rank_genes_groups_heatmap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` groups: `str` or `list` of `str` adata: :class:`~anndata.AnnData` groups: `str` or `list` of `str` @_doc_params(show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:512: UserWarning: Parameters in `scanpy.pl.rank_genes_groups_stacked_violin` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: groups: `str` or `list` of `str` n_genes: `int`, optional (default: 10) groupby: `str` or `None`, optional (default: `None`) groups: `str` or `list` of `str` n_genes: `int`, optional (default: 10) groupby: `str` or `None`, optional (default: `None`) @_doc_params(show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:590: UserWarning: Parameters in `scanpy.pl.rank_genes_groups_violin` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: use_raw: `bool`, optional (default: `None`) use_raw: `bool`, optional (default: `None`) @_doc_params(show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:41: UserWarning: Parameters in `scanpy.pl.scatter` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: basis: {`'pca'`, `'tsne'`, `'umap'`, `'diffmap'`, `'draw_graph_fr'`, etc.} legend_fontweight: {`'normal'`, `'bold'`, ...} basis: {`'pca'`, `'tsne'`, `'umap'`, `'diffmap'`, `'draw_graph_fr'`, etc.} legend_fontweight: {`'normal'`, `'bold'`, ...} @_doc_params(scatter_temp=doc_scatter_basic, show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:723: UserWarning: Parameters in `scanpy.pl.stacked_violin` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) @_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:1912: UserWarning: Parameters in `scanpy.pl.tracksplot` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) @_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:24: UserWarning: Parameters in `scanpy.pl.tsne` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: edges_color: matplotlib color(s), optional (default: `'grey'`) legend_fontweight: {`'normal'`, `'bold'`, ...} edges_color: matplotlib color(s), optional (default: `'grey'`) legend_fontweight: {`'normal'`, `'bold'`, ...} @_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:24: UserWarning: Parameters in `scanpy.pl.umap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: edges_color: matplotlib color(s), optional (default: `'grey'`) legend_fontweight: {`'normal'`, `'bold'`, ...} edges_color: matplotlib color(s), optional (default: `'grey'`) legend_fontweight: {`'normal'`, `'bold'`, ...} @_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp/_dca.py:6: UserWarning: Parameters in `scanpy.external.pp.dca` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: mode: `str`, optional. `denoise`(default), or `latent`. ae_type: `str`, optional. `zinb-conddisp`(default), `zinb`, `nb-conddisp` or `nb`. normalize_per_cell: `bool`, optional. Default: `True`. scale: `bool`, optional. Default: `True`. log1p: `bool`, optional. Default: `True`. hidden_size: `tuple` or `list`, optional. Default: (64, 32, 64). hidden_dropout: `float`, `tuple` or `list`, optional. Default: 0.0. batchnorm: `bool`, optional. Default: `True`. activation: `str`, optional. Default: `relu`. init: `str`, optional. Default: `glorot_uniform`. network_kwds: `dict`, optional. epochs: `int`, optional. Default: 300. reduce_lr: `int`, optional. Default: 10. early_stop: `int`, optional. Default: 15. batch_size: `int`, optional. Default: 32. optimizer: `str`, optional. Default: "rmsprop". random_state: `int`, optional. Default: 0. threads: `int` or None, optional. Default: None learning_rate: `float`, optional. Default: None. verbose: `bool`, optional. Default: `False`. training_kwds: `dict`, optional. return_model: `bool`, optional. Default: `False`. return_info: `bool`, optional. Default: `False`. copy: `bool`, optional. Default: `False`. mode: `str`, optional. `denoise`(default), or `latent`. ae_type: `str`, optional. `zinb-conddisp`(default), `zinb`, `nb-conddisp` or `nb`. normalize_per_cell: `bool`, optional. Default: `True`. scale: `bool`, optional. Default: `True`. log1p: `bool`, optional. Default: `True`. hidden_size: `tuple` or `list`, optional. Default: (64, 32, 64). hidden_dropout: `float`, `tuple` or `list`, optional. Default: 0.0. batchnorm: `bool`, optional. Default: `True`. activation: `str`, optional. Default: `relu`. init: `str`, optional. Default: `glorot_uniform`. network_kwds: `dict`, optional. epochs: `int`, optional. Default: 300. reduce_lr: `int`, optional. Default: 10. early_stop: `int`, optional. Default: 15. batch_size: `int`, optional. Default: 32. optimizer: `str`, optional. Default: "rmsprop". random_state: `int`, optional. Default: 0. threads: `int` or None, optional. Default: None learning_rate: `float`, optional. Default: None. verbose: `bool`, optional. Default: `False`. training_kwds: `dict`, optional. return_model: `bool`, optional. Default: `False`. return_info: `bool`, optional. Default: `False`. copy: `bool`, optional. Default: `False`. def dca( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:24: UserWarning: Parameters in `scanpy.external.pl.phate` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: edges_color: matplotlib color(s), optional (default: `'grey'`) legend_fontweight: {`'normal'`, `'bold'`, ...} edges_color: matplotlib color(s), optional (default: `'grey'`) legend_fontweight: {`'normal'`, `'bold'`, ...} @_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax) Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/cmd/build.py", line 276, in build_main app.build(args.force_all, filenames) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 346, in build self.builder.build_update() File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 299, in build_update len(to_build)) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 361, in build self.write(docnames, list(updated_docnames), method) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 535, in write self._write_serial(sorted(docnames)) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 545, in _write_serial self.write_doc(docname, doctree) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/contextlib.py", line 88, in __exit__ next(self.gen) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 219, in pending_warnings memhandler.flushTo(logger) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 184, in flushTo logger.handle(record) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1454, in handle self.callHandlers(record) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1516, in callHandlers hdlr.handle(record) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 861, in handle rv = self.filter(record) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 720, in filter result = f.filter(record) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 404, in filter raise SphinxWarning(location + ":" + message) sphinx.errors.SphinxWarning: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:docstring of scanpy.pl.diffmap:36:py:func reference target not found: matplotlib.text.Text.set_fontsize Warning, treated as error: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:docstring of scanpy.pl.diffmap:36:py:func reference target not found: matplotlib.text.Text.set_fontsize