Read the Docs build information
Build id: 612161
Project: life-epigenetics-methylprep
Version: latest
Commit: 88c6ee40c42c6bcfff010352311bf223e9dc29fd
Date: 2021-04-13T18:06:00.126264Z
State: finished
Success: True


[rtd-command-info] start-time: 2021-04-13T18:06:01.680671Z, end-time: 2021-04-13T18:06:12.506670Z, duration: 10, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/FOXOBioScience/methylprep.git .
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[rtd-command-info] start-time: 2021-04-13T18:06:12.648346Z, end-time: 2021-04-13T18:06:13.349903Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out 'origin/master'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

HEAD is now at 88c6ee4 version bump for unit test fixes

[rtd-command-info] start-time: 2021-04-13T18:06:13.457465Z, end-time: 2021-04-13T18:06:13.535224Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-04-13T18:06:16.535846Z, end-time: 2021-04-13T18:06:21.937268Z, duration: 5, exit-code: 0
python3.7 -mvirtualenv --system-site-packages 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-04-13T18:06:22.065333Z, end-time: 2021-04-13T18:06:23.790107Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
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[rtd-command-info] start-time: 2021-04-13T18:06:23.940429Z, end-time: 2021-04-13T18:06:34.066505Z, duration: 10, exit-code: 0
python -m pip install --upgrade --no-cache-dir -I 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<2.2
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Building wheels for collected packages: mock, future
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  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23755 sha256=986a7d65ba573ce081a4fd0edfae35fcf931198011a0afe18ee476cc0e248002
  Stored in directory: /tmp/pip-ephem-wheel-cache-ttmlo47w/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
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Successfully built mock future
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ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible.
Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.8.1 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.17 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.25.1 setuptools-56.0.0 six-1.15.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.4

[rtd-command-info] start-time: 2021-04-13T18:06:34.177064Z, end-time: 2021-04-13T18:06:48.290526Z, duration: 14, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-websupport->sphinx>=1.8->nbsphinx->-r requirements.txt (line 10)) (1.1.4)
Building wheels for collected packages: bs4, m2r, pandocfilters, pyrsistent
  Building wheel for bs4 (setup.py): started
  Building wheel for bs4 (setup.py): finished with status 'done'
  Created wheel for bs4: filename=bs4-0.0.1-py3-none-any.whl size=1273 sha256=51b665ca4d0dc8329c8081c6de8dec2dbdd83c76bbd7c91db8932a7b3e2f854d
  Stored in directory: /tmp/pip-ephem-wheel-cache-bv8g88qn/wheels/0a/9e/ba/20e5bbc1afef3a491f0b3bb74d508f99403aabe76eda2167ca
  Building wheel for m2r (setup.py): started
  Building wheel for m2r (setup.py): finished with status 'done'
  Created wheel for m2r: filename=m2r-0.2.1-py3-none-any.whl size=10465 sha256=5c87b00ca4a3d7b0dde7c25d32129f3520bd75d3751a3694f0027ab0ee7b76c0
  Stored in directory: /tmp/pip-ephem-wheel-cache-bv8g88qn/wheels/02/47/3a/e1c46c2cca442c8781612542397c9559a579f10e2dd87e7c9f
  Building wheel for pandocfilters (setup.py): started
  Building wheel for pandocfilters (setup.py): finished with status 'done'
  Created wheel for pandocfilters: filename=pandocfilters-1.4.3-py3-none-any.whl size=7992 sha256=207f52521e9f87d569ec2f5753095989822b501ab89939a54d12fcdb4dc715b4
  Stored in directory: /tmp/pip-ephem-wheel-cache-bv8g88qn/wheels/42/81/34/545dc2fbf0e9137811e901108d37fc04650e81d48f97078000
  Building wheel for pyrsistent (setup.py): started
  Building wheel for pyrsistent (setup.py): finished with status 'done'
  Created wheel for pyrsistent: filename=pyrsistent-0.17.3-cp37-cp37m-linux_x86_64.whl size=115328 sha256=5911dbf7a825ef34e84d9e0d9906fca127f10b83d814b82eae959e707c68fcfe
  Stored in directory: /tmp/pip-ephem-wheel-cache-bv8g88qn/wheels/a5/52/bf/71258a1d7b3c8cbe1ee53f9314c6f65f20385481eaee573cc5
Successfully built bs4 m2r pandocfilters pyrsistent
Installing collected packages: zipp, typing-extensions, ipython-genutils, traitlets, pyrsistent, importlib-metadata, attrs, tornado, pyzmq, jupyter-core, jsonschema, webencodings, nest-asyncio, nbformat, jupyter-client, async-generator, testpath, soupsieve, pandocfilters, nbclient, mistune, jupyterlab-pygments, entrypoints, defusedxml, bleach, toml, PyYAML, py, pluggy, pbr, patsy, nbconvert, iniconfig, coverage, beautifulsoup4, tqdm, statsmodels, sphinxcontrib-apidoc, python-coveralls, pytest, nbsphinx, m2r, lxml, bs4
Successfully installed PyYAML-5.4.1 async-generator-1.10 attrs-20.3.0 beautifulsoup4-4.9.3 bleach-3.3.0 bs4-0.0.1 coverage-5.5 defusedxml-0.7.1 entrypoints-0.3 importlib-metadata-3.10.1 iniconfig-1.1.1 ipython-genutils-0.2.0 jsonschema-3.2.0 jupyter-client-6.1.12 jupyter-core-4.7.1 jupyterlab-pygments-0.1.2 lxml-4.6.3 m2r-0.2.1 mistune-0.8.4 nbclient-0.5.3 nbconvert-6.0.7 nbformat-5.1.3 nbsphinx-0.8.3 nest-asyncio-1.5.1 pandocfilters-1.4.3 patsy-0.5.1 pbr-5.5.1 pluggy-0.13.1 py-1.10.0 pyrsistent-0.17.3 pytest-6.2.3 python-coveralls-2.9.3 pyzmq-22.0.3 soupsieve-2.2.1 sphinxcontrib-apidoc-0.3.0 statsmodels-0.12.2 testpath-0.4.4 toml-0.10.2 tornado-6.1 tqdm-4.60.0 traitlets-5.0.5 typing-extensions-3.7.4.3 webencodings-0.5.1 zipp-3.4.1

[rtd-command-info] start-time: 2021-04-13T18:06:48.436294Z, end-time: 2021-04-13T18:06:49.788961Z, duration: 1, exit-code: 0
python /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/setup.py install --force
running install
running bdist_egg
running egg_info
creating methylprep.egg-info
writing methylprep.egg-info/PKG-INFO
writing dependency_links to methylprep.egg-info/dependency_links.txt
writing entry points to methylprep.egg-info/entry_points.txt
writing requirements to methylprep.egg-info/requires.txt
writing top-level names to methylprep.egg-info/top_level.txt
writing manifest file 'methylprep.egg-info/SOURCES.txt'
adding license file 'LICENSE' (matched pattern 'LICEN[CS]E*')
reading manifest file 'methylprep.egg-info/SOURCES.txt'
writing manifest file 'methylprep.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/methylprep
copying methylprep/cli.py -> build/lib/methylprep
copying methylprep/__main__.py -> build/lib/methylprep
copying methylprep/version.py -> build/lib/methylprep
copying methylprep/__init__.py -> build/lib/methylprep
creating build/lib/methylprep/utils
copying methylprep/utils/progress_bar.py -> build/lib/methylprep/utils
copying methylprep/utils/parsing.py -> build/lib/methylprep/utils
copying methylprep/utils/files.py -> build/lib/methylprep/utils
copying methylprep/utils/data_frames.py -> build/lib/methylprep/utils
copying methylprep/utils/__init__.py -> build/lib/methylprep/utils
creating build/lib/methylprep/files
copying methylprep/files/idat.py -> build/lib/methylprep/files
copying methylprep/files/manifests.py -> build/lib/methylprep/files
copying methylprep/files/sample_sheets.py -> build/lib/methylprep/files
copying methylprep/files/__init__.py -> build/lib/methylprep/files
creating build/lib/methylprep/processing
copying methylprep/processing/pipeline.py -> build/lib/methylprep/processing
copying methylprep/processing/p_value_probe_detection.py -> build/lib/methylprep/processing
copying methylprep/processing/infer_channel_switch.py -> build/lib/methylprep/processing
copying methylprep/processing/postprocess.py -> build/lib/methylprep/processing
copying methylprep/processing/read_geo_processed.py -> build/lib/methylprep/processing
copying methylprep/processing/dye_bias.py -> build/lib/methylprep/processing
copying methylprep/processing/preprocess.py -> build/lib/methylprep/processing
copying methylprep/processing/__init__.py -> build/lib/methylprep/processing
creating build/lib/methylprep/download
copying methylprep/download/samplesheet_sync_idat.py -> build/lib/methylprep/download
copying methylprep/download/miniml.py -> build/lib/methylprep/download
copying methylprep/download/process_data.py -> build/lib/methylprep/download
copying methylprep/download/array_express.py -> build/lib/methylprep/download
copying methylprep/download/geo.py -> build/lib/methylprep/download
copying methylprep/download/__init__.py -> build/lib/methylprep/download
creating build/lib/methylprep/models
copying methylprep/models/meth_dataset.py -> build/lib/methylprep/models
copying methylprep/models/samples.py -> build/lib/methylprep/models
copying methylprep/models/raw_dataset.py -> build/lib/methylprep/models
copying methylprep/models/arrays.py -> build/lib/methylprep/models
copying methylprep/models/controls.py -> build/lib/methylprep/models
copying methylprep/models/sketchy_probes.py -> build/lib/methylprep/models
copying methylprep/models/__init__.py -> build/lib/methylprep/models
copying methylprep/models/probes.py -> build/lib/methylprep/models
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/methylprep
copying build/lib/methylprep/cli.py -> build/bdist.linux-x86_64/egg/methylprep
creating build/bdist.linux-x86_64/egg/methylprep/utils
copying build/lib/methylprep/utils/progress_bar.py -> build/bdist.linux-x86_64/egg/methylprep/utils
copying build/lib/methylprep/utils/parsing.py -> build/bdist.linux-x86_64/egg/methylprep/utils
copying build/lib/methylprep/utils/files.py -> build/bdist.linux-x86_64/egg/methylprep/utils
copying build/lib/methylprep/utils/data_frames.py -> build/bdist.linux-x86_64/egg/methylprep/utils
copying build/lib/methylprep/utils/__init__.py -> build/bdist.linux-x86_64/egg/methylprep/utils
creating build/bdist.linux-x86_64/egg/methylprep/files
copying build/lib/methylprep/files/idat.py -> build/bdist.linux-x86_64/egg/methylprep/files
copying build/lib/methylprep/files/manifests.py -> build/bdist.linux-x86_64/egg/methylprep/files
copying build/lib/methylprep/files/sample_sheets.py -> build/bdist.linux-x86_64/egg/methylprep/files
copying build/lib/methylprep/files/__init__.py -> build/bdist.linux-x86_64/egg/methylprep/files
creating build/bdist.linux-x86_64/egg/methylprep/processing
copying build/lib/methylprep/processing/pipeline.py -> build/bdist.linux-x86_64/egg/methylprep/processing
copying build/lib/methylprep/processing/p_value_probe_detection.py -> build/bdist.linux-x86_64/egg/methylprep/processing
copying build/lib/methylprep/processing/infer_channel_switch.py -> build/bdist.linux-x86_64/egg/methylprep/processing
copying build/lib/methylprep/processing/postprocess.py -> build/bdist.linux-x86_64/egg/methylprep/processing
copying build/lib/methylprep/processing/read_geo_processed.py -> build/bdist.linux-x86_64/egg/methylprep/processing
copying build/lib/methylprep/processing/dye_bias.py -> build/bdist.linux-x86_64/egg/methylprep/processing
copying build/lib/methylprep/processing/preprocess.py -> build/bdist.linux-x86_64/egg/methylprep/processing
copying build/lib/methylprep/processing/__init__.py -> build/bdist.linux-x86_64/egg/methylprep/processing
copying build/lib/methylprep/__main__.py -> build/bdist.linux-x86_64/egg/methylprep
copying build/lib/methylprep/version.py -> build/bdist.linux-x86_64/egg/methylprep
creating build/bdist.linux-x86_64/egg/methylprep/download
copying build/lib/methylprep/download/samplesheet_sync_idat.py -> build/bdist.linux-x86_64/egg/methylprep/download
copying build/lib/methylprep/download/miniml.py -> build/bdist.linux-x86_64/egg/methylprep/download
copying build/lib/methylprep/download/process_data.py -> build/bdist.linux-x86_64/egg/methylprep/download
copying build/lib/methylprep/download/array_express.py -> build/bdist.linux-x86_64/egg/methylprep/download
copying build/lib/methylprep/download/geo.py -> build/bdist.linux-x86_64/egg/methylprep/download
copying build/lib/methylprep/download/__init__.py -> build/bdist.linux-x86_64/egg/methylprep/download
creating build/bdist.linux-x86_64/egg/methylprep/models
copying build/lib/methylprep/models/meth_dataset.py -> build/bdist.linux-x86_64/egg/methylprep/models
copying build/lib/methylprep/models/samples.py -> build/bdist.linux-x86_64/egg/methylprep/models
copying build/lib/methylprep/models/raw_dataset.py -> build/bdist.linux-x86_64/egg/methylprep/models
copying build/lib/methylprep/models/arrays.py -> build/bdist.linux-x86_64/egg/methylprep/models
copying build/lib/methylprep/models/controls.py -> build/bdist.linux-x86_64/egg/methylprep/models
copying build/lib/methylprep/models/sketchy_probes.py -> build/bdist.linux-x86_64/egg/methylprep/models
copying build/lib/methylprep/models/__init__.py -> build/bdist.linux-x86_64/egg/methylprep/models
copying build/lib/methylprep/models/probes.py -> build/bdist.linux-x86_64/egg/methylprep/models
copying build/lib/methylprep/__init__.py -> build/bdist.linux-x86_64/egg/methylprep
byte-compiling build/bdist.linux-x86_64/egg/methylprep/cli.py to cli.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/utils/progress_bar.py to progress_bar.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/utils/parsing.py to parsing.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/utils/files.py to files.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/utils/data_frames.py to data_frames.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/utils/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/files/idat.py to idat.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/files/manifests.py to manifests.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/files/sample_sheets.py to sample_sheets.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/files/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/processing/pipeline.py to pipeline.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/processing/p_value_probe_detection.py to p_value_probe_detection.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/processing/infer_channel_switch.py to infer_channel_switch.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/processing/postprocess.py to postprocess.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/processing/read_geo_processed.py to read_geo_processed.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/processing/dye_bias.py to dye_bias.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/processing/preprocess.py to preprocess.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/processing/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/__main__.py to __main__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/version.py to version.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/download/samplesheet_sync_idat.py to samplesheet_sync_idat.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/download/miniml.py to miniml.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/download/process_data.py to process_data.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/download/array_express.py to array_express.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/download/geo.py to geo.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/download/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/models/meth_dataset.py to meth_dataset.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/models/samples.py to samples.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/models/raw_dataset.py to raw_dataset.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/models/arrays.py to arrays.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/models/controls.py to controls.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/models/sketchy_probes.py to sketchy_probes.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/models/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/models/probes.py to probes.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/methylprep/__init__.py to __init__.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying methylprep.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying methylprep.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying methylprep.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying methylprep.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying methylprep.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying methylprep.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating dist
creating 'dist/methylprep-1.4.1-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing methylprep-1.4.1-py3.7.egg
Copying methylprep-1.4.1-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages
Adding methylprep 1.4.1 to easy-install.pth file
Installing methylprep-cli script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin

Installed /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages/methylprep-1.4.1-py3.7.egg
Processing dependencies for methylprep==1.4.1
Searching for lxml==4.6.3
Best match: lxml 4.6.3
Adding lxml 4.6.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages
Searching for bs4==0.0.1
Best match: bs4 0.0.1
Adding bs4 0.0.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages
Searching for tqdm==4.60.0
Best match: tqdm 4.60.0
Adding tqdm 4.60.0 to easy-install.pth file
Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages
Searching for statsmodels==0.12.2
Best match: statsmodels 0.12.2
Adding statsmodels 0.12.2 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages
Searching for scipy==1.5.3
Best match: scipy 1.5.3
Adding scipy 1.5.3 to easy-install.pth file

Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages
Searching for pandas==1.1.3
Best match: pandas 1.1.3
pandas 1.1.3 is already the active version in easy-install.pth

Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages
Searching for numpy==1.19.2
Best match: numpy 1.19.2
numpy 1.19.2 is already the active version in easy-install.pth
Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin
Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin
Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin

Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages
Searching for beautifulsoup4==4.9.3
Best match: beautifulsoup4 4.9.3
Adding beautifulsoup4 4.9.3 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages
Searching for patsy==0.5.1
Best match: patsy 0.5.1
Adding patsy 0.5.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages
Searching for python-dateutil==2.8.1
Best match: python-dateutil 2.8.1
python-dateutil 2.8.1 is already the active version in easy-install.pth

Using /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages
Searching for pytz==2021.1
Best match: pytz 2021.1
Adding pytz 2021.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages
Searching for soupsieve==2.2.1
Best match: soupsieve 2.2.1
Adding soupsieve 2.2.1 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages
Searching for six==1.15.0
Best match: six 1.15.0
Adding six 1.15.0 to easy-install.pth file

Using /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages
Finished processing dependencies for methylprep==1.4.1

[rtd-command-info] start-time: 2021-04-13T18:06:50.629297Z, end-time: 2021-04-13T18:06:50.698703Z, duration: 0, exit-code: 0
cat conf.py
# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config

# -- Path setup --------------------------------------------------------------

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
import sys
sys.path.insert(0, os.path.abspath('.'))


# -- Project information -----------------------------------------------------

project = 'methylprep'
copyright = '2021, FOXO Technologies, inc.'
author = 'FOXO Technologies, inc.'

# The short X.Y version
version = '1.4'
# The full version, including alpha/beta/rc tags
release = '1.4.1'


# -- General configuration ---------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    'sphinx.ext.autodoc',
    'sphinxcontrib.apidoc',
    'm2r',
    'nbsphinx',
    'sphinx.ext.autosummary'
]

# instead of CLI "sphinx-autodoc . _build/html" you write this
apidoc_module_dir = '.'
apidoc_output_dir = '_sphinx_build'
apidoc_excluded_paths = ['tests']
apidoc_separate_modules = False

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_sphinx_templates']

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
source_suffix = ['.rst', '.md']
# source_suffix = '.rst'

# The master toctree document.
master_doc = 'index'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path .
exclude_patterns = ['_sphinx_build', 'Thumbs.db', '.DS_Store']

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'


# -- Options for HTML output -------------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
#
html_theme =  'sphinx_rtd_theme' #'alabaster'

# Theme options are theme-specific and customize the look and feel of a theme
# further.  For a list of options available for each theme, see the
# documentation.
#
# html_theme_options = {}

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_sphinx_static']

# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself.  Builtin themes are using these templates by
# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
# 'searchbox.html']``.
#
# html_sidebars = {}


# -- Options for HTMLHelp output ---------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = 'methylpredoc'


# -- Options for LaTeX output ------------------------------------------------

latex_elements = {
    # The paper size ('letterpaper' or 'a4paper').
    #
    # 'papersize': 'letterpaper',

    # The font size ('10pt', '11pt' or '12pt').
    #
    # 'pointsize': '10pt',

    # Additional stuff for the LaTeX preamble.
    #
    # 'preamble': '',

    # Latex figure (float) alignment
    #
    # 'figure_align': 'htbp',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
    (master_doc, 'methylprep.tex', 'methylprep Documentation',
     'Life Epigenetics', 'manual'),
]


# -- Options for manual page output ------------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    (master_doc, 'methylprep', 'methylprep Documentation',
     [author], 1)
]


# -- Options for Texinfo output ----------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (master_doc, 'methylprep', 'methylprep Documentation',
     author, 'methylprep', 'One line description of project.',
     'Miscellaneous'),
]


# -- Extension configuration -------------------------------------------------




###########################################################################
#          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
#
# Note: this file should't rely on extra depencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

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):
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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://assets.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://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ],
    'downloads': [ 
    ("html", "//life-epigenetics-methylprep.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'life-epigenetics-methylprep',
    'name': u'methylprep',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://life-epigenetics-methylprep.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'FOXOBioScience',
    'proxied_api_host': '/_',
    'github_repo': 'methylprep',
    '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,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '88c6ee40',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





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")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/life-epigenetics-methylprep/builds/612161/'

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'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2021-04-13T18:06:50.816381Z, end-time: 2021-04-13T18:07:14.443188Z, duration: 23, exit-code: 0
python -m sphinx -T -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/conf.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/setup.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.download.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.files.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.models.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.processing.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.utils.rst.
Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/modules.rst.
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 14 source files that are out of date
updating environment: 14 added, 0 changed, 0 removed
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reading sources... [ 14%] docs/README
reading sources... [ 21%] docs/cli
reading sources... [ 28%] docs/debug_notebooks/float16_error
reading sources... [ 35%] docs/debug_notebooks/improving idat.py
reading sources... [ 42%] docs/example_download
reading sources... [ 50%] docs/faq
reading sources... [ 57%] docs/how_to_add_new_array_type
reading sources... [ 64%] docs/installation
reading sources... [ 71%] docs/methylprep_tutorial
reading sources... [ 78%] docs/package
reading sources... [ 85%] docs/release-history
reading sources... [ 92%] docs/source/modules
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: 
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   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/README.md:302: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 2 does not contain the same number of items as row 1 (3 vs 4).

.. list-table::
   :header-rows: 1

   * - Argument
     - Type
     - Default
     - Description
   * - -h, --help
     -
     - show this help message and exit
   * -   -d , --data_dir
     - ``str``
     - [required path]
     - path to where the data series will be saved. Folder must exist already.
   * -   -i ID, --id ID
     - ``str``
     - [required ID]
     - The dataset's reference ID (Starts with ``GSE`` for GEO or ``E-MTAB-`` for ArrayExpress)
   * -   -l LIST, --list LIST
     - ``multiple strings``
     - optional
     - List of series IDs (can be either GEO or ArrayExpress), for partial downloading
   * -   -o, --dict_only
     - ``True``
     - pass flag only
     - If passed, will only create dictionaries and not process any samples
   * -   -b BATCH_SIZE, --batch_size BATCH_SIZE
     - ``int``
     - optional
     - Number of samples to process at a time, 100 by default.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/debug_notebooks/float16_error.ipynb:1: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/debug_notebooks/improving idat.py.ipynb:1: WARNING: Each notebook should have at least one section title
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:203: WARNING: Title level inconsistent:

list of code edits by file in methylprep for mouse support
----------------------------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:266: WARNING: Title level inconsistent:

testing
-------
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:278: WARNING: Title level inconsistent:

other bugs discovered:
~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:285: WARNING: Title level inconsistent:

data flow through methylprep
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/how_to_add_new_array_type.md:124: WARNING: Unknown target name: "ctl".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylprep".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:6: WARNING: Duplicate explicit target name: "methylcheck".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/methylprep_tutorial.md:370: WARNING: Title level inconsistent:

Visual Filtering Functions
~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md:161: WARNING: Title level inconsistent:

``get_sample_sheet``
~~~~~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md:191: WARNING: Title level inconsistent:

``get_manifest``
~~~~~~~~~~~~~~~~~~~~
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/docs/package.md:225: WARNING: Title level inconsistent:

``get_raw_datasets``
~~~~~~~~~~~~~~~~~~~~~~~~
WARNING: missing attribute mentioned in :members: or __all__: module methylprep, attribute make_pipeline
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_pipeline:92: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_pipeline:105: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.run_pipeline:106: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.read_geo:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.read_geo:27: WARNING: Unexpected indentation.
WARNING: missing attribute mentioned in :members: or __all__: module methylprep.processing, attribute make_pipeline,consolidate_values_for_sheet
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/processing/pipeline.py:docstring of methylprep.processing.SampleDataContainer:9: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/processing/__init__.py:docstring of methylprep.processing.run_pipeline:92: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/processing/__init__.py:docstring of methylprep.processing.run_pipeline:105: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/processing/__init__.py:docstring of methylprep.processing.run_pipeline:106: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/processing/__init__.py:docstring of methylprep.processing.read_geo:24: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/processing/__init__.py:docstring of methylprep.processing.read_geo:25: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/processing/__init__.py:docstring of methylprep.processing.read_geo:27: WARNING: Unexpected indentation.
WARNING: missing attribute mentioned in :members: or __all__: module methylprep.models, attribute Sesame
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/files/idat.py:docstring of methylprep.files.IdatDataset:12: WARNING: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/download/__init__.py:docstring of methylprep.download.pipeline_find_betas_any_source:34: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/__init__.py:docstring of methylprep.read_geo:19: WARNING: Unknown target name: "matrix".
/home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/methylprep/processing/__init__.py:docstring of methylprep.processing.read_geo:19: WARNING: Unknown target name: "matrix".
README.md:302: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 2 does not contain the same number of items as row 1 (3 vs 4).

.. list-table::
   :header-rows: 1

   * - Argument
     - Type
     - Default
     - Description
   * - -h, --help
     -
     - show this help message and exit
   * -   -d , --data_dir
     - ``str``
     - [required path]
     - path to where the data series will be saved. Folder must exist already.
   * -   -i ID, --id ID
     - ``str``
     - [required ID]
     - The dataset's reference ID (Starts with ``GSE`` for GEO or ``E-MTAB-`` for ArrayExpress)
   * -   -l LIST, --list LIST
     - ``multiple strings``
     - optional
     - List of series IDs (can be either GEO or ArrayExpress), for partial downloading
   * -   -o, --dict_only
     - ``True``
     - pass flag only
     - If passed, will only create dictionaries and not process any samples
   * -   -b BATCH_SIZE, --batch_size BATCH_SIZE
     - ``int``
     - optional
     - Number of samples to process at a time, 100 by default.
looking for now-outdated files... none found
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[rtd-command-info] start-time: 2021-04-13T18:07:14.624917Z, end-time: 2021-04-13T18:07:16.316754Z, duration: 1, exit-code: 0
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build succeeded, 2 warnings.

The HTML page is in _build/localmedia.
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