Read the Docs build information
Build id: 21436
Project: european-xfel-offline-calibration
Version: latest
Commit: 2610ad4cba18ff4e292a18c697c18fd9c7221af7
Date: 2021-03-08T11:33:17.667406Z
State: finished
Success: False


[rtd-command-info] start-time: 2021-03-08T11:33:18.636805Z, end-time: 2021-03-08T11:33:39.133436Z, duration: 20, exit-code: 0
git clone --no-single-branch --depth 50 http://git.xfel.eu/gitlab/detectors/pycalibration.git .
Cloning into '.'...

[rtd-command-info] start-time: 2021-03-08T11:33:39.540180Z, end-time: 2021-03-08T11:33:39.777147Z, duration: 0, exit-code: 0
git checkout --force origin/doc/run_rtd
Note: checking out 'origin/doc/run_rtd'.

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 2610ad4 add mock up for imports

[rtd-command-info] start-time: 2021-03-08T11:33:39.911622Z, end-time: 2021-03-08T11:33:39.990474Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-03-08T11:33:41.510492Z, end-time: 2021-03-08T11:33:46.637379Z, duration: 5, exit-code: 0
python3.7 -mvirtualenv /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest
Using base prefix '/home/docs/.pyenv/versions/3.7.3'
New python executable in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python3.7
Also creating executable in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-03-08T11:33:46.778998Z, end-time: 2021-03-08T11:33:47.833685Z, duration: 1, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python -m pip install --upgrade --no-cache-dir pip
Requirement already satisfied: pip in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages (21.0.1)

[rtd-command-info] start-time: 2021-03-08T11:33:47.971582Z, end-time: 2021-03-08T11:34:00.283041Z, duration: 12, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python -m pip install --upgrade --no-cache-dir 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
Collecting Pygments==2.3.1
  Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB)
Collecting setuptools==41.0.1
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Collecting docutils==0.14
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Collecting mock==1.0.1
  Downloading mock-1.0.1.zip (861 kB)
Collecting pillow==5.4.1
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Collecting alabaster!=0.7.5,<0.8,>=0.7
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Collecting future
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Collecting requests
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Collecting Jinja2>=2.9
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Collecting imagesize
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Collecting packaging
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Collecting babel!=2.0,>=1.3
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Collecting snowballstemmer>=1.1
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Collecting sphinxcontrib-websupport
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Collecting pytz>=2015.7
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Collecting MarkupSafe>=0.23
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Collecting urllib3<1.27,>=1.21.1
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Collecting chardet<5,>=3.0.2
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Collecting idna<3,>=2.5
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Collecting certifi>=2017.4.17
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Collecting pyparsing>=2.0.2
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Collecting sphinxcontrib-serializinghtml
  Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB)
Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23755 sha256=e9d6fa212411a8c58699a27914fce3824b540ea1048b441afca264e19b85b80b
  Stored in directory: /tmp/pip-ephem-wheel-cache-9xwzvqqz/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=9e307676089ad5eb0cd38619fae380a0398edff437a64fca571bb1fe48e9e233
  Stored in directory: /tmp/pip-ephem-wheel-cache-9xwzvqqz/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock
  Attempting uninstall: setuptools
    Found existing installation: setuptools 54.1.1
    Uninstalling setuptools-54.1.1:
      Successfully uninstalled setuptools-54.1.1
Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.14 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-1.0.4 recommonmark-0.5.0 requests-2.25.1 setuptools-41.0.1 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 urllib3-1.26.3

[rtd-command-info] start-time: 2021-03-08T11:34:00.420797Z, end-time: 2021-03-08T11:34:06.128699Z, duration: 5, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Collecting Cython==0.29.21
  Downloading Cython-0.29.21-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB)
Collecting numpy==1.19.1
  Downloading numpy-1.19.1-cp37-cp37m-manylinux2010_x86_64.whl (14.5 MB)
Installing collected packages: numpy, Cython
Successfully installed Cython-0.29.21 numpy-1.19.1

[rtd-command-info] start-time: 2021-03-08T11:34:06.264132Z, end-time: 2021-03-08T11:34:09.850042Z, duration: 3, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python ./setup.py install --force
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/cal_tools
copying cal_tools/cal_tools/metrology.py -> build/lib.linux-x86_64-3.7/cal_tools
copying cal_tools/cal_tools/__init__.py -> build/lib.linux-x86_64-3.7/cal_tools
copying cal_tools/cal_tools/agipdutils.py -> build/lib.linux-x86_64-3.7/cal_tools
copying cal_tools/cal_tools/agipdutils_ff.py -> build/lib.linux-x86_64-3.7/cal_tools
copying cal_tools/cal_tools/step_timing.py -> build/lib.linux-x86_64-3.7/cal_tools
copying cal_tools/cal_tools/pnccdlib.py -> build/lib.linux-x86_64-3.7/cal_tools
copying cal_tools/cal_tools/mdc_config.py -> build/lib.linux-x86_64-3.7/cal_tools
copying cal_tools/cal_tools/agipdlib.py -> build/lib.linux-x86_64-3.7/cal_tools
copying cal_tools/cal_tools/tools.py -> build/lib.linux-x86_64-3.7/cal_tools
copying cal_tools/cal_tools/enums.py -> build/lib.linux-x86_64-3.7/cal_tools
copying cal_tools/cal_tools/plotting.py -> build/lib.linux-x86_64-3.7/cal_tools
copying cal_tools/cal_tools/ana_tools.py -> build/lib.linux-x86_64-3.7/cal_tools
copying cal_tools/cal_tools/dssclib.py -> build/lib.linux-x86_64-3.7/cal_tools
copying cal_tools/cal_tools/lpdlib.py -> build/lib.linux-x86_64-3.7/cal_tools
creating build/lib.linux-x86_64-3.7/xfel_calibrate
copying xfel_calibrate/__init__.py -> build/lib.linux-x86_64-3.7/xfel_calibrate
copying xfel_calibrate/VERSION.py -> build/lib.linux-x86_64-3.7/xfel_calibrate
copying xfel_calibrate/settings.py -> build/lib.linux-x86_64-3.7/xfel_calibrate
copying xfel_calibrate/notebooks.py -> build/lib.linux-x86_64-3.7/xfel_calibrate
copying xfel_calibrate/calibrate.py -> build/lib.linux-x86_64-3.7/xfel_calibrate
copying xfel_calibrate/finalize.py -> build/lib.linux-x86_64-3.7/xfel_calibrate
creating build/lib.linux-x86_64-3.7/xfel_calibrate/bin
copying xfel_calibrate/bin/slurm_calibrate.sh -> build/lib.linux-x86_64-3.7/xfel_calibrate/bin
copying xfel_calibrate/bin/pre-commit-diff.sh -> build/lib.linux-x86_64-3.7/xfel_calibrate/bin
copying xfel_calibrate/titlepage.tmpl -> build/lib.linux-x86_64-3.7/xfel_calibrate
copying xfel_calibrate/xfel.pdf -> build/lib.linux-x86_64-3.7/xfel_calibrate
creating build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks
creating build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD
copying xfel_calibrate/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD
creating build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/generic
copying xfel_calibrate/notebooks/generic/overallmodules_Darks_Summary_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/generic
copying xfel_calibrate/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD
copying xfel_calibrate/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD
copying xfel_calibrate/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_Summary.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD
copying xfel_calibrate/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD
copying xfel_calibrate/notebooks/AGIPD/AGIPD_Correct_and_Verify_Summary_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD
copying xfel_calibrate/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD
copying xfel_calibrate/notebooks/AGIPD/AGIPD_Characterize_Gain_Combine_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD
copying xfel_calibrate/notebooks/AGIPD/AGIPD_FF_Histogramming.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD
creating build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD/playground
copying xfel_calibrate/notebooks/AGIPD/playground/AGIPD_SingleM_test_Dark.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD/playground
creating build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/LPD
copying xfel_calibrate/notebooks/LPD/LPDChar_Darks_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/LPD
copying xfel_calibrate/notebooks/LPD/Characterize_LPD_GAIN_CI_per_pixel_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/LPD
copying xfel_calibrate/notebooks/LPD/LPD_FlatField_Radial_per_pixel_CI_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/LPD
copying xfel_calibrate/notebooks/LPD/LPD_Correct_and_Verify.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/LPD
copying xfel_calibrate/notebooks/LPD/Mine_RadIntensity_vs_XGM_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/LPD
creating build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/pnCCD
copying xfel_calibrate/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/pnCCD
copying xfel_calibrate/notebooks/pnCCD/Characterize_pnCCD_Gain.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/pnCCD
copying xfel_calibrate/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/pnCCD
copying xfel_calibrate/notebooks/generic/DB_Constants_to_HDF5_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/generic
copying xfel_calibrate/notebooks/generic/PlotFromCalDB_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/generic
copying xfel_calibrate/notebooks/generic/PlotFromCalDB_Summary_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/generic
creating build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/Tutorial
copying xfel_calibrate/notebooks/Tutorial/calversion.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/Tutorial
creating build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/FastCCD
copying xfel_calibrate/notebooks/FastCCD/Characterize_Darks_NewDAQ_FastCCD_NBC_New_Common_Mode.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/FastCCD
copying xfel_calibrate/notebooks/FastCCD/CorrectionNotebook_NewDAQ_FastCCD_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/FastCCD
creating build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/Jungfrau
copying xfel_calibrate/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/Jungfrau
copying xfel_calibrate/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/Jungfrau
creating build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/ePix100
copying xfel_calibrate/notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/ePix100
copying xfel_calibrate/notebooks/ePix100/Correction_ePix100_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/ePix100
creating build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/ePix10K
copying xfel_calibrate/notebooks/ePix10K/Characterize_Darks_ePix10K_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/ePix10K
copying xfel_calibrate/notebooks/ePix10K/Correction_ePix10K_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/ePix10K
creating build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/DSSC
copying xfel_calibrate/notebooks/DSSC/Characterize_DSSC_Darks_NBC.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/DSSC
copying xfel_calibrate/notebooks/DSSC/DSSC_Correct_and_Verify.ipynb -> build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/DSSC
running build_ext
cythoning cal_tools/cython/agipdalgs.pyx to cal_tools/cython/agipdalgs.c
building 'cal_tools.cython.agipdalgs' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/cal_tools
creating build/temp.linux-x86_64-3.7/cal_tools/cython
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/numpy/core/include -I/home/docs/.pyenv/versions/3.7.3/include/python3.7m -c cal_tools/cython/agipdalgs.c -o build/temp.linux-x86_64-3.7/cal_tools/cython/agipdalgs.o -fopenmp -march=native
In file included from /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0,
                 from /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from cal_tools/cython/agipdalgs.c:610:
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
creating build/lib.linux-x86_64-3.7/cal_tools/cython
gcc -pthread -shared -L/home/docs/.pyenv/versions/3.7.3/lib -L/home/docs/.pyenv/versions/3.7.3/lib build/temp.linux-x86_64-3.7/cal_tools/cython/agipdalgs.o -o build/lib.linux-x86_64-3.7/cal_tools/cython/agipdalgs.cpython-37m-x86_64-linux-gnu.so -fopenmp
running install_lib
creating /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools
copying build/lib.linux-x86_64-3.7/cal_tools/metrology.py -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools
copying build/lib.linux-x86_64-3.7/cal_tools/__init__.py -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools
copying build/lib.linux-x86_64-3.7/cal_tools/agipdutils.py -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools
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byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/settings.py to settings.cpython-37.pyc
byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks.py to notebooks.cpython-37.pyc
byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/calibrate.py to calibrate.cpython-37.pyc
byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/finalize.py to finalize.cpython-37.pyc
running install_egg_info
running egg_info
creating European_XFEL_Offline_Calibration.egg-info
writing European_XFEL_Offline_Calibration.egg-info/PKG-INFO
writing dependency_links to European_XFEL_Offline_Calibration.egg-info/dependency_links.txt
writing entry points to European_XFEL_Offline_Calibration.egg-info/entry_points.txt
writing requirements to European_XFEL_Offline_Calibration.egg-info/requires.txt
writing top-level names to European_XFEL_Offline_Calibration.egg-info/top_level.txt
writing manifest file 'European_XFEL_Offline_Calibration.egg-info/SOURCES.txt'
reading manifest file 'European_XFEL_Offline_Calibration.egg-info/SOURCES.txt'
writing manifest file 'European_XFEL_Offline_Calibration.egg-info/SOURCES.txt'
Copying European_XFEL_Offline_Calibration.egg-info to /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/European_XFEL_Offline_Calibration-1.0-py3.7.egg-info
running install_scripts
Installing xfel-calibrate script to /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/cal_tools/cython/agipdalgs.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
Python environment seems to not be a Karabo environment. Please install PyDetLib manually.

[rtd-command-info] start-time: 2021-03-08T11:34:10.877685Z, end-time: 2021-03-08T11:34:10.955330Z, duration: 0, exit-code: 0
cat docs/source/conf.py
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# European XFEL Offline Calibration documentation build configuration file, created by
# sphinx-quickstart on Sun Jun 10 17:32:30 2018.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.

# 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('.'))

# -- 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',
    'sphinx.ext.intersphinx',
    'sphinx.ext.todo',
    'sphinx.ext.mathjax',
    'sphinx.ext.ifconfig',
    'sphinx.ext.viewcode',
]

import glob
import os
import sys
from subprocess import Popen

sys.path.append(os.path.abspath("../pycalibration/"))
p = Popen(["./makeAllDocs.sh"])
p.communicate()

import mock
autodoc_mock_imports = ['Cython']

MOCK_MODULES = ['numpy', 'matplotlib', 'matplotlib.pyplot','Cython']
for mod_name in MOCK_MODULES:
    sys.modules[mod_name] = mock.Mock()
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_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 encoding of source files.
#
# source_encoding = 'utf-8-sig'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = 'European XFEL Offline Calibration'
copyright = '2018, The European XFEL Detector Group'
author = 'The European XFEL Detector Group'

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = '1.0'
# The full version, including alpha/beta/rc tags.
release = '1.0'

# 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

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#
# today = ''
#
# Else, today_fmt is used as the format for a strftime call.
#
# today_fmt = '%B %d, %Y'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = []

# The reST default role (used for this markup: `text`) to use for all
# documents.
#
# default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.
#
# add_function_parentheses = True

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#
# add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#
# show_authors = False

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

# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []

# If true, keep warnings as "system message" paragraphs in the built documents.
# keep_warnings = False

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = True


# -- 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 = ''

# 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 themes here, relative to this directory.
# html_theme_path = []

# The name for this set of Sphinx documents.
# "<project> v<release> documentation" by default.
#
# html_title = 'European XFEL Offline Calibration v1.0'

# A shorter title for the navigation bar.  Default is the same as html_title.
#
# html_short_title = None

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#
# html_logo = None

# The name of an image file (relative to this directory) to use as a favicon of
# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#
# html_favicon = None

# 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 = ['_static']

# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#
# html_extra_path = []

# If not None, a 'Last updated on:' timestamp is inserted at every page
# bottom, using the given strftime format.
# The empty string is equivalent to '%b %d, %Y'.
#
# html_last_updated_fmt = None

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#
# html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
#
# html_sidebars = {}

# Additional templates that should be rendered to pages, maps page names to
# template names.
#
# html_additional_pages = {}

# If false, no module index is generated.
#
# html_domain_indices = True

# If false, no index is generated.
#
# html_use_index = True

# If true, the index is split into individual pages for each letter.
#
# html_split_index = False

# If true, links to the reST sources are added to the pages.
#
# html_show_sourcelink = True

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#
# html_show_sphinx = True

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#
# html_show_copyright = True

# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it.  The value of this option must be the
# base URL from which the finished HTML is served.
#
# html_use_opensearch = ''

# This is the file name suffix for HTML files (e.g. ".xhtml").
# html_file_suffix = None

# Language to be used for generating the HTML full-text search index.
# Sphinx supports the following languages:
#   'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'
#   'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr', 'zh'
#
# html_search_language = 'en'

# A dictionary with options for the search language support, empty by default.
# 'ja' uses this config value.
# 'zh' user can custom change `jieba` dictionary path.
#
# html_search_options = {'type': 'default'}

# The name of a javascript file (relative to the configuration directory) that
# implements a search results scorer. If empty, the default will be used.
#
# html_search_scorer = 'scorer.js'

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

# -- 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',
    'extraclassoptions': 'openany, oneside',
}

# 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, 'EuropeanXFELOfflineCalibration.tex', 'European XFEL Offline Calibration Documentation',
     'The European XFEL Detector Group', 'manual', True),
]

# The name of an image file (relative to this directory) to place at the top of
# the title page.
#
# latex_logo = None

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#
# latex_use_parts = False

# If true, show page references after internal links.
#
# latex_show_pagerefs = False

# If true, show URL addresses after external links.
#
# latex_show_urls = False

# Documents to append as an appendix to all manuals.
#
# latex_appendices = []

# It false, will not define \strong, \code, 	itleref, \crossref ... but only
# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
# packages.
#
# latex_keep_old_macro_names = True

# If false, no module index is generated.
#
# latex_domain_indices = True


# -- 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, 'europeanxfelofflinecalibration', 'European XFEL Offline Calibration Documentation',
     [author], 1)
]

# If true, show URL addresses after external links.
#
# man_show_urls = False


# -- 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, 'EuropeanXFELOfflineCalibration', 'European XFEL Offline Calibration Documentation',
     author, 'EuropeanXFELOfflineCalibration', 'One line description of project.',
     'Miscellaneous'),
]

# Documents to append as an appendix to all manuals.
#
# texinfo_appendices = []

# If false, no module index is generated.
#
# texinfo_domain_indices = True

# How to display URL addresses: 'footnote', 'no', or 'inline'.
#
# texinfo_show_urls = 'footnote'

# If true, do not generate a @detailmenu in the "Top" node's menu.
#
# texinfo_no_detailmenu = False


# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'https://docs.python.org/': None}



# first install pandoc if necessary, this is mainly meant for the RTD builds
try:
    from nbconvert.utils.pandoc import check_pandoc_version
    check_pandoc_version()
    print("Pandoc was found!")
except:
    print("Installing Pandoc!")
    from subprocess import check_call
    pandoc_url = "https://github.com/jgm/pandoc/releases/download/2.2.1/pandoc-2.2.1-1-amd64.deb"
    pandoc_pack = "pandoc-2.2.1-1-amd64.deb"
    check_call(["wget", pandoc_url])
    check_call(["dpkg", "-i", pandoc_pack])

import os
from subprocess import check_output
from textwrap import dedent, indent

import nbformat
from nbconvert import RSTExporter

# generate the list of available notebooks
from xfel_calibrate import notebooks

rst_exporter = RSTExporter()

with open("available_notebooks.rst", "w") as f:
    f.write(dedent("""
            .. _available_notebooks:

            Available Notebooks
            ===================

            The following notebooks are currently integrated into the European XFEL
            Offline Calibration tool chain.


            """))

    for detector in sorted(notebooks.notebooks.keys()):
        values = notebooks.notebooks[detector]
        f.write("{}\n".format(detector))
        f.write("{}\n".format("-"*len(detector)))
        f.write("\n")

        for caltype in sorted(values.keys()):
            data = values[caltype]

            nbpath = os.path.abspath("{}/../../../{}".format(__file__, data["notebook"]))
            with open(nbpath, "r") as nf:
                nb = nbformat.read(nf, as_version=4)
                def first_markdown_cell(nb):
                    for cell in nb.cells:
                        if cell.cell_type == 'markdown':
                            return cell
                mdcell = first_markdown_cell(nb)
                nb.cells = [mdcell]  # we only want this single cell
                body, _ = rst_exporter.from_notebook_node(nb)
                adjusted = []
                # adjust titles
                for line in body.split("\n"):
                    if line.startswith("=="):
                        line = line.replace("=", "+")
                    if line.startswith("--"):
                        line = line.replace("-", "~")
                    adjusted.append(line)
                f.write("\n".join(adjusted))
                f.write("\n")

            f.write("To invoke this notebook and display help use:\n\n")
            f.write(".. code-block:: bash\n\n")
            f.write("    xfel-calibrate {} {} --help\n\n".format(detector, caltype))
            f.write("The full parameter list of this notebook (with defaults is): \n\n")
            f.write(".. code-block:: bash\n\n")
            nb_help = ["xfel-calibrate", detector, caltype, "--help"]
            output = check_output(nb_help).decode('utf8')
            f.write(indent(output.replace("DETECTOR", detector).replace("TYPE", caltype), " "*4))
            f.write("\n\n")

# add test results
test_artefact_dir = os.path.realpath("../../tests/artefacts")

import shutil
import textwrap
from datetime import datetime
from uuid import uuid4

import tabulate
from dateutil.parser import parse
from lxml import etree


def xml_to_rst_report(xml, git_tag, reports=[]):
    e = etree.fromstring(xml.encode())
    rst = [""]
    rst += ["Test execution for {test_name} on {ex_date}"]
    test_name, ex_date = e.get("name").split("-")
    ex_date = parse(ex_date)
    rst[-1] = rst[-1].format(test_name=test_name, ex_date=ex_date)
    rst += ["="*len(rst[-1])]
    rst += [""]

    num_tests = e.get("tests")
    num_err = int(e.get("errors"))
    num_fail = int(e.get("failures"))
    num_skip = int(e.get("skipped"))

    # create a summary header
    if num_err + num_fail == 0:
        rst += [":header-passed:`✓`"]
    else:
        rst += [":header-failed:`❌`"]

    if num_skip > 0:
        rst[-1] += ":header-skipped:`⚠`"
    rst += [""]

    # give a summary
    rst += [":Git tag: {git_tag}".format(git_tag=git_tag)]
    rst += [":Tests: {num_tests}".format(num_tests=num_tests)]
    rst += [":Errors: {num_err}".format(num_err=num_err)]
    rst += [":Failures: {num_fail}".format(num_fail=num_fail)]
    rst += [":Skipped: {num_skip}".format(num_skip=num_skip)]
    rst += [":Duration: {duration}s".format(duration=e.get("time"))]
    for rname, rpath in reports:
        rst += [":Report: `{} <{}>`_".format(rname, rpath)]
    rst += [""]

    # now the details
    rst += ["Detailed Results"]
    rst += ["-"*len(rst[-1])]
    rst += [""]

    detailed_failures = []
    rows = []
    for child in e:
        if child.tag != "testcase":
            continue
        name = child.get("name")
        extime = child.get("time")
        status = ":passed:`passed`"
        msg = ""
        etype = ""
        if len(child):  # children are pressent so test failed or skipped
            detail = child[0]
            etype = detail.get("type")
            msg = detail.get("message")
            if etype == "skip":
                status = ":skipped:`skipped`"
            else:
                status= ":failed:`failed`"
                detailed_failures.append((name, detail.text))
        msg = "\n".join(textwrap.wrap(msg, 20))
        row = [status, name, etype, msg, extime ]
        rows.append(row)

    header = ["Result", "Test", "Error", "Message", "Duration (s)"]
    tblrst =  tabulate.tabulate(rows, headers=header, tablefmt="rst")
    rst += tblrst.split("\n")
    rst += [""]

    for test, report in detailed_failures:
        rst += ["Failure report for: {}".format(test)]
        rst += ["~"*len(rst[-1])]
        rst += [""]
        rst += [".. code-block:: python"]
        rst += textwrap.indent(report, " "*4).split("\n")
        rst += [""]

    do_console = False
    for child in e:
        if child.tag == "system-out" and len(child.text.strip()):
            do_console = True
            break

    if do_console:

        # console output
        rst += ["Console Output"]
        rst += ["-"*len(rst[-1])]
        rst += [""]

        for child in e:
            if child.tag != "system-out":
                continue

            rst += [".. code-block:: console"]
            rst += textwrap.indent(child.text, " "*4).split("\n")


    return "\n".join(rst)

def sorted_dir(folder):
    def getmtime(name):
        path = os.path.join(folder, name)
        return os.path.getmtime(path)

    sort = sorted(os.listdir(folder), key=getmtime, reverse=True)
    return [(s, datetime.fromtimestamp(getmtime(s))) for s in sort]

header = """
Test Results
++++++++++++

Results are organized by git commit, and sorted descending by date.

Contents:

.. toctree::
   :maxdepth: 2


"""
if not os.path.exists("./test_rsts"):
    os.makedirs("./test_rsts")

with open("test_results.rst", "w") as f:
    f.write(header)
    for commit, modtime in sorted_dir(test_artefact_dir):
        with open("./test_rsts/{}.rst".format(commit), "w") as fr:
            rst = [".. include:: roles.rst"]
            rst += [""]
            rst += ["{} - {}".format(commit[:8], modtime)]
            rst += ["+"*len(rst[-1])]
            rst += [""]
            fr.write("\n".join(rst))

            # copy reports
            pdfs = glob.glob("{}/{}/*/*.pdf".format(test_artefact_dir, commit))
            if not os.path.exists("./_static/reports/{}".format(commit)):
                os.makedirs("./_static/reports/{}".format(commit))
            reports = {}
            for pdf in pdfs:
                ppath = "{}/{}.pdf".format(commit, uuid4())
                shutil.copyfile(pdf, "./_static/reports/{}".format(ppath))
                rloc = pdf.split("/")[-2]
                rlist = reports.get(rloc, [])
                rname = os.path.basename(pdf).split(".")[0]
                rlist.append((rname, "../_static/reports/{}".format(ppath)))
                reports[rloc] = rlist

            xmls = glob.glob("{}/{}/*/TEST*.xml".format(test_artefact_dir, commit))
            for xml in xmls:
                rloc = xml.split("/")[-2]
                with open(xml, "r") as xf:
                    xs = xf.read()
                    rst = xml_to_rst_report(xs, commit, reports=reports.get(rloc, []))
                    fr.write(rst)
            f.write("   test_rsts/{}\n".format(commit))

def setup(app):
    app.add_stylesheet('css/test_decorators.css')




###########################################################################
#          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 = 'http://rtd.xfel.eu/websupport'
    websupport2_static_url = '/static/'


#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': "media/",
    'STATIC_URL': "/static/",
    'PRODUCTION_DOMAIN': "rtd.xfel.eu",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("doc-commonspace", "/en/doc-commonspace/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'european-xfel-offline-calibration',
    'name': u'European XFEL Offline Calibration',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'http://rtd.xfel.eu/docs/european-xfel-offline-calibration/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/source/',
    'api_host': 'http://rtd.xfel.eu',
    'github_user': 'None',
    'proxied_api_host': '/_',
    'github_repo': 'None',
    'github_version': 'doc/run_rtd',
    'display_github': False,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'doc/run_rtd',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'doc/run_rtd',
    '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': 'None',
    'commit': '2610ad4c',
}




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'

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

[rtd-command-info] start-time: 2021-03-08T11:34:11.100886Z, end-time: 2021-03-08T11:34:15.522701Z, duration: 4, exit-code: 2
python /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.8.5
./makeAllDocs.sh: line 23: jupyter: command not found
sed: can't read calversion.rst: No such file or directory
sed: can't read calversion.rst: No such file or directory
sed: can't read calversion.rst: No such file or directory
sed: can't read calversion.rst: No such file or directory
mv: cannot stat 'calversion.rst': No such file or directory
cat: calversion.rst.end: No such file or directory
rm: cannot remove 'calversion.rst.end': No such file or directory
rm: cannot remove '*.bak': No such file or directory
--2021-03-08 11:34:11--  https://github.com/jgm/pandoc/releases/download/2.2.1/pandoc-2.2.1-1-amd64.deb
Resolving github.com (github.com)... 140.82.121.3
Connecting to github.com (github.com)|140.82.121.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://github-releases.githubusercontent.com/571770/794e039e-5511-11e8-8698-24e0327313f5?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210308%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210308T113411Z&X-Amz-Expires=300&X-Amz-Signature=b126115c15eee9baa4125a2af6a4766dd3cff0ef154bca2cb90bd643308a8c48&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=571770&response-content-disposition=attachment%3B%20filename%3Dpandoc-2.2.1-1-amd64.deb&response-content-type=application%2Foctet-stream [following]
--2021-03-08 11:34:11--  https://github-releases.githubusercontent.com/571770/794e039e-5511-11e8-8698-24e0327313f5?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210308%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210308T113411Z&X-Amz-Expires=300&X-Amz-Signature=b126115c15eee9baa4125a2af6a4766dd3cff0ef154bca2cb90bd643308a8c48&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=571770&response-content-disposition=attachment%3B%20filename%3Dpandoc-2.2.1-1-amd64.deb&response-content-type=application%2Foctet-stream
Resolving github-releases.githubusercontent.com (github-releases.githubusercontent.com)... 185.199.108.154, 185.199.109.154, 185.199.111.154, ...
Connecting to github-releases.githubusercontent.com (github-releases.githubusercontent.com)|185.199.108.154|:443... connected.
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 13950K .......... .......... .......... .......... .......... 87% 42.4M 0s
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 14150K .......... .......... .......... .......... .......... 89% 48.2M 0s
 14200K .......... .......... .......... .......... .......... 89% 54.0M 0s
 14250K .......... .......... .......... .......... .......... 89% 64.6M 0s
 14300K .......... .......... .......... .......... .......... 90% 45.3M 0s
 14350K .......... .......... .......... .......... .......... 90%  167M 0s
 14400K .......... .......... .......... .......... .......... 90%  175M 0s
 14450K .......... .......... .......... .......... .......... 91% 43.4M 0s
 14500K .......... .......... .......... .......... .......... 91% 62.1M 0s
 14550K .......... .......... .......... .......... .......... 91% 46.8M 0s
 14600K .......... .......... .......... .......... .......... 92%  143M 0s
 14650K .......... .......... .......... .......... .......... 92% 48.3M 0s
 14700K .......... .......... .......... .......... .......... 92% 68.1M 0s
 14750K .......... .......... .......... .......... .......... 92% 5.50M 0s
 14800K .......... .......... .......... .......... .......... 93%  158M 0s
 14850K .......... .......... .......... .......... .......... 93% 29.2M 0s
 14900K .......... .......... .......... .......... .......... 93%  168M 0s
 14950K .......... .......... .......... .......... .......... 94% 65.2M 0s
 15000K .......... .......... .......... .......... .......... 94% 56.5M 0s
 15050K .......... .......... .......... .......... .......... 94% 48.2M 0s
 15100K .......... .......... .......... .......... .......... 95%  120M 0s
 15150K .......... .......... .......... .......... .......... 95% 19.1M 0s
 15200K .......... .......... .......... .......... .......... 95%  141M 0s
 15250K .......... .......... .......... .......... .......... 96% 41.1M 0s
 15300K .......... .......... .......... .......... .......... 96%  139M 0s
 15350K .......... .......... .......... .......... .......... 96% 99.5M 0s
 15400K .......... .......... .......... .......... .......... 97% 34.4M 0s
 15450K .......... .......... .......... .......... .......... 97% 46.5M 0s
 15500K .......... .......... .......... .......... .......... 97% 44.1M 0s
 15550K .......... .......... .......... .......... .......... 97%  101M 0s
 15600K .......... .......... .......... .......... .......... 98% 48.5M 0s
 15650K .......... .......... .......... .......... .......... 98% 17.0M 0s
 15700K .......... .......... .......... .......... .......... 98%  106M 0s
 15750K .......... .......... .......... .......... .......... 99% 29.4M 0s
 15800K .......... .......... .......... .......... .......... 99%  124M 0s
 15850K .......... .......... .......... .......... .......... 99%  148M 0s
 15900K .......... .......... .                               100%  133M=0.8s

2021-03-08 11:34:12 (18.7 MB/s) - ‘pandoc-2.2.1-1-amd64.deb’ saved [16303576/16303576]

(Reading database ... 223555 files and directories currently installed.)
Preparing to unpack pandoc-2.2.1-1-amd64.deb ...
Unpacking pandoc (2.2.1-1) over (1.19.2.4~dfsg-1build4) ...
Setting up pandoc (2.2.1-1) ...

Traceback (most recent call last):
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/conf.py", line 387, in <module>
    import nbformat
ModuleNotFoundError: No module named 'nbformat'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/sphinx/cmd/build.py", line 303, in build_main
    args.tags, args.verbosity, args.jobs, args.keep_going)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 201, in __init__
    self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 203, in read
    namespace = eval_config_file(filename, tags)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 380, in eval_config_file
    raise ConfigError(msg % traceback.format_exc())
sphinx.errors.ConfigError: There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/conf.py", line 387, in <module>
    import nbformat
ModuleNotFoundError: No module named 'nbformat'


Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/conf.py", line 387, in <module>
    import nbformat
ModuleNotFoundError: No module named 'nbformat'

Installing Pandoc!