Read the Docs build information Build id: 21434 Project: european-xfel-offline-calibration Version: latest Commit: 71d24d970875075a5b5b983d5e1a78b63ce2e3ab Date: 2021-03-08T11:28:56.712482Z State: finished Success: False [rtd-command-info] start-time: 2021-03-08T11:28:57.702805Z, end-time: 2021-03-08T11:29:17.674926Z, duration: 19, 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: 2021-03-08T11:29:18.077795Z, end-time: 2021-03-08T11:29:19.087454Z, duration: 1, 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 HEAD is now at 71d24d9 add mock up for imports [rtd-command-info] start-time: 2021-03-08T11:29:19.228633Z, end-time: 2021-03-08T11:29:19.320061Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-03-08T11:29:20.705239Z, end-time: 2021-03-08T11:29:25.857382Z, duration: 5, exit-code: 0 python3.7 -mvirtualenv --system-site-packages /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: 2021-03-08T11:29:25.996995Z, end-time: 2021-03-08T11:29:27.083746Z, 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: 2021-03-08T11:29:27.211077Z, end-time: 2021-03-08T11:29:39.504621Z, 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 -I 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 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting Jinja2>=2.9 Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB) Collecting requests Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting packaging Downloading packaging-20.9-py2.py3-none-any.whl (40 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.0-py2.py3-none-any.whl (8.8 MB) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux2010_x86_64.whl (33 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.3-py2.py3-none-any.whl (137 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.12.5-py2.py3-none-any.whl (147 kB) Collecting chardet<5,>=3.0.2 Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) 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=e68f28e02b7bdc00a5182d65269ab0822b69645e5f87cadc0deee28a6ffa15f5 Stored in directory: /tmp/pip-ephem-wheel-cache-fhsnfrd_/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=d62d719057c562532a4038ccbe70253feb5f3071b6741e1163934a4da1e6361e Stored in directory: /tmp/pip-ephem-wheel-cache-fhsnfrd_/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 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-54.1.1 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: 2021-03-08T11:29:39.628713Z, end-time: 2021-03-08T11:29:42.091774Z, duration: 2, 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) Installing collected packages: Cython Successfully installed Cython-0.29.21 [rtd-command-info] start-time: 2021-03-08T11:29:42.224627Z, end-time: 2021-03-08T11:29:45.761279Z, 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/home/docs/.pyenv/versions/3.7.3/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 /home/docs/.pyenv/versions/3.7.3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0, from /home/docs/.pyenv/versions/3.7.3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/docs/.pyenv/versions/3.7.3/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from cal_tools/cython/agipdalgs.c:610: /home/docs/.pyenv/versions/3.7.3/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 copying build/lib.linux-x86_64-3.7/cal_tools/agipdutils_ff.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/step_timing.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/pnccdlib.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/mdc_config.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/agipdlib.py -> 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build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/FastCCD/CorrectionNotebook_NewDAQ_FastCCD_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/FastCCD creating /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/pnCCD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/pnCCD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/pnCCD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/pnCCD/Characterize_pnCCD_Gain.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/pnCCD creating /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/Tutorial copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/Tutorial/calversion.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/Tutorial creating /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/generic copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/generic/overallmodules_Darks_Summary_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/generic copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/generic/PlotFromCalDB_Summary_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/generic copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/generic/DB_Constants_to_HDF5_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/generic copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/generic/PlotFromCalDB_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/generic creating /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD/AGIPD_Characterize_Gain_Combine_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD/AGIPD_FF_Histogramming.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/AGIPD creating /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/AGIPD/playground copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD/playground/AGIPD_SingleM_test_Dark.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/AGIPD/playground copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD/AGIPD_Correct_and_Verify_Summary_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_Summary.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/AGIPD creating /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/ePix100 copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/ePix100/Correction_ePix100_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/ePix100 copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/ePix100 creating /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/ePix10K copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/ePix10K/Characterize_Darks_ePix10K_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/ePix10K copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/ePix10K/Correction_ePix10K_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/ePix10K creating /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/LPD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/LPD/LPD_Correct_and_Verify.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/LPD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/LPD/Characterize_LPD_GAIN_CI_per_pixel_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/LPD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/LPD/LPD_FlatField_Radial_per_pixel_CI_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/LPD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/LPD/Mine_RadIntensity_vs_XGM_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/LPD copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/LPD/LPDChar_Darks_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/LPD creating /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/DSSC copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/DSSC/DSSC_Correct_and_Verify.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/DSSC copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/DSSC/Characterize_DSSC_Darks_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/DSSC creating /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/Jungfrau copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/Jungfrau copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/notebooks/Jungfrau copying build/lib.linux-x86_64-3.7/xfel_calibrate/settings.py -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate copying build/lib.linux-x86_64-3.7/xfel_calibrate/notebooks.py -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate copying build/lib.linux-x86_64-3.7/xfel_calibrate/calibrate.py -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate creating /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/bin copying build/lib.linux-x86_64-3.7/xfel_calibrate/bin/slurm_calibrate.sh -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/bin copying build/lib.linux-x86_64-3.7/xfel_calibrate/bin/pre-commit-diff.sh -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate/bin copying build/lib.linux-x86_64-3.7/xfel_calibrate/titlepage.tmpl -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate copying build/lib.linux-x86_64-3.7/xfel_calibrate/finalize.py -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate copying build/lib.linux-x86_64-3.7/xfel_calibrate/xfel.pdf -> /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/xfel_calibrate byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools/metrology.py to metrology.cpython-37.pyc byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools/__init__.py to __init__.cpython-37.pyc byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools/agipdutils.py to agipdutils.cpython-37.pyc byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools/agipdutils_ff.py to agipdutils_ff.cpython-37.pyc byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools/step_timing.py to step_timing.cpython-37.pyc byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools/pnccdlib.py to pnccdlib.cpython-37.pyc byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools/mdc_config.py to mdc_config.cpython-37.pyc byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools/agipdlib.py to agipdlib.cpython-37.pyc byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools/tools.py to tools.cpython-37.pyc byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools/enums.py to enums.cpython-37.pyc byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools/plotting.py to plotting.cpython-37.pyc byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools/ana_tools.py to ana_tools.cpython-37.pyc byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools/dssclib.py to dssclib.cpython-37.pyc byte-compiling /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.7/site-packages/cal_tools/lpdlib.py to lpdlib.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/__init__.py to __init__.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/VERSION.py to VERSION.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/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: 2021-03-08T11:29:46.753447Z, end-time: 2021-03-08T11:29:46.845080Z, 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. # " v 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 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': '71d24d97', } 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: 2021-03-08T11:29:46.979782Z, end-time: 2021-03-08T11:29:51.201881Z, 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 11:29:47-- 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=20210308T112947Z&X-Amz-Expires=300&X-Amz-Signature=8d511fdb065e135983b49878bf0ae0d4d3db8bb0a7044e434a3651a3936fa701&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 11:29:47-- 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=20210308T112947Z&X-Amz-Expires=300&X-Amz-Signature=8d511fdb065e135983b49878bf0ae0d4d3db8bb0a7044e434a3651a3936fa701&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)... 185.199.110.154, 185.199.108.154, 185.199.111.154, ... 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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 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 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 import nbformat ModuleNotFoundError: No module named 'nbformat' Installing Pandoc!