Read the Docs build information Build id: 12685 Project: pydetlib-test2 Version: latest Commit: 0119153e69825d410fa8b4c462be2f2a4b5707e1 Date: 2019-10-09T07:57:01.867454Z State: finished Success: False [rtd-command-info] start-time: 2019-10-09T12:57:08.047000Z, end-time: 2019-10-09T12:57:23.687000Z, duration: 15, exit-code: 0 python3 -mvirtualenv --no-site-packages --no-download /user_builds/pydetlib-test2/envs/latest Using base prefix '/usr' New python executable in /user_builds/pydetlib-test2/envs/latest/bin/python3 Not overwriting existing python script /user_builds/pydetlib-test2/envs/latest/bin/python (you must use /user_builds/pydetlib-test2/envs/latest/bin/python3) Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2019-10-09T12:57:23.749000Z, end-time: 2019-10-09T12:57:47.297000Z, duration: 23, exit-code: 0 python /user_builds/pydetlib-test2/envs/latest/bin/pip install --use-wheel -U --cache-dir /user_builds/pydetlib-test2/.cache/pip sphinx==1.3.5 Pygments==2.1.3 setuptools==20.1.1 docutils==0.12 mkdocs==0.15.0 mock==1.0.1 pillow==2.6.1 git+https://github.com/rtfd/readthedocs-sphinx-ext.git@0.6-alpha#egg=readthedocs-sphinx-ext sphinx-rtd-theme==0.1.9 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.1.1 Requirement already up-to-date: sphinx==1.3.5 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: Pygments==2.1.3 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages Collecting setuptools==20.1.1 Using cached https://files.pythonhosted.org/packages/e8/82/3b5455f74bf9ac0757d09c625b7741e6fc284d7519cffc3babb6c5173cf5/setuptools-20.1.1-py2.py3-none-any.whl Requirement already up-to-date: docutils==0.12 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: mkdocs==0.15.0 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: mock==1.0.1 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: pillow==2.6.1 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages Collecting readthedocs-sphinx-ext from git+https://github.com/rtfd/readthedocs-sphinx-ext.git@0.6-alpha#egg=readthedocs-sphinx-ext Cloning https://github.com/rtfd/readthedocs-sphinx-ext.git (to 0.6-alpha) to /tmp/pip-build-h4tnaa7j/readthedocs-sphinx-ext Requirement already up-to-date: sphinx-rtd-theme==0.1.9 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: commonmark==0.5.4 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: recommonmark==0.1.1 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: six>=1.4 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from sphinx==1.3.5) Requirement already up-to-date: babel!=2.0,>=1.3 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from sphinx==1.3.5) Requirement already up-to-date: Jinja2>=2.3 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from sphinx==1.3.5) Requirement already up-to-date: snowballstemmer>=1.1 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from sphinx==1.3.5) Requirement already up-to-date: livereload>=2.3.2 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: click>=4.0 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: PyYAML>=3.10 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: tornado>=4.1 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: mkdocs-bootswatch>=0.1.0 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: mkdocs-bootstrap>=0.1.1 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: Markdown>=2.3.1 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: requests in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from readthedocs-sphinx-ext) Requirement already up-to-date: nilsimsa>=0.3.7 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from readthedocs-sphinx-ext) Requirement already up-to-date: pytz>=2015.7 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from babel!=2.0,>=1.3->sphinx==1.3.5) Requirement already up-to-date: MarkupSafe>=0.23 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from Jinja2>=2.3->sphinx==1.3.5) Requirement already up-to-date: backports-abc>=0.4 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from tornado>=4.1->mkdocs==0.15.0) Requirement already up-to-date: idna<2.9,>=2.5 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from requests->readthedocs-sphinx-ext) Requirement already up-to-date: urllib3<1.25,>=1.21.1 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from requests->readthedocs-sphinx-ext) Requirement already up-to-date: certifi>=2017.4.17 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from requests->readthedocs-sphinx-ext) Requirement already up-to-date: chardet<3.1.0,>=3.0.2 in /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from requests->readthedocs-sphinx-ext) Installing collected packages: setuptools, readthedocs-sphinx-ext Found existing installation: setuptools 28.8.0 Uninstalling setuptools-28.8.0: Successfully uninstalled setuptools-28.8.0 Found existing installation: readthedocs-sphinx-ext 0.5.4 Uninstalling readthedocs-sphinx-ext-0.5.4: Successfully uninstalled readthedocs-sphinx-ext-0.5.4 Running setup.py install for readthedocs-sphinx-ext: started Running setup.py install for readthedocs-sphinx-ext: finished with status 'done' Successfully installed readthedocs-sphinx-ext-0.5.4 setuptools-20.1.1 You are using pip version 9.0.1, however version 19.2.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2019-10-09T12:57:47.364000Z, end-time: 2019-10-09T13:09:32.716000Z, duration: 705, exit-code: 0 python /user_builds/pydetlib-test2/envs/latest/bin/pip install --exists-action=w --cache-dir /user_builds/pydetlib-test2/.cache/pip -rrequirements.txt Collecting git+https://haufs:s--zGku2dzxtv6so2xsu@git.xfel.eu/gitlab/detectors/nbparameterise.git (from -r requirements.txt (line 1)) Cloning https://haufs:s--zGku2dzxtv6so2xsu@git.xfel.eu/gitlab/detectors/nbparameterise.git to /tmp/pip-uuznvaxs-build Collecting git+https://haufs:s--zGku2dzxtv6so2xsu@git.xfel.eu/gitlab/detectors/cal_db_interactive.git (from -r requirements.txt (line 2)) Cloning https://haufs:s--zGku2dzxtv6so2xsu@git.xfel.eu/gitlab/detectors/cal_db_interactive.git to /tmp/pip-i32irx63-build Processing ./cal_tools Processing /user_builds/pydetlib-test2/checkouts/latest Collecting fabio (from -r requirements.txt (line 3)) Using cached 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cached https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl Collecting pyzmq (from zmq->-r requirements.txt (line 12)) Downloading https://files.pythonhosted.org/packages/7a/d2/1eb3a994374802b352d4911f3317313a5b4ea786bc830cc5e343dad9b06d/pyzmq-18.1.0.tar.gz (1.2MB) Collecting gitdb2>=2.0.0 (from gitpython->-r requirements.txt (line 14)) Downloading https://files.pythonhosted.org/packages/03/6c/99296f89bad2ef85626e1df9f677acbee8885bb043ad82ad3ed4746d2325/gitdb2-2.0.6-py2.py3-none-any.whl (63kB) Collecting matplotlib (from karabo_data->-r requirements.txt (line 15)) Using cached https://files.pythonhosted.org/packages/e1/3d/b080b49d6927a20ee621127503fbe1b42c918ceb0157c8666cccbc0df1fc/matplotlib-2.2.4-cp34-cp34m-manylinux1_x86_64.whl Collecting msgpack>=0.5.4 (from karabo_data->-r requirements.txt (line 15)) Downloading 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jupyter->-r requirements.txt (line 18)) Downloading https://files.pythonhosted.org/packages/d4/16/43f51f65a8a08addf04f909a0938b06ba1ee1708b398a9282474531bd893/ipykernel-5.1.2-py3-none-any.whl (116kB) Collecting ipywidgets (from jupyter->-r requirements.txt (line 18)) Downloading https://files.pythonhosted.org/packages/56/a0/dbcf5881bb2f51e8db678211907f16ea0a182b232c591a6d6f276985ca95/ipywidgets-7.5.1-py2.py3-none-any.whl (121kB) Collecting qtconsole (from jupyter->-r requirements.txt (line 18)) Downloading https://files.pythonhosted.org/packages/d0/fc/4936c60be8d56acedfefcc13cf9f3d881e4036147d78e86160463c92d1b7/qtconsole-4.5.5-py2.py3-none-any.whl (121kB) Collecting notebook (from jupyter->-r requirements.txt (line 18)) Using cached https://files.pythonhosted.org/packages/f6/36/89ebfffc9dd8c8dbd81c1ffb53e3d4233ee666414c143959477cb07cc5f5/notebook-5.7.8-py2.py3-none-any.whl Collecting prompt-toolkit<2.0.0,>=1.0.0 (from jupyter_console->-r requirements.txt (line 19)) Downloading 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/user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages (from tornado>=4.2->ipykernel->jupyter->-r requirements.txt (line 18)) Collecting ptyprocess; os_name != "nt" (from terminado>=0.8.1->notebook->jupyter->-r requirements.txt (line 18)) Using cached https://files.pythonhosted.org/packages/d1/29/605c2cc68a9992d18dada28206eeada56ea4bd07a239669da41674648b6f/ptyprocess-0.6.0-py2.py3-none-any.whl Collecting parso>=0.5.0 (from jedi>=0.10->ipython->jupyter_console->-r requirements.txt (line 19)) Downloading https://files.pythonhosted.org/packages/a3/bd/bf4e5bd01d79906e5b945a7af033154da49fd2b0d5b5c705a21330323305/parso-0.5.1-py2.py3-none-any.whl (95kB) Building wheels for collected packages: tabulate, numpy, pyzmq, msgpack, prometheus-client, pyrsistent Running setup.py bdist_wheel for tabulate: started Running setup.py bdist_wheel for tabulate: finished with status 'done' Stored in directory: /user_builds/pydetlib-test2/.cache/pip/wheels/e1/41/5e/e201f95d90fc84f93aa629b6638adacda680fe63aac47174ab Running setup.py bdist_wheel for numpy: started Running setup.py bdist_wheel for numpy: still running... Running setup.py bdist_wheel for numpy: still running... Running setup.py bdist_wheel for numpy: finished with status 'done' Stored in directory: /user_builds/pydetlib-test2/.cache/pip/wheels/f3/c6/40/1c3d8725494e976f620d535731122a7944523aeda91aad0d68 Running setup.py bdist_wheel for pyzmq: started Running setup.py bdist_wheel for pyzmq: still running... Running setup.py bdist_wheel for pyzmq: still running... Running setup.py bdist_wheel for pyzmq: still running... Running setup.py bdist_wheel for pyzmq: finished with status 'done' Stored in directory: /user_builds/pydetlib-test2/.cache/pip/wheels/b5/cd/9c/179949d7d4aa9cd61eac63409f99310ac2d7c44eead30b8738 Running setup.py bdist_wheel for msgpack: started Running setup.py bdist_wheel for msgpack: finished with status 'done' Stored in directory: /user_builds/pydetlib-test2/.cache/pip/wheels/27/e6/c7/adc38b19993e22e1f7bea6ff388c7fcda941a2a17258d6e8f3 Running setup.py bdist_wheel for prometheus-client: started Running setup.py bdist_wheel for prometheus-client: finished with status 'done' Stored in directory: /user_builds/pydetlib-test2/.cache/pip/wheels/1c/54/34/fd47cd9b308826cc4292b54449c1899a30251ef3b506bc91ea Running setup.py bdist_wheel for pyrsistent: started Running setup.py bdist_wheel for pyrsistent: finished with status 'done' Stored in directory: /user_builds/pydetlib-test2/.cache/pip/wheels/bb/46/00/6d471ef0b813e3621f0abe6cb723c20d529d39a061de3f7c51 Successfully built tabulate numpy pyzmq msgpack prometheus-client pyrsistent Installing collected packages: numpy, fabio, pypandoc, pyrsistent, attrs, jsonschema, ipython-genutils, decorator, traitlets, jupyter-core, nbformat, entrypoints, testpath, mistune, defusedxml, webencodings, bleach, pandocfilters, nbconvert, astcheck, astsearch, python-dateutil, influxdb, tabulate, h5py, unittest-xml-reporting, pyzmq, zmq, lxml, smmap2, gitdb2, gitpython, kiwisolver, cycler, pyparsing, matplotlib, msgpack, msgpack-numpy, future, cfelpyutils, scipy, pandas, xarray, karabo-bridge, karabo-data, scikit-learn, sklearn, prettytable, backcall, parso, jedi, simplegeneric, typing, ptyprocess, pexpect, wcwidth, prompt-toolkit, pickleshare, ipython, jupyter-client, ipykernel, prometheus-client, terminado, Send2Trash, notebook, widgetsnbextension, ipywidgets, qtconsole, jupyter-console, jupyter, imagesize, sphinx, nbparameterise, iCalibrationDB, calTools, European-XFEL-Offline-Calibration Found existing installation: Sphinx 1.3.5 Uninstalling Sphinx-1.3.5: Successfully uninstalled Sphinx-1.3.5 Running setup.py install for nbparameterise: started Running setup.py install for nbparameterise: finished with status 'done' Running setup.py install for iCalibrationDB: started Running setup.py install for iCalibrationDB: finished with status 'done' Running setup.py install for calTools: started Running setup.py install for calTools: finished with status 'done' Running setup.py install for European-XFEL-Offline-Calibration: started Running setup.py install for European-XFEL-Offline-Calibration: finished with status 'done' Successfully installed European-XFEL-Offline-Calibration-1.0 Send2Trash-1.5.0 astcheck-0.2.5 astsearch-0.1.3 attrs-19.2.0 backcall-0.1.0 bleach-3.1.0 calTools-0.1 cfelpyutils-1.0.0 cycler-0.10.0 decorator-4.4.0 defusedxml-0.5.0 entrypoints-0.3 fabio-0.9.0 future-0.17.1 gitdb2-2.0.6 gitpython-3.0.3 h5py-2.10.0 iCalibrationDB-0.1 imagesize-1.1.0 influxdb-5.2.3 ipykernel-5.1.2 ipython-6.5.0 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.15.1 jsonschema-3.0.2 jupyter-1.0.0 jupyter-client-5.2.4 jupyter-console-5.2.0 jupyter-core-4.6.0 karabo-bridge-0.4.0 karabo-data-0.3.0 kiwisolver-1.1.0 lxml-4.3.4 matplotlib-2.2.4 mistune-0.8.4 msgpack-0.6.2 msgpack-numpy-0.4.4.3 nbconvert-5.4.1 nbformat-4.4.0 nbparameterise-1.0xfel notebook-5.7.8 numpy-1.16.5 pandas-0.20.3 pandocfilters-1.4.2 parso-0.5.1 pexpect-4.7.0 pickleshare-0.7.5 prettytable-0.7.2 prometheus-client-0.7.1 prompt-toolkit-1.0.18 ptyprocess-0.6.0 pypandoc-1.4 pyparsing-2.4.2 pyrsistent-0.15.4 python-dateutil-2.8.0 pyzmq-18.1.0 qtconsole-4.5.5 scikit-learn-0.20.4 scipy-1.2.2 simplegeneric-0.8.1 sklearn-0.0 smmap2-2.0.5 sphinx-1.4.5 tabulate-0.8.5 terminado-0.8.2 testpath-0.4.2 traitlets-4.3.3 typing-3.7.4.1 unittest-xml-reporting-2.5.1 wcwidth-0.1.7 webencodings-0.5.1 widgetsnbextension-3.5.1 xarray-0.10.9 zmq-0.0.0 You are using pip version 9.0.1, however version 19.2.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2019-10-09T13:09:32.795000Z, end-time: 2019-10-09T13:09:37.481000Z, duration: 4, exit-code: 0 python setup.py install --force running install running build running build_py creating build creating build/lib creating build/lib/cal_tools copying cal_tools/cal_tools/__init__.py -> build/lib/cal_tools copying cal_tools/cal_tools/agipdlib.py -> build/lib/cal_tools copying cal_tools/cal_tools/ana_tools.py -> build/lib/cal_tools copying cal_tools/cal_tools/enums.py -> build/lib/cal_tools copying cal_tools/cal_tools/influx.py -> build/lib/cal_tools copying cal_tools/cal_tools/lpdlib.py -> build/lib/cal_tools copying cal_tools/cal_tools/mdc_config.py -> build/lib/cal_tools copying cal_tools/cal_tools/metrology.py -> build/lib/cal_tools copying cal_tools/cal_tools/plotting.py -> build/lib/cal_tools copying cal_tools/cal_tools/tools.py -> build/lib/cal_tools creating build/lib/xfel_calibrate copying xfel_calibrate/__init__.py -> build/lib/xfel_calibrate copying xfel_calibrate/automode.py -> build/lib/xfel_calibrate copying xfel_calibrate/calibrate.py -> build/lib/xfel_calibrate copying xfel_calibrate/check_proc_files.py -> build/lib/xfel_calibrate copying xfel_calibrate/notebooks.py -> build/lib/xfel_calibrate copying xfel_calibrate/settings.py -> build/lib/xfel_calibrate copying xfel_calibrate/VERSION.py -> build/lib/xfel_calibrate creating build/lib/xfel_calibrate/bin copying xfel_calibrate/bin/automode.sh -> build/lib/xfel_calibrate/bin copying xfel_calibrate/bin/cal_influx_feeder.sh -> build/lib/xfel_calibrate/bin copying xfel_calibrate/bin/slurm_calibrate.sh -> build/lib/xfel_calibrate/bin creating build/lib/xfel_calibrate/notebooks creating build/lib/xfel_calibrate/notebooks/Jungfrau copying xfel_calibrate/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/Jungfrau copying xfel_calibrate/notebooks/Jungfrau/PlotFromCalDB_Jungfrau_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/Jungfrau copying xfel_calibrate/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/Jungfrau creating build/lib/xfel_calibrate/notebooks/LPD copying xfel_calibrate/notebooks/LPD/LPDChar_Darks_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/LPD copying xfel_calibrate/notebooks/LPD/LPD_FlatField_Radial_per_pixel_CI_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/LPD copying xfel_calibrate/notebooks/LPD/PlotFromCalDB_LPD_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/LPD copying xfel_calibrate/notebooks/LPD/Characterize_LPD_GAIN_CI_per_pixel_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/LPD copying xfel_calibrate/notebooks/LPD/Mine_RadIntensity_vs_XGM_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/LPD copying xfel_calibrate/notebooks/LPD/LPD_Correct_and_Verify.ipynb -> build/lib/xfel_calibrate/notebooks/LPD creating build/lib/xfel_calibrate/notebooks/Tutorial copying xfel_calibrate/notebooks/Tutorial/calversion.ipynb -> build/lib/xfel_calibrate/notebooks/Tutorial creating build/lib/xfel_calibrate/notebooks/AGIPD copying xfel_calibrate/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/AGIPD copying xfel_calibrate/notebooks/AGIPD/AGIPD_Characterize_Gain_Combine_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/AGIPD copying xfel_calibrate/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/AGIPD copying xfel_calibrate/notebooks/AGIPD/PlotFromCalDB_AGIPD_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/AGIPD copying xfel_calibrate/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/AGIPD copying xfel_calibrate/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb -> build/lib/xfel_calibrate/notebooks/AGIPD creating build/lib/xfel_calibrate/notebooks/FastCCD copying xfel_calibrate/notebooks/FastCCD/Characterize_Darks_NewDAQ_FastCCD_NBC_New_Common_Mode.ipynb -> build/lib/xfel_calibrate/notebooks/FastCCD copying xfel_calibrate/notebooks/FastCCD/PlotFromCalDB_FastCCD_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/FastCCD copying xfel_calibrate/notebooks/FastCCD/CorrectionNotebook_NewDAQ_FastCCD_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/FastCCD creating build/lib/xfel_calibrate/notebooks/pnCCD copying xfel_calibrate/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/pnCCD copying xfel_calibrate/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/pnCCD creating build/lib/xfel_calibrate/notebooks/DSSC copying xfel_calibrate/notebooks/DSSC/Characterize_DSSC_Darks_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/DSSC copying xfel_calibrate/notebooks/DSSC/DSSC_Correct_and_Verify.ipynb -> build/lib/xfel_calibrate/notebooks/DSSC creating build/lib/xfel_calibrate/notebooks/generic copying xfel_calibrate/notebooks/generic/DB_Constants_to_HDF5_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/generic creating build/lib/xfel_calibrate/notebooks/ePix copying xfel_calibrate/notebooks/ePix/Characterize_Darks_ePix_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/ePix copying xfel_calibrate/notebooks/ePix/PlotFromCalDB_ePix100_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/ePix copying xfel_calibrate/notebooks/ePix/Correction_ePix_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/ePix copying xfel_calibrate/notebooks/ePix/Characterize_Darks_ePix10K_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/ePix copying xfel_calibrate/notebooks/ePix/Correction_ePix10K_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/ePix running install_lib copying build/lib/cal_tools/__init__.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/agipdlib.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/ana_tools.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/enums.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/influx.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/lpdlib.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/mdc_config.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/metrology.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/plotting.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/tools.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/xfel_calibrate/__init__.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate copying build/lib/xfel_calibrate/automode.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate copying build/lib/xfel_calibrate/calibrate.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate copying build/lib/xfel_calibrate/check_proc_files.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate copying build/lib/xfel_calibrate/notebooks.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate copying build/lib/xfel_calibrate/settings.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate copying build/lib/xfel_calibrate/VERSION.py -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate copying build/lib/xfel_calibrate/bin/automode.sh -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/bin copying build/lib/xfel_calibrate/bin/cal_influx_feeder.sh -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/bin copying build/lib/xfel_calibrate/bin/slurm_calibrate.sh -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/bin copying build/lib/xfel_calibrate/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/Jungfrau copying build/lib/xfel_calibrate/notebooks/Jungfrau/PlotFromCalDB_Jungfrau_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/Jungfrau copying build/lib/xfel_calibrate/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/Jungfrau copying build/lib/xfel_calibrate/notebooks/LPD/LPDChar_Darks_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/LPD copying build/lib/xfel_calibrate/notebooks/LPD/LPD_FlatField_Radial_per_pixel_CI_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/LPD copying build/lib/xfel_calibrate/notebooks/LPD/PlotFromCalDB_LPD_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/LPD copying build/lib/xfel_calibrate/notebooks/LPD/Characterize_LPD_GAIN_CI_per_pixel_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/LPD copying build/lib/xfel_calibrate/notebooks/LPD/Mine_RadIntensity_vs_XGM_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/LPD copying build/lib/xfel_calibrate/notebooks/LPD/LPD_Correct_and_Verify.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/LPD copying build/lib/xfel_calibrate/notebooks/Tutorial/calversion.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/Tutorial copying build/lib/xfel_calibrate/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib/xfel_calibrate/notebooks/AGIPD/AGIPD_Characterize_Gain_Combine_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib/xfel_calibrate/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib/xfel_calibrate/notebooks/AGIPD/PlotFromCalDB_AGIPD_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib/xfel_calibrate/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib/xfel_calibrate/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib/xfel_calibrate/notebooks/FastCCD/Characterize_Darks_NewDAQ_FastCCD_NBC_New_Common_Mode.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/FastCCD copying build/lib/xfel_calibrate/notebooks/FastCCD/PlotFromCalDB_FastCCD_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/FastCCD copying build/lib/xfel_calibrate/notebooks/FastCCD/CorrectionNotebook_NewDAQ_FastCCD_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/FastCCD copying build/lib/xfel_calibrate/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/pnCCD copying build/lib/xfel_calibrate/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/pnCCD copying build/lib/xfel_calibrate/notebooks/DSSC/Characterize_DSSC_Darks_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/DSSC copying build/lib/xfel_calibrate/notebooks/DSSC/DSSC_Correct_and_Verify.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/DSSC copying build/lib/xfel_calibrate/notebooks/generic/DB_Constants_to_HDF5_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/generic copying build/lib/xfel_calibrate/notebooks/ePix/Characterize_Darks_ePix_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/ePix copying build/lib/xfel_calibrate/notebooks/ePix/PlotFromCalDB_ePix100_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/ePix copying build/lib/xfel_calibrate/notebooks/ePix/Correction_ePix_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/ePix copying build/lib/xfel_calibrate/notebooks/ePix/Characterize_Darks_ePix10K_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/ePix copying build/lib/xfel_calibrate/notebooks/ePix/Correction_ePix10K_NBC.ipynb -> /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/ePix byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools/__init__.py to __init__.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools/agipdlib.py to agipdlib.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools/ana_tools.py to ana_tools.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools/enums.py to enums.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools/influx.py to influx.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools/lpdlib.py to lpdlib.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools/mdc_config.py to mdc_config.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools/metrology.py to metrology.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools/plotting.py to plotting.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools/tools.py to tools.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/__init__.py to __init__.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/automode.py to automode.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/calibrate.py to calibrate.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/check_proc_files.py to check_proc_files.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks.py to notebooks.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/settings.py to settings.cpython-34.pyc byte-compiling /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/VERSION.py to VERSION.cpython-34.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 top-level names to European_XFEL_Offline_Calibration.egg-info/top_level.txt writing entry points to European_XFEL_Offline_Calibration.egg-info/entry_points.txt writing dependency_links to European_XFEL_Offline_Calibration.egg-info/dependency_links.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' removing '/user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/European_XFEL_Offline_Calibration-1.0-py3.4.egg-info' (and everything under it) Copying European_XFEL_Offline_Calibration.egg-info to /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/European_XFEL_Offline_Calibration-1.0-py3.4.egg-info running install_scripts Installing xfel-calibrate script to /user_builds/pydetlib-test2/envs/latest/bin Python environment seems to not be a Karabo environment. Please install PyDetLib manually. [rtd-command-info] start-time: 2019-10-09T13:09:37.989000Z, end-time: 2019-10-09T13:09:38.023000Z, duration: 0, exit-code: 0 cat 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 sys import os from subprocess import Popen sys.path.append(os.path.abspath("../pycalibration/")) p = Popen(["./makeAllDocs.sh"]) p.communicate() # 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]) # generate the list of available notebooks from xfel_calibrate import notebooks from subprocess import check_output from textwrap import dedent, indent from nbconvert import RSTExporter import os import nbformat 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") from datetime import datetime from dateutil.parser import parse from lxml import etree import shutil import tabulate import textwrap from uuid import uuid4 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 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 else: SUFFIX = source_suffix[0] 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') html_static_path.append('/rtd_root/readthedocs/templates/sphinx/_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = False if 'html_theme' in globals(): if html_theme in ['default']: # Allow people to bail with a hack of having an html_style if not 'html_style' in globals(): import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True else: import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.org/websupport' if 'http' not in settings.MEDIA_URL: websupport2_static_url = '/static/' else: websupport2_static_url = '/media//static' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'MEDIA_URL': "/media/", 'PRODUCTION_DOMAIN': "exflrtd.desy.de", 'versions': [ ("latest", "/en/latest/"), ("doc-installation_modifications", "/en/doc-installation_modifications/"), ], 'downloads': [ ("pdf", "//exflrtd.desy.de/projects/pydetlib-test2/downloads/pdf/latest/"), ("htmlzip", "//exflrtd.desy.de/projects/pydetlib-test2/downloads/htmlzip/latest/"), ("epub", "//exflrtd.desy.de/projects/pydetlib-test2/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'pydetlib-test2', 'name': u'offline calibration test', 'rtd_language': u'en', 'canonical_url': 'http://exflrtd.desy.de/docs/pydetlib-test2/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/docs/source/', 'api_host': 'https://readthedocs.org', 'github_user': 'None', 'github_repo': 'None', 'github_version': 'doc/installation_modifications', 'display_github': False, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'doc/installation_modifications', 'display_bitbucket': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-1', 'commit': '0119153e', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): extensions.append("readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] [rtd-command-info] start-time: 2019-10-09T13:09:38.098000Z, end-time: 2019-10-09T13:10:03.254000Z, duration: 25, exit-code: 1 python /user_builds/pydetlib-test2/envs/latest/bin/sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.4.5 making output directory... [NbConvertApp] Converting notebook ../../../notebooks/Tutorial/calversion.ipynb to rst /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/nbconvert/utils/pandoc.py:52: RuntimeWarning: You are using an unsupported version of pandoc (2.2.1). Your version must be at least (1.12.1) but less than (2.0.0). Refer to http://pandoc.org/installing.html. Continuing with doubts... check_pandoc_version() /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/nbconvert/utils/pandoc.py:52: RuntimeWarning: You are using an unsupported version of pandoc (2.2.1). Your version must be at least (1.12.1) but less than (2.0.0). Refer to http://pandoc.org/installing.html. Continuing with doubts... check_pandoc_version() /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/nbconvert/utils/pandoc.py:52: RuntimeWarning: You are using an unsupported version of pandoc (2.2.1). Your version must be at least (1.12.1) but less than (2.0.0). Refer to http://pandoc.org/installing.html. Continuing with doubts... check_pandoc_version() /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/nbconvert/utils/pandoc.py:52: RuntimeWarning: You are using an unsupported version of pandoc (2.2.1). Your version must be at least (1.12.1) but less than (2.0.0). Refer to http://pandoc.org/installing.html. Continuing with doubts... check_pandoc_version() /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/nbconvert/utils/pandoc.py:52: RuntimeWarning: You are using an unsupported version of pandoc (2.2.1). Your version must be at least (1.12.1) but less than (2.0.0). Refer to http://pandoc.org/installing.html. Continuing with doubts... check_pandoc_version() /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/nbconvert/utils/pandoc.py:52: RuntimeWarning: You are using an unsupported version of pandoc (2.2.1). Your version must be at least (1.12.1) but less than (2.0.0). Refer to http://pandoc.org/installing.html. Continuing with doubts... check_pandoc_version() /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/nbconvert/utils/pandoc.py:52: RuntimeWarning: You are using an unsupported version of pandoc (2.2.1). Your version must be at least (1.12.1) but less than (2.0.0). Refer to http://pandoc.org/installing.html. Continuing with doubts... check_pandoc_version() /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/nbconvert/utils/pandoc.py:52: RuntimeWarning: You are using an unsupported version of pandoc (2.2.1). Your version must be at least (1.12.1) but less than (2.0.0). Refer to http://pandoc.org/installing.html. Continuing with doubts... check_pandoc_version() [NbConvertApp] Writing 4428 bytes to ./calversion.rst Traceback (most recent call last): File "/user_builds/pydetlib-test2/envs/latest/bin/xfel-calibrate", line 9, in load_entry_point('European-XFEL-Offline-Calibration==1.0', 'console_scripts', 'xfel-calibrate')() File "/user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/pkg_resources/__init__.py", line 547, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/pkg_resources/__init__.py", line 2720, in load_entry_point return ep.load() File "/user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/pkg_resources/__init__.py", line 2380, in load return self.resolve() File "/user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/pkg_resources/__init__.py", line 2386, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "/user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/xfel_calibrate/calibrate.py", line 24, in from cal_tools.tools import tex_escape File "/user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/cal_tools/tools.py", line 18, in from metadata_client.metadata_client import MetadataClient ImportError: No module named 'metadata_client' /user_builds/pydetlib-test2/checkouts/latest/docs/source/conf.py:368: RuntimeWarning: You are using an unsupported version of pandoc (2.2.1). Your version must be at least (1.12.1) but less than (2.0.0). Refer to http://pandoc.org/installing.html. Continuing with doubts... check_pandoc_version() /user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/nbconvert/utils/pandoc.py:52: RuntimeWarning: You are using an unsupported version of pandoc (2.2.1). Your version must be at least (1.12.1) but less than (2.0.0). Refer to http://pandoc.org/installing.html. Continuing with doubts... check_pandoc_version() Traceback (most recent call last): File "/user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/sphinx/cmdline.py", line 243, in main opts.warningiserror, opts.tags, opts.verbosity, opts.jobs) File "/user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/sphinx/application.py", line 137, in __init__ confoverrides or {}, self.tags) File "/user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/sphinx/config.py", line 292, in __init__ execfile_(filename, config) File "/user_builds/pydetlib-test2/envs/latest/lib/python3.4/site-packages/sphinx/util/pycompat.py", line 130, in execfile_ exec_(code, _globals) File "conf.py", line 436, in output = check_output(nb_help).decode('utf8') File "/usr/lib/python3.4/subprocess.py", line 620, in check_output raise CalledProcessError(retcode, process.args, output=output) subprocess.CalledProcessError: Command '['xfel-calibrate', 'AGIPD', 'COMBINE', '--help']' returned non-zero exit status 1 Exception occurred: File "/usr/lib/python3.4/subprocess.py", line 620, in check_output raise CalledProcessError(retcode, process.args, output=output) subprocess.CalledProcessError: Command '['xfel-calibrate', 'AGIPD', 'COMBINE', '--help']' returned non-zero exit status 1 The full traceback has been saved in /tmp/sphinx-err-7l13ubg1.log, if you want to report the issue to the developers. Please also report this if it was a user error, so that a better error message can be provided next time. A bug report can be filed in the tracker at . Thanks! Pandoc was found!