Read the Docs build information Build id: 8826 Project: european-xfel-offline-calibration Version: latest Commit: a8c41e22e325e06dff097afd272b965ec6d9a91c Date: 2018-12-13T01:58:42.366316Z State: finished Success: False [rtd-command-info] start-time: 2018-12-13T07:58:55.071000Z, end-time: 2018-12-13T07:59:02.970000Z, duration: 7, exit-code: 0 python3 -mvirtualenv --system-site-packages --no-download /user_builds/european-xfel-offline-calibration/envs/latest Using base prefix '/usr' New python executable in /user_builds/european-xfel-offline-calibration/envs/latest/bin/python3 Not overwriting existing python script /user_builds/european-xfel-offline-calibration/envs/latest/bin/python (you must use /user_builds/european-xfel-offline-calibration/envs/latest/bin/python3) Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2018-12-13T07:59:03.032000Z, end-time: 2018-12-13T07:59:44.217000Z, duration: 41, exit-code: 0 python /user_builds/european-xfel-offline-calibration/envs/latest/bin/pip install --use-wheel -U --cache-dir /user_builds/european-xfel-offline-calibration/.cache/pip -I 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 Collecting sphinx==1.3.5 Using cached https://files.pythonhosted.org/packages/ff/91/45883bc962bda1be7e78039b41cc15e1eb3327ec75679eedd067b5d07bd5/Sphinx-1.3.5-py2.py3-none-any.whl Collecting Pygments==2.1.3 Using cached https://files.pythonhosted.org/packages/9e/d0/d692085518c6a2dc875fe421c866fb6a08e0d9796ca507803c1e545fa116/Pygments-2.1.3-py2.py3-none-any.whl Collecting setuptools==20.1.1 Using cached https://files.pythonhosted.org/packages/e8/82/3b5455f74bf9ac0757d09c625b7741e6fc284d7519cffc3babb6c5173cf5/setuptools-20.1.1-py2.py3-none-any.whl Collecting docutils==0.12 Using cached https://files.pythonhosted.org/packages/c7/16/29d8de2404c5b90243b51f91315b3ce375169ceb48a68aeec0862e0143c4/docutils-0.12-py3-none-any.whl Collecting mkdocs==0.15.0 Using cached https://files.pythonhosted.org/packages/a7/10/c839adfd209aba3a5905d4a766ea354a1d03a414d6d437e10988574de70a/mkdocs-0.15.0-py2.py3-none-any.whl Collecting mock==1.0.1 Collecting pillow==2.6.1 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-xqg0sal0/readthedocs-sphinx-ext Collecting sphinx-rtd-theme==0.1.9 Using cached https://files.pythonhosted.org/packages/97/d9/e27ef5a2b6b92d2cf29724c25daf0683adacc43ab5ad15dc0e9b69b464f8/sphinx_rtd_theme-0.1.9-py3-none-any.whl Collecting alabaster!=0.7.5,<0.8,>=0.7 Using cached https://files.pythonhosted.org/packages/10/ad/00b090d23a222943eb0eda509720a404f531a439e803f6538f35136cae9e/alabaster-0.7.12-py2.py3-none-any.whl Collecting commonmark==0.5.4 Collecting recommonmark==0.1.1 Using cached https://files.pythonhosted.org/packages/cb/65/0c893f1be31b8892ddd491ff05a9d539459ac07b9b1c9804034589ad7eb2/recommonmark-0.1.1-py2.py3-none-any.whl Collecting snowballstemmer>=1.1 (from sphinx==1.3.5) Using cached https://files.pythonhosted.org/packages/d4/6c/8a935e2c7b54a37714656d753e4187ee0631988184ed50c0cf6476858566/snowballstemmer-1.2.1-py2.py3-none-any.whl Collecting six>=1.4 (from sphinx==1.3.5) Downloading https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl Collecting Jinja2>=2.3 (from sphinx==1.3.5) Using cached https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl Collecting babel!=2.0,>=1.3 (from sphinx==1.3.5) Using cached https://files.pythonhosted.org/packages/b8/ad/c6f60602d3ee3d92fbed87675b6fb6a6f9a38c223343ababdb44ba201f10/Babel-2.6.0-py2.py3-none-any.whl Collecting Markdown>=2.3.1 (from mkdocs==0.15.0) Using cached https://files.pythonhosted.org/packages/7a/6b/5600647404ba15545ec37d2f7f58844d690baf2f81f3a60b862e48f29287/Markdown-3.0.1-py2.py3-none-any.whl Collecting livereload>=2.3.2 (from mkdocs==0.15.0) Downloading https://files.pythonhosted.org/packages/ae/dd/f518bb99d84a3d26f45c281030b4d74b8cbe23bf8ad311b42e413aa33e51/livereload-2.6.0-py2.py3-none-any.whl Collecting tornado>=4.1 (from mkdocs==0.15.0) Collecting mkdocs-bootstrap>=0.1.1 (from mkdocs==0.15.0) Using cached https://files.pythonhosted.org/packages/e4/26/8823a7e45fad6ede3da31147514fb029dffb134e363bb0f64f7a2bd9448d/mkdocs_bootstrap-1.0.1-py2.py3-none-any.whl Collecting click>=4.0 (from mkdocs==0.15.0) Using cached https://files.pythonhosted.org/packages/fa/37/45185cb5abbc30d7257104c434fe0b07e5a195a6847506c074527aa599ec/Click-7.0-py2.py3-none-any.whl Collecting mkdocs-bootswatch>=0.1.0 (from mkdocs==0.15.0) Using cached https://files.pythonhosted.org/packages/42/06/1cdc2c3889c3c5803ae830bae3bf7c3fa5a0841109665d93bac81f287088/mkdocs_bootswatch-1.0-py2.py3-none-any.whl Collecting PyYAML>=3.10 (from mkdocs==0.15.0) Collecting requests (from readthedocs-sphinx-ext) Downloading https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl (57kB) Collecting nilsimsa>=0.3.7 (from readthedocs-sphinx-ext) Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx==1.3.5) Using cached https://files.pythonhosted.org/packages/3e/a6/230a77104000937d717c300bcefe907a960d437e1a721e49c5fb40deb1c0/MarkupSafe-1.1.0-cp34-cp34m-manylinux1_x86_64.whl Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx==1.3.5) Using cached https://files.pythonhosted.org/packages/f8/0e/2365ddc010afb3d79147f1dd544e5ee24bf4ece58ab99b16fbb465ce6dc0/pytz-2018.7-py2.py3-none-any.whl Collecting backports-abc>=0.4 (from tornado>=4.1->mkdocs==0.15.0) Using cached https://files.pythonhosted.org/packages/7d/56/6f3ac1b816d0cd8994e83d0c4e55bc64567532f7dc543378bd87f81cebc7/backports_abc-0.5-py2.py3-none-any.whl Collecting idna<2.9,>=2.5 (from requests->readthedocs-sphinx-ext) Downloading https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl (58kB) Collecting certifi>=2017.4.17 (from requests->readthedocs-sphinx-ext) Downloading https://files.pythonhosted.org/packages/9f/e0/accfc1b56b57e9750eba272e24c4dddeac86852c2bebd1236674d7887e8a/certifi-2018.11.29-py2.py3-none-any.whl (154kB) Collecting urllib3<1.25,>=1.21.1 (from requests->readthedocs-sphinx-ext) Using cached https://files.pythonhosted.org/packages/62/00/ee1d7de624db8ba7090d1226aebefab96a2c71cd5cfa7629d6ad3f61b79e/urllib3-1.24.1-py2.py3-none-any.whl Collecting chardet<3.1.0,>=3.0.2 (from requests->readthedocs-sphinx-ext) Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl Installing collected packages: snowballstemmer, alabaster, six, MarkupSafe, Jinja2, docutils, Pygments, pytz, babel, sphinx-rtd-theme, sphinx, setuptools, Markdown, backports-abc, tornado, livereload, mkdocs-bootstrap, click, mkdocs-bootswatch, PyYAML, mkdocs, mock, pillow, idna, certifi, urllib3, chardet, requests, nilsimsa, readthedocs-sphinx-ext, commonmark, recommonmark Running setup.py install for readthedocs-sphinx-ext: started Running setup.py install for readthedocs-sphinx-ext: finished with status 'done' Successfully installed Jinja2-2.10 Markdown-3.0.1 MarkupSafe-1.1.0 PyYAML-4.1 Pygments-2.1.3 alabaster-0.7.12 babel-2.6.0 backports-abc-0.5 certifi-2018.11.29 chardet-3.0.4 click-7.0 commonmark-0.5.4 docutils-0.12 idna-2.8 livereload-2.6.0 mkdocs-0.15.0 mkdocs-bootstrap-1.0.1 mkdocs-bootswatch-1.0 mock-1.0.1 nilsimsa-0.3.8 pillow-2.6.1 pytz-2018.7 readthedocs-sphinx-ext-0.5.4 recommonmark-0.1.1 requests-2.21.0 setuptools-28.8.0 six-1.12.0 snowballstemmer-1.2.1 sphinx-1.3.5 sphinx-rtd-theme-0.1.9 tornado-5.1.1 urllib3-1.24.1 You are using pip version 9.0.1, however version 18.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2018-12-13T07:59:44.283000Z, end-time: 2018-12-13T08:00:06.827000Z, duration: 22, exit-code: 0 python /user_builds/european-xfel-offline-calibration/envs/latest/bin/pip install --exists-action=w --cache-dir /user_builds/european-xfel-offline-calibration/.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-xhwb91_n-build Requirement already satisfied (use --upgrade to upgrade): nbparameterise===1.0xfel from git+https://haufs:s--zGku2dzxtv6so2xsu@git.xfel.eu/gitlab/detectors/nbparameterise.git in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 1)) 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-lwyx8cfi-build Requirement already satisfied (use --upgrade to upgrade): iCalibrationDB==0.1 from git+https://haufs:s--zGku2dzxtv6so2xsu@git.xfel.eu/gitlab/detectors/cal_db_interactive.git in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 2)) Processing ./cal_tools Requirement already satisfied (use --upgrade to upgrade): calTools==0.1 from file:///user_builds/european-xfel-offline-calibration/checkouts/latest/cal_tools in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 9)) Processing /user_builds/european-xfel-offline-calibration/checkouts/latest Requirement already satisfied (use --upgrade to upgrade): European-XFEL-Offline-Calibration==1.0 from file:///user_builds/european-xfel-offline-calibration/checkouts/latest in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 10)) Requirement already satisfied: pypandoc in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied: nbconvert in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: astcheck in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: astsearch in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: influxdb in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: tabulate in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: pip>=8.1.0 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from pypandoc->-r requirements.txt (line 3)) Requirement already satisfied: setuptools in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from pypandoc->-r requirements.txt (line 3)) Requirement already satisfied: wheel>=0.25.0 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from pypandoc->-r requirements.txt (line 3)) Requirement already satisfied: mistune>=0.7.4 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: pygments in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: entrypoints>=0.2.2 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: jinja2 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: bleach in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: traitlets>=4.2 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: nbformat>=4.4 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: jupyter-core in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: pandocfilters>=1.4.1 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: testpath in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: python-dateutil>=2.6.0 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from influxdb->-r requirements.txt (line 7)) Requirement already satisfied: six>=1.10.0 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from influxdb->-r requirements.txt (line 7)) Requirement already satisfied: requests>=2.17.0 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from influxdb->-r requirements.txt (line 7)) Requirement already satisfied: pytz in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from influxdb->-r requirements.txt (line 7)) Requirement already satisfied: MarkupSafe>=0.23 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from jinja2->nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: html5lib!=1.0b1,!=1.0b2,!=1.0b3,!=1.0b4,!=1.0b5,!=1.0b6,!=1.0b7,!=1.0b8,>=0.99999999pre in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from bleach->nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: decorator in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from traitlets>=4.2->nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: ipython-genutils in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from traitlets>=4.2->nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbformat>=4.4->nbconvert->-r requirements.txt (line 4)) Requirement already satisfied: certifi>=2017.4.17 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from requests>=2.17.0->influxdb->-r requirements.txt (line 7)) Requirement already satisfied: urllib3<1.25,>=1.21.1 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from requests>=2.17.0->influxdb->-r requirements.txt (line 7)) Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from requests>=2.17.0->influxdb->-r requirements.txt (line 7)) Requirement already satisfied: idna<2.9,>=2.5 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from requests>=2.17.0->influxdb->-r requirements.txt (line 7)) Requirement already satisfied: webencodings in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from html5lib!=1.0b1,!=1.0b2,!=1.0b3,!=1.0b4,!=1.0b5,!=1.0b6,!=1.0b7,!=1.0b8,>=0.99999999pre->bleach->nbconvert->-r requirements.txt (line 4)) You are using pip version 9.0.1, however version 18.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2018-12-13T08:00:06.891000Z, end-time: 2018-12-13T08:00:09.827000Z, duration: 2, 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/influx.py -> build/lib/cal_tools copying cal_tools/cal_tools/enums.py -> build/lib/cal_tools copying cal_tools/cal_tools/agipdlib.py -> build/lib/cal_tools copying cal_tools/cal_tools/lpdlib.py -> build/lib/cal_tools copying cal_tools/cal_tools/__init__.py -> build/lib/cal_tools copying cal_tools/cal_tools/conf_latex.py -> build/lib/cal_tools copying cal_tools/cal_tools/conf_orig.py -> build/lib/cal_tools copying cal_tools/cal_tools/tools.py -> build/lib/cal_tools copying cal_tools/cal_tools/plotting.py -> build/lib/cal_tools copying cal_tools/cal_tools/metrology.py -> build/lib/cal_tools creating build/lib/xfel_calibrate copying xfel_calibrate/settings.py -> build/lib/xfel_calibrate copying xfel_calibrate/check_proc_files.py -> build/lib/xfel_calibrate copying xfel_calibrate/__init__.py -> build/lib/xfel_calibrate copying xfel_calibrate/notebooks.py -> build/lib/xfel_calibrate copying xfel_calibrate/automode.py -> build/lib/xfel_calibrate copying xfel_calibrate/calibrate.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/slurm_calibrate.sh -> build/lib/xfel_calibrate/bin copying xfel_calibrate/bin/cal_influx_feeder.sh -> build/lib/xfel_calibrate/bin creating build/lib/xfel_calibrate/notebooks creating 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/PlotFromCalDB.ipynb -> build/lib/xfel_calibrate/notebooks/LPD copying xfel_calibrate/notebooks/LPD/LPD_Correct_and_Verify.ipynb -> 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/Characterize_LPD_GAIN_CI_per_pixel_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 creating build/lib/xfel_calibrate/notebooks/pnCCD copying xfel_calibrate/notebooks/pnCCD/Characterize_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/pnCCD creating build/lib/xfel_calibrate/notebooks/AGIPD copying xfel_calibrate/notebooks/AGIPD/AGIPD_Correct_and_Verify.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/Chracterize_AGIPD_Gain_PC_NBC.ipynb -> 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/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/AGIPD creating build/lib/xfel_calibrate/notebooks/FastCCD copying xfel_calibrate/notebooks/FastCCD/CorrectionNotebook_NewDAQ_FastCCD_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/FastCCD copying xfel_calibrate/notebooks/FastCCD/Characterize_Darks_NewDAQ_FastCCD_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/FastCCD copying xfel_calibrate/notebooks/FastCCD/Characterize_FlatFields_FastCCD_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/FastCCD 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/generic copying xfel_calibrate/notebooks/generic/DB_Constants_to_HDF5_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/generic running install_lib copying build/lib/xfel_calibrate/settings.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate copying build/lib/xfel_calibrate/check_proc_files.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate copying build/lib/xfel_calibrate/__init__.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate copying build/lib/xfel_calibrate/notebooks.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate copying build/lib/xfel_calibrate/notebooks/generic/DB_Constants_to_HDF5_NBC.ipynb -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/generic copying build/lib/xfel_calibrate/notebooks/LPD/LPDChar_Darks_NBC.ipynb -> /user_builds/european-xfel-offline-calibration/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/european-xfel-offline-calibration/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/european-xfel-offline-calibration/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/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/LPD copying build/lib/xfel_calibrate/notebooks/LPD/PlotFromCalDB.ipynb -> /user_builds/european-xfel-offline-calibration/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/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/LPD copying build/lib/xfel_calibrate/notebooks/FastCCD/CorrectionNotebook_NewDAQ_FastCCD_NBC.ipynb -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/FastCCD copying build/lib/xfel_calibrate/notebooks/FastCCD/Characterize_Darks_NewDAQ_FastCCD_NBC.ipynb -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/FastCCD copying build/lib/xfel_calibrate/notebooks/FastCCD/Characterize_FlatFields_FastCCD_NBC.ipynb -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/FastCCD copying build/lib/xfel_calibrate/notebooks/Tutorial/calversion.ipynb -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/Tutorial copying build/lib/xfel_calibrate/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb -> /user_builds/european-xfel-offline-calibration/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/european-xfel-offline-calibration/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/european-xfel-offline-calibration/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/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib/xfel_calibrate/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/AGIPD copying build/lib/xfel_calibrate/notebooks/pnCCD/Characterize_NBC.ipynb -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks/pnCCD copying build/lib/xfel_calibrate/bin/automode.sh -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/bin copying build/lib/xfel_calibrate/bin/slurm_calibrate.sh -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/bin copying build/lib/xfel_calibrate/bin/cal_influx_feeder.sh -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/bin copying build/lib/xfel_calibrate/automode.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate copying build/lib/xfel_calibrate/calibrate.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate copying build/lib/cal_tools/influx.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/enums.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/agipdlib.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/lpdlib.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/__init__.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/conf_latex.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/conf_orig.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/tools.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/plotting.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools copying build/lib/cal_tools/metrology.py -> /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/settings.py to settings.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/check_proc_files.py to check_proc_files.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/__init__.py to __init__.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/notebooks.py to notebooks.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/automode.py to automode.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/calibrate.py to calibrate.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools/influx.py to influx.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools/enums.py to enums.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools/agipdlib.py to agipdlib.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools/lpdlib.py to lpdlib.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools/__init__.py to __init__.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools/conf_latex.py to conf_latex.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools/conf_orig.py to conf_orig.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools/tools.py to tools.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools/plotting.py to plotting.cpython-34.pyc byte-compiling /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/cal_tools/metrology.py to metrology.cpython-34.pyc running install_egg_info running egg_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 European_XFEL_Offline_Calibration.egg-info/PKG-INFO 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/european-xfel-offline-calibration/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/european-xfel-offline-calibration/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/european-xfel-offline-calibration/envs/latest/bin Python environment seems to not be a Karabo environment. Please install PyDetLib manually. [rtd-command-info] start-time: 2018-12-13T08:00:10.288000Z, end-time: 2018-12-13T08:00:10.321000Z, 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 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 = 'alabaster' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # html_theme_options = {} # Add any paths that contain custom 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") ########################################################################### # 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/"), ("feat-reproducibility", "/en/feat-reproducibility/"), ], 'downloads': [ ("pdf", "//exflrtd.desy.de/projects/european-xfel-offline-calibration/downloads/pdf/latest/"), ("htmlzip", "//exflrtd.desy.de/projects/european-xfel-offline-calibration/downloads/htmlzip/latest/"), ("epub", "//exflrtd.desy.de/projects/european-xfel-offline-calibration/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'european-xfel-offline-calibration', 'name': u'European XFEL Offline Calibration', 'rtd_language': u'en', 'canonical_url': 'http://exflrtd.desy.de/docs/european-xfel-offline-calibration/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': 'master', 'display_github': False, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', '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': 'a8c41e22', } 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: 2018-12-13T08:00:10.387000Z, end-time: 2018-12-13T08:00:33.469000Z, duration: 23, exit-code: 1 python /user_builds/european-xfel-offline-calibration/envs/latest/bin/sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.3.5 making output directory... ./makeAllDocs.sh: line 8: cd: _notebooks: No such file or directory [NbConvertApp] WARNING | pattern '../../../notebooks/Tutorial/calversion.ipynb' matched no files This application is used to convert notebook files (*.ipynb) to various other formats. WARNING: THE COMMANDLINE INTERFACE MAY CHANGE IN FUTURE RELEASES. Options ------- Arguments that take values are actually convenience aliases to full Configurables, whose aliases are listed on the help line. For more information on full configurables, see '--help-all'. --stdout Write notebook output to stdout instead of files. --no-prompt Exclude input and output prompts from converted document. --clear-output Clear output of current file and save in place, overwriting the existing notebook. -y Answer yes to any questions instead of prompting. --allow-errors Continue notebook execution even if one of the cells throws an error and include the error message in the cell output (the default behaviour is to abort conversion). This flag is only relevant if '--execute' was specified, too. --stdin read a single notebook file from stdin. Write the resulting notebook with default basename 'notebook.*' --execute Execute the notebook prior to export. --inplace Run nbconvert in place, overwriting the existing notebook (only relevant when converting to notebook format) --debug set log level to logging.DEBUG (maximize logging output) --generate-config generate default config file --nbformat= (NotebookExporter.nbformat_version) Default: 4 Choices: [1, 2, 3, 4] The nbformat version to write. Use this to downgrade notebooks. --writer= (NbConvertApp.writer_class) Default: 'FilesWriter' Writer class used to write the results of the conversion --config= (JupyterApp.config_file) Default: '' Full path of a config file. --output= (NbConvertApp.output_base) Default: '' overwrite base name use for output files. can only be used when converting one notebook at a time. --output-dir= (FilesWriter.build_directory) Default: '' Directory to write output(s) to. Defaults to output to the directory of each notebook. To recover previous default behaviour (outputting to the current working directory) use . as the flag value. --log-level= (Application.log_level) Default: 30 Choices: (0, 10, 20, 30, 40, 50, 'DEBUG', 'INFO', 'WARN', 'ERROR', 'CRITICAL') Set the log level by value or name. --post= (NbConvertApp.postprocessor_class) Default: '' PostProcessor class used to write the results of the conversion --reveal-prefix= (SlidesExporter.reveal_url_prefix) Default: '' The URL prefix for reveal.js. This can be a a relative URL for a local copy of reveal.js, or point to a CDN. For speaker notes to work, a local reveal.js prefix must be used. --template= (TemplateExporter.template_file) Default: '' Name of the template file to use --to= (NbConvertApp.export_format) Default: 'html' The export format to be used, either one of the built-in formats, or a dotted object name that represents the import path for an `Exporter` class To see all available configurables, use `--help-all` Examples -------- The simplest way to use nbconvert is > jupyter nbconvert mynotebook.ipynb which will convert mynotebook.ipynb to the default format (probably HTML). You can specify the export format with `--to`. Options include ['asciidoc', 'custom', 'html', 'latex', 'markdown', 'notebook', 'pdf', 'python', 'rst', 'script', 'slides'] > jupyter nbconvert --to latex mynotebook.ipynb Both HTML and LaTeX support multiple output templates. LaTeX includes 'base', 'article' and 'report'. HTML includes 'basic' and 'full'. You can specify the flavor of the format used. > jupyter nbconvert --to html --template basic mynotebook.ipynb You can also pipe the output to stdout, rather than a file > jupyter nbconvert mynotebook.ipynb --stdout PDF is generated via latex > jupyter nbconvert mynotebook.ipynb --to pdf You can get (and serve) a Reveal.js-powered slideshow > jupyter nbconvert myslides.ipynb --to slides --post serve Multiple notebooks can be given at the command line in a couple of different ways: > jupyter nbconvert notebook*.ipynb > jupyter nbconvert notebook1.ipynb notebook2.ipynb or you can specify the notebooks list in a config file, containing:: c.NbConvertApp.notebooks = ["my_notebook.ipynb"] > jupyter nbconvert --config mycfg.py 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 Traceback (most recent call last): File "/user_builds/european-xfel-offline-calibration/envs/latest/bin/xfel-calibrate", line 9, in load_entry_point('European-XFEL-Offline-Calibration==1.0', 'console_scripts', 'xfel-calibrate')() File "/user_builds/european-xfel-offline-calibration/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/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/pkg_resources/__init__.py", line 2720, in load_entry_point return ep.load() File "/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/pkg_resources/__init__.py", line 2380, in load return self.resolve() File "/user_builds/european-xfel-offline-calibration/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/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/xfel_calibrate/calibrate.py", line 327, in extention = f(*callargs) File "", line 2, in extend_parms File "/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/iCalibrationDB/__init__.py", line 3, in from .meta_data import ConstantMetaData File "/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/iCalibrationDB/meta_data.py", line 5, in import h5py ImportError: No module named 'h5py' Traceback (most recent call last): File "/user_builds/european-xfel-offline-calibration/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/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/sphinx/application.py", line 127, in __init__ confoverrides or {}, self.tags) File "/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/sphinx/config.py", line 277, in __init__ execfile_(filename, config) File "/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages/sphinx/util/pycompat.py", line 128, in execfile_ exec_(code, _globals) File "conf.py", line 434, 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', 'GENERIC', 'DB_TO_H5', '--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', 'GENERIC', 'DB_TO_H5', '--help']' returned non-zero exit status 1 The full traceback has been saved in /tmp/sphinx-err-_85hc233.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!