Read the Docs build information Build id: 9342 Project: european-xfel-offline-calibration Version: latest Commit: f273618dbca286ec0c895fefa8b471968d3984ba Date: 2019-02-01T02:35:33.322672Z State: finished Success: False [rtd-command-info] start-time: 2019-02-01T08:35:40.953000Z, end-time: 2019-02-01T08:35:48.362000Z, 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: 2019-02-01T08:35:48.425000Z, end-time: 2019-02-01T08:36:32.219000Z, duration: 43, 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-2kirdbph/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 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 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 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 six>=1.4 (from sphinx==1.3.5) Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl Collecting PyYAML>=3.10 (from mkdocs==0.15.0) 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 livereload>=2.3.2 (from mkdocs==0.15.0) Using cached https://files.pythonhosted.org/packages/ae/dd/f518bb99d84a3d26f45c281030b4d74b8cbe23bf8ad311b42e413aa33e51/livereload-2.6.0-py2.py3-none-any.whl 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 tornado>=4.1 (from mkdocs==0.15.0) 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 requests (from readthedocs-sphinx-ext) Using cached https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl Collecting nilsimsa>=0.3.7 (from readthedocs-sphinx-ext) Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx==1.3.5) Downloading https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl (510kB) 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 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 certifi>=2017.4.17 (from requests->readthedocs-sphinx-ext) Using cached https://files.pythonhosted.org/packages/9f/e0/accfc1b56b57e9750eba272e24c4dddeac86852c2bebd1236674d7887e8a/certifi-2018.11.29-py2.py3-none-any.whl Collecting idna<2.9,>=2.5 (from requests->readthedocs-sphinx-ext) Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-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 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 Installing collected packages: pytz, babel, snowballstemmer, MarkupSafe, Jinja2, docutils, sphinx-rtd-theme, Pygments, alabaster, six, sphinx, setuptools, PyYAML, click, mkdocs-bootswatch, backports-abc, tornado, livereload, mkdocs-bootstrap, Markdown, mkdocs, mock, pillow, certifi, idna, chardet, urllib3, 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-2018.9 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 19.0.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2019-02-01T08:36:32.287000Z, end-time: 2019-02-01T08:38:00.444000Z, duration: 88, 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-s6ree68c-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-gbdjl_02-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 17)) 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 18)) Collecting fabio (from -r requirements.txt (line 3)) Downloading https://files.pythonhosted.org/packages/d5/d2/c7f578c1ab539c742916aa42f2aa010c93520a5e05271e2a18c8b31a32af/fabio-0.8.0-cp34-cp34m-manylinux1_x86_64.whl (1.6MB) Requirement already satisfied: pypandoc in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied: nbconvert in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied: astcheck in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 6)) Requirement already satisfied: astsearch in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied: influxdb in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied: tabulate in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from -r requirements.txt (line 9)) Collecting h5py (from -r requirements.txt (line 10)) Downloading https://files.pythonhosted.org/packages/9c/fb/16dfe209a415c700577e41d16b46ca3514f920b96ebeed2895d01bf97316/h5py-2.9.0-cp34-cp34m-manylinux1_x86_64.whl (2.8MB) Collecting unittest-xml-reporting (from -r requirements.txt (line 11)) Downloading https://files.pythonhosted.org/packages/2b/44/3895d13a64f76e9a4f1d58ab72964d99d0292d440f21422a7c4aa5074534/unittest_xml_reporting-2.2.1-py2.py3-none-any.whl Collecting zmq (from -r requirements.txt (line 12)) Collecting lxml (from -r requirements.txt (line 13)) Downloading https://files.pythonhosted.org/packages/c1/03/0e0948f35788721343bc7ad9ff09169244ac89948985b29bd86b7e613f9d/lxml-4.3.0-cp34-cp34m-manylinux1_x86_64.whl (5.7MB) Collecting gitpython (from -r requirements.txt (line 14)) Downloading https://files.pythonhosted.org/packages/fe/e5/fafe827507644c32d6dc553a1c435cdf882e0c28918a5bab29f7fbebfb70/GitPython-2.1.11-py2.py3-none-any.whl (448kB) Collecting karabo_data (from -r requirements.txt (line 15)) Downloading https://files.pythonhosted.org/packages/18/39/818947599b992a742f97ffa56c1b335da2cab58b4a44c6f433f62633bc2a/karabo_data-0.2.0-py3-none-any.whl (51kB) Collecting sklearn (from -r requirements.txt (line 16)) Downloading https://files.pythonhosted.org/packages/1e/7a/dbb3be0ce9bd5c8b7e3d87328e79063f8b263b2b1bfa4774cb1147bfcd3f/sklearn-0.0.tar.gz Requirement already satisfied: setuptools in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from fabio->-r requirements.txt (line 3)) Requirement already satisfied: numpy in /usr/local/lib/python3.4/dist-packages (from fabio->-r requirements.txt (line 3)) 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 4)) 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 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 5)) Requirement already satisfied: pygments in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbconvert->-r requirements.txt (line 5)) Requirement already satisfied: bleach in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbconvert->-r requirements.txt (line 5)) 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 5)) Requirement already satisfied: jinja2 in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbconvert->-r requirements.txt (line 5)) 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 5)) Requirement already satisfied: testpath in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbconvert->-r requirements.txt (line 5)) 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 5)) 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 5)) 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 5)) 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 8)) 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 8)) 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 8)) Requirement already satisfied: pytz in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from influxdb->-r requirements.txt (line 8)) Collecting pyzmq (from zmq->-r requirements.txt (line 12)) Collecting gitdb2>=2.0.0 (from gitpython->-r requirements.txt (line 14)) Downloading https://files.pythonhosted.org/packages/da/30/a407568aa8d8f25db817cf50121a958722f3fc5f87e3a6fba1f40c0633e3/gitdb2-2.0.5-py2.py3-none-any.whl (62kB) Collecting karabo-bridge (from karabo_data->-r requirements.txt (line 15)) Downloading https://files.pythonhosted.org/packages/be/3a/63a361afe60eca0fea4b4b677818f0136332889730c8b5adca0ac72845db/karabo_bridge-0.2.0-py3-none-any.whl Collecting pandas<0.21; python_version < "3.5" (from karabo_data->-r requirements.txt (line 15)) Downloading https://files.pythonhosted.org/packages/aa/cb/43ce8e01cf980f2381aa85ad6d0aff5e62c64d498b94a379e19f3a011e1a/pandas-0.20.3-cp34-cp34m-manylinux1_x86_64.whl (24.4MB) Collecting xarray (from karabo_data->-r requirements.txt (line 15)) Downloading https://files.pythonhosted.org/packages/d2/40/e3d9a6b679a7b4ba80e8cdf0b0226809ef454773f7b79ef1b2bd1898bd48/xarray-0.10.9-py2.py3-none-any.whl (473kB) Collecting msgpack>=0.5.4 (from karabo_data->-r requirements.txt (line 15)) Downloading https://files.pythonhosted.org/packages/81/9c/0036c66234482044070836cc622266839e2412f8108849ab0bfdeaab8578/msgpack-0.6.1.tar.gz (118kB) Requirement already satisfied: matplotlib in /usr/local/lib/python3.4/dist-packages (from karabo_data->-r requirements.txt (line 15)) Collecting msgpack-numpy>=0.4.3 (from karabo_data->-r requirements.txt (line 15)) Downloading https://files.pythonhosted.org/packages/b4/1c/68fcaeb72ac4a9c7f44cf4d19082bd4e486cd035134b118ddea6eff10e7d/msgpack_numpy-0.4.4.2-py2.py3-none-any.whl Collecting scikit-learn (from sklearn->-r requirements.txt (line 16)) Downloading https://files.pythonhosted.org/packages/38/5a/4b1c9c56cfcdc727d977d6698de10b749a8e0f487c519125d9eecd9613ed/scikit_learn-0.20.2-cp34-cp34m-manylinux1_x86_64.whl (5.3MB) 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 5)) 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 5)) Requirement already satisfied: ipython-genutils in /user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.4/site-packages (from nbformat>=4.4->nbconvert->-r requirements.txt (line 5)) 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 5)) 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 5)) 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 8)) 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 8)) 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 8)) 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 8)) Collecting smmap2>=2.0.0 (from gitdb2>=2.0.0->gitpython->-r requirements.txt (line 14)) Downloading https://files.pythonhosted.org/packages/55/d2/866d45e3a121ee15a1dc013824d58072fd5c7799c9c34d01378eb262ca8f/smmap2-2.0.5-py2.py3-none-any.whl Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.4/dist-packages (from matplotlib->karabo_data->-r requirements.txt (line 15)) Requirement already satisfied: pyparsing!=2.0.0,!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /usr/local/lib/python3.4/dist-packages (from matplotlib->karabo_data->-r requirements.txt (line 15)) Collecting scipy>=0.13.3 (from scikit-learn->sklearn->-r requirements.txt (line 16)) Downloading https://files.pythonhosted.org/packages/bf/47/6e6b4136e1ca4729f67b0ef45b93dcf7523c33c95050a2bc75f8f26c4199/scipy-1.2.0-cp34-cp34m-manylinux1_x86_64.whl (26.5MB) 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 5)) Building wheels for collected packages: sklearn, msgpack Running setup.py bdist_wheel for sklearn: started Running setup.py bdist_wheel for sklearn: finished with status 'done' Stored in directory: /user_builds/european-xfel-offline-calibration/.cache/pip/wheels/76/03/bb/589d421d27431bcd2c6da284d5f2286c8e3b2ea3cf1594c074 Running setup.py bdist_wheel for msgpack: started Running setup.py bdist_wheel for msgpack: finished with status 'done' Stored in directory: /user_builds/european-xfel-offline-calibration/.cache/pip/wheels/e0/eb/73/79c4057260fcb51c5f12cee027dda5cf79b92b618a82529c74 Successfully built sklearn msgpack Installing collected packages: fabio, h5py, unittest-xml-reporting, pyzmq, zmq, lxml, smmap2, gitdb2, gitpython, msgpack, msgpack-numpy, karabo-bridge, pandas, xarray, karabo-data, scipy, scikit-learn, sklearn Successfully installed fabio-0.8.0 gitdb2-2.0.5 gitpython-2.1.11 h5py-2.9.0 karabo-bridge-0.2.0 karabo-data-0.2.0 lxml-4.3.0 msgpack-0.6.1 msgpack-numpy-0.4.4.2 pandas-0.20.3 pyzmq-17.1.2 scikit-learn-0.20.2 scipy-1.2.0 sklearn-0.0 smmap2-2.0.5 unittest-xml-reporting-2.2.1 xarray-0.10.9 zmq-0.0.0 You are using pip version 9.0.1, however version 19.0.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2019-02-01T08:38:00.510000Z, end-time: 2019-02-01T08:38:03.305000Z, 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/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/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/AGIPD_Correct_and_Verify.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/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/LPDChar_Darks_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/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 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/generic copying xfel_calibrate/notebooks/generic/DB_Constants_to_HDF5_NBC.ipynb -> build/lib/xfel_calibrate/notebooks/generic creating 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/CorrectionNotebook_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 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 European_XFEL_Offline_Calibration.egg-info/PKG-INFO writing dependency_links to European_XFEL_Offline_Calibration.egg-info/dependency_links.txt writing entry points to European_XFEL_Offline_Calibration.egg-info/entry_points.txt writing top-level names to European_XFEL_Offline_Calibration.egg-info/top_level.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/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: 2019-02-01T08:38:03.752000Z, end-time: 2019-02-01T08:38:04.111000Z, 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 = '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") # add test results test_artifact_dir = os.path.realpath("../../tests/artifacts") 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_artifact_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_artifact_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_artifact_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/"), ("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': 'f273618d', } 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: 2019-02-01T08:38:04.246000Z, end-time: 2019-02-01T08:38:39.708000Z, duration: 35, 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... [NbConvertApp] Converting notebook ../../../notebooks/Tutorial/calversion.ipynb to rst [NbConvertApp] Support files will be in calversion_files/ [NbConvertApp] Making directory ./calversion_files [NbConvertApp] Making directory ./calversion_files [NbConvertApp] Writing 4643 bytes to ./calversion.rst 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 578, in for commit, modtime in sorted_dir(test_artifact_dir): File "conf.py", line 557, in sorted_dir sort = sorted(os.listdir(folder), key=getmtime, reverse=True) FileNotFoundError: [Errno 2] No such file or directory: '/user_builds/european-xfel-offline-calibration/checkouts/latest/tests/artifacts' Exception occurred: File "conf.py", line 557, in sorted_dir sort = sorted(os.listdir(folder), key=getmtime, reverse=True) FileNotFoundError: [Errno 2] No such file or directory: '/user_builds/european-xfel-offline-calibration/checkouts/latest/tests/artifacts' The full traceback has been saved in /tmp/sphinx-err-_vgfmj_7.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!