Read the Docs build information Build id: 22649 Project: data-analysis-user-documentation Version: latest Commit: 834d29a30c4c1756cbd9f982316ec21ab70cf576 Date: 2021-11-11T13:24:10.634712Z State: finished Success: True [rtd-command-info] start-time: 2021-11-11T13:24:12.091115Z, end-time: 2021-11-11T13:24:14.043224Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 http://git.xfel.eu/gitlab/dataAnalysis/user-documentation . Cloning into '.'... warning: redirecting to https://git.xfel.eu/gitlab/dataAnalysis/user-documentation.git/ [rtd-command-info] start-time: 2021-11-11T13:24:14.485090Z, end-time: 2021-11-11T13:24:14.624549Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 834d29a Fix link to Singularity docs [rtd-command-info] start-time: 2021-11-11T13:24:14.781388Z, end-time: 2021-11-11T13:24:14.858345Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-11-11T13:24:16.060900Z, end-time: 2021-11-11T13:24:23.118066Z, duration: 7, exit-code: 0 python3.7 -mvirtualenv /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/bin/python3.7 Also creating executable in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-11-11T13:24:23.252421Z, end-time: 2021-11-11T13:24:24.850754Z, duration: 1, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/bin/python -m pip install --upgrade --no-cache-dir pip Requirement already satisfied: pip in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (21.3.1) [rtd-command-info] start-time: 2021-11-11T13:24:25.028506Z, end-time: 2021-11-11T13:24:36.716734Z, duration: 11, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/bin/python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting packaging Downloading packaging-21.2-py3-none-any.whl (40 kB) Collecting requests>=2.0.0 Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB) Collecting imagesize Downloading imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting pytz>=2015.7 Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (31 kB) Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.7-py3-none-any.whl (38 kB) Collecting idna<4,>=2.5 Downloading idna-3.3-py3-none-any.whl (61 kB) Collecting certifi>=2017.4.17 Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.7-py2.py3-none-any.whl (138 kB) Collecting pyparsing<3,>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23772 sha256=267ef4260cd46fe1e2d8bae03416f80bd892a8ac0511577bb1c6024dc9c25bc4 Stored in directory: /tmp/pip-ephem-wheel-cache-p4nelplz/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=c50038385a2c49b9ab6cc5555bee0259f977f2a238ab8a2264eb3320f009ba33 Stored in directory: /tmp/pip-ephem-wheel-cache-p4nelplz/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Attempting uninstall: setuptools Found existing installation: setuptools 58.5.3 Uninstalling setuptools-58.5.3: Successfully uninstalled setuptools-58.5.3 Successfully installed Jinja2-3.0.3 MarkupSafe-2.0.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.7 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-3.3 imagesize-1.3.0 mock-1.0.1 packaging-21.2 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.3 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.26.0 setuptools-41.0.1 six-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.7 [rtd-command-info] start-time: 2021-11-11T13:24:36.858787Z, end-time: 2021-11-11T13:24:48.351448Z, duration: 11, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/bin/python -m pip install --exists-action=w --no-cache-dir -r source/requirements.txt Requirement already satisfied: sphinx>=1.8 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from -r source/requirements.txt (line 1)) (1.8.5) Requirement already satisfied: sphinx_rtd_theme in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from -r source/requirements.txt (line 2)) (0.4.3) Collecting nbsphinx Downloading nbsphinx-0.8.7-py3-none-any.whl (25 kB) Collecting karabo_bridge Downloading karabo_bridge-0.6.1.tar.gz (17 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: Pygments>=2.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.8->-r source/requirements.txt (line 1)) (2.3.1) Requirement already satisfied: alabaster<0.8,>=0.7 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.8->-r source/requirements.txt (line 1)) (0.7.12) Requirement already satisfied: setuptools in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.8->-r source/requirements.txt (line 1)) (41.0.1) Requirement already satisfied: sphinxcontrib-websupport in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.8->-r source/requirements.txt (line 1)) (1.2.4) Requirement already satisfied: babel!=2.0,>=1.3 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.8->-r source/requirements.txt (line 1)) (2.9.1) Requirement already satisfied: six>=1.5 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.8->-r source/requirements.txt (line 1)) (1.16.0) Requirement already satisfied: snowballstemmer>=1.1 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.8->-r source/requirements.txt (line 1)) (2.1.0) Requirement already satisfied: requests>=2.0.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.8->-r source/requirements.txt (line 1)) (2.26.0) Requirement already satisfied: packaging in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.8->-r source/requirements.txt (line 1)) (21.2) Requirement already satisfied: imagesize in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.8->-r source/requirements.txt (line 1)) (1.3.0) Requirement already satisfied: docutils>=0.11 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.8->-r source/requirements.txt (line 1)) (0.14) Requirement already satisfied: Jinja2>=2.3 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.8->-r source/requirements.txt (line 1)) (3.0.3) Collecting nbformat Downloading nbformat-5.1.3-py3-none-any.whl (178 kB) Collecting nbconvert!=5.4 Downloading nbconvert-6.2.0-py3-none-any.whl (553 kB) Collecting traitlets Downloading traitlets-5.1.1-py3-none-any.whl (102 kB) Collecting msgpack>=0.5.4 Downloading msgpack-1.0.2-cp37-cp37m-manylinux1_x86_64.whl (273 kB) Collecting msgpack-numpy Downloading msgpack_numpy-0.4.7.1-py2.py3-none-any.whl (6.7 kB) Collecting numpy Downloading numpy-1.21.4-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB) Collecting pyzmq>=17.0.0 Downloading pyzmq-22.3.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.1 MB) Requirement already satisfied: pytz>=2015.7 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.8->-r source/requirements.txt (line 1)) (2021.3) Requirement already satisfied: MarkupSafe>=2.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx>=1.8->-r source/requirements.txt (line 1)) (2.0.1) Collecting pandocfilters>=1.4.1 Downloading pandocfilters-1.5.0-py2.py3-none-any.whl (8.7 kB) Collecting entrypoints>=0.2.2 Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB) Collecting nbclient<0.6.0,>=0.5.0 Downloading nbclient-0.5.5-py3-none-any.whl (69 kB) Collecting testpath Downloading testpath-0.5.0-py3-none-any.whl (84 kB) Collecting defusedxml Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Collecting jupyterlab-pygments Downloading jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB) Collecting bleach Downloading bleach-4.1.0-py2.py3-none-any.whl (157 kB) Collecting Pygments>=2.0 Downloading Pygments-2.10.0-py3-none-any.whl (1.0 MB) Collecting mistune<2,>=0.8.1 Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB) Collecting jupyter-core Downloading jupyter_core-4.9.1-py3-none-any.whl (86 kB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Collecting jsonschema!=2.5.0,>=2.4 Downloading jsonschema-4.2.1-py3-none-any.whl (69 kB) Requirement already satisfied: certifi>=2017.4.17 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.8->-r source/requirements.txt (line 1)) (2021.10.8) Requirement already satisfied: idna<4,>=2.5 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.8->-r source/requirements.txt (line 1)) (3.3) Requirement already satisfied: charset-normalizer~=2.0.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.8->-r source/requirements.txt (line 1)) (2.0.7) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.8->-r source/requirements.txt (line 1)) (1.26.7) Requirement already satisfied: pyparsing<3,>=2.0.2 in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from packaging->sphinx>=1.8->-r source/requirements.txt (line 1)) (2.4.7) Requirement already satisfied: sphinxcontrib-serializinghtml in /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-websupport->sphinx>=1.8->-r source/requirements.txt (line 1)) (1.1.5) Collecting attrs>=17.4.0 Downloading attrs-21.2.0-py2.py3-none-any.whl (53 kB) Collecting importlib-metadata Downloading importlib_metadata-4.8.2-py3-none-any.whl (17 kB) Collecting importlib-resources>=1.4.0 Downloading importlib_resources-5.4.0-py3-none-any.whl (28 kB) Collecting pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 Downloading pyrsistent-0.18.0-cp37-cp37m-manylinux1_x86_64.whl (119 kB) Collecting jupyter-client>=6.1.5 Downloading jupyter_client-7.0.6-py3-none-any.whl (125 kB) Collecting nest-asyncio Downloading nest_asyncio-1.5.1-py3-none-any.whl (5.0 kB) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Collecting zipp>=3.1.0 Downloading zipp-3.6.0-py3-none-any.whl (5.3 kB) Collecting tornado>=4.1 Downloading tornado-6.1-cp37-cp37m-manylinux2010_x86_64.whl (428 kB) Collecting python-dateutil>=2.1 Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Collecting typing-extensions>=3.6.4 Downloading typing_extensions-3.10.0.2-py3-none-any.whl (26 kB) Building wheels for collected packages: karabo-bridge Building wheel for karabo-bridge (setup.py): started Building wheel for karabo-bridge (setup.py): finished with status 'done' Created wheel for karabo-bridge: filename=karabo_bridge-0.6.1-py3-none-any.whl size=23572 sha256=052e6a5d03a71c903a4b52c92094c86ef3a08525aaa50ab40af64397b8bb74d7 Stored in directory: /tmp/pip-ephem-wheel-cache-x4gp9ove/wheels/57/83/bf/dcf5e32ce3fed4fd11a76d307d2d7818fc2c32fcc7a537bc55 Successfully built karabo-bridge Installing collected packages: zipp, typing-extensions, traitlets, pyrsistent, importlib-resources, importlib-metadata, attrs, tornado, pyzmq, python-dateutil, nest-asyncio, jupyter-core, jsonschema, ipython-genutils, entrypoints, webencodings, Pygments, nbformat, jupyter-client, testpath, pandocfilters, numpy, nbclient, msgpack, mistune, jupyterlab-pygments, defusedxml, bleach, nbconvert, msgpack-numpy, nbsphinx, karabo-bridge Attempting uninstall: Pygments Found existing installation: Pygments 2.3.1 Uninstalling Pygments-2.3.1: Successfully uninstalled Pygments-2.3.1 Successfully installed Pygments-2.10.0 attrs-21.2.0 bleach-4.1.0 defusedxml-0.7.1 entrypoints-0.3 importlib-metadata-4.8.2 importlib-resources-5.4.0 ipython-genutils-0.2.0 jsonschema-4.2.1 jupyter-client-7.0.6 jupyter-core-4.9.1 jupyterlab-pygments-0.1.2 karabo-bridge-0.6.1 mistune-0.8.4 msgpack-1.0.2 msgpack-numpy-0.4.7.1 nbclient-0.5.5 nbconvert-6.2.0 nbformat-5.1.3 nbsphinx-0.8.7 nest-asyncio-1.5.1 numpy-1.21.4 pandocfilters-1.5.0 pyrsistent-0.18.0 python-dateutil-2.8.2 pyzmq-22.3.0 testpath-0.5.0 tornado-6.1 traitlets-5.1.1 typing-extensions-3.10.0.2 webencodings-0.5.1 zipp-3.6.0 [rtd-command-info] start-time: 2021-11-11T13:24:49.413284Z, end-time: 2021-11-11T13:24:49.490717Z, duration: 0, exit-code: 0 cat source/conf.py #!/usr/bin/env python3 # -*- coding: utf-8 -*- # # User documentation documentation build configuration file, created by # sphinx-quickstart on Mon Jun 26 08:59:34 2017. # # 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.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'nbsphinx', 'sphinx_rtd_theme', ] # 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 = 'User Documentation' copyright = 'European XFEL' author = 'Hans Fangohr, Sandor Brockhauser and others from CAS and ITDM at XFEL' # 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 = ['_build', 'Thumbs.db', '.DS_Store'] # 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 # If true, figures, tables and code-blocks are automatically numbered if # they have a caption. At same time, the numref role is enabled. For now, # it works only with the HTML builder and LaTeX builder. Default is False. numfig = True on_rtd = os.environ.get('READTHEDOCS') == 'True' if on_rtd: tags.add('readthedocs') # -- 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 = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # html_theme_options = {} # Add any paths that contain custom themes here, relative to this directory. # html_theme_path = [] # The name for this set of Sphinx documents. # " v documentation" by default. # # html_title = 'Karabo Commissioning Guidelines v1.4.7' # 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' # -- Options for HTMLHelp output ------------------------------------------ # Output file base name for HTML help builder. htmlhelp_basename = 'Userdocumentationdoc' # -- 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', } # 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, 'Userdocumentation.tex', 'User Documentation', 'European XFEL', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. # latex_logo = "_templates/european-xfel-logo_cmyk.eps" # 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, 'userdocumentation', 'User documentation 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, 'Userdocumentation', 'User documentation Documentation', author, 'Userdocumentation', '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} # We have trouble with some of the links in link check # (see https://git.xfel.eu/gitlab/dataAnalysis/user-documentation/issues/2) # -> we ignore the links for which the link check fails on CI linkcheck_ignore = [ 'https://in.xfel.eu/.*', 'https://max-display.desy.de:3443', 'https://confluence.desy.de/display/IS/Docker+containers+on+Maxwell', 'https://confluence.desy.de/display/IS/Alphabetical+List+of+Packages', 'https://www.sigmaaldrich.com/.*', # No idea why this fails on CI , but it does. ] # Limit to 1 minute waiting if a server is stalling linkcheck_timeout = 60 ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'http://rtd.xfel.eu/websupport' websupport2_static_url = '/static/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "media/", 'STATIC_URL': "/static/", 'PRODUCTION_DOMAIN': "rtd.xfel.eu", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//rtd.xfel.eu/downloads/data-analysis-user-documentation/latest/pdf/"), ("html", "//rtd.xfel.eu/downloads/data-analysis-user-documentation/latest/htmlzip/"), ("epub", "//rtd.xfel.eu/downloads/data-analysis-user-documentation/latest/epub/"), ], 'subprojects': [ ], 'slug': 'data-analysis-user-documentation', 'name': u'Data Analysis User Documentation', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'http://rtd.xfel.eu/docs/data-analysis-user-documentation/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/source/', 'api_host': 'http://rtd.xfel.eu', 'github_user': 'None', 'proxied_api_host': '/_', 'github_repo': 'None', 'github_version': 'master', 'display_github': False, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'None', 'commit': '834d29a3', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2021-11-11T13:24:49.628446Z, end-time: 2021-11-11T13:24:54.006385Z, duration: 4, exit-code: 0 python /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/bin/sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading intersphinx inventory from https://docs.python.org/objects.inv... intersphinx inventory has moved: https://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 17 source files that are out of date updating environment: 17 added, 0 changed, 0 removed reading sources... [ 5%] candidate-frame-lists reading sources... [ 11%] changes reading sources... [ 17%] citations reading sources... [ 23%] computing reading sources... [ 29%] datafiles reading sources... [ 35%] hdf5_virtualise/hdf5_virtualise reading sources... [ 41%] index reading sources... [ 47%] jhub reading sources... [ 52%] karabo_bridge/cpp-client reading sources... [ 58%] karabo_bridge/protocol reading sources... [ 64%] karabo_bridge/py-client reading sources... [ 70%] karabo_bridge/recorder reading sources... [ 76%] online reading sources... [ 82%] overview reading sources... [ 88%] resources reading sources... [ 94%] software reading sources... [100%] usecases /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages/karabo_bridge/client.py:docstring of karabo_bridge.Client:21: WARNING: Unknown interpreted text role "method". /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages/karabo_bridge/client.py:docstring of karabo_bridge.Client:26: WARNING: Unexpected indentation. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 5%] candidate-frame-lists writing output... [ 11%] changes writing output... [ 17%] citations writing output... [ 23%] computing writing output... [ 29%] datafiles writing output... [ 35%] hdf5_virtualise/hdf5_virtualise writing output... [ 41%] index writing output... [ 47%] jhub writing output... [ 52%] karabo_bridge/cpp-client writing output... [ 58%] karabo_bridge/protocol writing output... [ 64%] karabo_bridge/py-client writing output... [ 70%] karabo_bridge/recorder writing output... [ 76%] online writing output... [ 82%] overview writing output... [ 88%] resources writing output... [ 94%] software writing output... [100%] usecases generating indices... genindex py-modindex writing additional pages... search copying images... [ 6%] _images/Level1_workstations.jpg copying images... [ 12%] _images/Level2_workstations.jpg copying images... [ 18%] _images/h5.png copying images... [ 25%] _images/max-jhub-partitions.png copying images... [ 31%] _images/max-jupyter_manual_token.png copying images... [ 37%] _images/lpd2tile_gui.png copying images... [ 43%] _images/trains_pulses.png copying images... [ 50%] _images/EXtra-foam-LPD_azimuthal_integration.png copying images... [ 56%] _images/EXtra-foam-ImageTool.png copying images... [ 62%] _images/EXtra-foam-ROI.png copying images... [ 68%] _images/geoAssembler.png copying images... [ 75%] _images/FastCCDCorrelatorScene.png copying images... [ 81%] _images/EXtra-foam_FastCCD_SCS.png copying images... [ 87%] _images/XasTimProcessorScene.png copying images... [ 93%] _images/xas-tim-view.png copying images... [100%] _images/correlations.png copying downloadable files... [100%] _static/XHQ_Map.pdf copying static files... done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 2 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2021-11-11T13:24:54.200472Z, end-time: 2021-11-11T13:24:57.568568Z, duration: 3, exit-code: 0 python /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/bin/sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading intersphinx inventory from https://docs.python.org/objects.inv... intersphinx inventory has moved: https://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 17 added, 0 changed, 0 removed reading sources... [ 5%] candidate-frame-lists reading sources... [ 11%] changes reading sources... [ 17%] citations reading sources... [ 23%] computing reading sources... [ 29%] datafiles reading sources... [ 35%] hdf5_virtualise/hdf5_virtualise reading sources... [ 41%] index reading sources... [ 47%] jhub reading sources... [ 52%] karabo_bridge/cpp-client reading sources... [ 58%] karabo_bridge/protocol reading sources... [ 64%] karabo_bridge/py-client reading sources... [ 70%] karabo_bridge/recorder reading sources... [ 76%] online reading sources... [ 82%] overview reading sources... [ 88%] resources reading sources... [ 94%] software reading sources... [100%] usecases /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages/karabo_bridge/client.py:docstring of karabo_bridge.Client:21: WARNING: Unknown interpreted text role "method". /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages/karabo_bridge/client.py:docstring of karabo_bridge.Client:26: WARNING: Unexpected indentation. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... overview online datafiles hdf5_virtualise/hdf5_virtualise computing jhub software karabo_bridge/py-client karabo_bridge/cpp-client karabo_bridge/recorder karabo_bridge/protocol usecases resources citations changes writing... done writing additional files... copying images... [ 6%] _images/trains_pulses.png copying images... [ 12%] _images/lpd2tile_gui.png copying images... [ 18%] _images/h5.png copying images... [ 25%] _images/Level1_workstations.jpg copying images... [ 31%] _images/Level2_workstations.jpg copying images... [ 37%] _images/max-jhub-partitions.png copying images... [ 43%] _images/max-jupyter_manual_token.png copying images... [ 50%] _images/EXtra-foam-LPD_azimuthal_integration.png copying images... [ 56%] _images/EXtra-foam-ImageTool.png copying images... [ 62%] _images/EXtra-foam-ROI.png copying images... [ 68%] _images/geoAssembler.png copying images... [ 75%] _images/FastCCDCorrelatorScene.png copying images... [ 81%] _images/EXtra-foam_FastCCD_SCS.png copying images... [ 87%] _images/XasTimProcessorScene.png copying images... [ 93%] _images/xas-tim-view.png copying images... [100%] _images/correlations.png copying downloadable files... [100%] _static/XHQ_Map.pdf copying static files... done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 2 warnings. The HTML page is in _build/localmedia. [rtd-command-info] start-time: 2021-11-11T13:24:57.784886Z, end-time: 2021-11-11T13:25:00.807062Z, duration: 3, exit-code: 0 python /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/bin/sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading intersphinx inventory from https://docs.python.org/objects.inv... intersphinx inventory has moved: https://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 17 added, 0 changed, 0 removed reading sources... [ 5%] candidate-frame-lists reading sources... [ 11%] changes reading sources... [ 17%] citations reading sources... [ 23%] computing reading sources... [ 29%] datafiles reading sources... [ 35%] hdf5_virtualise/hdf5_virtualise reading sources... [ 41%] index reading sources... [ 47%] jhub reading sources... [ 52%] karabo_bridge/cpp-client reading sources... [ 58%] karabo_bridge/protocol reading sources... [ 64%] karabo_bridge/py-client reading sources... [ 70%] karabo_bridge/recorder reading sources... [ 76%] online reading sources... [ 82%] overview reading sources... [ 88%] resources reading sources... [ 94%] software reading sources... [100%] usecases looking for now-outdated files... /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages/karabo_bridge/client.py:docstring of karabo_bridge.Client:21: WARNING: Unknown interpreted text role "method". /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages/karabo_bridge/client.py:docstring of karabo_bridge.Client:26: WARNING: Unexpected indentation. none found pickling environment... done checking consistency... done processing Userdocumentation.tex...index overview online datafiles hdf5_virtualise/hdf5_virtualise computing jhub software karabo_bridge/py-client karabo_bridge/cpp-client karabo_bridge/recorder karabo_bridge/protocol usecases resources citations changes resolving references... writing... done copying images... [ 6%] _images/trains_pulses.png copying images... [ 12%] _images/lpd2tile_gui.png copying images... [ 18%] _images/h5.png copying images... [ 25%] _images/Level1_workstations.jpg copying images... [ 31%] _images/Level2_workstations.jpg copying images... [ 37%] _images/max-jhub-partitions.png copying images... [ 43%] _images/max-jupyter_manual_token.png copying images... [ 50%] _images/EXtra-foam-LPD_azimuthal_integration.png copying images... [ 56%] _images/EXtra-foam-ImageTool.png copying images... [ 62%] _images/EXtra-foam-ROI.png copying images... [ 68%] _images/geoAssembler.png copying images... [ 75%] _images/FastCCDCorrelatorScene.png copying images... [ 81%] _images/EXtra-foam_FastCCD_SCS.png copying images... [ 87%] _images/XasTimProcessorScene.png copying images... [ 93%] _images/xas-tim-view.png copying images... [100%] _images/correlations.png copying TeX support files... done build succeeded, 2 warnings. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2021-11-11T13:25:04.000434Z, end-time: 2021-11-11T13:25:04.092836Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2021-11-11T13:25:04.231338Z, end-time: 2021-11-11T13:25:29.917398Z, duration: 25, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=data-analysis-user-documentation -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="data-analysis-user-documentation" "Userdocumentation.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Userdocumentation.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb> Output written on data-analysis-user-documentation.pdf (75 pages, 3876041 bytes ). Transcript written on data-analysis-user-documentation.log. Latexmk: Index file 'data-analysis-user-documentation.idx' was written Latexmk: Missing input file: 'data-analysis-user-documentation.ind' from line 'No file data-analysis-user-documentation.ind.' Latexmk: References changed. Latexmk: References changed. 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Latexmk: Index file 'data-analysis-user-documentation.idx' was written Latexmk: References changed. Latexmk: Log file says output to 'data-analysis-user-documentation.pdf' Latexmk: Log file says output to 'data-analysis-user-documentation.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'data-analysis-user-documentation.aux' 'data-analysis-user-documentation.out' 'data-analysis-user-documentation.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="data-analysis-user-documentation" "Userdocumentation.tex"' ------------ === european-xfel-logo_cmyk.eps -> european-xfel-logo_cmyk-eps-converted-to.pdf === european-xfel-logo_cmyk.eps -> european-xfel-logo_cmyk-eps-converted-to.pdf Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Userdocumentation.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[21] [22] [23] [24 <./Level1_workstations.jpg>] [25 <./Level2_workstations.jpg> ] [26] [27] [28] [29] [30] Chapter 5. Overfull \hbox (189.8773pt too wide) in paragraph at lines 2376--2377 | []| [31] [32 <./max-jhub-partitions.png>] [33] [34 <./max-jupyter_manual_token.png> ] [35] Underfull \hbox (badness 10000) in paragraph at lines 2712--2713 []\T1/pcr/m/n/10 ssh -L 8000:localhost:8000 exflgateway -t ssh -L 8000:localhos t:8000 [36] [37] [38] Chapter 6. Underfull \hbox (badness 10000) in paragraph at lines 2829--2829 []\T1/ptm/m/it/10 endpoint\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sock='REQ'\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 ser='msgpack'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 time-out=N one\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con- [39] [40] [41] [42] [43] [44] Overfull \hbox (663.22504pt too wide) in paragraph at lines 3280--3281 [] LaTeX Warning: Float too large for page by 198.75769pt on input line 3281. Overfull \hbox (131.77739pt too wide) in paragraph at lines 3286--3287 [] Overfull \hbox (658.02417pt too wide) in paragraph at lines 3292--3293 [] LaTeX Warning: Float too large for page by 143.78525pt on input line 3293. [45] [46 <./EXtra-foam-LPD_azimuthal_integration.png>] [47 <./EXtra-foam-ImageT ool.png>] [48 <./EXtra-foam-ROI.png>] Overfull \hbox (675.36504pt too wide) in paragraph at lines 3394--3395 [] LaTeX Warning: Float too large for page by 22.0137pt on input line 3395. [49] [50 <./geoAssembler.png>] [51] [52] Chapter 7. Overfull \hbox (310.90964pt too wide) in paragraph at lines 3593--3594 [] [53] [54 <./FastCCDCorrelatorScene.png>] Overfull \hbox (979.46448pt too wide) in paragraph at lines 3650--3651 [] LaTeX Warning: Float too large for page by 349.32288pt on input line 3651. Overfull \hbox (645.18027pt too wide) in paragraph at lines 3681--3682 [] LaTeX Warning: Float too large for page by 42.15579pt on input line 3682. Overfull \hbox (971.90674pt too wide) in paragraph at lines 3710--3711 [] LaTeX Warning: Float too large for page by 167.87518pt on input line 3711. Overfull \hbox (444.92853pt too wide) in paragraph at lines 3725--3726 [] LaTeX Warning: Float too large for page by 49.71239pt on input line 3726. [55] [56 <./EXtra-foam_FastCCD_SCS.png>] [57 <./XasTimProcessorScene.png>] [58 <./xas-tim-view.png>] [59 <./correlations.png (PNG copy)>] [60] Chapter 8. [61] [62] Chapter 9. [63] Overfull \vbox (132.9832pt too high) detected at line 3975 [64] [65] [66] Chapter 10. [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 4062--4065 []\T1/ptm/m/n/10 Fangohr, Hans, et al. ^^PData Anal-y-sis Sup-port in Karabo at Eu-ro-pean XFEL^^Q Underfull \hbox (badness 10000) in paragraph at lines 4062--4065 \T1/ptm/m/n/10 ICALEPCS 2017. Avail-able on-line: [][]$http : / / accelconf . w eb . cern . ch / AccelConf / icalepcs2017 / doi / [69] [70] [71] (./data-analysis-user-documentation.ind [72] Underfull \hbox (badness 10000) in paragraph at lines 38--40 []| \T1/pcr/m/n/10 -g , --geometry Underfull \hbox (badness 10000) in paragraph at lines 41--43 []| \T1/pcr/m/n/10 -l , --level \T1/ptm/m/n/10 , [73]) (./data-analysis-user-documentation.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb> Output written on data-analysis-user-documentation.pdf (77 pages, 3890347 bytes ). Transcript written on data-analysis-user-documentation.log. Latexmk: Index file 'data-analysis-user-documentation.idx' was written Latexmk: Log file says output to 'data-analysis-user-documentation.pdf' Latexmk: Log file says output to 'data-analysis-user-documentation.pdf' === european-xfel-logo_cmyk.eps -> european-xfel-logo_cmyk-eps-converted-to.pdf === european-xfel-logo_cmyk.eps -> european-xfel-logo_cmyk-eps-converted-to.pdf Latexmk: All targets (data-analysis-user-documentation.pdf) are up-to-date [rtd-command-info] start-time: 2021-11-11T13:25:30.107607Z, end-time: 2021-11-11T13:25:30.224153Z, duration: 0, exit-code: 0 mv -f /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/checkouts/latest/source/_build/latex/data-analysis-user-documentation.pdf /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/artifacts/latest/sphinx_pdf/data-analysis-user-documentation.pdf [rtd-command-info] start-time: 2021-11-11T13:25:30.362982Z, end-time: 2021-11-11T13:25:34.009704Z, duration: 3, exit-code: 0 python /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/bin/sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading intersphinx inventory from https://docs.python.org/objects.inv... intersphinx inventory has moved: https://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv building [mo]: targets for 0 po files that are out of date building [epub]: targets for 17 source files that are out of date updating environment: 17 added, 0 changed, 0 removed reading sources... 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[100%] usecases /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages/karabo_bridge/client.py:docstring of karabo_bridge.Client:21: WARNING: Unknown interpreted text role "method". /usr/src/app/checkouts/readthedocs.org/user_builds/data-analysis-user-documentation/envs/latest/lib/python3.7/site-packages/karabo_bridge/client.py:docstring of karabo_bridge.Client:26: WARNING: Unexpected indentation. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 5%] candidate-frame-lists writing output... [ 11%] changes writing output... [ 17%] citations writing output... [ 23%] computing writing output... [ 29%] datafiles writing output... [ 35%] hdf5_virtualise/hdf5_virtualise writing output... [ 41%] index writing output... [ 47%] jhub writing output... [ 52%] karabo_bridge/cpp-client writing output... 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