Read the Docs build information Build id: 10742 Project: pydetlib Version: latest Commit: 827bdcb03e0d6ac7398acb3700c9a041f714d212 Date: 2019-06-12T07:15:53.146011Z State: finished Success: True [rtd-command-info] start-time: 2019-06-12T12:16:08.357000Z, end-time: 2019-06-12T12:16:21.414000Z, duration: 13, exit-code: 0 python3 -mvirtualenv --no-site-packages --no-download /user_builds/pydetlib/envs/latest Using base prefix '/usr' New python executable in /user_builds/pydetlib/envs/latest/bin/python3 Not overwriting existing python script /user_builds/pydetlib/envs/latest/bin/python (you must use /user_builds/pydetlib/envs/latest/bin/python3) Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2019-06-12T12:16:21.476000Z, end-time: 2019-06-12T12:17:00.856000Z, duration: 39, exit-code: 0 python /user_builds/pydetlib/envs/latest/bin/pip install --use-wheel -U --cache-dir /user_builds/pydetlib/.cache/pip sphinx==1.3.5 Pygments==2.1.3 setuptools==20.1.1 docutils==0.12 mkdocs==0.15.0 mock==1.0.1 pillow==2.6.1 git+https://github.com/rtfd/readthedocs-sphinx-ext.git@0.6-alpha#egg=readthedocs-sphinx-ext sphinx-rtd-theme==0.1.9 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.1.1 Collecting sphinx==1.3.5 Using cached https://files.pythonhosted.org/packages/ff/91/45883bc962bda1be7e78039b41cc15e1eb3327ec75679eedd067b5d07bd5/Sphinx-1.3.5-py2.py3-none-any.whl Requirement already up-to-date: Pygments==2.1.3 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Collecting setuptools==20.1.1 Using cached https://files.pythonhosted.org/packages/e8/82/3b5455f74bf9ac0757d09c625b7741e6fc284d7519cffc3babb6c5173cf5/setuptools-20.1.1-py2.py3-none-any.whl Requirement already up-to-date: docutils==0.12 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: mkdocs==0.15.0 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: mock==1.0.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: pillow==2.6.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Collecting readthedocs-sphinx-ext from git+https://github.com/rtfd/readthedocs-sphinx-ext.git@0.6-alpha#egg=readthedocs-sphinx-ext Cloning https://github.com/rtfd/readthedocs-sphinx-ext.git (to 0.6-alpha) to /tmp/pip-build-ti8pqr34/readthedocs-sphinx-ext Requirement already up-to-date: sphinx-rtd-theme==0.1.9 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: commonmark==0.5.4 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: recommonmark==0.1.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: Jinja2>=2.3 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx==1.3.5) Requirement already up-to-date: babel!=2.0,>=1.3 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx==1.3.5) Requirement already up-to-date: snowballstemmer>=1.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx==1.3.5) Requirement already up-to-date: six>=1.4 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx==1.3.5) Requirement already up-to-date: Markdown>=2.3.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: PyYAML>=3.10 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: mkdocs-bootswatch>=0.1.0 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: livereload>=2.3.2 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: mkdocs-bootstrap>=0.1.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: click>=4.0 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: tornado>=4.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: requests in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from readthedocs-sphinx-ext) Requirement already up-to-date: nilsimsa>=0.3.7 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from readthedocs-sphinx-ext) Requirement already up-to-date: MarkupSafe>=0.23 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from Jinja2>=2.3->sphinx==1.3.5) Requirement already up-to-date: pytz>=2015.7 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from babel!=2.0,>=1.3->sphinx==1.3.5) Requirement already up-to-date: backports-abc>=0.4 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from tornado>=4.1->mkdocs==0.15.0) Requirement already up-to-date: chardet<3.1.0,>=3.0.2 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from requests->readthedocs-sphinx-ext) Requirement already up-to-date: certifi>=2017.4.17 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from requests->readthedocs-sphinx-ext) Requirement already up-to-date: urllib3<1.25,>=1.21.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from requests->readthedocs-sphinx-ext) Requirement already up-to-date: idna<2.9,>=2.5 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from requests->readthedocs-sphinx-ext) Installing collected packages: sphinx, setuptools, readthedocs-sphinx-ext Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Found existing installation: setuptools 28.8.0 Uninstalling setuptools-28.8.0: Successfully uninstalled setuptools-28.8.0 Found existing installation: readthedocs-sphinx-ext 0.5.4 Uninstalling readthedocs-sphinx-ext-0.5.4: Successfully uninstalled readthedocs-sphinx-ext-0.5.4 Running setup.py install for readthedocs-sphinx-ext: started Running setup.py install for readthedocs-sphinx-ext: finished with status 'done' Successfully installed readthedocs-sphinx-ext-0.5.4 setuptools-20.1.1 sphinx-1.3.5 You are using pip version 9.0.1, however version 19.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2019-06-12T12:17:00.920000Z, end-time: 2019-06-12T12:17:25.895000Z, duration: 24, exit-code: 0 python /user_builds/pydetlib/envs/latest/bin/pip install --exists-action=w --cache-dir /user_builds/pydetlib/.cache/pip -rlib/docs/requirements.txt Collecting sphinx>=1.4.5 (from -r lib/docs/requirements.txt (line 1)) Using cached https://files.pythonhosted.org/packages/7d/66/a4af242b4348b729b9d46ce5db23943ce9bca7da9bbe2ece60dc27f26420/Sphinx-1.8.5-py2.py3-none-any.whl Requirement already satisfied: ipython in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 2)) Requirement already satisfied: ipyparallel in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 3)) Requirement already satisfied: jupyter in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 4)) Requirement already satisfied: matplotlib>=2.0.0 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 5)) Requirement already satisfied: numpy>=1.12 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 6)) Requirement already satisfied: tornado>=4.3 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 7)) Requirement already satisfied: pandas==0.18 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 8)) Requirement already satisfied: seaborn>=0.7.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 9)) Requirement already satisfied: brewer2mpl>=1.4 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 10)) Requirement already satisfied: dill>=0.2.5 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 11)) Requirement already satisfied: sphinxcontrib-napoleon>=0.5.2 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 12)) Requirement already satisfied: pypandoc in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 13)) Requirement already satisfied: snowballstemmer>=1.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx>=1.4.5->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: imagesize in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx>=1.4.5->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: requests>=2.0.0 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx>=1.4.5->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: docutils>=0.11 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx>=1.4.5->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: babel!=2.0,>=1.3 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx>=1.4.5->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: alabaster<0.8,>=0.7 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx>=1.4.5->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: six>=1.5 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx>=1.4.5->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: setuptools in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx>=1.4.5->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: packaging in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx>=1.4.5->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: sphinxcontrib-websupport in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx>=1.4.5->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: Pygments>=2.0 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx>=1.4.5->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: Jinja2>=2.3 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx>=1.4.5->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: typing; python_version < "3.5" in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx>=1.4.5->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: prompt-toolkit<2.0.0,>=1.0.4 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipython->-r lib/docs/requirements.txt (line 2)) Requirement already satisfied: decorator in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipython->-r lib/docs/requirements.txt (line 2)) Requirement already satisfied: pexpect; sys_platform != "win32" in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipython->-r lib/docs/requirements.txt (line 2)) Requirement already satisfied: pickleshare in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipython->-r lib/docs/requirements.txt (line 2)) Requirement already satisfied: traitlets>=4.2 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipython->-r lib/docs/requirements.txt (line 2)) Requirement already satisfied: simplegeneric>0.8 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipython->-r lib/docs/requirements.txt (line 2)) Requirement already satisfied: ipython-genutils in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipyparallel->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: jupyter-client in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipyparallel->-r lib/docs/requirements.txt 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tornado>=4.3->-r lib/docs/requirements.txt (line 7)) Requirement already satisfied: scipy in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from seaborn>=0.7.1->-r lib/docs/requirements.txt (line 9)) Requirement already satisfied: pockets>=0.3 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinxcontrib-napoleon>=0.5.2->-r lib/docs/requirements.txt (line 12)) Requirement already satisfied: pip>=8.1.0 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from pypandoc->-r lib/docs/requirements.txt (line 13)) Requirement already satisfied: wheel>=0.25.0 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from pypandoc->-r lib/docs/requirements.txt (line 13)) Requirement already satisfied: urllib3<1.25,>=1.21.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from requests>=2.0.0->sphinx>=1.4.5->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: chardet<3.1.0,>=3.0.2 in 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lib/docs/requirements.txt (line 4)) Requirement already satisfied: html5lib!=0.9999,!=0.99999,<0.99999999,>=0.999 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from bleach->nbconvert->jupyter->-r lib/docs/requirements.txt (line 4)) Installing collected packages: sphinx Found existing installation: Sphinx 1.3.5 Uninstalling Sphinx-1.3.5: Successfully uninstalled Sphinx-1.3.5 Successfully installed sphinx-1.8.5 You are using pip version 9.0.1, however version 19.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2019-06-12T12:17:28.100000Z, end-time: 2019-06-12T12:17:28.129000Z, duration: 0, exit-code: 0 cat conf.py # -*- coding: utf-8 -*- # # src documentation build configuration file, created by # sphinx-quickstart on Tue Sep 30 09:45:40 2014. # # 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. import subprocess import sys import os sys.path.append(os.path.abspath("../src/")) p = subprocess.Popen(["./makeAllDocs.sh"]) p.communicate() from unittest.mock import MagicMock class Mock(MagicMock): @classmethod def __getattr__(cls, name): return Mock() MOCK_MODULES = ['pycuda', 'pycuda.driver', 'pycuda.compiler', 'pycuda.autoinit', 'h5py', 'brewer2mpl', 'matplotlib', 'matplotlib.pyplot', 'matplotlib.colors', 'matplotlib.axes', 'scipy', 'scipy.stats', 'matplotlib.patches', 'scipy.ndimage', 'scipy.ndimage.filters', 'iminuit', 'mpl_toolkits', 'mpl_toolkits.mplot3d', 'mpl_toolkits.axes_grid1', 'mpl_toolkits.axes_grid1.inset_locator', 'pandoc', 'pypandoc'] sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES) # 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. #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.viewcode', 'sphinxcontrib.napoleon', 'sphinx.ext.mathjax', 'sphinx.ext.intersphinx', 'sphinx.ext.autosectionlabel', ] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix of source filenames. 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 = u'XFEL Detector Tools' copyright = u'2014, European X-ray Free Electron Laser Facility GmbH' # 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 = '' # The full version, including alpha/beta/rc tags. release = '' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #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. exclude_patterns = ['_build'] # 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 # -- 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. If None, it defaults to # " v documentation". #html_title = None # 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 (within the static path) to use as 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 '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. #html_last_updated_fmt = '%b %d, %Y' # 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 # Output file base name for HTML help builder. htmlhelp_basename = 'srcdoc' # -- 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': '', } # 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 = [ ('index', 'src.tex', u'XFEL Detector Tools', u'Steffen Hauf', 'manual'), ] # 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 = [] # 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 = [ ('index', 'src', u'XFEL Detector Tools', [u'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 = [ ('index', 'src', u'XFEL Detector Tools', u'Author', 'src', '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 # -- Options for Epub output ---------------------------------------------- # Bibliographic Dublin Core info. epub_title = u'XFEL Detector Tools' epub_author = u'Steffen Hauf' epub_publisher = u'European X-ray Free Electron Laser GmbH' epub_copyright = u'2014, Steffen Hauf' # The basename for the epub file. It defaults to the project name. #epub_basename = u'src' # The HTML theme for the epub output. Since the default themes are not optimized # for small screen space, using the same theme for HTML and epub output is # usually not wise. This defaults to 'epub', a theme designed to save visual # space. #epub_theme = 'epub' # The language of the text. It defaults to the language option # or en if the language is not set. #epub_language = '' # The scheme of the identifier. Typical schemes are ISBN or URL. #epub_scheme = '' # The unique identifier of the text. This can be a ISBN number # or the project homepage. #epub_identifier = '' # A unique identification for the text. #epub_uid = '' # A tuple containing the cover image and cover page html template filenames. #epub_cover = () # A sequence of (type, uri, title) tuples for the guide element of content.opf. #epub_guide = () # HTML files that should be inserted before the pages created by sphinx. # The format is a list of tuples containing the path and title. #epub_pre_files = [] # HTML files shat should be inserted after the pages created by sphinx. # The format is a list of tuples containing the path and title. #epub_post_files = [] # A list of files that should not be packed into the epub file. epub_exclude_files = ['search.html'] # The depth of the table of contents in toc.ncx. #epub_tocdepth = 3 # Allow duplicate toc entries. #epub_tocdup = True # Choose between 'default' and 'includehidden'. #epub_tocscope = 'default' # Fix unsupported image types using the PIL. #epub_fix_images = False # Scale large images. #epub_max_image_width = 0 # How to display URL addresses: 'footnote', 'no', or 'inline'. #epub_show_urls = 'inline' # If false, no index is generated. #epub_use_index = True autoclass_content = 'both' napoleon_google_docstring = True napoleon_numpy_docstring = True napoleon_include_private_with_doc = True napoleon_include_special_with_doc = False napoleon_use_admonition_for_examples = False napoleon_use_admonition_for_notes = False napoleon_use_admonition_for_references = False napoleon_use_ivar = False napoleon_use_param = True napoleon_use_rtype = True intersphinx_mapping = {'python': ('http://docs.python.org/2.7', None), 'numpy': ('http://docs.scipy.org/doc/numpy/', None), 'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None), 'matplotlib': ('http://matplotlib.sourceforge.net/', None)} ########################################################################### # 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/"), ("stable", "/en/stable/"), ], 'downloads': [ ("pdf", "//exflrtd.desy.de/projects/pydetlib/downloads/pdf/latest/"), ("htmlzip", "//exflrtd.desy.de/projects/pydetlib/downloads/htmlzip/latest/"), ("epub", "//exflrtd.desy.de/projects/pydetlib/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'pydetlib', 'name': u'PyDetLib', 'rtd_language': u'en', 'canonical_url': 'http://exflrtd.desy.de/docs/pydetlib/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/doc/', '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': '827bdcb0', } 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: 2019-06-12T12:17:29.595000Z, end-time: 2019-06-12T12:18:29.623000Z, duration: 60, exit-code: 0 python /user_builds/pydetlib/envs/latest/bin/sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 mkdir: cannot create directory ‘_notebooks’: File exists [NbConvertApp] Converting notebook ../examples/gainMapStability.ipynb to rst [NbConvertApp] Support files will be in gainMapStability_files/ [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Writing 48113 bytes to ./gainMapStability.rst [NbConvertApp] Converting notebook ../examples/DataGeneratorExample.ipynb to rst [NbConvertApp] Support files will be in DataGeneratorExample_files/ [NbConvertApp] Making directory ./DataGeneratorExample_files [NbConvertApp] Writing 1984559 bytes to ./DataGeneratorExample.rst [NbConvertApp] Converting notebook ../examples/calculatorCreation.ipynb to rst [NbConvertApp] Writing 15602 bytes to ./calculatorCreation.rst [NbConvertApp] Converting notebook ../examples/PlotExamples.ipynb to rst [NbConvertApp] Support files will be in PlotExamples_files/ [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Writing 23677 bytes to ./PlotExamples.rst Creating file ./api/XFELDetAna.rst. Creating file ./api/XFELDetAna.algorithms.rst. Creating file ./api/XFELDetAna.algorithms.cython.rst. Creating file ./api/XFELDetAna.algorithms.gpu.rst. Creating file ./api/XFELDetAna.algorithms.gpu.kernels.rst. Creating file ./api/XFELDetAna.algorithms.tests.rst. Creating file ./api/XFELDetAna.core.rst. Creating file ./api/XFELDetAna.detectors.rst. Creating file ./api/XFELDetAna.detectors.agipd.rst. Creating file ./api/XFELDetAna.detectors.agipd.dyrange_algorithms.rst. Creating file ./api/XFELDetAna.detectors.agipd.gpu.rst. Creating file ./api/XFELDetAna.detectors.agipd.gpu.kernels.rst. Creating file ./api/XFELDetAna.detectors.agipd.tests.rst. Creating file ./api/XFELDetAna.detectors.dssc.rst. Creating file ./api/XFELDetAna.detectors.edf_data.rst. Creating file ./api/XFELDetAna.detectors.epix.rst. Creating file ./api/XFELDetAna.detectors.fastccd.rst. Creating file ./api/XFELDetAna.detectors.generator.rst. Creating file ./api/XFELDetAna.detectors.jungfrau.rst. Creating file ./api/XFELDetAna.detectors.lpd.rst. Creating file ./api/XFELDetAna.detectors.pnccd.rst. Creating file ./api/XFELDetAna.plotting.rst. Creating file ./api/XFELDetAna.util.rst. Creating file ./api/modules.rst. loading translations [en]... done making output directory... loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 33 source files that are out of date updating environment: [] 0 added, 28 changed, 0 removed reading sources... [ 3%] _notebooks/DataGeneratorExample reading sources... [ 7%] _notebooks/PlotExamples reading sources... [ 10%] _notebooks/calculatorCreation reading sources... [ 14%] _notebooks/gainMapStability reading sources... [ 17%] _notebooks/index reading sources... [ 21%] api/XFELDetAna Plotting not available No module named 'matplotlib.collections' reading sources... [ 25%] api/XFELDetAna.algorithms reading sources... [ 28%] api/XFELDetAna.algorithms.gpu reading sources... [ 32%] api/XFELDetAna.algorithms.gpu.kernels reading sources... [ 35%] api/XFELDetAna.algorithms.tests reading sources... [ 39%] api/XFELDetAna.core reading sources... [ 42%] api/XFELDetAna.detectors reading sources... [ 46%] api/XFELDetAna.detectors.agipd reading sources... [ 50%] api/XFELDetAna.detectors.agipd.dyrange_algorithms reading sources... [ 53%] api/XFELDetAna.detectors.agipd.gpu reading sources... [ 57%] api/XFELDetAna.detectors.agipd.gpu.kernels reading sources... [ 60%] api/XFELDetAna.detectors.agipd.tests reading sources... [ 64%] api/XFELDetAna.detectors.dssc reading sources... [ 67%] api/XFELDetAna.detectors.edf_data reading sources... [ 71%] api/XFELDetAna.detectors.epix reading sources... [ 75%] api/XFELDetAna.detectors.fastccd reading sources... [ 78%] api/XFELDetAna.detectors.generator reading sources... [ 82%] api/XFELDetAna.detectors.jungfrau reading sources... [ 85%] api/XFELDetAna.detectors.lpd reading sources... [ 89%] api/XFELDetAna.detectors.pnccd reading sources... [ 92%] api/XFELDetAna.plotting reading sources... [ 96%] api/XFELDetAna.util reading sources... [100%] api/modules /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages/sphinx/websupport/__init__.py:25: RemovedInSphinx20Warning: sphinx.websupport module is now provided as sphinxcontrib-websupport. sphinx.websupport will be removed at Sphinx-2.0. Please use the package instead. RemovedInSphinx20Warning) /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/DataGeneratorExample.rst:4: WARNING: duplicate label example usage with a random data generator, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/DataGeneratorExample.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:13: WARNING: duplicate label using plotting tools, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:20: WARNING: duplicate label simple plots, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:53: WARNING: duplicate label draw and linestyles, coloring things, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:144: WARNING: duplicate label bar plots, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:191: WARNING: duplicate label defining axis ranges and logarithmic rendering, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:227: WARNING: duplicate label combining multiple data series into a single plot, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:258: WARNING: duplicate label stacked bar plots and adding a legend, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:318: WARNING: duplicate label adding uncertainties, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:354: WARNING: duplicate label systematic uncertainties, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:415: WARNING: duplicate label error bands, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:503: WARNING: duplicate label adding a second plot panel (for residuals), other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:563: WARNING: duplicate label adding an inset, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:618: WARNING: duplicate label usage with histplot, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:666: WARNING: duplicate label heatmaps, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:18: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:24: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:44: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:48: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:54: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:4: WARNING: duplicate label pdf-weighted gain map calculation, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/gainMapStability.rst WARNING: autodoc: failed to import module 'xfelpycaltools' from module 'XFELDetAna'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:16: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:45: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:7: WARNING: toctree contains reference to nonexisting document 'api/XFELDetAna.algorithms.cython' WARNING: autodoc: failed to import module 'characterize_cti' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'characterize_noise' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'characterize_relgain' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_cti' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_offset' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_relgain' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correction' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator:38: WARNING: Unknown interpreted text role "method". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator.get:26: WARNING: Definition list ends without a blank line; unexpected unindent. WARNING: autodoc: failed to import module 'statistics' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:14: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:88: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/gpu/correct_common_mode.py:docstring of XFELDetAna.algorithms.gpu.correct_common_mode._gpuCommonMode:11: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:12: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:56: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst:49: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst WARNING: autodoc: failed to import module 'test_characterize_cti' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_characterize_noise' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_characterize_offset' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_characterize_rel_gain' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_characterize_split_events' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_common_mode' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_cti' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_correct_offset' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_relgain' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_statistics' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_unitary' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'testing_base' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst:69: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/core/reader.py:docstring of XFELDetAna.core.reader.ChunkReader.readChunks:8: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst:34: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst:20: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst WARNING: autodoc: failed to import module 'characterize_dynrange' from module 'XFELDetAna.detectors.agipd'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'threshold_gain' from module 'XFELDetAna.detectors.agipd'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:14: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:38: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:5: WARNING: Unexpected section title or transition. ____________ /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:6: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:6: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:7: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:8: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:15: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:18: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:20: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:20: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:20: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:21: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:22: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:29: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:5: WARNING: Unexpected section title or transition. ____________ /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:6: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:6: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:7: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:8: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:15: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:18: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:20: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:20: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:20: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:21: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:22: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:29: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:7: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:11: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:21: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:21: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:25: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:25: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:7: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:11: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:21: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:21: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:25: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:25: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.dyrange_algorithms.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.dyrange_algorithms.rst:24: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.rst:12: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.dyrange_algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.rst:21: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.dyrange_algorithms.rst 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Use sphinx.util.logging instead. app.info('done') [rtd-command-info] start-time: 2019-06-12T12:18:47.149000Z, end-time: 2019-06-12T12:19:42.332000Z, duration: 55, exit-code: 0 python /user_builds/pydetlib/envs/latest/bin/sphinx-build -T -b json -d _build/doctrees-json -D language=en . _build/json Running Sphinx v1.8.5 mkdir: cannot create directory ‘_notebooks’: File exists [NbConvertApp] Converting notebook ../examples/gainMapStability.ipynb to rst [NbConvertApp] Support files will be in gainMapStability_files/ [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Writing 48113 bytes to ./gainMapStability.rst [NbConvertApp] Converting notebook ../examples/DataGeneratorExample.ipynb to rst [NbConvertApp] Support files will be in DataGeneratorExample_files/ [NbConvertApp] Making directory ./DataGeneratorExample_files [NbConvertApp] Writing 1984559 bytes to ./DataGeneratorExample.rst [NbConvertApp] Converting notebook ../examples/calculatorCreation.ipynb to rst [NbConvertApp] Writing 15602 bytes to ./calculatorCreation.rst [NbConvertApp] Converting notebook ../examples/PlotExamples.ipynb to rst [NbConvertApp] Support files will be in PlotExamples_files/ [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Writing 23677 bytes to ./PlotExamples.rst Creating file ./api/XFELDetAna.rst. Creating file ./api/XFELDetAna.algorithms.rst. Creating file ./api/XFELDetAna.algorithms.cython.rst. Creating file ./api/XFELDetAna.algorithms.gpu.rst. Creating file ./api/XFELDetAna.algorithms.gpu.kernels.rst. Creating file ./api/XFELDetAna.algorithms.tests.rst. Creating file ./api/XFELDetAna.core.rst. Creating file ./api/XFELDetAna.detectors.rst. Creating file ./api/XFELDetAna.detectors.agipd.rst. Creating file ./api/XFELDetAna.detectors.agipd.dyrange_algorithms.rst. Creating file ./api/XFELDetAna.detectors.agipd.gpu.rst. Creating file ./api/XFELDetAna.detectors.agipd.gpu.kernels.rst. Creating file ./api/XFELDetAna.detectors.agipd.tests.rst. Creating file ./api/XFELDetAna.detectors.dssc.rst. Creating file ./api/XFELDetAna.detectors.edf_data.rst. Creating file ./api/XFELDetAna.detectors.epix.rst. Creating file ./api/XFELDetAna.detectors.fastccd.rst. Creating file ./api/XFELDetAna.detectors.generator.rst. Creating file ./api/XFELDetAna.detectors.jungfrau.rst. Creating file ./api/XFELDetAna.detectors.lpd.rst. Creating file ./api/XFELDetAna.detectors.pnccd.rst. Creating file ./api/XFELDetAna.plotting.rst. Creating file ./api/XFELDetAna.util.rst. Creating file ./api/modules.rst. loading translations [en]... done making output directory... loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [json]: targets for 33 source files that are out of date updating environment: [] 0 added, 28 changed, 0 removed reading sources... [ 3%] _notebooks/DataGeneratorExample reading sources... [ 7%] _notebooks/PlotExamples reading sources... [ 10%] _notebooks/calculatorCreation reading sources... [ 14%] _notebooks/gainMapStability reading sources... [ 17%] _notebooks/index reading sources... [ 21%] api/XFELDetAna Plotting not available No module named 'matplotlib.collections' reading sources... [ 25%] api/XFELDetAna.algorithms reading sources... [ 28%] api/XFELDetAna.algorithms.gpu reading sources... [ 32%] api/XFELDetAna.algorithms.gpu.kernels reading sources... [ 35%] api/XFELDetAna.algorithms.tests reading sources... [ 39%] api/XFELDetAna.core reading sources... [ 42%] api/XFELDetAna.detectors reading sources... [ 46%] api/XFELDetAna.detectors.agipd reading sources... [ 50%] api/XFELDetAna.detectors.agipd.dyrange_algorithms reading sources... [ 53%] api/XFELDetAna.detectors.agipd.gpu reading sources... [ 57%] api/XFELDetAna.detectors.agipd.gpu.kernels reading sources... [ 60%] api/XFELDetAna.detectors.agipd.tests reading sources... [ 64%] api/XFELDetAna.detectors.dssc reading sources... [ 67%] api/XFELDetAna.detectors.edf_data reading sources... [ 71%] api/XFELDetAna.detectors.epix reading sources... [ 75%] api/XFELDetAna.detectors.fastccd reading sources... [ 78%] api/XFELDetAna.detectors.generator reading sources... [ 82%] api/XFELDetAna.detectors.jungfrau reading sources... [ 85%] api/XFELDetAna.detectors.lpd reading sources... 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RemovedInSphinx20Warning) /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/DataGeneratorExample.rst:4: WARNING: duplicate label example usage with a random data generator, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/DataGeneratorExample.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:13: WARNING: duplicate label using plotting tools, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:20: WARNING: duplicate label simple plots, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:53: WARNING: duplicate label draw and linestyles, coloring things, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:144: WARNING: duplicate label bar plots, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:191: WARNING: duplicate label defining axis ranges and logarithmic rendering, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:227: WARNING: duplicate label combining multiple data series into a single plot, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:258: WARNING: duplicate label stacked bar plots and adding a legend, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:318: WARNING: duplicate label adding uncertainties, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:354: WARNING: duplicate label systematic uncertainties, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:415: WARNING: duplicate label error bands, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:503: WARNING: duplicate label adding a second plot panel (for residuals), other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:563: WARNING: duplicate label adding an inset, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:618: WARNING: duplicate label usage with histplot, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:666: WARNING: duplicate label heatmaps, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:18: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:24: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:44: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:48: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:54: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:4: WARNING: duplicate label pdf-weighted gain map calculation, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/gainMapStability.rst WARNING: autodoc: failed to import module 'xfelpycaltools' from module 'XFELDetAna'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:16: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:45: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:7: WARNING: toctree contains reference to nonexisting document 'api/XFELDetAna.algorithms.cython' WARNING: autodoc: failed to import module 'characterize_cti' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'characterize_noise' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'characterize_relgain' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_cti' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_offset' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_relgain' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correction' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator:38: WARNING: Unknown interpreted text role "method". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator.get:26: WARNING: Definition list ends without a blank line; unexpected unindent. WARNING: autodoc: failed to import module 'statistics' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:14: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:88: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/gpu/correct_common_mode.py:docstring of XFELDetAna.algorithms.gpu.correct_common_mode._gpuCommonMode:11: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:12: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:56: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst:49: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst WARNING: autodoc: failed to import module 'test_characterize_cti' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_characterize_noise' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_characterize_offset' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_characterize_rel_gain' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_characterize_split_events' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_common_mode' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_cti' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_correct_offset' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_relgain' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_statistics' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_unitary' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'testing_base' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst:69: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/core/reader.py:docstring of XFELDetAna.core.reader.ChunkReader.readChunks:8: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst:34: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst:20: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst WARNING: autodoc: failed to import module 'characterize_dynrange' from module 'XFELDetAna.detectors.agipd'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'threshold_gain' from module 'XFELDetAna.detectors.agipd'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:14: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:38: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:5: WARNING: Unexpected section title or transition. ____________ /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:6: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:6: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:7: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:8: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:15: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:18: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of 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XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:6: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:6: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:7: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:8: WARNING: Block quote ends without a blank line; unexpected 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/user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:7: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:11: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:21: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:21: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:25: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:25: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.dyrange_algorithms.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst 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unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile:31: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile:44: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile:50: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile.EdfFile.GetData:4: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile.EdfFile.GetData:10: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile.EdfFile.GetData:22: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile.EdfFile.WriteImage:3: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile.EdfFile.WriteImage:5: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile.EdfFile.WriteImage:18: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile.EdfFile.WriteImage:31: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.edf_data.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.dssc.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.edf_data.rst:24: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.dssc.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.epix.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.edf_data.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.epix.rst:14: WARNING: duplicate label module contents, other instance in 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/user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.jungfrau.rst:39: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.generator.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.lpd.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.jungfrau.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.lpd.rst:14: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.jungfrau.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.pnccd.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.lpd.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.pnccd.rst:19: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.lpd.rst WARNING: autodoc: failed to import module 'heatmap' from module 'XFELDetAna.plotting'; the following exception was raised: No module named 'matplotlib.collections' WARNING: autodoc: failed to import module 'multidim' from module 'XFELDetAna.plotting'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.plotting.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.pnccd.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.plotting.rst:34: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.pnccd.rst 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You can now process the JSON files in _build/json. [rtd-command-info] start-time: 2019-06-12T12:19:51.291000Z, end-time: 2019-06-12T12:20:40.331000Z, duration: 49, exit-code: 0 python /user_builds/pydetlib/envs/latest/bin/sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.8.5 mkdir: cannot create directory ‘_notebooks’: File exists [NbConvertApp] Converting notebook ../examples/gainMapStability.ipynb to rst [NbConvertApp] Support files will be in gainMapStability_files/ [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Writing 48113 bytes to ./gainMapStability.rst [NbConvertApp] Converting notebook ../examples/DataGeneratorExample.ipynb to rst [NbConvertApp] Support files will be in DataGeneratorExample_files/ [NbConvertApp] Making directory ./DataGeneratorExample_files [NbConvertApp] Writing 1984559 bytes to ./DataGeneratorExample.rst [NbConvertApp] Converting notebook ../examples/calculatorCreation.ipynb to rst [NbConvertApp] Writing 15602 bytes to ./calculatorCreation.rst [NbConvertApp] Converting notebook ../examples/PlotExamples.ipynb to rst [NbConvertApp] Support files will be in PlotExamples_files/ [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Writing 23677 bytes to ./PlotExamples.rst Creating file ./api/XFELDetAna.rst. Creating file ./api/XFELDetAna.algorithms.rst. Creating file ./api/XFELDetAna.algorithms.cython.rst. Creating file ./api/XFELDetAna.algorithms.gpu.rst. Creating file ./api/XFELDetAna.algorithms.gpu.kernels.rst. Creating file ./api/XFELDetAna.algorithms.tests.rst. Creating file ./api/XFELDetAna.core.rst. Creating file ./api/XFELDetAna.detectors.rst. Creating file ./api/XFELDetAna.detectors.agipd.rst. Creating file ./api/XFELDetAna.detectors.agipd.dyrange_algorithms.rst. Creating file ./api/XFELDetAna.detectors.agipd.gpu.rst. Creating file ./api/XFELDetAna.detectors.agipd.gpu.kernels.rst. Creating file ./api/XFELDetAna.detectors.agipd.tests.rst. Creating file ./api/XFELDetAna.detectors.dssc.rst. Creating file ./api/XFELDetAna.detectors.edf_data.rst. Creating file ./api/XFELDetAna.detectors.epix.rst. Creating file ./api/XFELDetAna.detectors.fastccd.rst. Creating file ./api/XFELDetAna.detectors.generator.rst. Creating file ./api/XFELDetAna.detectors.jungfrau.rst. 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RemovedInSphinx20Warning) /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/DataGeneratorExample.rst:4: WARNING: duplicate label example usage with a random data generator, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/DataGeneratorExample.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:13: WARNING: duplicate label using plotting tools, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:20: WARNING: duplicate label simple plots, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:53: WARNING: duplicate label draw and linestyles, coloring things, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:144: WARNING: duplicate label bar plots, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:191: WARNING: duplicate label defining axis ranges and logarithmic rendering, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:227: WARNING: duplicate label combining multiple data series into a single plot, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:258: WARNING: duplicate label stacked bar plots and adding a legend, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:318: WARNING: duplicate label adding uncertainties, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:354: WARNING: duplicate label systematic uncertainties, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:415: WARNING: duplicate label error bands, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:503: WARNING: duplicate label adding a second plot panel (for residuals), other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:563: WARNING: duplicate label adding an inset, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:618: WARNING: duplicate label usage with histplot, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:666: WARNING: duplicate label heatmaps, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:18: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:24: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:44: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:48: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:54: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:4: WARNING: duplicate label pdf-weighted gain map calculation, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/gainMapStability.rst WARNING: autodoc: failed to import module 'xfelpycaltools' from module 'XFELDetAna'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:16: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:45: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:7: WARNING: toctree contains reference to nonexisting document 'api/XFELDetAna.algorithms.cython' WARNING: autodoc: failed to import module 'characterize_cti' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'characterize_noise' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'characterize_relgain' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_cti' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_offset' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_relgain' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correction' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator:38: WARNING: Unknown interpreted text role "method". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator.get:26: WARNING: Definition list ends without a blank line; unexpected unindent. WARNING: autodoc: failed to import module 'statistics' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:14: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:88: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/gpu/correct_common_mode.py:docstring of XFELDetAna.algorithms.gpu.correct_common_mode._gpuCommonMode:11: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:12: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:56: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst:49: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst WARNING: autodoc: failed to import module 'test_characterize_cti' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_characterize_noise' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_characterize_offset' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_characterize_rel_gain' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_characterize_split_events' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_common_mode' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_cti' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_correct_offset' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_relgain' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_statistics' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_unitary' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'testing_base' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst:69: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/core/reader.py:docstring of XFELDetAna.core.reader.ChunkReader.readChunks:8: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst:34: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst:20: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst WARNING: autodoc: failed to import module 'characterize_dynrange' from module 'XFELDetAna.detectors.agipd'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'threshold_gain' from module 'XFELDetAna.detectors.agipd'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:14: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:38: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:5: WARNING: Unexpected section title or transition. ____________ /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:6: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:6: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:7: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:8: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:15: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:18: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:20: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:20: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:20: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:21: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:22: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:29: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:5: WARNING: Unexpected section title or transition. ____________ /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:6: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:6: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:7: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:8: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:15: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:18: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:20: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:20: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:20: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:21: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:22: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:29: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:7: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:11: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:21: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:21: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:25: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:25: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:7: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:11: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:21: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of 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[rtd-command-info] start-time: 2019-06-12T12:20:42.367000Z, end-time: 2019-06-12T12:21:31.048000Z, duration: 48, exit-code: 0 python /user_builds/pydetlib/envs/latest/bin/sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.8.5 mkdir: cannot create directory ‘_notebooks’: File exists [NbConvertApp] Converting notebook ../examples/gainMapStability.ipynb to rst [NbConvertApp] Support files will be in gainMapStability_files/ [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Writing 48113 bytes to ./gainMapStability.rst [NbConvertApp] Converting notebook ../examples/DataGeneratorExample.ipynb to rst [NbConvertApp] Support files will be in DataGeneratorExample_files/ [NbConvertApp] Making directory ./DataGeneratorExample_files [NbConvertApp] Writing 1984559 bytes to ./DataGeneratorExample.rst [NbConvertApp] Converting notebook ../examples/calculatorCreation.ipynb to rst [NbConvertApp] Writing 15602 bytes to ./calculatorCreation.rst [NbConvertApp] Converting notebook ../examples/PlotExamples.ipynb to rst [NbConvertApp] Support files will be in PlotExamples_files/ [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Writing 23677 bytes to ./PlotExamples.rst Creating file ./api/XFELDetAna.rst. Creating file ./api/XFELDetAna.algorithms.rst. Creating file ./api/XFELDetAna.algorithms.cython.rst. Creating file ./api/XFELDetAna.algorithms.gpu.rst. Creating file ./api/XFELDetAna.algorithms.gpu.kernels.rst. Creating file ./api/XFELDetAna.algorithms.tests.rst. Creating file ./api/XFELDetAna.core.rst. Creating file ./api/XFELDetAna.detectors.rst. Creating file ./api/XFELDetAna.detectors.agipd.rst. Creating file ./api/XFELDetAna.detectors.agipd.dyrange_algorithms.rst. Creating file ./api/XFELDetAna.detectors.agipd.gpu.rst. Creating file ./api/XFELDetAna.detectors.agipd.gpu.kernels.rst. Creating file ./api/XFELDetAna.detectors.agipd.tests.rst. Creating file ./api/XFELDetAna.detectors.dssc.rst. Creating file ./api/XFELDetAna.detectors.edf_data.rst. Creating file ./api/XFELDetAna.detectors.epix.rst. Creating file ./api/XFELDetAna.detectors.fastccd.rst. Creating file ./api/XFELDetAna.detectors.generator.rst. Creating file ./api/XFELDetAna.detectors.jungfrau.rst. Creating file ./api/XFELDetAna.detectors.lpd.rst. Creating file ./api/XFELDetAna.detectors.pnccd.rst. Creating file ./api/XFELDetAna.plotting.rst. Creating file ./api/XFELDetAna.util.rst. Creating file ./api/modules.rst. loading translations [en]... done making output directory... loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: [] 0 added, 28 changed, 0 removed reading sources... [ 3%] _notebooks/DataGeneratorExample reading sources... [ 7%] _notebooks/PlotExamples reading sources... [ 10%] _notebooks/calculatorCreation reading sources... [ 14%] _notebooks/gainMapStability reading sources... [ 17%] _notebooks/index reading sources... [ 21%] api/XFELDetAna Plotting not available No module named 'matplotlib.collections' reading sources... [ 25%] api/XFELDetAna.algorithms reading sources... [ 28%] api/XFELDetAna.algorithms.gpu reading sources... [ 32%] api/XFELDetAna.algorithms.gpu.kernels reading sources... [ 35%] api/XFELDetAna.algorithms.tests reading sources... [ 39%] api/XFELDetAna.core reading sources... [ 42%] api/XFELDetAna.detectors reading sources... [ 46%] api/XFELDetAna.detectors.agipd reading sources... [ 50%] api/XFELDetAna.detectors.agipd.dyrange_algorithms reading sources... [ 53%] api/XFELDetAna.detectors.agipd.gpu reading sources... [ 57%] api/XFELDetAna.detectors.agipd.gpu.kernels reading sources... [ 60%] api/XFELDetAna.detectors.agipd.tests reading sources... [ 64%] api/XFELDetAna.detectors.dssc reading sources... [ 67%] api/XFELDetAna.detectors.edf_data reading sources... [ 71%] api/XFELDetAna.detectors.epix reading sources... [ 75%] api/XFELDetAna.detectors.fastccd reading sources... [ 78%] api/XFELDetAna.detectors.generator reading sources... [ 82%] api/XFELDetAna.detectors.jungfrau reading sources... [ 85%] api/XFELDetAna.detectors.lpd reading sources... [ 89%] api/XFELDetAna.detectors.pnccd reading sources... [ 92%] api/XFELDetAna.plotting reading sources... [ 96%] api/XFELDetAna.util reading sources... [100%] api/modules /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages/sphinx/websupport/__init__.py:25: RemovedInSphinx20Warning: sphinx.websupport module is now provided as sphinxcontrib-websupport. sphinx.websupport will be removed at Sphinx-2.0. Please use the package instead. RemovedInSphinx20Warning) /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/DataGeneratorExample.rst:4: WARNING: duplicate label example usage with a random data generator, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/DataGeneratorExample.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:13: WARNING: duplicate label using plotting tools, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:20: WARNING: duplicate label simple plots, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:53: WARNING: duplicate label draw and linestyles, coloring things, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:144: WARNING: duplicate label bar plots, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:191: WARNING: duplicate label defining axis ranges and logarithmic rendering, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:227: WARNING: duplicate label combining multiple data series into a single plot, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:258: WARNING: duplicate label stacked bar plots and adding a legend, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:318: WARNING: duplicate label adding uncertainties, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:354: WARNING: duplicate label systematic uncertainties, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:415: WARNING: duplicate label error bands, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:503: WARNING: duplicate label adding a second plot panel (for residuals), other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:563: WARNING: duplicate label adding an inset, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:618: WARNING: duplicate label usage with histplot, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:666: WARNING: duplicate label heatmaps, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:18: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:24: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:44: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:48: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:54: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:4: WARNING: duplicate label pdf-weighted gain map calculation, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/gainMapStability.rst WARNING: autodoc: failed to import module 'xfelpycaltools' from module 'XFELDetAna'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:16: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:45: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:7: WARNING: toctree contains reference to nonexisting document 'api/XFELDetAna.algorithms.cython' WARNING: autodoc: failed to import module 'characterize_cti' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'characterize_noise' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'characterize_relgain' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_cti' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_offset' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_relgain' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correction' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator:38: WARNING: Unknown interpreted text role "method". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator.get:26: WARNING: Definition list ends without a blank line; unexpected unindent. WARNING: autodoc: failed to import module 'statistics' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:14: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:88: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/gpu/correct_common_mode.py:docstring of XFELDetAna.algorithms.gpu.correct_common_mode._gpuCommonMode:11: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:12: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:56: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst:49: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst WARNING: autodoc: failed to import module 'test_characterize_cti' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_characterize_noise' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_characterize_offset' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_characterize_rel_gain' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_characterize_split_events' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_common_mode' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_cti' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_correct_offset' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_relgain' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_statistics' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_unitary' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'testing_base' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst:69: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/core/reader.py:docstring of XFELDetAna.core.reader.ChunkReader.readChunks:8: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst:34: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst:20: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst WARNING: autodoc: failed to import module 'characterize_dynrange' from module 'XFELDetAna.detectors.agipd'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'threshold_gain' from module 'XFELDetAna.detectors.agipd'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:14: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:38: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:5: WARNING: Unexpected section title or transition. ____________ /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:6: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:6: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:7: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:8: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:15: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:18: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:20: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:20: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:20: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:21: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:22: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:29: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:5: WARNING: Unexpected section title or transition. ____________ /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of 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/user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile.EdfFile.GetData:22: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile.EdfFile.WriteImage:3: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile.EdfFile.WriteImage:5: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile.EdfFile.WriteImage:18: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of 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WARNING: autodoc: failed to import module 'cluster' from module 'XFELDetAna.util'; the following exception was raised: No module named 'psutil' WARNING: __all__ should be a list of strings, not .wrapped at 0x7f47b9967730> (in module XFELDetAna.util.knumpy) -- ignoring __all__ /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.plotting.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst:34: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.plotting.rst looking for now-outdated files... none found pickling environment... done checking consistency... /user_builds/pydetlib/checkouts/latest/lib/docs/examples/DataGeneratorExample.rst: WARNING: document isn't included in any toctree /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst: 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dType=\T1/ptm/m/n/10 , Overfull \hbox (13.76465pt too wide) in paragraph at lines 3491--3491 \T1/ptm/m/it/10 **kwargs\T1/pcr/m/n/10 ) LaTeX Warning: Hyper reference `api/XFELDetAna.core:XFELDetAna.core.mapcalculat or.MapCalculator' on page 90 undefined on input line 3492. 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paragraph at lines 5843--5843 \T1/ptm/m/it/10 9\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 10\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 11\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 12\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 13\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 14\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 15\T1/ptm/m/n/10 , Overfull \hbox (0.96486pt too wide) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 16])\T1/ptm/m/n/10 , Overfull \hbox (21.05455pt too wide) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , Overfull \hbox (38.44444pt too wide) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , Overfull 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[110] [111] [112] Underfull \hbox (badness 10000) in paragraph at lines 6121--6123 []\T1/ptm/m/n/10 Usually the Underfull \hbox (badness 10000) in paragraph at lines 6161--6169 []\T1/ptm/m/n/10 __init__(self,FileName) Get-N-u-mIm-ages(self) def Get-Data(se lf,Index, Underfull \hbox (badness 10000) in paragraph at lines 6161--6169 \T1/ptm/m/n/10 DataType=^^Q^^P,Pos=None,Size=None): Get-Pixel(self,Index,Positi on) Get-H-eader(self,Index) Get-Static- Overfull \hbox (4.81061pt too wide) in paragraph at lines 6161--6169 \T1/ptm/m/n/10 Header(self,Index) WriteIm-age (self,Header,Data,Append=1,DataTy pe=^^Q^^P,WriteAsUnsigened=0,ByteOrder=^^Q^^P) [113] LaTeX Warning: Hyper reference `api/XFELDetAna.detectors.edf_data:XFELDetAna.de tectors.edf_data.EdfFile.EdfFile' on page 114 undefined on input line 6248. [114] LaTeX Warning: Hyper reference `api/XFELDetAna.detectors.edf_data:XFELDetAna.de tectors.edf_data.EdfFile.EdfFile' on page 115 undefined on input line 6417. 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[119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 7257--7259 []\T1/ptm/m/n/10 Usually the [123] [124] [125] Underfull \hbox (badness 10000) in paragraph at lines 7725--7726 []\T1/pcr/b/n/10 will be passed to the matplotlib fill_between() function. [126] [127] [128] [129] [130] LaTeX Warning: Hyper reference `api/XFELDetAna.util:XFELDetAna.util.knumpy.axis Meaning' on page 131 undefined on input line 8737. [131] [132] [133] LaTeX Warning: Hyper reference `api/XFELDetAna.util:XFELDetAna.util.knumpy.axis Meaning' on page 134 undefined on input line 9273. LaTeX Warning: Hyper reference `api/XFELDetAna.util:XFELDetAna.util.knumpy.axis Meaning' on page 134 undefined on input line 9281. LaTeX Warning: Hyper reference `api/XFELDetAna.util:XFELDetAna.util.knumpy.axis Meaning' on page 134 undefined on input line 9289. [134] [135] [136] [137] [138] LaTeX Warning: Hyper reference `api/XFELDetAna.util:XFELDetAna.util.knumpy.axis Meaning' on page 139 undefined on input line 10323. [139] [140] LaTeX Warning: Hyper reference `api/XFELDetAna.util:XFELDetAna.util.knumpy.axis Meaning' on page 141 undefined on input line 10781. [141] [142] Underfull \hbox (badness 10000) in paragraph at lines 11090--11090 []\T1/ptm/m/it/10 host=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 port=None\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 read-Han- Underfull \hbox (badness 10000) in paragraph at lines 11110--11110 []\T1/ptm/m/it/10 host=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 port=None\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 read-Han- [143] [144] Chapter 5. [145] [146] LaTeX Warning: Reference `api/XFELDetAna:module-XFELDetAna' on page 147 undefin ed on input line 11308. LaTeX Warning: Reference `api/XFELDetAna.algorithms:module-XFELDetAna.algorithm s' on page 147 undefined on input line 11309. 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LaTeX Warning: Reference `api/XFELDetAna.util:module-XFELDetAna.util.pattern_ke rnels' on page 148 undefined on input line 11385. LaTeX Warning: Reference `api/XFELDetAna:module-XFELDetAna.xfelprofiler' on pag e 148 undefined on input line 11386. LaTeX Warning: Reference `api/XFELDetAna:module-XFELDetAna.xfelpyanatools' on p age 148 undefined on input line 11387. LaTeX Warning: Reference `api/XFELDetAna:module-XFELDetAna.xfelreaders' on page 148 undefined on input line 11388. LaTeX Warning: Reference `api/XFELDetAna:module-XFELDetAna.xfelsettings' on pag e 148 undefined on input line 11389. [148] No file src.ind. (./src.aux) Package rerunfilecheck Warning: File `src.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. 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} Output written on src.pdf (152 pages, 2425985 bytes). Transcript written on src.log. [rtd-command-info] start-time: 2019-06-12T12:21:38.088000Z, end-time: 2019-06-12T12:21:38.194000Z, duration: 0, exit-code: 0 makeindex -s python.ist src.idx This is makeindex, version 2.15 [TeX Live 2015/dev] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file src.idx....done (890 entries accepted, 0 rejected). Sorting entries...........done (11345 comparisons). Generating output file src.ind....done (1254 lines written, 0 warnings). Output written in src.ind. Transcript written in src.ilg. [rtd-command-info] start-time: 2019-06-12T12:21:38.253000Z, end-time: 2019-06-12T12:21:45.511000Z, duration: 7, exit-code: 0 pdflatex -interaction=nonstopmode /user_builds/pydetlib/checkouts/latest/doc/_build/latex/src.tex This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2015/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/user_builds/pydetlib/checkouts/latest/doc/_build/latex/src.tex LaTeX2e <2014/05/01> Babel <3.9l> and hyphenation patterns for 2 languages loaded. 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dType=\T1/ptm/m/n/10 , Overfull \hbox (13.76465pt too wide) in paragraph at lines 3491--3491 \T1/ptm/m/it/10 **kwargs\T1/pcr/m/n/10 ) [90] Underfull \hbox (badness 10000) in paragraph at lines 3633--3633 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bins\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3633--3633 \T1/ptm/m/it/10 range\T1/ptm/m/n/10 , \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , [91] Underfull \hbox (badness 5954) in paragraph at lines 3687--3689 []\T1/ptm/m/n/10 complete sen-sor but on a per- [92] [93] [94] Underfull \hbox (badness 10000) in paragraph at lines 4060--4061 []\T1/pcr/b/n/10 function. For any 1-d vector in this list it will be Underfull \hbox (badness 10000) in paragraph at lines 4063--4064 []\T1/pcr/b/n/10 to mask/remove data as is done with the data block. Underfull \hbox (badness 10000) in paragraph at lines 4069--4070 []\T1/pcr/b/n/10 where True denotes remove of an image at this position. Underfull \hbox (badness 10000) in paragraph at lines 4072--4073 []\T1/pcr/b/n/10 indices is given, the evaluation function is NOT evaluated. Underfull \hbox (badness 10000) in paragraph at lines 4093--4093 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fil-l-Value=None\T1/ptm /m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4093--4093 \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dType= for immediate help. ... l.4293 \item {} \begin{description} [97] Underfull \hbox (badness 5711) in paragraph at lines 4331--4334 []\T1/ptm/m/n/10 the iden-ti-fied pat- [98] Underfull \hbox (badness 10000) in paragraph at lines 4485--4485 \T1/ptm/m/it/10 nCells=1, dType=\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4552--4552 []\T1/ptm/m/it/10 offsetmap\T1/ptm/m/n/10 , \T1/ptm/m/it/10 noisemap\T1/ptm/m/n /10 , [99] Underfull \hbox (badness 10000) in paragraph at lines 4661--4661 []\T1/ptm/m/it/10 offsetmap\T1/ptm/m/n/10 , \T1/ptm/m/it/10 noisemap\T1/ptm/m/n /10 , [100] Underfull \hbox (badness 10000) in paragraph at lines 4735--4735 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , \T1/ptm/m/it/10 par-al-lel=Tru e\T1/ptm/m/n/10 , [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 5067--5067 []\T1/ptm/m/it/10 functionsToProfile\T1/ptm/m/n/10 , \T1/ptm/m/it/10 val-uesTo- VaryCpu\T1/ptm/m/n/10 , \T1/ptm/m/it/10 val-uesTo- Underfull \hbox (badness 10000) in paragraph at lines 5067--5067 \T1/ptm/m/it/10 VaryGpu=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 nRe-peats=None\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 val-uesTo-P-re- [103] Underfull \hbox (badness 7081) in paragraph at lines 5079--5079 []\T1/ptm/m/it/10 filename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 read-Fun\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 size\T1/ptm/m/n/10 , \T1/ptm/m/it/10 chunk-Size\T1/ptm/m/n /10 , \T1/ptm/m/it/10 *args\T1/ptm/m/n/10 , Overfull \hbox (131.85474pt too wide) in paragraph at lines 5188--5188 []\T1/ptm/m/it/10 asic, Overfull \hbox (124.35486pt too wide) in paragraph at lines 5188--5188 \T1/ptm/m/it/10 in- Overfull \hbox (145.64474pt too wide) in paragraph at lines 5188--5188 \T1/ptm/m/it/10 put_file, Overfull \hbox (129.35486pt too wide) in paragraph at lines 5188--5188 \T1/ptm/m/it/10 out- Overfull \hbox (172.30466pt too wide) in paragraph at lines 5188--5188 \T1/ptm/m/it/10 put_file_name, Overfull \hbox (181.83458pt too wide) in paragraph at lines 5188--5188 \T1/ptm/m/it/10 max_part=None, Overfull \hbox (173.7644pt too wide) in paragraph at lines 5188--5188 \T1/ptm/m/it/10 col_spec=[0]\T1/pcr/m/n/10 ) [104] [105] Overfull \hbox (101.85474pt too wide) in paragraph at lines 5380--5380 []\T1/ptm/m/it/10 asic, Overfull \hbox (94.35486pt too wide) in paragraph at lines 5380--5380 \T1/ptm/m/it/10 in- Overfull \hbox (115.64474pt too wide) in paragraph at lines 5380--5380 \T1/ptm/m/it/10 put_file, Overfull \hbox (99.35486pt too wide) in paragraph at lines 5380--5380 \T1/ptm/m/it/10 out- Overfull \hbox (142.30466pt too wide) in paragraph at lines 5380--5380 \T1/ptm/m/it/10 put_file_name, Overfull \hbox (151.83458pt too wide) in paragraph at lines 5380--5380 \T1/ptm/m/it/10 max_part=None, Overfull \hbox (140.2644pt too wide) in paragraph at lines 5380--5380 \T1/ptm/m/it/10 col_spec=[0], Overfull \hbox (105.2549pt too wide) in paragraph at lines 5380--5380 \T1/ptm/m/it/10 back- Overfull \hbox (151.74435pt too wide) in paragraph at lines 5380--5380 \T1/ptm/m/it/10 ing_store=True\T1/pcr/m/n/10 ) [106] [107] Overfull \hbox (29.85474pt too wide) in paragraph at lines 5611--5611 []\T1/ptm/m/it/10 asic\T1/ptm/m/n/10 , Overfull \hbox (22.35486pt too wide) in paragraph at lines 5611--5611 \T1/ptm/m/it/10 in- Overfull \hbox (55.9647pt too wide) in paragraph at lines 5611--5611 \T1/ptm/m/it/10 put_fname\T1/ptm/m/n/10 , Overfull \hbox (59.85419pt too wide) in paragraph at lines 5611--5611 \T1/ptm/m/it/10 pixel_v_list\T1/ptm/m/n/10 , Overfull \hbox (60.41425pt too wide) in paragraph at lines 5611--5611 \T1/ptm/m/it/10 pixel_u_list\T1/ptm/m/n/10 , Overfull \hbox (69.29413pt too wide) in paragraph at lines 5611--5611 \T1/ptm/m/it/10 mem_cell_list\T1/ptm/m/n/10 , Overfull \hbox (62.17444pt too wide) in paragraph at lines 5611--5611 \T1/ptm/m/it/10 n_processes\T1/ptm/m/n/10 , Overfull \hbox (65.96419pt too wide) in paragraph at lines 5611--5611 \T1/ptm/m/it/10 safety_factor\T1/ptm/m/n/10 , Overfull \hbox (27.35486pt too wide) in paragraph at lines 5611--5611 \T1/ptm/m/it/10 out- Overfull \hbox (55.9647pt too wide) in paragraph at lines 5611--5611 \T1/ptm/m/it/10 put_fname\T1/ptm/m/n/10 , Overfull \hbox (69.83406pt too wide) in paragraph at lines 5611--5611 \T1/ptm/m/it/10 reuse_results\T1/pcr/m/n/10 ) Overfull \hbox (11.85474pt too wide) in paragraph at lines 5661--5661 []\T1/ptm/m/it/10 asic\T1/ptm/m/n/10 , Overfull \hbox (4.35486pt too wide) in paragraph at lines 5661--5661 \T1/ptm/m/it/10 in- Overfull \hbox (65.82457pt too wide) in paragraph at lines 5661--5661 \T1/ptm/m/it/10 put_fname=None\T1/ptm/m/n/10 , Overfull \hbox (9.35486pt too wide) in paragraph at lines 5661--5661 \T1/ptm/m/it/10 out- Overfull \hbox (65.82457pt too wide) in paragraph at lines 5661--5661 \T1/ptm/m/it/10 put_fname=None\T1/ptm/m/n/10 , Overfull \hbox (74.71419pt too wide) in paragraph at lines 5661--5661 \T1/ptm/m/it/10 safety_factor=1000\T1/ptm/m/n/10 , Overfull \hbox (66.56442pt too wide) in paragraph at lines 5661--5661 \T1/ptm/m/it/10 plot_prefix=None\T1/ptm/m/n/10 , Overfull \hbox (55.83444pt too wide) in paragraph at lines 5661--5661 \T1/ptm/m/it/10 plot_dir=None\T1/ptm/m/n/10 , Overfull \hbox (8.97473pt too wide) in paragraph at lines 5661--5661 \T1/ptm/m/it/10 cre- Overfull \hbox (60.63423pt too wide) in paragraph at lines 5661--5661 \T1/ptm/m/it/10 ate_plots=False\T1/ptm/m/n/10 , Overfull \hbox (64.62431pt too wide) in paragraph at lines 5661--5661 \T1/ptm/m/it/10 log_level='info'\T1/pcr/m/n/10 ) [108] Overfull \hbox (30.16438pt too wide) in paragraph at lines 5763--5763 []\T1/ptm/m/it/10 list_to_check\T1/ptm/m/n/10 , Overfull \hbox (32.12476pt too wide) in paragraph at lines 5769--5769 []\T1/ptm/m/it/10 file_name\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 5775--5775 []\T1/ptm/m/it/10 asic\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in- Underfull \hbox (badness 10000) in paragraph at lines 5775--5775 \T1/ptm/m/it/10 put_file\T1/ptm/m/n/10 , Overfull \hbox (5.85419pt too wide) in paragraph at lines 5775--5775 \T1/ptm/m/it/10 pixel_v_list\T1/ptm/m/n/10 , Overfull \hbox (6.41425pt too wide) in paragraph at lines 5775--5775 \T1/ptm/m/it/10 pixel_u_list\T1/ptm/m/n/10 , Overfull \hbox (15.29413pt too wide) in paragraph at lines 5775--5775 \T1/ptm/m/it/10 mem_cell_list\T1/ptm/m/n/10 , Overfull \hbox (15.69415pt too wide) in paragraph at lines 5775--5775 \T1/ptm/m/it/10 safety_factor\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 5781--5781 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , Overfull \hbox (23.85419pt too wide) in paragraph at lines 5787--5787 []\T1/ptm/m/it/10 pixel_v_list\T1/ptm/m/n/10 , Overfull \hbox (24.41425pt too wide) in paragraph at lines 5787--5787 \T1/ptm/m/it/10 pixel_u_list\T1/ptm/m/n/10 , Overfull \hbox (33.29413pt too wide) in paragraph at lines 5787--5787 \T1/ptm/m/it/10 mem_cell_list\T1/ptm/m/n/10 , Overfull \hbox (35.32454pt too wide) in paragraph at lines 5787--5787 \T1/ptm/m/it/10 n_gain_stages\T1/ptm/m/n/10 , Overfull \hbox (22.74435pt too wide) in paragraph at lines 5787--5787 \T1/ptm/m/it/10 n_intervals\T1/ptm/m/n/10 , Overfull \hbox (71.82416pt too wide) in paragraph at lines 5787--5787 \T1/ptm/m/it/10 n_diff_changes_stored\T1/pcr/m/n/10 ) Overfull \hbox (14.12476pt too wide) in paragraph at lines 5799--5799 []\T1/ptm/m/it/10 file_name\T1/pcr/m/n/10 ) [109] Overfull \hbox (7.07484pt too wide) in paragraph at lines 5843--5843 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 pro- Overfull \hbox (31.70407pt too wide) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 cess_results\T1/ptm/m/n/10 , Overfull \hbox (37.2843pt too wide) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 asics=array([ Underfull \hbox (badness 10000) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 9\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 10\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 11\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 12\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 13\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 14\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 15\T1/ptm/m/n/10 , Overfull \hbox (0.96486pt too wide) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 16])\T1/ptm/m/n/10 , Overfull \hbox (21.05455pt too wide) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , Overfull \hbox (38.44444pt too wide) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , Overfull \hbox (25.76465pt too wide) in paragraph at lines 5843--5843 \T1/ptm/m/it/10 **kwargs\T1/pcr/m/n/10 ) [110] [111] [112] Underfull \hbox (badness 10000) in paragraph at lines 6121--6123 []\T1/ptm/m/n/10 Usually the Underfull \hbox (badness 10000) in paragraph at lines 6161--6169 []\T1/ptm/m/n/10 __init__(self,FileName) Get-N-u-mIm-ages(self) def Get-Data(se lf,Index, Underfull \hbox (badness 10000) in paragraph at lines 6161--6169 \T1/ptm/m/n/10 DataType=^^Q^^P,Pos=None,Size=None): Get-Pixel(self,Index,Positi on) Get-H-eader(self,Index) Get-Static- Overfull \hbox (4.81061pt too wide) in paragraph at lines 6161--6169 \T1/ptm/m/n/10 Header(self,Index) WriteIm-age (self,Header,Data,Append=1,DataTy pe=^^Q^^P,WriteAsUnsigened=0,ByteOrder=^^Q^^P) [113] [114] [115] [116] [117] Underfull \hbox (badness 10000) in paragraph at lines 6816--6816 []\T1/ptm/m/it/10 filename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path='/stream'\T1/pt m/m/n/10 , [118] Underfull \hbox (badness 10000) in paragraph at lines 6903--6903 []\T1/ptm/m/it/10 filename\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6903--6903 \T1/ptm/m/it/10 read- Underfull \hbox (badness 10000) in paragraph at lines 6903--6903 \T1/ptm/m/it/10 Fun\T1/ptm/m/n/10 , \T1/ptm/m/it/10 size\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6903--6903 \T1/ptm/m/it/10 chunk-Size\T1/ptm/m/n/10 , Overfull \hbox (23.16454pt too wide) in paragraph at lines 6903--6903 \T1/ptm/m/it/10 filesRange=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 6903--6903 \T1/ptm/m/it/10 *args\T1/ptm/m/n/10 , [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 7257--7259 []\T1/ptm/m/n/10 Usually the [123] [124] [125] Underfull \hbox (badness 10000) in paragraph at lines 7725--7726 []\T1/pcr/b/n/10 will be passed to the matplotlib fill_between() function. [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 10000) in paragraph at lines 11090--11090 []\T1/ptm/m/it/10 host=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 port=None\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 read-Han- Underfull \hbox (badness 10000) in paragraph at lines 11110--11110 []\T1/ptm/m/it/10 host=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 port=None\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 read-Han- [143] [144] Chapter 5. [145] [146] Overfull \hbox (18.6225pt too wide) in paragraph at lines 11310--11311 []\T1/pcr/m/n/10 XFELDetAna.algorithms.correct_common_mode\T1/ptm/m/n/10 , Overfull \hbox (54.6225pt too wide) in paragraph at lines 11312--11313 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.calc_offset_and_noise\T1/ptm/m/n/10 , Overfull \hbox (42.6225pt too wide) in paragraph at lines 11313--11314 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.correct_common_mode\T1/ptm/m/n/10 , Overfull \hbox (12.6225pt too wide) in paragraph at lines 11314--11315 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.correct_offset\T1/ptm/m/n/10 , Overfull \hbox (18.6225pt too wide) in paragraph at lines 11315--11316 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.correct_relgain\T1/ptm/m/n/10 , Overfull \hbox (102.6225pt too wide) in paragraph at lines 11317--11318 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.calc_offset_and_noise\T1/ptm /m/n/10 , Overfull \hbox (90.6225pt too wide) in paragraph at lines 11318--11319 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.correct_common_mode\T1/ptm/m /n/10 , Overfull \hbox (138.6225pt too wide) in paragraph at lines 11319--11320 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.correct_common_mode_batcher\ T1/ptm/m/n/10 , Overfull \hbox (78.6225pt too wide) in paragraph at lines 11320--11321 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.simple_correction\T1/ptm/m/n /10 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 11321--11322 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.split_events\T1/ptm/m/n/10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 11322--11323 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.statistics\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 11323--11324 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.util\T1/ptm/m/n/10 , Overfull \hbox (60.6225pt too wide) in paragraph at lines 11324--11325 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.xfelgpukernels\T1/ptm/m/n/10 , Overfull 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XFELDetAna.detectors.agipd.dyrange_algorithms.util\T1/ptm/m/n/ 10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 11348--11349 []\T1/pcr/m/n/10 XFELDetAna.detectors.agipd.gpu.kernels\T1/ptm/m/n/10 , Overfull \hbox (90.6225pt too wide) in paragraph at lines 11349--11350 []\T1/pcr/m/n/10 XFELDetAna.detectors.agipd.gpu.kernels.threshold_gain\T1/ptm/m /n/10 , Overfull \hbox (42.6225pt too wide) in paragraph at lines 11350--11351 []\T1/pcr/m/n/10 XFELDetAna.detectors.agipd.gpu.threshold_gain\T1/ptm/m/n/10 , Overfull \hbox (18.6225pt too wide) in paragraph at lines 11351--11352 []\T1/pcr/m/n/10 XFELDetAna.detectors.agipd.merge_dynrange\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 11357--11358 []\T1/pcr/m/n/10 XFELDetAna.detectors.edf_data.EdfFile\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 11358--11359 []\T1/pcr/m/n/10 XFELDetAna.detectors.edf_data.loadedf\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 11359--11360 []\T1/pcr/m/n/10 XFELDetAna.detectors.edf_data.reader\T1/ptm/m/n/10 , [147] Underfull \hbox (badness 10000) in paragraph at lines 11364--11365 []\T1/pcr/m/n/10 XFELDetAna.detectors.fastccd.readerh5\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 11366--11367 []\T1/pcr/m/n/10 XFELDetAna.detectors.generator.reader\T1/ptm/m/n/10 , Overfull \hbox (42.6225pt too wide) in paragraph at lines 11368--11369 []\T1/pcr/m/n/10 XFELDetAna.detectors.jungfrau.jf_chunk_reader\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 11369--11370 []\T1/pcr/m/n/10 XFELDetAna.detectors.jungfrau.reader\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 11370--11371 []\T1/pcr/m/n/10 XFELDetAna.detectors.jungfrau.readerPSI\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 11375--11376 []\T1/pcr/m/n/10 XFELDetAna.detectors.pnccd.frm6reader\T1/ptm/m/n/10 , [148] (./src.ind Underfull \hbox (badness 10000) in paragraph at lines 8--9 []\T1/pcr/m/n/10 _axisFuncWrapper() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 9--11 []\T1/pcr/m/n/10 _commonmodeBase3d \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule X FELDe- Overfull \hbox (26.01056pt too wide) in paragraph at lines 9--11 \T1/ptm/m/it/10 tAna.algorithms.gpu.kernels.correct_common_mode\T1/ptm/m/n/10 ) , Overfull \hbox (26.01056pt too wide) in paragraph at lines 11--13 \T1/ptm/m/it/10 tAna.algorithms.gpu.kernels.correct_common_mode\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 13--15 []\T1/pcr/m/n/10 _commonmodeBase3dBitonicZ1 Underfull \hbox (badness 10000) in paragraph at lines 13--15 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Overfull \hbox (26.01056pt too wide) in paragraph at lines 13--15 \T1/ptm/m/it/10 tAna.algorithms.gpu.kernels.correct_common_mode\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 15--16 []\T1/pcr/m/n/10 _decorateModule() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule X FELDe- Underfull \hbox (badness 5331) in paragraph at lines 16--18 []\T1/pcr/m/n/10 _fill_between_steps() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 18--20 []\T1/pcr/m/n/10 _gpuCommonMode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XF ELDe- Underfull \hbox (badness 10000) in paragraph at lines 18--20 \T1/ptm/m/it/10 tAna.algorithms.gpu.correct_common_mode\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 20--22 []\T1/pcr/m/n/10 _gpuCommonMode2D() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 20--22 \T1/ptm/m/it/10 tAna.algorithms.gpu.correct_common_mode\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/pcr/m/n/10 _gpuCommonMode3D() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 22--24 \T1/ptm/m/it/10 tAna.algorithms.gpu.correct_common_mode\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 30--32 []\T1/pcr/m/n/10 add_can_expand \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 32--34 []\T1/pcr/m/n/10 add_can_expand \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 32--34 \T1/ptm/m/it/10 tAna.util.knumpy.krbMaskedArray at-tribute\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 34--35 []\T1/pcr/m/n/10 add_docstring() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFE LDe- Underfull \hbox (badness 10000) in paragraph at lines 36--37 []\T1/pcr/m/n/10 add_newdoc_ufunc() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 37--38 []\T1/pcr/m/n/10 add_newdocs() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 38--40 []\T1/pcr/m/n/10 AgipdDynamicRangeGatherSingleAsic Underfull \hbox (badness 10000) in paragraph at lines 38--40 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELDe- Overfull \hbox (11.28064pt too wide) in paragraph at lines 38--40 \T1/ptm/m/it/10 tAna.detectors.agipd.dyrange_algorithms.gather\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 40--42 []\T1/pcr/m/n/10 AgipdDynamicRangeSingleAsic Underfull \hbox (badness 10000) in paragraph at lines 40--42 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELDe- Overfull \hbox (15.04054pt too wide) in paragraph at lines 40--42 \T1/ptm/m/it/10 tAna.detectors.agipd.dyrange_algorithms.process\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 42--44 []\T1/pcr/m/n/10 AgipdMergeDynamicRange \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class i n XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 45--47 []\T1/pcr/m/n/10 algorithmDescription() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Overfull \hbox (6.0305pt too wide) in paragraph at lines 45--47 \T1/ptm/m/it/10 tAna.algorithms.histogram.HistogramCalculator Underfull \hbox (badness 10000) in paragraph at lines 47--49 []\T1/pcr/m/n/10 algorithmDescription() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 47--49 \T1/ptm/m/it/10 tAna.algorithms.split_event.PatternClassifier Underfull \hbox (badness 10000) in paragraph at lines 49--51 []\T1/pcr/m/n/10 algorithmDescription() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 49--51 \T1/ptm/m/it/10 tAna.core.mapcalculator.MapCalculator Underfull \hbox (badness 10000) in paragraph at lines 51--53 []\T1/pcr/m/n/10 algorithmSpecificSettings() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XF ELDe- Underfull \hbox (badness 10000) in paragraph at lines 51--53 \T1/ptm/m/it/10 tAna.core.mapcalculator.MapCalculator Underfull \hbox (badness 10000) in paragraph at lines 55--56 []\T1/pcr/m/n/10 ALLOW_THREADS() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFE LDe- [149] Underfull \hbox (badness 10000) in paragraph at lines 65--66 []\T1/pcr/m/n/10 apply_along_axis() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 66--67 []\T1/pcr/m/n/10 apply_over_axes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule X FELDe- Underfull \hbox (badness 10000) in paragraph at lines 77--78 []\T1/pcr/m/n/10 argpartition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFEL De- Underfull \hbox (badness 10000) in paragraph at lines 82--83 []\T1/pcr/m/n/10 array2string() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFEL De- Underfull \hbox (badness 10000) in paragraph at lines 83--84 []\T1/pcr/m/n/10 array_equal() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 84--85 []\T1/pcr/m/n/10 array_equiv() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 86--87 []\T1/pcr/m/n/10 array_split() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 90--91 []\T1/pcr/m/n/10 asarray_chkfinite() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 91--92 []\T1/pcr/m/n/10 ascontiguousarray() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 93--94 []\T1/pcr/m/n/10 asfortranarray() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XF ELDe- Underfull \hbox (badness 10000) in paragraph at lines 96--97 []\T1/pcr/m/n/10 AsyncHandler \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 97--98 []\T1/pcr/m/n/10 AsyncServer \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 105--107 []\T1/pcr/m/n/10 axis_scales \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 105--107 \T1/ptm/m/it/10 tAna.util.knumpy.krbMaskedArray at-tribute\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 117--119 []\T1/pcr/m/n/10 baseArrayType \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 117--119 \T1/ptm/m/it/10 tAna.util.knumpy.krbMaskedArray at-tribute\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 119--121 []\T1/pcr/m/n/10 biggest_entries() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule X FELDe- Overfull \hbox (15.04054pt too wide) in paragraph at lines 119--121 \T1/ptm/m/it/10 tAna.detectors.agipd.dyrange_algorithms.process\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 121--122 []\T1/pcr/m/n/10 binary_repr() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 123--124 []\T1/pcr/m/n/10 bitwise_and() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 124--125 []\T1/pcr/m/n/10 bitwise_not() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 126--127 []\T1/pcr/m/n/10 bitwise_xor() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 131--132 []\T1/pcr/m/n/10 broadcast_arrays() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 132--133 []\T1/pcr/m/n/10 broadcast_to() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFEL De- Underfull \hbox (badness 10000) in paragraph at lines 134--135 []\T1/pcr/m/n/10 busday_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFEL De- [150] Underfull \hbox (badness 10000) in paragraph at lines 135--136 []\T1/pcr/m/n/10 busday_offset() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFE LDe- Underfull \hbox (badness 10000) in paragraph at lines 136--137 []\T1/pcr/m/n/10 byte_bounds() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 140--142 []\T1/pcr/m/n/10 calc_gain_median() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Overfull \hbox (66.14977pt too wide) in paragraph at lines 140--142 \T1/ptm/m/it/10 tAna.detectors.agipd.dyrange_algorithms.process.ProcessDrscs Underfull \hbox (badness 10000) in paragraph at lines 142--144 []\T1/pcr/m/n/10 calc_gain_regions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Overfull \hbox (66.14977pt too wide) in paragraph at lines 142--144 \T1/ptm/m/it/10 tAna.detectors.agipd.dyrange_algorithms.process.ProcessDrscs Underfull \hbox (badness 10000) in paragraph at lines 144--146 []\T1/pcr/m/n/10 calc_thresholds() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Overfull \hbox (66.14977pt too wide) in paragraph at lines 144--146 \T1/ptm/m/it/10 tAna.detectors.agipd.dyrange_algorithms.process.ProcessDrscs Underfull \hbox (badness 10000) in paragraph at lines 146--148 []\T1/pcr/m/n/10 calculate_mapped_asic() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe - Overfull \hbox (162.59938pt 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[]\T1/pcr/m/n/10 commonmode3d \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe - Overfull \hbox (26.01056pt too wide) in paragraph at lines 185--187 \T1/ptm/m/it/10 tAna.algorithms.gpu.kernels.correct_common_mode\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 187--189 []\T1/pcr/m/n/10 commonmode3dBitonic \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Overfull \hbox (26.01056pt too wide) in paragraph at lines 187--189 \T1/ptm/m/it/10 tAna.algorithms.gpu.kernels.correct_common_mode\T1/ptm/m/n/10 ) , Underfull \hbox (badness 5331) in paragraph at lines 189--191 []\T1/pcr/m/n/10 commonmode3dBitonicZ1 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le XFELDe- Overfull \hbox (26.01056pt too wide) in paragraph at lines 189--191 \T1/ptm/m/it/10 tAna.algorithms.gpu.kernels.correct_common_mode\T1/ptm/m/n/10 ) , Underfull \hbox (badness 5331) in paragraph at lines 191--193 []\T1/pcr/m/n/10 commonmode3dNetwork() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le XFELDe- Overfull 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paragraph at lines 227--229 []\T1/pcr/m/n/10 current_list_to_ndarray() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFEL De- Overfull \hbox (76.21066pt too wide) in paragraph at lines 227--229 \T1/ptm/m/it/10 tAna.detectors.agipd.merge_dynrange.AgipdMergeDynamicRange Underfull \hbox (badness 10000) in paragraph at lines 234--235 []\T1/pcr/m/n/10 data \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.knumpy.p ulseAxis at-tribute\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 235--236 []\T1/pcr/m/n/10 data \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.knumpy.s tackAxis at-tribute\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 237--238 []\T1/pcr/m/n/10 dataReceiver() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFEL De- Underfull \hbox (badness 10000) in paragraph at lines 238--239 []\T1/pcr/m/n/10 DataSelector \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 240--242 []\T1/pcr/m/n/10 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[]\T1/pcr/m/n/10 histPlot() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 541--543 []\T1/pcr/m/n/10 histSimplePlot() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XF ELDe- Underfull \hbox (badness 10000) in paragraph at lines 543--545 []\T1/pcr/m/n/10 histWithStats() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFE LDe- Underfull \hbox (badness 10000) in paragraph at lines 555--556 []\T1/pcr/m/n/10 Image \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELDe- Overfull \hbox (4.94975pt too wide) in paragraph at lines 556--558 []\T1/pcr/m/n/10 IMAGES \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.algorithms. selection.DataSelector Overfull \hbox (10.94975pt too wide) in paragraph at lines 562--564 []\T1/pcr/m/n/10 INDICES \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.algorithms .selection.DataSelector Underfull \hbox (badness 10000) in paragraph at lines 571--573 []\T1/pcr/m/n/10 init_metadata() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Overfull 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tAna.detectors.agipd.dyrange_algorithms.process\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 579--581 []\T1/pcr/m/n/10 initiate_result() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Overfull \hbox (74.74982pt too wide) in paragraph at lines 579--581 \T1/ptm/m/it/10 tAna.detectors.agipd.dyrange_algorithms.process.ParallelProcess Underfull \hbox (badness 10000) in paragraph at lines 581--583 []\T1/pcr/m/n/10 initKernel() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Overfull \hbox (69.05994pt too wide) in paragraph at lines 581--583 \T1/ptm/m/it/10 tAna.algorithms.gpu.calc_offset_and_noise.GpuOffsetNoiseCalc Underfull \hbox (badness 10000) in paragraph at lines 585--586 []\T1/pcr/m/n/10 int_asbuffer() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFEL De- Underfull \hbox (badness 10000) in paragraph at lines 586--588 []\T1/pcr/m/n/10 integrate_result() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Overfull \hbox (74.74982pt too wide) in paragraph at lines 586--588 \T1/ptm/m/it/10 tAna.detectors.agipd.dyrange_algorithms.process.ParallelProcess Underfull \hbox (badness 10000) in paragraph at lines 589--590 []\T1/pcr/m/n/10 intersect1d() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 593--594 []\T1/pcr/m/n/10 invertADC \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 599--600 []\T1/pcr/m/n/10 iscomplexobj() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFEL De- Underfull \hbox (badness 10000) in paragraph at lines 600--601 []\T1/pcr/m/n/10 isEnabled() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.core.p rofiler.Profiler [156] Underfull \hbox (badness 10000) in paragraph at lines 611--612 []\T1/pcr/m/n/10 issubclass_() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 613--614 []\T1/pcr/m/n/10 issubsctype() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 619--621 []\T1/pcr/m/n/10 JFChunkReader \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 619--621 \T1/ptm/m/it/10 tAna.detectors.jungfrau.jf_chunk_reader\T1/ptm/m/n/10 ), Overfull \hbox (12.9695pt too wide) in paragraph at lines 625--627 []\T1/pcr/m/n/10 kernelC \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patte rn_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 627--629 []\T1/pcr/m/n/10 kernelD0 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 629--631 []\T1/pcr/m/n/10 kernelD1 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 631--633 []\T1/pcr/m/n/10 kernelD2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 633--635 []\T1/pcr/m/n/10 kernelD3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 635--637 []\T1/pcr/m/n/10 kernelQ0 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 637--639 []\T1/pcr/m/n/10 kernelQ1 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 639--641 []\T1/pcr/m/n/10 kernelQ2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 641--643 []\T1/pcr/m/n/10 kernelQ3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (12.9695pt too wide) in paragraph at lines 643--645 []\T1/pcr/m/n/10 kernelS \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patte rn_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 645--647 []\T1/pcr/m/n/10 kernelT0 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 647--649 []\T1/pcr/m/n/10 kernelT1 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 649--651 []\T1/pcr/m/n/10 kernelT2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 651--653 []\T1/pcr/m/n/10 kernelT3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 653--655 []\T1/pcr/m/n/10 kernelT4 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 655--657 []\T1/pcr/m/n/10 kernelT5 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 657--659 []\T1/pcr/m/n/10 kernelT6 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 659--661 []\T1/pcr/m/n/10 kernelT7 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 661--663 []\T1/pcr/m/n/10 kernelT8 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Overfull \hbox (18.9701pt too wide) in paragraph at lines 663--665 []\T1/pcr/m/n/10 kernelT9 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patt ern_kernels.patternkernels Underfull \hbox (badness 10000) in paragraph at lines 666--667 []\T1/pcr/m/n/10 krbMaskedArray \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELDe - Underfull \hbox (badness 5331) in paragraph at lines 671--673 []\T1/pcr/m/n/10 latexLabelFormatter() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 681--682 []\T1/pcr/m/n/10 little_endian() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFE LDe- Underfull \hbox (badness 10000) in paragraph at lines 683--685 []\T1/pcr/m/n/10 load_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Overfull \hbox (66.14977pt too wide) in paragraph at lines 683--685 \T1/ptm/m/it/10 tAna.detectors.agipd.dyrange_algorithms.process.ProcessDrscs Underfull \hbox (badness 10000) in paragraph at lines 685--687 []\T1/pcr/m/n/10 loadedf() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 694--695 []\T1/pcr/m/n/10 logical_and() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 695--696 []\T1/pcr/m/n/10 logical_not() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 697--698 []\T1/pcr/m/n/10 logical_xor() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- [157] Underfull \hbox (badness 10000) in paragraph at lines 707--708 []\T1/pcr/m/n/10 make_colormap() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFE LDe- Underfull \hbox (badness 10000) in paragraph at lines 708--710 []\T1/pcr/m/n/10 makeReport() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 708--710 \T1/ptm/m/it/10 tAna.core.mapcalculator.MapCalculator Underfull \hbox (badness 10000) in paragraph at lines 710--711 []\T1/pcr/m/n/10 MapCalculator \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELDe- Underfull \hbox (badness 7963) in paragraph at lines 711--713 []\T1/pcr/m/n/10 MASK \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.algorithms.se lection.DataSelector Underfull \hbox (badness 10000) in paragraph at lines 713--714 []\T1/pcr/m/n/10 mask_indices() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFEL De- Underfull \hbox (badness 10000) in paragraph at lines 722--723 []\T1/pcr/m/n/10 maximum_sctype() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XF ELDe- Underfull \hbox (badness 10000) in paragraph at lines 723--724 []\T1/pcr/m/n/10 MAY_SHARE_BOUNDS() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 724--725 []\T1/pcr/m/n/10 MAY_SHARE_EXACT() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule X FELDe- Underfull \hbox (badness 10000) in paragraph at lines 725--726 []\T1/pcr/m/n/10 may_share_memory() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 728--730 []\T1/pcr/m/n/10 median3d \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Overfull \hbox (26.01056pt too wide) in paragraph at lines 728--730 \T1/ptm/m/it/10 tAna.algorithms.gpu.kernels.correct_common_mode\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 730--732 []\T1/pcr/m/n/10 median3dBitonic \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFE LDe- Overfull \hbox (26.01056pt too wide) in paragraph at lines 730--732 \T1/ptm/m/it/10 tAna.algorithms.gpu.kernels.correct_common_mode\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 732--734 []\T1/pcr/m/n/10 median3dNetwork() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule X FELDe- Overfull \hbox (61.64029pt too wide) in paragraph at lines 732--734 \T1/ptm/m/it/10 tAna.algorithms.gpu.kernels.correct_common_mode_batcher\T1/ptm/ m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 735--737 []\T1/pcr/m/n/10 MergeDrscs \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 740--741 []\T1/pcr/m/n/10 min_scalar_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule X FELDe- Underfull \hbox (badness 10000) in paragraph at lines 742--743 []\T1/pcr/m/n/10 mintypecode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 746--748 []\T1/pcr/m/n/10 ModuleDeprecationWarning() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 766--767 []\T1/pcr/m/n/10 nanpercentile() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFE LDe- Underfull \hbox (badness 10000) in paragraph at lines 772--773 []\T1/pcr/m/n/10 ndenumerate() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- [158] Underfull \hbox (badness 10000) in paragraph at lines 777--778 []\T1/pcr/m/n/10 nested_iters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFEL De- Underfull \hbox (badness 10000) in paragraph at lines 781--783 []\T1/pcr/m/n/10 non_empty_trains() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 793--795 []\T1/pcr/m/n/10 oddeven_merge() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFE LDe- Overfull \hbox (61.64029pt too wide) in paragraph at lines 793--795 \T1/ptm/m/it/10 tAna.algorithms.gpu.kernels.correct_common_mode_batcher\T1/ptm/ m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 795--797 []\T1/pcr/m/n/10 oddeven_merge_sort() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e XFELDe- Overfull \hbox (61.64029pt too wide) in paragraph at lines 795--797 \T1/ptm/m/it/10 tAna.algorithms.gpu.kernels.correct_common_mode_batcher\T1/ptm/ m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 797--799 []\T1/pcr/m/n/10 oddeven_merge_sort_range() Underfull \hbox (badness 10000) in paragraph at lines 797--799 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Overfull \hbox (61.64029pt too wide) in paragraph at lines 797--799 \T1/ptm/m/it/10 tAna.algorithms.gpu.kernels.correct_common_mode_batcher\T1/ptm/ m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 805--806 []\T1/pcr/m/n/10 outputPipe() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe - Underfull \hbox (badness 10000) in paragraph at lines 809--810 []\T1/pcr/m/n/10 P2pInterface \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 810--811 []\T1/pcr/m/n/10 PackageLoader() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFE LDe- Underfull \hbox (badness 10000) in paragraph at lines 813--815 []\T1/pcr/m/n/10 ParallelProcess \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELD e- Overfull \hbox (15.04054pt too wide) in paragraph at lines 813--815 \T1/ptm/m/it/10 tAna.detectors.agipd.dyrange_algorithms.process\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 816--818 []\T1/pcr/m/n/10 PatternClassifier \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFE LDe- Underfull \hbox (badness 10000) in paragraph at lines 818--820 []\T1/pcr/m/n/10 patternkernels \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELDe - Underfull \hbox (badness 10000) in paragraph at lines 820--822 []\T1/pcr/m/n/10 PatternSelector \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 823--824 []\T1/pcr/m/n/10 pertinent_kwargs() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Overfull \hbox (12.9701pt too wide) in paragraph at lines 827--829 []\T1/pcr/m/n/10 pkernel \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe-tAna.util.patte rn_kernels.patternkernels Underfull \hbox (badness 10000) in paragraph at lines 845--846 []\T1/pcr/m/n/10 prepare_maxwell() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule X FELDe- Underfull \hbox (badness 10000) in paragraph at lines 846--848 []\T1/pcr/m/n/10 print() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Overfull \hbox (15.04054pt too wide) in paragraph at lines 846--848 \T1/ptm/m/it/10 tAna.detectors.agipd.dyrange_algorithms.process\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 848--850 []\T1/pcr/m/n/10 printFormattedLogs() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 850--852 []\T1/pcr/m/n/10 process() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Overfull \hbox (76.21066pt too wide) in paragraph at lines 850--852 \T1/ptm/m/it/10 tAna.detectors.agipd.merge_dynrange.AgipdMergeDynamicRange Underfull \hbox (badness 10000) in paragraph at lines 852--854 []\T1/pcr/m/n/10 process_data_point() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Overfull \hbox (66.14977pt too wide) in paragraph at lines 852--854 \T1/ptm/m/it/10 tAna.detectors.agipd.dyrange_algorithms.process.ProcessDrscs Underfull \hbox (badness 10000) in paragraph at lines 854--856 []\T1/pcr/m/n/10 ProcessDrscs \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in XFELDe- Overfull \hbox (15.04054pt too wide) in paragraph at lines 854--856 \T1/ptm/m/it/10 tAna.detectors.agipd.dyrange_algorithms.process\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 858--859 []\T1/pcr/m/n/10 profilable() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe - [159] Underfull \hbox (badness 10000) in paragraph at lines 860--861 []\T1/pcr/m/n/10 profilerMethod() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XF ELDe- Underfull \hbox (badness 10000) in paragraph at lines 861--862 []\T1/pcr/m/n/10 promote_types() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFE LDe- Underfull \hbox (badness 10000) in paragraph at lines 876--877 []\T1/pcr/m/n/10 RankWarning() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELD e- Underfull \hbox (badness 10000) in paragraph at lines 879--881 []\T1/pcr/m/n/10 ravel_multi_index() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 881--883 []\T1/pcr/m/n/10 read_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Overfull \hbox (74.74982pt too wide) in paragraph at lines 881--883 \T1/ptm/m/it/10 tAna.detectors.agipd.dyrange_algorithms.process.ParallelProcess Underfull \hbox (badness 10000) in paragraph at lines 883--885 []\T1/pcr/m/n/10 readChunks() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 883--885 \T1/ptm/m/it/10 tAna.core.reader.ChunkReader method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 885--887 []\T1/pcr/m/n/10 readChunks() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 XFELDe- Overfull 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lines 1161--1162 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.correct_common_mode Overfull \hbox (10.1225pt too wide) in paragraph at lines 1162--1163 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.correct_offset Overfull \hbox (16.1225pt too wide) in paragraph at lines 1163--1164 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.correct_relgain Overfull \hbox (100.1225pt too wide) in paragraph at lines 1165--1167 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.calc_offset_and_noise Overfull \hbox (88.1225pt too wide) in paragraph at lines 1167--1169 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.correct_common_mode Overfull \hbox (136.1225pt too wide) in paragraph at lines 1169--1171 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.correct_common_mode_batcher Overfull \hbox (76.1225pt too wide) in paragraph at lines 1171--1173 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.simple_correction Overfull \hbox (46.1225pt too wide) in paragraph at lines 1173--1174 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.split_events Overfull \hbox (34.1225pt too wide) in paragraph at lines 1174--1175 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.statistics Underfull \hbox (badness 10000) in paragraph at lines 1175--1176 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.util Overfull \hbox (58.1225pt too wide) in paragraph at lines 1176--1178 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.xfelgpukernels Underfull \hbox (badness 10000) in paragraph at lines 1178--1179 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.split_events Underfull \hbox (badness 10000) in paragraph at lines 1179--1180 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.statistics Underfull \hbox (badness 10000) in paragraph at lines 1180--1181 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.util \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mod-ule\T1/ptm/m/n/10 ), Overfull \hbox (16.1225pt too wide) in paragraph at lines 1181--1182 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.xfelcalgputools Underfull \hbox (badness 10000) in paragraph at lines 1190--1191 []\T1/pcr/m/n/10 XFELDetAna.core.mapcalculator \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mod-ule\T1/ptm/m/n/10 ), Overfull \hbox (40.1225pt too wide) in paragraph at lines 1196--1197 []\T1/pcr/m/n/10 XFELDetAna.detectors.agipd.dyrange_algorithms Overfull \hbox (82.1225pt too wide) in paragraph at lines 1197--1199 []\T1/pcr/m/n/10 XFELDetAna.detectors.agipd.dyrange_algorithms.gather [163] Overfull \hbox (88.1225pt too wide) in paragraph at lines 1199--1201 []\T1/pcr/m/n/10 XFELDetAna.detectors.agipd.dyrange_algorithms.process Overfull \hbox (70.1225pt too wide) in paragraph at lines 1201--1203 []\T1/pcr/m/n/10 XFELDetAna.detectors.agipd.dyrange_algorithms.util Underfull \hbox (badness 10000) in paragraph at lines 1203--1204 []\T1/pcr/m/n/10 XFELDetAna.detectors.agipd.gpu \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mod-ule\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 1204--1205 []\T1/pcr/m/n/10 XFELDetAna.detectors.agipd.gpu.kernels Overfull \hbox (88.1225pt too wide) in paragraph at lines 1205--1207 []\T1/pcr/m/n/10 XFELDetAna.detectors.agipd.gpu.kernels.threshold_gain Overfull \hbox (40.1225pt too wide) in paragraph at lines 1207--1208 []\T1/pcr/m/n/10 XFELDetAna.detectors.agipd.gpu.threshold_gain Overfull \hbox (16.1225pt too wide) in paragraph at lines 1208--1209 []\T1/pcr/m/n/10 XFELDetAna.detectors.agipd.merge_dynrange Underfull \hbox (badness 10000) in paragraph at lines 1210--1211 []\T1/pcr/m/n/10 XFELDetAna.detectors.agipd.tests \T1/ptm/m/n/10 (\T1/ptm/m/it/ 10 mod- Underfull \hbox (badness 10000) in paragraph at lines 1212--1213 []\T1/pcr/m/n/10 XFELDetAna.detectors.dssc.reader \T1/ptm/m/n/10 (\T1/ptm/m/it/ 10 mod- Underfull \hbox (badness 10000) in paragraph at lines 1213--1214 []\T1/pcr/m/n/10 XFELDetAna.detectors.edf_data \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mod-ule\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 1214--1215 []\T1/pcr/m/n/10 XFELDetAna.detectors.edf_data.EdfFile Underfull \hbox (badness 10000) in paragraph at lines 1215--1216 []\T1/pcr/m/n/10 XFELDetAna.detectors.edf_data.loadedf Underfull \hbox (badness 10000) in paragraph at lines 1216--1217 []\T1/pcr/m/n/10 XFELDetAna.detectors.edf_data.reader Underfull \hbox (badness 10000) in paragraph at lines 1218--1219 []\T1/pcr/m/n/10 XFELDetAna.detectors.epix.reader \T1/ptm/m/n/10 (\T1/ptm/m/it/ 10 mod- Underfull \hbox (badness 10000) in paragraph at lines 1220--1221 []\T1/pcr/m/n/10 XFELDetAna.detectors.fastccd.reader Underfull \hbox (badness 10000) in paragraph at lines 1221--1222 []\T1/pcr/m/n/10 XFELDetAna.detectors.fastccd.readerh5 Underfull \hbox (badness 10000) in paragraph at lines 1222--1223 []\T1/pcr/m/n/10 XFELDetAna.detectors.generator \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mod-ule\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 1223--1224 []\T1/pcr/m/n/10 XFELDetAna.detectors.generator.reader Underfull \hbox (badness 10000) in paragraph at lines 1224--1225 []\T1/pcr/m/n/10 XFELDetAna.detectors.jungfrau \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mod-ule\T1/ptm/m/n/10 ), Overfull \hbox (40.1225pt too wide) in paragraph at lines 1225--1227 []\T1/pcr/m/n/10 XFELDetAna.detectors.jungfrau.jf_chunk_reader Underfull \hbox (badness 10000) in paragraph at lines 1227--1228 []\T1/pcr/m/n/10 XFELDetAna.detectors.jungfrau.reader Overfull \hbox (4.1225pt too wide) in paragraph at lines 1228--1229 []\T1/pcr/m/n/10 XFELDetAna.detectors.jungfrau.readerPSI Underfull \hbox (badness 10000) in paragraph at lines 1233--1234 []\T1/pcr/m/n/10 XFELDetAna.detectors.pnccd.frm6reader Underfull \hbox (badness 10000) in paragraph at lines 1236--1237 []\T1/pcr/m/n/10 XFELDetAna.plotting.histogram \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mod-ule\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 1237--1238 []\T1/pcr/m/n/10 XFELDetAna.plotting.simpleplot \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mod-ule\T1/ptm/m/n/10 ), [164]) (./src.aux) Package rerunfilecheck Warning: File `src.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on src.pdf (168 pages, 2474718 bytes). Transcript written on src.log. [rtd-command-info] start-time: 2019-06-12T12:21:45.632000Z, end-time: 2019-06-12T12:21:45.663000Z, duration: 0, exit-code: 0 mv -f /user_builds/pydetlib/checkouts/latest/doc/_build/latex/src.pdf /user_builds/pydetlib/artifacts/latest/sphinx_pdf/pydetlib.pdf [rtd-command-info] start-time: 2019-06-12T12:21:47.880000Z, end-time: 2019-06-12T12:22:39.685000Z, duration: 51, exit-code: 0 python /user_builds/pydetlib/envs/latest/bin/sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub Running Sphinx v1.8.5 mkdir: cannot create directory ‘_notebooks’: File exists [NbConvertApp] Converting notebook ../examples/gainMapStability.ipynb to rst [NbConvertApp] Support files will be in gainMapStability_files/ [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Making directory ./gainMapStability_files [NbConvertApp] Writing 48113 bytes to ./gainMapStability.rst [NbConvertApp] Converting notebook ../examples/DataGeneratorExample.ipynb to rst [NbConvertApp] Support files will be in DataGeneratorExample_files/ [NbConvertApp] Making directory ./DataGeneratorExample_files [NbConvertApp] Writing 1984559 bytes to ./DataGeneratorExample.rst [NbConvertApp] Converting notebook ../examples/calculatorCreation.ipynb to rst [NbConvertApp] Writing 15602 bytes to ./calculatorCreation.rst [NbConvertApp] Converting notebook ../examples/PlotExamples.ipynb to rst [NbConvertApp] Support files will be in PlotExamples_files/ [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Making directory ./PlotExamples_files [NbConvertApp] Writing 23677 bytes to ./PlotExamples.rst Creating file ./api/XFELDetAna.rst. Creating file ./api/XFELDetAna.algorithms.rst. Creating file ./api/XFELDetAna.algorithms.cython.rst. Creating file ./api/XFELDetAna.algorithms.gpu.rst. Creating file ./api/XFELDetAna.algorithms.gpu.kernels.rst. Creating file ./api/XFELDetAna.algorithms.tests.rst. Creating file ./api/XFELDetAna.core.rst. Creating file ./api/XFELDetAna.detectors.rst. Creating file ./api/XFELDetAna.detectors.agipd.rst. Creating file ./api/XFELDetAna.detectors.agipd.dyrange_algorithms.rst. Creating file ./api/XFELDetAna.detectors.agipd.gpu.rst. Creating file ./api/XFELDetAna.detectors.agipd.gpu.kernels.rst. Creating file ./api/XFELDetAna.detectors.agipd.tests.rst. Creating file ./api/XFELDetAna.detectors.dssc.rst. Creating file ./api/XFELDetAna.detectors.edf_data.rst. Creating file ./api/XFELDetAna.detectors.epix.rst. Creating file ./api/XFELDetAna.detectors.fastccd.rst. Creating file ./api/XFELDetAna.detectors.generator.rst. Creating file ./api/XFELDetAna.detectors.jungfrau.rst. Creating file ./api/XFELDetAna.detectors.lpd.rst. Creating file ./api/XFELDetAna.detectors.pnccd.rst. Creating file ./api/XFELDetAna.plotting.rst. Creating file ./api/XFELDetAna.util.rst. Creating file ./api/modules.rst. loading translations [en]... done making output directory... loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [epub]: targets for 33 source files that are out of date updating environment: [] 0 added, 28 changed, 0 removed reading sources... [ 3%] _notebooks/DataGeneratorExample reading sources... [ 7%] _notebooks/PlotExamples reading sources... [ 10%] _notebooks/calculatorCreation reading sources... [ 14%] _notebooks/gainMapStability reading sources... [ 17%] _notebooks/index reading sources... [ 21%] api/XFELDetAna Plotting not available No module named 'matplotlib.collections' reading sources... [ 25%] api/XFELDetAna.algorithms reading sources... [ 28%] api/XFELDetAna.algorithms.gpu reading sources... [ 32%] api/XFELDetAna.algorithms.gpu.kernels reading sources... [ 35%] api/XFELDetAna.algorithms.tests reading sources... [ 39%] api/XFELDetAna.core reading sources... [ 42%] api/XFELDetAna.detectors reading sources... [ 46%] api/XFELDetAna.detectors.agipd reading sources... [ 50%] api/XFELDetAna.detectors.agipd.dyrange_algorithms reading sources... [ 53%] api/XFELDetAna.detectors.agipd.gpu reading sources... [ 57%] api/XFELDetAna.detectors.agipd.gpu.kernels reading sources... [ 60%] api/XFELDetAna.detectors.agipd.tests reading sources... [ 64%] api/XFELDetAna.detectors.dssc reading sources... [ 67%] api/XFELDetAna.detectors.edf_data reading sources... [ 71%] api/XFELDetAna.detectors.epix reading sources... [ 75%] api/XFELDetAna.detectors.fastccd reading sources... [ 78%] api/XFELDetAna.detectors.generator reading sources... [ 82%] api/XFELDetAna.detectors.jungfrau reading sources... [ 85%] api/XFELDetAna.detectors.lpd reading sources... [ 89%] api/XFELDetAna.detectors.pnccd reading sources... [ 92%] api/XFELDetAna.plotting reading sources... [ 96%] api/XFELDetAna.util reading sources... [100%] api/modules /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages/sphinx/websupport/__init__.py:25: RemovedInSphinx20Warning: sphinx.websupport module is now provided as sphinxcontrib-websupport. sphinx.websupport will be removed at Sphinx-2.0. Please use the package instead. RemovedInSphinx20Warning) /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/DataGeneratorExample.rst:4: WARNING: duplicate label example usage with a random data generator, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/DataGeneratorExample.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:13: WARNING: duplicate label using plotting tools, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:20: WARNING: duplicate label simple plots, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:53: WARNING: duplicate label draw and linestyles, coloring things, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:144: WARNING: duplicate label bar plots, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:191: WARNING: duplicate label defining axis ranges and logarithmic rendering, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:227: WARNING: duplicate label combining multiple data series into a single plot, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:258: WARNING: duplicate label stacked bar plots and adding a legend, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:318: WARNING: duplicate label adding uncertainties, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:354: WARNING: duplicate label systematic uncertainties, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:415: WARNING: duplicate label error bands, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:503: WARNING: duplicate label adding a second plot panel (for residuals), other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:563: WARNING: duplicate label adding an inset, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:618: WARNING: duplicate label usage with histplot, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/PlotExamples.rst:666: WARNING: duplicate label heatmaps, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:18: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:24: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:44: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:48: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:54: WARNING: Unknown interpreted text role "raw-latex". /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/gainMapStability.rst:4: WARNING: duplicate label pdf-weighted gain map calculation, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/examples/gainMapStability.rst WARNING: autodoc: failed to import module 'xfelpycaltools' from module 'XFELDetAna'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:16: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst:45: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:7: WARNING: toctree contains reference to nonexisting document 'api/XFELDetAna.algorithms.cython' WARNING: autodoc: failed to import module 'characterize_cti' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'characterize_noise' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'characterize_relgain' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_cti' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_offset' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correct_relgain' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'correction' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator:38: WARNING: Unknown interpreted text role "method". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator.get:26: WARNING: Definition list ends without a blank line; unexpected unindent. WARNING: autodoc: failed to import module 'statistics' from module 'XFELDetAna.algorithms'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:14: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:88: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/gpu/correct_common_mode.py:docstring of XFELDetAna.algorithms.gpu.correct_common_mode._gpuCommonMode:11: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:12: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst:56: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst:49: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst WARNING: autodoc: failed to import module 'test_characterize_cti' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_characterize_noise' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_characterize_offset' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_characterize_rel_gain' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_characterize_split_events' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_common_mode' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_cti' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_correct_offset' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_correct_relgain' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'test_statistics' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'test_unitary' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' WARNING: autodoc: failed to import module 'testing_base' from module 'XFELDetAna.algorithms.tests'; the following exception was raised: No module named 'psutil' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst:69: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.kernels.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/core/reader.py:docstring of XFELDetAna.core.reader.ChunkReader.readChunks:8: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst:34: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.tests.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst:20: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst WARNING: autodoc: failed to import module 'characterize_dynrange' from module 'XFELDetAna.detectors.agipd'; the following exception was raised: No module named 'matplotlib.offsetbox' WARNING: autodoc: failed to import module 'threshold_gain' from module 'XFELDetAna.detectors.agipd'; the following exception was raised: No module named 'matplotlib.offsetbox' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:14: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.core.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst:38: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:5: WARNING: Unexpected section title or transition. ____________ /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:6: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:6: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:7: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:8: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:15: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:18: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:20: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:20: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:20: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:21: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:22: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:29: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:5: WARNING: Unexpected section title or transition. ____________ /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:6: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:6: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:7: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:8: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:15: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:18: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:20: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:20: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:20: WARNING: Inline substitution_reference start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:21: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:22: WARNING: Block quote ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:29: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:7: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:11: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:21: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:21: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:25: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/gather.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.gather.AgipdDynamicRangeGatherSingleAsic.get_data:25: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:7: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:11: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:21: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:21: WARNING: Undefined substitution referenced: "___________ |". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:25: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/agipd/dyrange_algorithms/process.py:docstring of XFELDetAna.detectors.agipd.dyrange_algorithms.process.AgipdDynamicRangeSingleAsic.get_data:25: WARNING: Undefined substitution referenced: "____________". /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.dyrange_algorithms.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.dyrange_algorithms.rst:24: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.rst:5: WARNING: duplicate label subpackages, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.rst:12: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.dyrange_algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.rst:21: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.dyrange_algorithms.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.kernels.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.kernels.rst:14: WARNING: duplicate label module contents, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.rst WARNING: autodoc: failed to import module 'test_threshold_gain' from module 'XFELDetAna.detectors.agipd.tests'; the following exception was raised: No module named 'psutil' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.tests.rst:5: WARNING: duplicate label submodules, other instance in /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.gpu.kernels.rst /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.agipd.tests.rst:14: 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unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile:31: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile:44: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile:50: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile.EdfFile.GetData:4: WARNING: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/detectors/edf_data/EdfFile.py:docstring of XFELDetAna.detectors.edf_data.EdfFile.EdfFile.GetData:10: WARNING: Unexpected indentation. 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