Read the Docs build information
Build id: 29771
Project: scs-toolbox
Version: latest
Commit: edf357736cca7a36c218b7c7f4d0ddbedcbc3764
Date: 2025-03-19T12:21:33.955729Z
State: finished
Success: True


[rtd-command-info] start-time: 2025-03-19T12:21:35.081446Z, end-time: 2025-03-19T12:21:37.630832Z, duration: 2, exit-code: 0
git clone --no-single-branch --depth 50 https://git.xfel.eu/SCS/ToolBox.git .
Cloning into '.'...

[rtd-command-info] start-time: 2025-03-19T12:21:38.086854Z, end-time: 2025-03-19T12:21:38.231706Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out 'origin/master'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

HEAD is now at edf3577 Merge branch 'integ_mode' into 'master'

[rtd-command-info] start-time: 2025-03-19T12:21:38.317394Z, end-time: 2025-03-19T12:21:38.376749Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2025-03-19T12:21:39.636436Z, end-time: 2025-03-19T12:21:44.473306Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest
Using base prefix '/home/docs/.pyenv/versions/3.7.3'
New python executable in /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/bin/python3.7
Also creating executable in /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2025-03-19T12:21:44.564041Z, end-time: 2025-03-19T12:21:45.494061Z, duration: 0, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/bin/python -m pip install --upgrade --no-cache-dir pip
Requirement already satisfied: pip in /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/lib/python3.7/site-packages (24.0)

[rtd-command-info] start-time: 2025-03-19T12:21:45.578803Z, end-time: 2025-03-19T12:21:53.942034Z, duration: 8, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/bin/python -m pip install --upgrade --no-cache-dir jinja2==2.11.3 markupsafe==2.0.1 Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1
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Building wheels for collected packages: mock
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23753 sha256=702d7e8e20e3dcfbe38cb434291232efcacac040640d320ae85ec8c525960a1b
  Stored in directory: /tmp/pip-ephem-wheel-cache-y01xwzir/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
Successfully built mock
Installing collected packages: snowballstemmer, pytz, Pygments, mock, docutils, urllib3, sphinxcontrib-serializinghtml, six, setuptools, pillow, packaging, markupsafe, imagesize, idna, future, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
  Attempting uninstall: setuptools
    Found existing installation: setuptools 68.0.0
    Uninstalling setuptools-68.0.0:
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Successfully installed Pygments-2.3.1 alabaster-0.7.13 babel-2.14.0 certifi-2025.1.31 charset-normalizer-3.4.1 commonmark-0.8.1 docutils-0.14 future-1.0.0 idna-3.10 imagesize-1.4.1 jinja2-2.11.3 markupsafe-2.0.1 mock-1.0.1 packaging-24.0 pillow-5.4.1 pytz-2025.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.31.0 setuptools-41.0.1 six-1.17.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-2.0.7

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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/bin/python -m pip install --exists-action=w --no-cache-dir -r doc/requirements.txt
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Building wheels for collected packages: autoapi
  Building wheel for autoapi (setup.py): started
  Building wheel for autoapi (setup.py): finished with status 'done'
  Created wheel for autoapi: filename=autoapi-2.0.1-py3-none-any.whl size=13606 sha256=a2dbe014210a397c85902004147cd21ba428775c469c85a9ffc3e492e4f3b9c7
  Stored in directory: /tmp/pip-ephem-wheel-cache-bu07i3me/wheels/ca/26/79/18abdd5beff508f752fdd093843eddd65c9247c2e8f819657e
Successfully built autoapi
Installing collected packages: webencodings, fastjsonschema, zipp, wrapt, urllib3, typing-extensions, typed-ast, traitlets, tornado, tinycss2, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, pyzmq, PyYAML, python-dateutil, pyrsistent, Pygments, pkgutil-resolve-name, pandocfilters, nest-asyncio, mistune, lazy-object-proxy, jupyterlab-pygments, Jinja2, entrypoints, docutils, defusedxml, bleach, anyascii, jupyter-core, importlib-resources, importlib-metadata, beautifulsoup4, astroid, sphinx, jupyter-client, attrs, sphinx-autoapi, jsonschema, autoapi, nbformat, nbclient, nbconvert, nbsphinx
  Attempting uninstall: urllib3
    Found existing installation: urllib3 2.0.7
    Uninstalling urllib3-2.0.7:
      Successfully uninstalled urllib3-2.0.7
  Attempting uninstall: Pygments
    Found existing installation: Pygments 2.3.1
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    Found existing installation: Jinja2 2.11.3
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  Attempting uninstall: docutils
    Found existing installation: docutils 0.14
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  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.6
    Uninstalling Sphinx-1.8.6:
      Successfully uninstalled Sphinx-1.8.6
Successfully installed Jinja2-3.1.6 PyYAML-6.0.1 Pygments-2.17.2 anyascii-0.3.2 astroid-2.15.8 attrs-24.2.0 autoapi-2.0.1 beautifulsoup4-4.13.3 bleach-6.0.0 defusedxml-0.7.1 docutils-0.19 entrypoints-0.4 fastjsonschema-2.21.1 importlib-metadata-6.7.0 importlib-resources-5.12.0 jsonschema-4.17.3 jupyter-client-7.4.9 jupyter-core-4.12.0 jupyterlab-pygments-0.2.2 lazy-object-proxy-1.9.0 mistune-3.0.2 nbclient-0.7.4 nbconvert-7.6.0 nbformat-5.8.0 nbsphinx-0.9.7 nest-asyncio-1.6.0 pandocfilters-1.5.1 pkgutil-resolve-name-1.3.10 pyrsistent-0.19.3 python-dateutil-2.9.0.post0 pyzmq-26.2.1 soupsieve-2.4.1 sphinx-5.3.0 sphinx-autoapi-2.1.1 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 tinycss2-1.2.1 tornado-6.2 traitlets-5.9.0 typed-ast-1.5.5 typing-extensions-4.7.1 urllib3-1.26.20 webencodings-0.5.1 wrapt-1.16.0 zipp-3.15.0

[rtd-command-info] start-time: 2025-03-19T12:22:06.340530Z, end-time: 2025-03-19T12:22:06.400828Z, duration: 0, exit-code: 0
cat doc/conf.py
# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config

# -- Path setup --------------------------------------------------------------

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
import sys
sys.path.insert(0, os.path.abspath('..'))

# -- Project information -----------------------------------------------------

project = 'SCS Toolbox'
copyright = '2021, SCS'
author = 'SCS'

# The short X.Y version
version = ''
# The full version, including alpha/beta/rc tags
release = ''


# -- 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.mathjax',
    'sphinx.ext.viewcode',
    'sphinx.ext.coverage',
    'sphinx.ext.napoleon',
    'sphinx.ext.extlinks',
    'autoapi.extension',
    'nbsphinx'
]

nbsphinx_execute = 'never'

autoapi_dirs = ['../src/toolbox_scs']
autoapi_ignore = ['*/deprecated/*']

extlinks = {'issue': ('https://git.xfel.eu/SCS/ToolBox/-/issues/%s',
                      'issue:%s'),
            'mr': ('https://git.xfel.eu/SCS/ToolBox/-/merge_requests/%s',
                   'MR:%s'),
            'commit': ('https://git.xfel.eu/SCS/ToolBox/-/commit/%s',
                       'commit:%s')
            }

# Don't add .txt suffix to source files:
html_sourcelink_suffix = ''

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'

# The master toctree document.
master_doc = 'index'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = None


# -- 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 = 'classic'

# 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 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']

# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself.  Builtin themes are using these templates by
# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
# 'searchbox.html']``.
#
# html_sidebars = {}


# -- Options for HTMLHelp output ---------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = 'SCSToolboxdoc'


# -- Options for LaTeX output ------------------------------------------------

latex_elements = {
    # The paper size ('letterpaper' or 'a4paper').
    #
    # 'papersize': 'letterpaper',

    # The font size ('10pt', '11pt' or '12pt').
    #
    # 'pointsize': '10pt',

    # Additional stuff for the LaTeX preamble.
    #
    # 'preamble': '',

    # Latex figure (float) alignment
    #
    # 'figure_align': 'htbp',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
    (master_doc, 'SCSToolbox.tex', 'SCS Toolbox Documentation',
     'SCS', 'manual'),
]


# -- Options for manual page output ------------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    (master_doc, 'scstoolbox', 'SCS Toolbox Documentation',
     [author], 1)
]


# -- Options for Texinfo output ----------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (master_doc, 'SCSToolbox', 'SCS Toolbox Documentation',
     author, 'SCSToolbox', 'One line description of project.',
     'Miscellaneous'),
]


# -- Options for Epub output -------------------------------------------------

# Bibliographic Dublin Core info.
epub_title = project

# 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 list of files that should not be packed into the epub file.
epub_exclude_files = ['search.html']


# -- Extension configuration -------------------------------------------------




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#


import importlib
import sys
import os.path
from six import string_types

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
    (
        'html_theme' in globals() and
        html_theme in ['default'] and
        # Allow people to bail with a hack of having an html_style
        'html_style' not in globals()
    ) or 'html_theme' not in globals()
)
if using_rtd_theme:
    theme = importlib.import_module('sphinx_rtd_theme')
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'http://rtd.xfel.eu/websupport'
    websupport2_static_url = '/static/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "media/",
    'STATIC_URL': "/static/",
    'PRODUCTION_DOMAIN': "rtd.xfel.eu",
    'versions': [
    ("latest", "/en/latest/"),
    ("fix-ci-autoapi-failure", "/en/fix-ci-autoapi-failure/"),
    ],
    'downloads': [ 
    ("pdf", "//rtd.xfel.eu/downloads/scs-toolbox/latest/pdf/"),
    ("html", "//rtd.xfel.eu/downloads/scs-toolbox/latest/htmlzip/"),
    ("epub", "//rtd.xfel.eu/downloads/scs-toolbox/latest/epub/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'scs-toolbox',
    'name': u'SCS ToolBox',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'http://rtd.xfel.eu/docs/scs-toolbox/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/doc/',
    'api_host': 'http://rtd.xfel.eu',
    'github_user': 'None',
    'proxied_api_host': '/_',
    'github_repo': 'None',
    'github_version': 'master',
    'display_github': False,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'master',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'None',
    'commit': 'edf35773',
}




if 'html_context' in globals():
    
    html_context.update(context)
    
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2025-03-19T12:22:06.492505Z, end-time: 2025-03-19T12:22:41.855035Z, duration: 35, exit-code: 0
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Running Sphinx v5.3.0
WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English).
making output directory... done
WARNING: html_static_path entry '_static' does not exist
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[autosummary] generating autosummary for: Analysis_of_Viking_spectrometer_data.ipynb, Azimuthal integration of DSSC with pyFAI.ipynb, BOZ analysis part I.a Correction determination.ipynb, BOZ analysis part I.b Correction validation.ipynb, BOZ analysis part II.1 Small data.ipynb, BOZ analysis part II.2 Binning.ipynb, DSSC create geometry.ipynb, DSSC fine delay with SCS toolbox.ipynb, DSSC scattering time-delay.ipynb, Dask DSSC module binning.ipynb, ..., OnlineGPU BOZ analysis part I.a Correction determination S K-egde.ipynb, PES_spectra_extraction.ipynb, Transient reflectivity measurement.ipynb, bunch_pattern_decoding.rst, changelog.rst, dssc/DSSCBinner.rst, howtos.rst, index.rst, load.rst, maintainers.rst
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/lib/python3.7/site-packages/nbsphinx/__init__.py:1075: RuntimeWarning: You are using an unsupported version of pandoc (1.19.2.4).
Your version must be at least (2.14.2) but less than (4.0.0).
Refer to https://pandoc.org/installing.html.
Continuing with doubts...
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3433: CRITICAL: Title level inconsistent:

Peak fluence calculation using knife-edge scans:
------------------------------------------------
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3451: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3451: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3506: CRITICAL: Title level inconsistent:

Load scanning motor and laser photodiode data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3572: CRITICAL: Title level inconsistent:

Check diode traces and region of integration for peak calculations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:5807: CRITICAL: Title level inconsistent:

Plot intensity vs. knife-edge positions, fit with erfc function
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:7990: CRITICAL: Title level inconsistent:

OL power measurement
^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:8016: CRITICAL: Title level inconsistent:

Fluence vs. laser power
^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:9096: CRITICAL: Title level inconsistent:

Load runs with horizontal and vertical scans, normalize the transmitted signal by XGM
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:9676: CRITICAL: Title level inconsistent:

Fit scan to erfc function and plot
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:11863: CRITICAL: Title level inconsistent:

Load XGM data
^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:12357: CRITICAL: Title level inconsistent:

Calibrate XGM fast data using photon flux and plot
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/base/knife_edge/index.rst:4: WARNING: duplicate object description of toolbox_scs.base.knife_edge, other instance in autoapi/toolbox_scs/base/index, use :noindex: for one of them
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/dssc_misc/index.rst:30: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/fccd/index.rst:6: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/hrixs/index.rst:7: WARNING: Inline interpreted text or phrase reference start-string without end-string.
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/index.rst:7: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:381: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:646: ERROR: Unexpected indentation.
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:7: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1581: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1600: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:31: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1716: WARNING: duplicate object description of toolbox_scs.__all__, other instance in autoapi/toolbox_scs/index, use :noindex: for one of them
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1727: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:8: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1812: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1869: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1880: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1893: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2007: WARNING: duplicate object description of toolbox_scs.__all__, other instance in autoapi/toolbox_scs/index, use :noindex: for one of them
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2018: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:7: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2025: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2041: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2120: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2196: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2267: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:8: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2287: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2398: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2421: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2470: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2526: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2541: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2544: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2547: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2566: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2687: WARNING: duplicate object description of toolbox_scs.__all__, other instance in autoapi/toolbox_scs/index, use :noindex: for one of them
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:: ERROR: Unknown target name: "numpy.s".
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:: ERROR: Unknown target name: "numpy.s".
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1636: ERROR: Unknown target name: "numpy.s".
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:4: WARNING: duplicate object description of toolbox_scs.load, other instance in autoapi/toolbox_scs/index, use :noindex: for one of them
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:49: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:68: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:31: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:: ERROR: Unknown target name: "numpy.s".
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:136: ERROR: Unknown target name: "numpy.s".
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:: ERROR: Unknown target name: "numpy.s".
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/bunch_pattern/index.rst:85: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/bunch_pattern/index.rst:8: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/bunch_pattern/index.rst:126: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/bunch_pattern/index.rst:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:61: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:8: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:146: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:203: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:214: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:227: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/laser_utils/index.rst:28: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/laser_utils/index.rst:41: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/laser_utils/index.rst:55: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/XAS/index.rst:40: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/XAS/index.rst:7: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/XAS/index.rst:47: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/XAS/index.rst:63: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:135: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:211: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:282: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:8: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:302: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:413: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:436: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:485: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:541: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:556: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:559: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:562: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:581: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:88: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:7: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:95: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:111: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:190: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:266: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:337: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:8: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:357: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:468: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:491: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:540: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:596: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:611: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:614: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:617: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:636: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/knife_edge/index.rst:4: WARNING: duplicate object description of toolbox_scs.routines.knife_edge, other instance in autoapi/toolbox_scs/routines/index, use :noindex: for one of them
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/test/test_dssc_cls/index.rst:89: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/test/test_dssc_cls/index.rst:27: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/test/test_hrixs/index.rst:47: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/test/test_hrixs/index.rst:27: WARNING: Block quote ends without a blank line; unexpected unindent.
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done
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writing output... [  1%] Analysis_of_Viking_spectrometer_data
writing output... [  2%] Azimuthal integration of DSSC with pyFAI
writing output... [  4%] BOZ analysis part I.a Correction determination
writing output... [  5%] BOZ analysis part I.b Correction validation
writing output... [  7%] BOZ analysis part II.1 Small data
writing output... [  8%] BOZ analysis part II.2 Binning
writing output... [ 10%] DSSC create geometry
writing output... [ 11%] DSSC fine delay with SCS toolbox
writing output... [ 13%] DSSC scattering time-delay
writing output... [ 14%] Dask DSSC module binning
writing output... [ 16%] HRIXS
writing output... [ 17%] How to extract peaks from digitizer traces
writing output... [ 19%] Knife edge scan and fluence calculation
writing output... [ 20%] Loading_data_in_memory
writing output... [ 22%] OnlineGPU BOZ analysis part I.a Correction determination S K-egde
writing output... [ 23%] PES_spectra_extraction
writing output... [ 25%] Transient reflectivity measurement
writing output... [ 26%] autoapi/index
writing output... [ 28%] autoapi/toolbox_scs/base/index
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writing output... [ 35%] autoapi/toolbox_scs/detectors/azimuthal_integrator/index
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writing output... [ 55%] autoapi/toolbox_scs/detectors/viking/index
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writing output... [ 70%] autoapi/toolbox_scs/routines/Reflectivity/index
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writing output... [ 79%] autoapi/toolbox_scs/test/test_dssc_cls/index
writing output... [ 80%] autoapi/toolbox_scs/test/test_hrixs/index
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writing output... [ 94%] dssc/DSSCBinner
writing output... [ 95%] howtos
writing output... [ 97%] index
writing output... [ 98%] load
writing output... [100%] maintainers

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[autosummary] generating autosummary for: Analysis_of_Viking_spectrometer_data.ipynb, Azimuthal integration of DSSC with pyFAI.ipynb, BOZ analysis part I.a Correction determination.ipynb, BOZ analysis part I.b Correction validation.ipynb, BOZ analysis part II.1 Small data.ipynb, BOZ analysis part II.2 Binning.ipynb, DSSC create geometry.ipynb, DSSC fine delay with SCS toolbox.ipynb, DSSC scattering time-delay.ipynb, Dask DSSC module binning.ipynb, ..., OnlineGPU BOZ analysis part I.a Correction determination S K-egde.ipynb, PES_spectra_extraction.ipynb, Transient reflectivity measurement.ipynb, bunch_pattern_decoding.rst, changelog.rst, dssc/DSSCBinner.rst, howtos.rst, index.rst, load.rst, maintainers.rst
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/lib/python3.7/site-packages/nbsphinx/__init__.py:1075: RuntimeWarning: You are using an unsupported version of pandoc (1.19.2.4).
Your version must be at least (2.14.2) but less than (4.0.0).
Refer to https://pandoc.org/installing.html.
Continuing with doubts...
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3433: CRITICAL: Title level inconsistent:

Peak fluence calculation using knife-edge scans:
------------------------------------------------
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3451: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3451: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3506: CRITICAL: Title level inconsistent:

Load scanning motor and laser photodiode data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3572: CRITICAL: Title level inconsistent:

Check diode traces and region of integration for peak calculations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:5807: CRITICAL: Title level inconsistent:

Plot intensity vs. knife-edge positions, fit with erfc function
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:7990: CRITICAL: Title level inconsistent:

OL power measurement
^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:8016: CRITICAL: Title level inconsistent:

Fluence vs. laser power
^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:9096: CRITICAL: Title level inconsistent:

Load runs with horizontal and vertical scans, normalize the transmitted signal by XGM
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:9676: CRITICAL: Title level inconsistent:

Fit scan to erfc function and plot
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:11863: CRITICAL: Title level inconsistent:

Load XGM data
^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:12357: CRITICAL: Title level inconsistent:

Calibrate XGM fast data using photon flux and plot
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/base/knife_edge/index.rst:4: WARNING: duplicate object description of toolbox_scs.base.knife_edge, other instance in autoapi/toolbox_scs/base/index, use :noindex: for one of them
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/digitizers/index.rst:155: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/dssc_misc/index.rst:71: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/dssc_misc/index.rst:30: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/fccd/index.rst:6: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/hrixs/index.rst:7: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/index.rst:307: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/index.rst:572: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/index.rst:30: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/index.rst:7: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:381: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:646: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:30: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:7: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1581: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1600: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:31: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1716: WARNING: duplicate object description of toolbox_scs.__all__, other instance in autoapi/toolbox_scs/index, use :noindex: for one of them
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:8: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1812: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:12: WARNING: Block quote ends without a blank line; unexpected unindent.
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1880: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1893: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2007: WARNING: duplicate object description of toolbox_scs.__all__, other instance in autoapi/toolbox_scs/index, use :noindex: for one of them
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:7: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2025: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2041: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2120: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2196: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2267: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:8: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2287: ERROR: Unexpected indentation.
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2398: ERROR: Unexpected indentation.
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2421: ERROR: Unexpected indentation.
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2470: ERROR: Unexpected indentation.
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2526: ERROR: Unexpected indentation.
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2544: ERROR: Unexpected indentation.
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2547: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2566: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:2687: WARNING: duplicate object description of toolbox_scs.__all__, other instance in autoapi/toolbox_scs/index, use :noindex: for one of them
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:: ERROR: Unknown target name: "numpy.s".
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:: ERROR: Unknown target name: "numpy.s".
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:1636: ERROR: Unknown target name: "numpy.s".
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:4: WARNING: duplicate object description of toolbox_scs.load, other instance in autoapi/toolbox_scs/index, use :noindex: for one of them
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:68: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:31: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:: ERROR: Unknown target name: "numpy.s".
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:136: ERROR: Unknown target name: "numpy.s".
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:: ERROR: Unknown target name: "numpy.s".
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/bunch_pattern/index.rst:85: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/bunch_pattern/index.rst:8: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/bunch_pattern/index.rst:126: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/bunch_pattern/index.rst:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:61: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:8: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:146: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:203: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:214: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:227: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/laser_utils/index.rst:28: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/laser_utils/index.rst:41: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/laser_utils/index.rst:55: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/XAS/index.rst:40: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/XAS/index.rst:7: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/XAS/index.rst:47: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/XAS/index.rst:63: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:135: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:211: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:282: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:8: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:302: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:413: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:436: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:485: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:541: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:556: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:559: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:12: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:562: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:581: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:88: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:7: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:95: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:111: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:190: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:266: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:337: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:8: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:357: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:468: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:491: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:540: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:10: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:596: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:611: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:614: ERROR: Unexpected indentation.
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[autosummary] generating autosummary for: Analysis_of_Viking_spectrometer_data.ipynb, Azimuthal integration of DSSC with pyFAI.ipynb, BOZ analysis part I.a Correction determination.ipynb, BOZ analysis part I.b Correction validation.ipynb, BOZ analysis part II.1 Small data.ipynb, BOZ analysis part II.2 Binning.ipynb, DSSC create geometry.ipynb, DSSC fine delay with SCS toolbox.ipynb, DSSC scattering time-delay.ipynb, Dask DSSC module binning.ipynb, ..., OnlineGPU BOZ analysis part I.a Correction determination S K-egde.ipynb, PES_spectra_extraction.ipynb, Transient reflectivity measurement.ipynb, bunch_pattern_decoding.rst, changelog.rst, dssc/DSSCBinner.rst, howtos.rst, index.rst, load.rst, maintainers.rst
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: [new config] 67 added, 0 changed, 0 removed
reading sources... [  1%] Analysis_of_Viking_spectrometer_data
reading sources... [  2%] Azimuthal integration of DSSC with pyFAI
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reading sources... [  7%] BOZ analysis part II.1 Small data
reading sources... [  8%] BOZ analysis part II.2 Binning
reading sources... [ 10%] DSSC create geometry
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reading sources... [ 13%] DSSC scattering time-delay
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reading sources... [ 16%] HRIXS
reading sources... [ 17%] How to extract peaks from digitizer traces
reading sources... [ 19%] Knife edge scan and fluence calculation
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reading sources... [ 23%] PES_spectra_extraction
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/lib/python3.7/site-packages/nbsphinx/__init__.py:1075: RuntimeWarning: You are using an unsupported version of pandoc (1.19.2.4).
Your version must be at least (2.14.2) but less than (4.0.0).
Refer to https://pandoc.org/installing.html.
Continuing with doubts...
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3433: CRITICAL: Title level inconsistent:

Peak fluence calculation using knife-edge scans:
------------------------------------------------
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3451: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3451: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3506: CRITICAL: Title level inconsistent:

Load scanning motor and laser photodiode data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3572: CRITICAL: Title level inconsistent:

Check diode traces and region of integration for peak calculations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:5807: CRITICAL: Title level inconsistent:

Plot intensity vs. knife-edge positions, fit with erfc function
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:7990: CRITICAL: Title level inconsistent:

OL power measurement
^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:8016: CRITICAL: Title level inconsistent:

Fluence vs. laser power
^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:9096: CRITICAL: Title level inconsistent:

Load runs with horizontal and vertical scans, normalize the transmitted signal by XGM
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:9676: CRITICAL: Title level inconsistent:

Fit scan to erfc function and plot
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:11863: CRITICAL: Title level inconsistent:

Load XGM data
^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:12357: CRITICAL: Title level inconsistent:

Calibrate XGM fast data using photon flux and plot
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/base/knife_edge/index.rst:4: WARNING: duplicate object description of toolbox_scs.base.knife_edge, other instance in autoapi/toolbox_scs/base/index, use :noindex: for one of them
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done
processing SCSToolbox.tex... index howtos maintainers changelog autoapi/index autoapi/toolbox_scs/index autoapi/toolbox_scs/base/index autoapi/toolbox_scs/base/tests/index autoapi/toolbox_scs/base/tests/test_knife_edge/index autoapi/toolbox_scs/base/knife_edge/index autoapi/toolbox_scs/detectors/index autoapi/toolbox_scs/detectors/azimuthal_integrator/index autoapi/toolbox_scs/detectors/bam_detectors/index autoapi/toolbox_scs/detectors/digitizers/index autoapi/toolbox_scs/detectors/dssc/index autoapi/toolbox_scs/detectors/dssc_data/index autoapi/toolbox_scs/detectors/dssc_misc/index autoapi/toolbox_scs/detectors/dssc_plot/index autoapi/toolbox_scs/detectors/dssc_processing/index autoapi/toolbox_scs/detectors/fccd/index autoapi/toolbox_scs/detectors/gotthard2/index autoapi/toolbox_scs/detectors/hrixs/index autoapi/toolbox_scs/detectors/pes/index autoapi/toolbox_scs/detectors/viking/index autoapi/toolbox_scs/detectors/xgm/index autoapi/toolbox_scs/misc/index autoapi/toolbox_scs/misc/bunch_pattern/index autoapi/toolbox_scs/misc/bunch_pattern_external/index autoapi/toolbox_scs/misc/laser_utils/index autoapi/toolbox_scs/misc/undulator/index autoapi/toolbox_scs/routines/index autoapi/toolbox_scs/routines/Reflectivity/index autoapi/toolbox_scs/routines/XAS/index autoapi/toolbox_scs/routines/boz/index autoapi/toolbox_scs/routines/knife_edge/index autoapi/toolbox_scs/test/index autoapi/toolbox_scs/test/test_dssc_cls/index autoapi/toolbox_scs/test/test_hrixs/index autoapi/toolbox_scs/test/test_misc/index autoapi/toolbox_scs/test/test_top_level/index autoapi/toolbox_scs/test/test_utils/index autoapi/toolbox_scs/util/index autoapi/toolbox_scs/util/exceptions/index autoapi/toolbox_scs/util/pkg/index autoapi/toolbox_scs/constants/index autoapi/toolbox_scs/load/index autoapi/toolbox_scs/mnemonics_machinery/index 
resolving references...
done
writing... done
copying images... [ 50%] sview.png
copying images... [100%] metadata.png

copying TeX support files... copying TeX support files...
done
build succeeded, 176 warnings.

The LaTeX files are in _build/latex.
Run 'make' in that directory to run these through (pdf)latex
(use `make latexpdf' here to do that automatically).

[rtd-command-info] start-time: 2025-03-19T12:23:41.775295Z, end-time: 2025-03-19T12:23:41.834085Z, duration: 0, exit-code: 0
cat latexmkrc
$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S';
$makeindex = 'makeindex -s python.ist %O -o %D %S';
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
 return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}

[rtd-command-info] start-time: 2025-03-19T12:23:41.936576Z, end-time: 2025-03-19T12:23:47.185297Z, duration: 5, exit-code: 0
latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=scs-toolbox -interaction=nonstopmode
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Subroutine makeglo redefined at (eval 11) line 7, <GEN2> chunk 1.
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Chapter 1.
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Chapter 2.
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Chapter 3.
[11] [12] [13] [14] [15] [16]
Chapter 4.

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[17]

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[18]

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[19]

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[20]

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[21]

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[25]

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mod-ule,

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[]|[][]\T1/txtt/m/sl/10 extract_GH2[][]\T1/qtm/m/n/10 (ds, run[, first-Frame, b
unch-Pat-tern,
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U sub-di-rec-tory. The data is stored in <pro-posal

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/10 ) ^^U If True, ex-tracts the val-ues from BAM vari-ables (e.g.
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/10 ) ^^U If True, ex-tracts the val-ues from BAM vari-ables (e.g.
[148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159]
[160] [161] [162] [163] [164] [165] [166]
Chapter 5.
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Chapter 6.
[169 <./metadata.png>] [170]
Chapter 7.
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Chapter 8.
[173] [174]
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[]\T1/txtt/m/n/10 toolbox_scs.detectors.azimuthal_integrator\T1/qtm/m/n/10 ,
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/10 ) ^^U If True, ex-tracts the val-ues from BAM vari-ables (e.g.
[148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159]
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Chapter 5.
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Chapter 6.
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Chapter 7.
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Chapter 8.
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(see the transcript file for additional information){/usr/share/texmf/fonts/enc
/dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}{
/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texmf/fon
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/qhvr.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qtmb.pfb></usr/share/te
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ex-gyre/qtmri.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1x
btt.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/txfonts/tcxbtt.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/txfonts/tcxtt.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
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Transcript written on scs-toolbox.log.
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Latexmk: Log file says output to 'scs-toolbox.pdf'
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[autosummary] generating autosummary for: Analysis_of_Viking_spectrometer_data.ipynb, Azimuthal integration of DSSC with pyFAI.ipynb, BOZ analysis part I.a Correction determination.ipynb, BOZ analysis part I.b Correction validation.ipynb, BOZ analysis part II.1 Small data.ipynb, BOZ analysis part II.2 Binning.ipynb, DSSC create geometry.ipynb, DSSC fine delay with SCS toolbox.ipynb, DSSC scattering time-delay.ipynb, Dask DSSC module binning.ipynb, ..., OnlineGPU BOZ analysis part I.a Correction determination S K-egde.ipynb, PES_spectra_extraction.ipynb, Transient reflectivity measurement.ipynb, bunch_pattern_decoding.rst, changelog.rst, dssc/DSSCBinner.rst, howtos.rst, index.rst, load.rst, maintainers.rst
building [mo]: targets for 0 po files that are out of date
building [epub]: targets for 24 source files that are out of date
updating environment: [new config] 67 added, 0 changed, 0 removed
reading sources... [  1%] Analysis_of_Viking_spectrometer_data
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reading sources... [ 10%] DSSC create geometry
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reading sources... [ 13%] DSSC scattering time-delay
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reading sources... [ 16%] HRIXS
reading sources... [ 17%] How to extract peaks from digitizer traces
reading sources... [ 19%] Knife edge scan and fluence calculation
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/lib/python3.7/site-packages/nbsphinx/__init__.py:1075: RuntimeWarning: You are using an unsupported version of pandoc (1.19.2.4).
Your version must be at least (2.14.2) but less than (4.0.0).
Refer to https://pandoc.org/installing.html.
Continuing with doubts...
  nbconvert.utils.pandoc.check_pandoc_version()
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3433: CRITICAL: Title level inconsistent:

Peak fluence calculation using knife-edge scans:
------------------------------------------------
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3451: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3451: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3506: CRITICAL: Title level inconsistent:

Load scanning motor and laser photodiode data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:3572: CRITICAL: Title level inconsistent:

Check diode traces and region of integration for peak calculations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:5807: CRITICAL: Title level inconsistent:

Plot intensity vs. knife-edge positions, fit with erfc function
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:7990: CRITICAL: Title level inconsistent:

OL power measurement
^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:8016: CRITICAL: Title level inconsistent:

Fluence vs. laser power
^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:9096: CRITICAL: Title level inconsistent:

Load runs with horizontal and vertical scans, normalize the transmitted signal by XGM
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:9676: CRITICAL: Title level inconsistent:

Fit scan to erfc function and plot
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:11863: CRITICAL: Title level inconsistent:

Load XGM data
^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb:12357: CRITICAL: Title level inconsistent:

Calibrate XGM fast data using photon flux and plot
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/base/knife_edge/index.rst:4: WARNING: duplicate object description of toolbox_scs.base.knife_edge, other instance in autoapi/toolbox_scs/base/index, use :noindex: for one of them
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/dssc_misc/index.rst:30: WARNING: Definition list ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/fccd/index.rst:6: WARNING: Definition list ends without a blank line; unexpected unindent.
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/detectors/index.rst:7: WARNING: Inline interpreted text or phrase reference start-string without end-string.
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/index.rst:: ERROR: Unknown target name: "numpy.s".
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:: ERROR: Unknown target name: "numpy.s".
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/load/index.rst:136: ERROR: Unknown target name: "numpy.s".
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:559: ERROR: Unexpected indentation.
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:12: WARNING: Block quote ends without a blank line; unexpected unindent.
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/test/test_hrixs/index.rst:47: ERROR: Unexpected indentation.
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WARNING: nbsphinx_widgets_path not given and ipywidgets module unavailable
looking for now-outdated files... none found
pickling environment... done
checking consistency... /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Analysis_of_Viking_spectrometer_data.ipynb: WARNING: document isn't included in any toctree
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/BOZ analysis part II.1 Small data.ipynb: WARNING: document isn't included in any toctree
/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/BOZ analysis part II.2 Binning.ipynb: WARNING: document isn't included in any toctree
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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Knife edge scan and fluence calculation.ipynb: WARNING: document isn't included in any toctree
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done
preparing documents... done
writing output... [  1%] Analysis_of_Viking_spectrometer_data
writing output... [  2%] Azimuthal integration of DSSC with pyFAI
writing output... [  4%] BOZ analysis part I.a Correction determination
writing output... [  5%] BOZ analysis part I.b Correction validation
writing output... [  7%] BOZ analysis part II.1 Small data
writing output... [  8%] BOZ analysis part II.2 Binning
writing output... [ 10%] DSSC create geometry
writing output... [ 11%] DSSC fine delay with SCS toolbox
writing output... [ 13%] DSSC scattering time-delay
writing output... [ 14%] Dask DSSC module binning
writing output... [ 16%] HRIXS
writing output... [ 17%] How to extract peaks from digitizer traces
writing output... [ 19%] Knife edge scan and fluence calculation
writing output... [ 20%] Loading_data_in_memory
writing output... [ 22%] OnlineGPU BOZ analysis part I.a Correction determination S K-egde
writing output... [ 23%] PES_spectra_extraction
writing output... [ 25%] Transient reflectivity measurement
writing output... [ 26%] autoapi/index
writing output... [ 28%] autoapi/toolbox_scs/base/index
writing output... [ 29%] autoapi/toolbox_scs/base/knife_edge/index
writing output... [ 31%] autoapi/toolbox_scs/base/tests/index
writing output... [ 32%] autoapi/toolbox_scs/base/tests/test_knife_edge/index
writing output... [ 34%] autoapi/toolbox_scs/constants/index
writing output... [ 35%] autoapi/toolbox_scs/detectors/azimuthal_integrator/index
writing output... [ 37%] autoapi/toolbox_scs/detectors/bam_detectors/index
writing output... [ 38%] autoapi/toolbox_scs/detectors/digitizers/index
writing output... [ 40%] autoapi/toolbox_scs/detectors/dssc/index
writing output... [ 41%] autoapi/toolbox_scs/detectors/dssc_data/index
writing output... [ 43%] autoapi/toolbox_scs/detectors/dssc_misc/index
writing output... [ 44%] autoapi/toolbox_scs/detectors/dssc_plot/index
writing output... [ 46%] autoapi/toolbox_scs/detectors/dssc_processing/index
writing output... [ 47%] autoapi/toolbox_scs/detectors/fccd/index
writing output... [ 49%] autoapi/toolbox_scs/detectors/gotthard2/index
writing output... [ 50%] autoapi/toolbox_scs/detectors/hrixs/index
writing output... [ 52%] autoapi/toolbox_scs/detectors/index
writing output... [ 53%] autoapi/toolbox_scs/detectors/pes/index
writing output... [ 55%] autoapi/toolbox_scs/detectors/viking/index
writing output... [ 56%] autoapi/toolbox_scs/detectors/xgm/index
writing output... [ 58%] autoapi/toolbox_scs/index
writing output... [ 59%] autoapi/toolbox_scs/load/index
writing output... [ 61%] autoapi/toolbox_scs/misc/bunch_pattern/index
writing output... [ 62%] autoapi/toolbox_scs/misc/bunch_pattern_external/index
writing output... [ 64%] autoapi/toolbox_scs/misc/index
writing output... [ 65%] autoapi/toolbox_scs/misc/laser_utils/index
writing output... [ 67%] autoapi/toolbox_scs/misc/undulator/index
writing output... [ 68%] autoapi/toolbox_scs/mnemonics_machinery/index
writing output... [ 70%] autoapi/toolbox_scs/routines/Reflectivity/index
writing output... [ 71%] autoapi/toolbox_scs/routines/XAS/index
writing output... [ 73%] autoapi/toolbox_scs/routines/boz/index
writing output... [ 74%] autoapi/toolbox_scs/routines/index
writing output... [ 76%] autoapi/toolbox_scs/routines/knife_edge/index
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writing output... [ 94%] dssc/DSSCBinner
writing output... [ 95%] howtos
writing output... [ 97%] index
writing output... [ 98%] load
writing output... [100%] maintainers

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build succeeded, 523 warnings.

The ePub file is in _build/epub.

[rtd-command-info] start-time: 2025-03-19T12:24:20.430344Z, end-time: 2025-03-19T12:24:20.512569Z, duration: 0, exit-code: 0
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