Read the Docs build information
Build id: 23250
Project: european-xfel-offline-calibration
Version: latest
Commit: c81d00593085ffe5ff8fd65891bdbd942d09a76f
Date: 2022-03-16T07:41:50.620727Z
State: finished
Success: True


[rtd-command-info] start-time: 2022-03-16T07:41:51.836902Z, end-time: 2022-03-16T07:42:14.660885Z, duration: 22, exit-code: 0
git clone --no-single-branch --depth 50 http://git.xfel.eu/gitlab/detectors/pycalibration.git .
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[rtd-command-info] start-time: 2022-03-16T07:42:15.315035Z, end-time: 2022-03-16T07:42:16.056428Z, duration: 0, exit-code: 0
git checkout --force origin/doc/update_pycalibration_documentation
Note: checking out 'origin/doc/update_pycalibration_documentation'.

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 c81d005 resolve conflicts with master

[rtd-command-info] start-time: 2022-03-16T07:42:16.185604Z, end-time: 2022-03-16T07:42:16.276611Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-03-16T07:42:18.345359Z, end-time: 2022-03-16T07:42:25.621742Z, duration: 7, exit-code: 0
python3.8 -mvirtualenv /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest
Using base prefix '/home/docs/.pyenv/versions/3.8.0'
New python executable in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python3.8
Also creating executable in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2022-03-16T07:42:25.770944Z, end-time: 2022-03-16T07:42:26.978365Z, duration: 1, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/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/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (22.0.4)

[rtd-command-info] start-time: 2022-03-16T07:42:27.117472Z, end-time: 2022-03-16T07:43:03.762480Z, duration: 36, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1
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Building wheels for collected packages: mock, pillow, future
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  Stored in directory: /tmp/pip-ephem-wheel-cache-c0zncu03/wheels/41/7c/21/90057f91c6ead7c77a90c52d6e85ca48bf82d8b0d3f8dfbb65
  Building wheel for pillow (setup.py): started
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  Created wheel for pillow: filename=Pillow-5.4.1-cp38-cp38-linux_x86_64.whl size=1263124 sha256=e55c055d64347939f2ea628217ef32f602ad127f42524b2df205cb084c95909c
  Stored in directory: /tmp/pip-ephem-wheel-cache-c0zncu03/wheels/5f/a8/6b/5b7b3f764d879214eb03570f74d2b086201eb514e6ffa68d6d
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=05887bf75309a6ac32c2d139183cc18df0ff3c891149d4738860f7e90f9cd715
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Successfully built mock pillow future
Installing collected packages: snowballstemmer, pytz, Pygments, mock, docutils, certifi, alabaster, urllib3, sphinxcontrib-serializinghtml, six, setuptools, pyparsing, pillow, MarkupSafe, imagesize, idna, future, charset-normalizer, babel, sphinxcontrib-websupport, requests, packaging, Jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
  Attempting uninstall: setuptools
    Found existing installation: setuptools 60.9.3
    Uninstalling setuptools-60.9.3:
      Successfully uninstalled setuptools-60.9.3
Successfully installed Jinja2-3.0.3 MarkupSafe-2.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-3.3 imagesize-1.3.0 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.7 pytz-2021.3 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.27.1 setuptools-41.0.1 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.8

[rtd-command-info] start-time: 2022-03-16T07:43:03.895558Z, end-time: 2022-03-16T07:43:13.531603Z, duration: 9, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Collecting iCalibrationDB@ git+https://xcalgitlab:dxh5vE8fFsEJHvatXjsV@git.xfel.eu/gitlab/detectors/cal_db_interactive.git@2.1.0
  Cloning https://xcalgitlab:****@git.xfel.eu/gitlab/detectors/cal_db_interactive.git (to revision 2.1.0) to /tmp/pip-install-p2rkx9xg/icalibrationdb_74110d4c264a4bbb8e905425f1f2c421
  Running command git clone --filter=blob:none --quiet 'https://xcalgitlab:****@git.xfel.eu/gitlab/detectors/cal_db_interactive.git' /tmp/pip-install-p2rkx9xg/icalibrationdb_74110d4c264a4bbb8e905425f1f2c421
  Running command git checkout -q 691d9ed616391a761fd88d6514c404436fbc83ff
  Resolved https://xcalgitlab:****@git.xfel.eu/gitlab/detectors/cal_db_interactive.git to commit 691d9ed616391a761fd88d6514c404436fbc83ff
  Preparing metadata (setup.py): started
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Collecting h5py
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Collecting numpy>=1.14.5
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Requirement already satisfied: six>=1.5 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from python-dateutil->iCalibrationDB@ git+https://xcalgitlab:dxh5vE8fFsEJHvatXjsV@git.xfel.eu/gitlab/detectors/cal_db_interactive.git@2.1.0->-r docs/requirements.txt (line 1)) (1.16.0)
Building wheels for collected packages: iCalibrationDB
  Building wheel for iCalibrationDB (setup.py): started
  Building wheel for iCalibrationDB (setup.py): finished with status 'done'
  Created wheel for iCalibrationDB: filename=iCalibrationDB-2.1.0-py3-none-any.whl size=32643 sha256=0c85a04f61340abc0e5301c28830b98dad1cc9fde0d22505d1a1feeda3088a82
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Successfully built iCalibrationDB
Installing collected packages: pyzmq, python-dateutil, numpy, h5py, iCalibrationDB
Successfully installed h5py-3.6.0 iCalibrationDB-2.1.0 numpy-1.22.3 python-dateutil-2.8.2 pyzmq-22.3.0

[rtd-command-info] start-time: 2022-03-16T07:43:13.668497Z, end-time: 2022-03-16T07:44:31.674517Z, duration: 78, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[docs]
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Building wheels for collected packages: dill, prettytable, pypandoc, pyyaml, sharedmem, tabulate, European-XFEL-Offline-Calibration, karabo-bridge
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  Building wheel for European-XFEL-Offline-Calibration (pyproject.toml): started
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  Created wheel for karabo-bridge: filename=karabo_bridge-0.6.1-py3-none-any.whl size=23572 sha256=c4406aa46ee19a47e52013485bc982a486a727933abf2c00587ce4d46e31b7ed
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Successfully built dill prettytable pypandoc pyyaml sharedmem tabulate European-XFEL-Offline-Calibration karabo-bridge
Installing collected packages: webencodings, wcwidth, tabulate, Send2Trash, ptyprocess, prettytable, pickleshare, msgpack, mistune, kafka-python, ipython-genutils, dynaconf, chardet, backcall, astcheck, zipp, urllib3, tornado, testpath, smmap, setuptools, pyzmq, pyyaml, python-dateutil, pyrsistent, pygments, pycparser, psutil, prompt-toolkit, prometheus-client, pillow, pexpect, parso, pandocfilters, oauthlib, numpy, nest-asyncio, markupsafe, lxml, kiwisolver, joblib, idna, entrypoints, docutils, dill, defusedxml, decorator, Cython, cycler, attrs, async-generator, astsearch, traitlets, terminado, sharedmem, scipy, requests, pypandoc, pasha, pandas, msgpack-numpy, matplotlib, Jinja2, jedi, importlib-resources, iminuit, h5py, gitdb, fabio, cffi, cfelpyutils, bleach, xarray, sphinx, scikit-learn, requests-oauthlib, karabo-bridge, jupyter-core, jsonschema, ipython, gitpython, extra-geom, argon2-cffi-bindings, oauth2-xfel-client, nbformat, karabo-data, jupyter-client, extra-data, argon2-cffi, nbconvert, nbclient, metadata-client, ipykernel, princess, notebook, nbsphinx, nbparameterise, jupyter-console, ipyparallel, European-XFEL-Offline-Calibration
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    Uninstalling Sphinx-1.8.6:
      Successfully uninstalled Sphinx-1.8.6
Successfully installed Cython-0.29.21 European-XFEL-Offline-Calibration-1.0 Jinja2-2.11.2 Send2Trash-1.8.0 argon2-cffi-21.3.0 argon2-cffi-bindings-21.2.0 astcheck-0.2.5 astsearch-0.2.0 async-generator-1.10 attrs-21.4.0 backcall-0.2.0 bleach-4.1.0 cfelpyutils-1.0.1 cffi-1.15.0 chardet-3.0.4 cycler-0.11.0 decorator-5.1.1 defusedxml-0.7.1 dill-0.3.0 docutils-0.17.1 dynaconf-3.1.4 entrypoints-0.4 extra-data-1.9.1 extra-geom-1.6.0 fabio-0.13.0 gitdb-4.0.9 gitpython-3.1.0 h5py-3.5.0 idna-2.8 iminuit-1.3.8 importlib-resources-5.4.0 ipykernel-5.1.4 ipyparallel-6.2.4 ipython-7.12.0 ipython-genutils-0.2.0 jedi-0.18.1 joblib-1.1.0 jsonschema-4.4.0 jupyter-client-6.1.7 jupyter-console-6.1.0 jupyter-core-4.6.1 kafka-python-2.0.2 karabo-bridge-0.6.1 karabo-data-0.7.0 kiwisolver-1.4.0 lxml-4.5.0 markupsafe-2.0.1 matplotlib-3.4.2 metadata-client-3.0.8 mistune-0.8.4 msgpack-1.0.3 msgpack-numpy-0.4.7.1 nbclient-0.5.1 nbconvert-5.6.1 nbformat-5.0.7 nbparameterise-0.5 nbsphinx-0.8.8 nest-asyncio-1.5.4 notebook-6.1.5 numpy-1.20.3 oauth2-xfel-client-6.0.1 oauthlib-3.2.0 pandas-1.4.1 pandocfilters-1.5.0 parso-0.8.3 pasha-0.1.0 pexpect-4.8.0 pickleshare-0.7.5 pillow-9.0.1 prettytable-0.7.2 princess-0.5 prometheus-client-0.13.1 prompt-toolkit-3.0.28 psutil-5.9.0 ptyprocess-0.7.0 pycparser-2.21 pygments-2.11.2 pypandoc-1.4 pyrsistent-0.18.1 python-dateutil-2.8.1 pyyaml-5.3 pyzmq-19.0.0 requests-2.22.0 requests-oauthlib-1.3.1 scikit-learn-0.22.2.post1 scipy-1.7.0 setuptools-60.9.3 sharedmem-0.3.8 smmap-5.0.0 sphinx-1.8.5 tabulate-0.8.6 terminado-0.13.3 testpath-0.6.0 tornado-6.1 traitlets-4.3.3 urllib3-1.25.11 wcwidth-0.2.5 webencodings-0.5.1 xarray-2022.3.0 zipp-3.7.0

[rtd-command-info] start-time: 2022-03-16T07:44:32.710988Z, end-time: 2022-03-16T07:44:33.069512Z, duration: 0, exit-code: 0
cat docs/source/conf.py
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# European XFEL Offline Calibration documentation build configuration file, created by
# sphinx-quickstart on Sun Jun 10 17:32:30 2018.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.

import glob

# 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('.'))
import os
import shutil
import sys
import textwrap
from datetime import datetime
from subprocess import Popen, check_output
from textwrap import dedent, indent
from uuid import uuid4

import nbformat
import tabulate
from dateutil.parser import parse
from lxml import etree
from nbconvert import RSTExporter

# generate the list of available notebooks
from xfel_calibrate import notebooks

# -- General configuration ------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    'sphinx.ext.autodoc',
    'sphinx.ext.intersphinx',
    'sphinx.ext.todo',
    'sphinx.ext.mathjax',
    'sphinx.ext.ifconfig',
    'sphinx.ext.viewcode',
]

sys.path.append(os.path.abspath("../pycalibration/"))
p = Popen(["./makeAllDocs.sh"])
p.communicate()

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

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

# The encoding of source files.
#
# source_encoding = 'utf-8-sig'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = 'European XFEL Offline Calibration'
copyright = '2018, The European XFEL Detector Group'
author = 'The European XFEL Detector Group'

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = '1.0'
# The full version, including alpha/beta/rc tags.
release = '1.0'

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

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#
# today = ''
#
# Else, today_fmt is used as the format for a strftime call.
#
# today_fmt = '%B %d, %Y'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = []

# The reST default role (used for this markup: `text`) to use for all
# documents.
#
# default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.
#
# add_function_parentheses = True

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#
# add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#
# show_authors = False

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'

# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []

# If true, keep warnings as "system message" paragraphs in the built documents.
# keep_warnings = False

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = True


# -- Options for HTML output ----------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
#
html_theme = 'sphinx_rtd_theme'

# Theme options are theme-specific and customize the look and feel of a theme
# further.  For a list of options available for each theme, see the
# documentation.
#
# html_theme_options = {}

# Add any paths that contain custom themes here, relative to this directory.
# html_theme_path = []

# The name for this set of Sphinx documents.
# "<project> v<release> documentation" by default.
#
# html_title = 'European XFEL Offline Calibration v1.0'

# A shorter title for the navigation bar.  Default is the same as html_title.
#
# html_short_title = None

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#
# html_logo = None

# The name of an image file (relative to this directory) to use as a favicon of
# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#
# html_favicon = None

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']

# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#
# html_extra_path = []

# If not None, a 'Last updated on:' timestamp is inserted at every page
# bottom, using the given strftime format.
# The empty string is equivalent to '%b %d, %Y'.
#
# html_last_updated_fmt = None

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#
# html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
#
# html_sidebars = {}

# Additional templates that should be rendered to pages, maps page names to
# template names.
#
# html_additional_pages = {}

# If false, no module index is generated.
#
# html_domain_indices = True

# If false, no index is generated.
#
# html_use_index = True

# If true, the index is split into individual pages for each letter.
#
# html_split_index = False

# If true, links to the reST sources are added to the pages.
#
# html_show_sourcelink = True

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#
# html_show_sphinx = True

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#
# html_show_copyright = True

# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it.  The value of this option must be the
# base URL from which the finished HTML is served.
#
# html_use_opensearch = ''

# This is the file name suffix for HTML files (e.g. ".xhtml").
# html_file_suffix = None

# Language to be used for generating the HTML full-text search index.
# Sphinx supports the following languages:
#   'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'
#   'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr', 'zh'
#
# html_search_language = 'en'

# A dictionary with options for the search language support, empty by default.
# 'ja' uses this config value.
# 'zh' user can custom change `jieba` dictionary path.
#
# html_search_options = {'type': 'default'}

# The name of a javascript file (relative to the configuration directory) that
# implements a search results scorer. If empty, the default will be used.
#
# html_search_scorer = 'scorer.js'

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

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

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

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

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

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

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
    (master_doc, 'EuropeanXFELOfflineCalibration.tex', 'European XFEL Offline Calibration Documentation',
     'The European XFEL Detector Group', 'manual', True),
]

# The name of an image file (relative to this directory) to place at the top of
# the title page.
#
# latex_logo = None

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#
# latex_use_parts = False

# If true, show page references after internal links.
#
# latex_show_pagerefs = False

# If true, show URL addresses after external links.
#
# latex_show_urls = False

# Documents to append as an appendix to all manuals.
#
# latex_appendices = []

# It false, will not define \strong, \code, 	itleref, \crossref ... but only
# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
# packages.
#
# latex_keep_old_macro_names = True

# If false, no module index is generated.
#
# latex_domain_indices = True


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

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    (master_doc, 'europeanxfelofflinecalibration', 'European XFEL Offline Calibration Documentation',
     [author], 1)
]

# If true, show URL addresses after external links.
#
# man_show_urls = False


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

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

# Documents to append as an appendix to all manuals.
#
# texinfo_appendices = []

# If false, no module index is generated.
#
# texinfo_domain_indices = True

# How to display URL addresses: 'footnote', 'no', or 'inline'.
#
# texinfo_show_urls = 'footnote'

# If true, do not generate a @detailmenu in the "Top" node's menu.
#
# texinfo_no_detailmenu = False


# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'https://docs.python.org/': None}



# first install pandoc if necessary, this is mainly meant for the RTD builds
try:
    from nbconvert.utils.pandoc import check_pandoc_version
    check_pandoc_version()
    print("Pandoc was found!")
except:
    print("Installing Pandoc!")
    from subprocess import check_call
    pandoc_url = "https://github.com/jgm/pandoc/releases/download/2.2.1/pandoc-2.2.1-1-amd64.deb"
    pandoc_pack = "pandoc-2.2.1-1-amd64.deb"
    check_call(["wget", pandoc_url])
    check_call(["dpkg", "-i", pandoc_pack])

rst_exporter = RSTExporter()
with open("available_notebooks.rst", "w") as f:
    f.write(dedent("""
            .. _available_notebooks:

            Available Notebooks
            ===================

            The following notebooks are currently integrated into the European XFEL
            Offline Calibration tool chain.


            """))

    for detector in sorted(notebooks.notebooks.keys()):
        # Avoid having test notebooks in detector notebooks documentations. 
        if "TEST" in detector.upper():
            continue
        values = notebooks.notebooks[detector]
        f.write("{}\n".format(detector))
        f.write("{}\n".format("-"*len(detector)))
        f.write("\n")

        for caltype in sorted(values.keys()):
            data = values[caltype]
            if data.get("notebook", None) is None:
                continue
            nbpath = os.path.abspath("{}/../../../{}".format(__file__, data["notebook"]))
            with open(nbpath, "r") as nf:
                nb = nbformat.read(nf, as_version=4)
                def first_markdown_cell(nb):
                    for cell in nb.cells:
                        if cell.cell_type == 'markdown':
                            return cell
                mdcell = first_markdown_cell(nb)
                nb.cells = [mdcell]  # we only want this single cell
                body, _ = rst_exporter.from_notebook_node(nb)
                adjusted = []
                # adjust titles
                for line in body.split("\n"):
                    if line.startswith("=="):
                        line = line.replace("=", "+")
                    if line.startswith("--"):
                        line = line.replace("-", "~")
                    adjusted.append(line)
                f.write("\n".join(adjusted))
                f.write("\n")

            f.write("To invoke this notebook and display help use:\n\n")
            f.write(".. code-block:: bash\n\n")
            f.write("    xfel-calibrate {} {} --help\n\n".format(detector, caltype))
            f.write("The full parameter list of this notebook (with defaults is): \n\n")
            f.write(".. code-block:: bash\n\n")
            nb_help = ["xfel-calibrate", detector, caltype, "--help"]
            output = check_output(nb_help).decode('utf8')
            f.write(indent(output.replace("DETECTOR", detector).replace("TYPE", caltype), " "*4))
            f.write("\n\n")

# add test results
test_artefact_dir = os.path.realpath("../../tests/legacy/artefacts")


def xml_to_rst_report(xml, git_tag, reports=[]):
    e = etree.fromstring(xml.encode())
    rst = [""]
    rst += ["Test execution for {test_name} on {ex_date}"]
    test_name, ex_date = e.get("name").split("-")
    ex_date = parse(ex_date)
    rst[-1] = rst[-1].format(test_name=test_name, ex_date=ex_date)
    rst += ["="*len(rst[-1])]
    rst += [""]

    num_tests = e.get("tests")
    num_err = int(e.get("errors"))
    num_fail = int(e.get("failures"))
    num_skip = int(e.get("skipped"))

    # create a summary header
    if num_err + num_fail == 0:
        rst += [":header-passed:`✓`"]
    else:
        rst += [":header-failed:`❌`"]

    if num_skip > 0:
        rst[-1] += ":header-skipped:`⚠`"
    rst += [""]

    # give a summary
    rst += [":Git tag: {git_tag}".format(git_tag=git_tag)]
    rst += [":Tests: {num_tests}".format(num_tests=num_tests)]
    rst += [":Errors: {num_err}".format(num_err=num_err)]
    rst += [":Failures: {num_fail}".format(num_fail=num_fail)]
    rst += [":Skipped: {num_skip}".format(num_skip=num_skip)]
    rst += [":Duration: {duration}s".format(duration=e.get("time"))]
    for rname, rpath in reports:
        rst += [":Report: `{} <{}>`_".format(rname, rpath)]
    rst += [""]

    # now the details
    rst += ["Detailed Results"]
    rst += ["-"*len(rst[-1])]
    rst += [""]

    detailed_failures = []
    rows = []
    for child in e:
        if child.tag != "testcase":
            continue
        name = child.get("name")
        extime = child.get("time")
        status = ":passed:`passed`"
        msg = ""
        etype = ""
        if len(child):  # children are pressent so test failed or skipped
            detail = child[0]
            etype = detail.get("type")
            msg = detail.get("message")
            if etype == "skip":
                status = ":skipped:`skipped`"
            else:
                status= ":failed:`failed`"
                detailed_failures.append((name, detail.text))
        msg = "\n".join(textwrap.wrap(msg, 20))
        row = [status, name, etype, msg, extime ]
        rows.append(row)

    header = ["Result", "Test", "Error", "Message", "Duration (s)"]
    tblrst =  tabulate.tabulate(rows, headers=header, tablefmt="rst")
    rst += tblrst.split("\n")
    rst += [""]

    for test, report in detailed_failures:
        rst += ["Failure report for: {}".format(test)]
        rst += ["~"*len(rst[-1])]
        rst += [""]
        rst += [".. code-block:: python"]
        rst += textwrap.indent(report, " "*4).split("\n")
        rst += [""]

    do_console = False
    for child in e:
        if child.tag == "system-out" and len(child.text.strip()):
            do_console = True
            break

    if do_console:

        # console output
        rst += ["Console Output"]
        rst += ["-"*len(rst[-1])]
        rst += [""]

        for child in e:
            if child.tag != "system-out":
                continue

            rst += [".. code-block:: console"]
            rst += textwrap.indent(child.text, " "*4).split("\n")


    return "\n".join(rst)

def sorted_dir(folder):
    def getmtime(name):
        path = os.path.join(folder, name)
        return os.path.getmtime(path)

    sort = sorted(os.listdir(folder), key=getmtime, reverse=True)
    return [(s, datetime.fromtimestamp(getmtime(s))) for s in sort]

header = """
Test Results
++++++++++++

Results are organized by git commit, and sorted descending by date.

Contents:

.. toctree::
   :maxdepth: 2


"""
if not os.path.exists("./test_rsts"):
    os.makedirs("./test_rsts")
with open("test_results.rst", "w") as f:
    f.write(header)
    for commit, modtime in sorted_dir(test_artefact_dir):
        with open("./test_rsts/{}.rst".format(commit), "w") as fr:
            rst = [".. include:: roles.rst"]
            rst += [""]
            rst += ["{} - {}".format(commit[:8], modtime)]
            rst += ["+"*len(rst[-1])]
            rst += [""]
            fr.write("\n".join(rst))

            # copy reports
            pdfs = glob.glob("{}/{}/*/*.pdf".format(test_artefact_dir, commit))
            if not os.path.exists("./_static/reports/{}".format(commit)):
                os.makedirs("./_static/reports/{}".format(commit))
            reports = {}
            for pdf in pdfs:
                ppath = "{}/{}.pdf".format(commit, uuid4())
                shutil.copyfile(pdf, "./_static/reports/{}".format(ppath))
                rloc = pdf.split("/")[-2]
                rlist = reports.get(rloc, [])
                rname = os.path.basename(pdf).split(".")[0]
                rlist.append((rname, "../_static/reports/{}".format(ppath)))
                reports[rloc] = rlist

            xmls = glob.glob("{}/{}/*/TEST*.xml".format(test_artefact_dir, commit))
            for xml in xmls:
                rloc = xml.split("/")[-2]
                with open(xml, "r") as xf:
                    xs = xf.read()
                    rst = xml_to_rst_report(xs, commit, reports=reports.get(rloc, []))
                    fr.write(rst)
            f.write("   test_rsts/{}\n".format(commit))


def setup(app):
    app.add_stylesheet('css/test_decorators.css')




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


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


import 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/"),
    ("stable", "/en/stable/"),
    ("doc-commonspace", "/en/doc-commonspace/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'european-xfel-offline-calibration',
    'name': u'European XFEL Offline Calibration',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'http://rtd.xfel.eu/docs/european-xfel-offline-calibration/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/source/',
    'api_host': 'http://rtd.xfel.eu',
    'github_user': 'None',
    'proxied_api_host': '/_',
    'github_repo': 'None',
    'github_version': 'doc/update_pycalibration_documentation',
    'display_github': False,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'doc/update_pycalibration_documentation',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'doc/update_pycalibration_documentation',
    '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': 'c81d0059',
}




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: 2022-03-16T07:44:33.221893Z, end-time: 2022-03-16T07:45:51.253662Z, duration: 78, exit-code: 0
python /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.8.5
[NbConvertApp] Converting notebook ../../../notebooks/Tutorial/calversion.ipynb to rst
[NbConvertApp] Writing 4434 bytes to ./calversion.rst
Matplotlib is building the font cache; this may take a moment.
Pandoc was found!
loading translations [en]... done
making output directory...
loading intersphinx inventory from https://docs.python.org/objects.inv...
intersphinx inventory has moved: https://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 17 source files that are out of date
updating environment: 17 added, 0 changed, 0 removed
reading sources... [  5%] _notebooks/calversion
reading sources... [ 11%] _notebooks/index
reading sources... [ 17%] advanced
reading sources... [ 23%] available_notebooks
reading sources... [ 29%] cal_tools_algorithms
reading sources... [ 35%] changelog
reading sources... [ 41%] configuration
reading sources... [ 47%] index
reading sources... [ 52%] installation
reading sources... [ 58%] test_results
reading sources... [ 64%] test_rsts/9088fa11013afe7bb5d4231fd4170c96e34db520
reading sources... [ 70%] test_rsts/ca3b513c64c05a29ae0f530c91b04349417c4fa0
reading sources... [ 76%] test_rsts/roles
reading sources... [ 82%] testing
reading sources... [ 88%] tutorial
reading sources... [ 94%] workflow
reading sources... [100%] xfel_calibrate_conf

/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/_notebooks/calversion.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/advanced.rst:46: WARNING: Literal block expected; none found.
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/index.rst:61: WARNING: toctree contains reference to nonexisting document 'architecture'
looking for now-outdated files... none found
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writing output... [ 11%] _notebooks/index
writing output... [ 17%] advanced
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writing output... [ 29%] cal_tools_algorithms
writing output... [ 35%] changelog
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writing output... [ 52%] installation
writing output... [ 58%] test_results
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writing output... [ 70%] test_rsts/ca3b513c64c05a29ae0f530c91b04349417c4fa0
writing output... [ 76%] test_rsts/roles
writing output... [ 82%] testing
writing output... [ 88%] tutorial
writing output... [ 94%] workflow
writing output... [100%] xfel_calibrate_conf

/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/available_notebooks.rst:43: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
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generating indices... genindex py-modindex
highlighting module code... [ 50%] cal_tools.agipdlib
highlighting module code... [100%] xfel_calibrate.calibrate

writing additional pages... search
copying static files... done
copying readthedocs static files... done
copying searchtools... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 27 warnings.

The HTML pages are in _build/html.