Read the Docs build information
Build id: 25735
Project: european-xfel-offline-calibration
Version: doc-mkdocs_new_documentations
Commit: 52a03a137d387018193b5562e777396396dcf9fa
Date: 2023-03-21T08:58:08.760314Z
State: finished
Success: False


[rtd-command-info] start-time: 2023-03-21T08:58:09.838940Z, end-time: 2023-03-21T08:58:26.577408Z, duration: 16, exit-code: 0
git clone --no-single-branch --depth 50 http://git.xfel.eu/calibration/pycalibration .
Cloning into '.'...
warning: redirecting to https://git.xfel.eu/calibration/pycalibration.git/

[rtd-command-info] start-time: 2023-03-21T08:58:26.875488Z, end-time: 2023-03-21T08:58:27.664536Z, duration: 0, exit-code: 0
git checkout --force origin/doc/mkdocs_new_documentations
Note: checking out 'origin/doc/mkdocs_new_documentations'.

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 52a03a13 update requirements

[rtd-command-info] start-time: 2023-03-21T08:58:27.749422Z, end-time: 2023-03-21T08:58:27.814296Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-03-21T08:58:29.584345Z, end-time: 2023-03-21T08:58:34.478523Z, duration: 4, exit-code: 0
python3.8 -mvirtualenv /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations
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/doc-mkdocs_new_documentations/bin/python3.8
Also creating executable in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2023-03-21T08:58:34.570582Z, end-time: 2023-03-21T08:58:35.494244Z, duration: 0, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/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/doc-mkdocs_new_documentations/lib/python3.8/site-packages (23.0.1)

[rtd-command-info] start-time: 2023-03-21T08:58:35.579876Z, end-time: 2023-03-21T08:59:00.469916Z, duration: 24, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/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, pillow, future
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Successfully built mock pillow future
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 67.6.0
    Uninstalling setuptools-67.6.0:
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Successfully installed Pygments-2.3.1 alabaster-0.7.13 babel-2.12.1 certifi-2022.12.7 charset-normalizer-3.1.0 commonmark-0.8.1 docutils-0.14 future-0.18.3 idna-3.4 imagesize-1.4.1 jinja2-2.11.3 markupsafe-2.0.1 mock-1.0.1 packaging-23.0 pillow-5.4.1 pytz-2022.7.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.28.2 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 urllib3-1.26.15

[rtd-command-info] start-time: 2023-03-21T08:59:00.557065Z, end-time: 2023-03-21T08:59:10.006237Z, duration: 9, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/bin/python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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[rtd-command-info] start-time: 2023-03-21T08:59:10.093500Z, end-time: 2023-03-21T09:00:16.170760Z, duration: 66, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/bin/python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[docs]
Processing /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/doc-mkdocs_new_documentations
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Collecting cffi>=1.0.1
  Downloading cffi-1.15.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (442 kB)
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Building wheels for collected packages: dill, prettytable, pypandoc, pyyaml, sharedmem, tabulate, European-XFEL-Offline-Calibration
  Building wheel for dill (setup.py): started
  Building wheel for dill (setup.py): finished with status 'done'
  Created wheel for dill: filename=dill-0.3.0-py3-none-any.whl size=77512 sha256=953b8a4ca66c4d63d35a9900869a10b433735277a9f4d8be537cb0a727b922d5
  Stored in directory: /tmp/pip-ephem-wheel-cache-c5l2blyy/wheels/ec/e7/fb/9b59e2dbda9eeefab51f7cb41df434ff463c4afe1985abff24
  Building wheel for prettytable (setup.py): started
  Building wheel for prettytable (setup.py): finished with status 'done'
  Created wheel for prettytable: filename=prettytable-0.7.2-py3-none-any.whl size=13699 sha256=2eb0aa088e2ea8578881a8d15a4353892e80a3c7e07ea0f2508ef4fb666f22e2
  Stored in directory: /tmp/pip-ephem-wheel-cache-c5l2blyy/wheels/48/6d/77/9517cb933af254f51a446f1a5ec9c2be3e45f17384940bce68
  Building wheel for pypandoc (setup.py): started
  Building wheel for pypandoc (setup.py): finished with status 'done'
  Created wheel for pypandoc: filename=pypandoc-1.4-py3-none-any.whl size=16716 sha256=9b9b7990011c844cb00684875ad66111b13a6b049ac871929969998ecc79e60d
  Stored in directory: /tmp/pip-ephem-wheel-cache-c5l2blyy/wheels/f7/d9/a0/ef1fe56c058e41d6271a4935caaeae89d43e2280504690a329
  Building wheel for pyyaml (setup.py): started
  Building wheel for pyyaml (setup.py): finished with status 'done'
  Created wheel for pyyaml: filename=PyYAML-5.3-cp38-cp38-linux_x86_64.whl size=44227 sha256=c4a97d284a10b0c3b8c90bfceb8e266abe031e0aff1c79576778769ec45b01fd
  Stored in directory: /tmp/pip-ephem-wheel-cache-c5l2blyy/wheels/e4/94/ec/65e430f66fda7a86c08f61ce59455581adc269a65881b4ffeb
  Building wheel for sharedmem (setup.py): started
  Building wheel for sharedmem (setup.py): finished with status 'done'
  Created wheel for sharedmem: filename=sharedmem-0.3.8-py3-none-any.whl size=18342 sha256=12dc7ef1bc7b2c1f580f26f83f33ec5f00c3203c815c4021d48ac4fc13fefddb
  Stored in directory: /tmp/pip-ephem-wheel-cache-c5l2blyy/wheels/ee/ef/25/9562dc56f11d2b55824c1b1547eff68b75f1a0117d3b0867dd
  Building wheel for tabulate (setup.py): started
  Building wheel for tabulate (setup.py): finished with status 'done'
  Created wheel for tabulate: filename=tabulate-0.8.6-py3-none-any.whl size=23273 sha256=3c3187a7e91a913204617f46627a31def9610d96857306343e7d28ab37ac7f62
  Stored in directory: /tmp/pip-ephem-wheel-cache-c5l2blyy/wheels/86/8c/d9/3b6c2f55efaefe656c52b725d2fdc5669085c83444979db8b3
  Building wheel for European-XFEL-Offline-Calibration (pyproject.toml): started
  Building wheel for European-XFEL-Offline-Calibration (pyproject.toml): finished with status 'done'
  Created wheel for European-XFEL-Offline-Calibration: filename=European_XFEL_Offline_Calibration-1.0-cp38-cp38-linux_x86_64.whl size=1598722 sha256=420c55972b50b500cffa79e3c941157d455f984a16570539d2508bed9bdcc66d
  Stored in directory: /tmp/pip-ephem-wheel-cache-c5l2blyy/wheels/1d/8e/2b/dcedca7f2ac9a173c60e54d723e1d361570bb0c374714b3976
Successfully built dill prettytable pypandoc pyyaml sharedmem tabulate European-XFEL-Offline-Calibration
Installing collected packages: webencodings, wcwidth, tabulate, Send2Trash, ptyprocess, prettytable, pickleshare, mistune, kafka-python, ipython-genutils, env-cache, dynaconf, chardet, backcall, urllib3, tornado, testpath, smmap, setuptools, pyzmq, pyyaml, pyrsistent, pyparsing, pycparser, prompt-toolkit, prometheus-client, pkgutil-resolve-name, pillow, pexpect, parso, pandocfilters, oauthlib, numpy, nest-asyncio, mypy-extensions, lxml, kiwisolver, joblib, Jinja2, importlib-resources, idna, entrypoints, docutils, dill, defusedxml, decorator, Cython, cycler, bleach, attrs, async-generator, astcheck, traitlets, terminado, sharedmem, scipy, requests, pypandoc, pasha, pandas, matplotlib, jsonschema, jedi, iminuit, h5py, gitdb, euxfel-bunch-pattern, cffi, xarray, sphinx, scikit-learn, requests-oauthlib, jupyter-core, ipython, gitpython, cfelpyutils, argon2-cffi-bindings, oauth2-xfel-client, nbformat, jupyter-client, extra-geom, extra-data, argon2-cffi, nbconvert, nbclient, metadata-client, ipykernel, EXtra-redu, calibration-client, princess, notebook, nbsphinx, nbparameterise, jupyter-console, ipyparallel, European-XFEL-Offline-Calibration
  Attempting uninstall: urllib3
    Found existing installation: urllib3 1.26.15
    Uninstalling urllib3-1.26.15:
      Successfully uninstalled urllib3-1.26.15
  Attempting uninstall: setuptools
    Found existing installation: setuptools 41.0.1
    Uninstalling setuptools-41.0.1:
      Successfully uninstalled setuptools-41.0.1
  Attempting uninstall: pyyaml
    Found existing installation: PyYAML 6.0
    Uninstalling PyYAML-6.0:
      Successfully uninstalled PyYAML-6.0
  Attempting uninstall: pillow
    Found existing installation: Pillow 5.4.1
    Uninstalling Pillow-5.4.1:
      Successfully uninstalled Pillow-5.4.1
  Attempting uninstall: Jinja2
    Found existing installation: Jinja2 3.1.2
    Uninstalling Jinja2-3.1.2:
      Successfully uninstalled Jinja2-3.1.2
  Attempting uninstall: idna
    Found existing installation: idna 3.4
    Uninstalling idna-3.4:
      Successfully uninstalled idna-3.4
  Attempting uninstall: docutils
    Found existing installation: docutils 0.14
    Uninstalling docutils-0.14:
      Successfully uninstalled docutils-0.14
  Attempting uninstall: requests
    Found existing installation: requests 2.28.2
    Uninstalling requests-2.28.2:
      Successfully uninstalled requests-2.28.2
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.6
    Uninstalling Sphinx-1.8.6:
      Successfully uninstalled Sphinx-1.8.6
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
mkdocs-material 9.1.3 requires jinja2>=3.0, but you have jinja2 2.11.2 which is incompatible.
mkdocs-material 9.1.3 requires requests>=2.26, but you have requests 2.22.0 which is incompatible.
Successfully installed Cython-0.29.21 EXtra-redu-0.0.7 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-0.3.0 async-generator-1.10 attrs-22.2.0 backcall-0.2.0 bleach-6.0.0 calibration-client-11.2.0 cfelpyutils-2.0.6 cffi-1.15.1 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 env-cache-0.1 euxfel-bunch-pattern-0.6 extra-data-1.12.0 extra-geom-1.8.0 gitdb-4.0.10 gitpython-3.1.0 h5py-3.5.0 idna-2.8 iminuit-1.3.8 importlib-resources-5.12.0 ipykernel-5.1.4 ipyparallel-6.2.4 ipython-7.12.0 ipython-genutils-0.2.0 jedi-0.18.2 joblib-1.2.0 jsonschema-4.17.3 jupyter-client-7.3.4 jupyter-console-6.1.0 jupyter-core-4.10.0 kafka-python-2.0.2 kiwisolver-1.4.4 lxml-4.5.0 matplotlib-3.4.2 metadata-client-3.0.8 mistune-0.8.4 mypy-extensions-1.0.0 nbclient-0.5.1 nbconvert-5.6.1 nbformat-5.0.7 nbparameterise-0.6 nbsphinx-0.8.8 nest-asyncio-1.5.6 notebook-6.1.5 numpy-1.20.3 oauth2-xfel-client-6.1.1 oauthlib-3.2.2 pandas-1.5.3 pandocfilters-1.5.0 parso-0.8.3 pasha-0.1.1 pexpect-4.8.0 pickleshare-0.7.5 pillow-9.4.0 pkgutil-resolve-name-1.3.10 prettytable-0.7.2 princess-0.5 prometheus-client-0.16.0 prompt-toolkit-3.0.38 ptyprocess-0.7.0 pycparser-2.21 pypandoc-1.4 pyparsing-3.0.9 pyrsistent-0.19.3 pyyaml-5.3 pyzmq-23.2.0 requests-2.22.0 requests-oauthlib-1.3.1 scikit-learn-0.22.2.post1 scipy-1.7.0 setuptools-67.6.0 sharedmem-0.3.8 smmap-5.0.0 sphinx-1.8.5 tabulate-0.8.6 terminado-0.17.1 testpath-0.6.0 tornado-6.2 traitlets-4.3.3 urllib3-1.25.11 wcwidth-0.2.6 webencodings-0.5.1 xarray-2022.3.0

[rtd-command-info] start-time: 2023-03-21T09:00:16.905354Z, end-time: 2023-03-21T09:00:16.971353Z, 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]
            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': "doc/mkdocs_new_documentations",
    'version_slug': "doc-mkdocs_new_documentations",
    'MEDIA_URL': "media/",
    'STATIC_URL': "/static/",
    'PRODUCTION_DOMAIN': "rtd.xfel.eu",
    'versions': [
    ("master", "/en/master/"),
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("doc-writing_new_notebook", "/en/doc-writing_new_notebook/"),
    ("doc-mkdocs_new_documentations", "/en/doc-mkdocs_new_documentations/"),
    ],
    '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/doc-mkdocs_new_documentations/',
    '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/mkdocs_new_documentations',
    'display_github': False,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'doc/mkdocs_new_documentations',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'doc/mkdocs_new_documentations',
    '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': '52a03a13',
}




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: 2023-03-21T09:00:17.061465Z, end-time: 2023-03-21T09:00:19.185361Z, duration: 2, exit-code: 2
python /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/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
Traceback (most recent call last):
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/bin/xfel-calibrate", line 7, in <module>
    from xfel_calibrate.calibrate import run
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/lib/python3.8/site-packages/xfel_calibrate/calibrate.py", line 25, in <module>
    import cal_tools.tools
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/lib/python3.8/site-packages/cal_tools/tools.py", line 24, in <module>
    from iCalibrationDB import ConstantMetaData, Versions
ModuleNotFoundError: No module named 'iCalibrationDB'
Pandoc was found!

Traceback (most recent call last):
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/lib/python3.8/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/lib/python3.8/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/doc-mkdocs_new_documentations/docs/source/conf.py", line 443, in <module>
    output = check_output(nb_help).decode('utf8')
  File "/home/docs/.pyenv/versions/3.8.0/lib/python3.8/subprocess.py", line 411, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/home/docs/.pyenv/versions/3.8.0/lib/python3.8/subprocess.py", line 512, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['xfel-calibrate', 'AGIPD', 'COMBINE', '--help']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/lib/python3.8/site-packages/sphinx/cmd/build.py", line 300, in build_main
    app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/lib/python3.8/site-packages/sphinx/application.py", line 201, in __init__
    self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/lib/python3.8/site-packages/sphinx/config.py", line 203, in read
    namespace = eval_config_file(filename, tags)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/lib/python3.8/site-packages/sphinx/config.py", line 380, in eval_config_file
    raise ConfigError(msg % traceback.format_exc())
sphinx.errors.ConfigError: There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/lib/python3.8/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/lib/python3.8/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/doc-mkdocs_new_documentations/docs/source/conf.py", line 443, in <module>
    output = check_output(nb_help).decode('utf8')
  File "/home/docs/.pyenv/versions/3.8.0/lib/python3.8/subprocess.py", line 411, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/home/docs/.pyenv/versions/3.8.0/lib/python3.8/subprocess.py", line 512, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['xfel-calibrate', 'AGIPD', 'COMBINE', '--help']' returned non-zero exit status 1.


Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/lib/python3.8/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/lib/python3.8/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/doc-mkdocs_new_documentations/docs/source/conf.py", line 443, in <module>
    output = check_output(nb_help).decode('utf8')
  File "/home/docs/.pyenv/versions/3.8.0/lib/python3.8/subprocess.py", line 411, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/home/docs/.pyenv/versions/3.8.0/lib/python3.8/subprocess.py", line 512, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['xfel-calibrate', 'AGIPD', 'COMBINE', '--help']' returned non-zero exit status 1.